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Conserved Signature Indels
Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein. The CSIs that are restricted to a particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, it is less likely that they could arise independently by either Convergent evolution, convergent or parallel evolution (i.e. homoplasy) and therefore are likely to represent synapomorphy. Other confounding factors such as differences in evolutionary rates at dif ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Indel
Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. Indels ≥ 50 bases in length are classified as structural variants. In coding regions of the genome, unless the length of an indel is a multiple of 3, it will produce a frameshift mutation. For example, a common microindel which results in a frameshift causes Bloom syndrome in the Jewish or Japanese population. Indels can be contrasted with a point mutation. An indel inserts or deletes nucleotides from a sequence, while a point mutation is a form of substitution that ''replaces'' one of the nucleotides without changing the overall number in the DNA. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed). In ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Planctomycetota
The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammonium oxidation, also known as anammox. Many Planctomycetota occur in relatively high abundance as biofilms, often associating with other organisms such as macroalgae and marine sponges. Planctomycetota are included in the PVC superphylum along with Verrucomicrobiota, Chlamydiota, Lentisphaerota, Kiritimatiellaeota, and ''Candidatus'' ''Omnitrophica''. The phylum Planctomycetota is composed of the classes Planctomycetia and Phycisphaerae. First described in 1924, members of the Planctomycetota were identified as eukaryotes and were only later described as bacteria in 1972. Early examination of members of the Planctomycetota suggested a cell plan differing considerably from other bacteria, although they are now confirmed as Gram-negative ba ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fusobacteriota
Fusobacteriota are obligately anaerobic non-sporeforming Gram-negative bacilli. Since the first reports in the late nineteenth century, various names have been applied to these organisms, sometimes with the same name being applied to different species. More recently, not only have there been changes to the nomenclature, but also attempts to differentiate between species which are believed to be either pathogenic or commensal or both. Because of their asaccharolytic nature, and a general paucity of positive results in routine biochemical tests, laboratory identification of the Fusobacteriota has been difficult. However, the application of novel molecular biological techniques to taxonomy has established a number of new species, together with the subspeciation of ''Fusobacterium necrophorum'' and ''F. nucleatum'', and provided new methods for identification. The involvement of Fusobacteriota in a wide spectrum of human infections causing tissue necrosis and septicaemia has long bee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Deinococcota
Deinococcota (synonym, Deinococcus-Thermus) is a phylum of bacteria with a single class, ''Deinococci'', that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. Taxonomy The phylum Deinococcota consists of a single class ( Deinococci) and two orders: * The Deinococcales include two families ( Deinococcaceae and Trueperaceae), with three genera, '' Deinococcus'', '' Deinobacterium'' and '' Truepera''.Garrity GM, Holt JG. (2001) Phylum BIV. "Deinococcus–Thermus". In: Bergey’s manual of systematic bacteriology, pp. 395-420. Eds D. R. Boone, R. W. Castenholz. Springer-: New York.Garrity GM, Bell JA, Lilburn TG. (2005) Phylum BIV. The revised road map to the Manual. In: Bergey’s manual of systematic bacteriology, pp. 159-220. Eds Brenner DJ, Krieg NR, Staley JT, Garrity GM. Sprin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacillota
The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', '' Pectinatus'', '' Selenomonas'', and '' Zymophilus'' from the class Negativicutes, have a porous pseudo-outer membrane that causes them to stain Gram-negative. Many Bacillota produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and the group includes some notable pathogens. Those in one family, the Heliobacteria, produce energy through anoxygenic photosynthesis. Bacillota play an important role in beer, wine, and cider spoilage. Taxonomy The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The name "Firmicutes" was derived from the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Markers
In molecular biology and other fields, a molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. For another example, some proteins can be molecular markers of Alzheimer's disease in a person from which they are taken. Molecular markers may be non-biological. Non-biological markers are often used in environmental studies. Genetic markers In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers are used in molecular biology and biotechnology to identify a particular sequence of DNA in a pool of unknown DNA. Types of genetic markers There are many types of genetic markers, each with particular limitations and strengths. Within genetic markers there are three different categories: "First Generation Markers", "Second Generatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
16S Ribosomal RNA
16S 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 genes 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. Terminology The descriptor ''16S'' refers to the size of these ribosomal subunits as reflected indirectly by the speed at which they sediment when samples are centrifuged. Thus ''16S'' means 16 Svedburg units. 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archea Phylogeny CSI
Archaea ( ) is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even though the domain Archaea cladistically includes eukaryotes, the term "archaea" (: archaeon , from the Greek "ἀρχαῖον", which means ancient) in English still generally refers specifically to prokaryotic members of Archaea. 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 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. It is unknown if they can produce endospores. Archaea are often similar to bacteria in size a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermotogae Phlogeny CSI Summary
The Thermotogae is a class of kingdom Thermotogati and domain Bacteria. It's the sole class in the phylum Thermotogota. The class Thermotogae is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-1015. Springer Berlin Heidelberg. Characteristics The name of this class is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or "toga", surrounding the cells of these species.Reysenbach, A.-L. (2001) Phylum BII. Thermotogae phy. nov. In: Bergey's Manual of Systematic Bacteriology, pp. 369-387. Eds D. R. Boone, R. W. Castenholz. Springer-Verlag: Berlin. Recently, some Thermotogae existing at moderate temperatures have also been identified. Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single-unit lipid membrane, hence they are monoderm bacteria. Because of the ability ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chlorobiota
The green sulfur bacteria are a phylum, Chlorobiota, of obligately anaerobic photoautotrophic bacteria that metabolize sulfur. Green sulfur bacteria are nonmotile (except ''Chloroherpeton thalassium'', which may glide) and capable of anoxygenic photosynthesis. They live in anaerobic aquatic environments. In contrast to plants, green sulfur bacteria mainly use sulfide ions as electron donors. They are autotrophs that utilize the reverse tricarboxylic acid cycle to perform carbon fixation. They are also mixotrophs and reduce nitrogen. Characteristics Green sulfur bacteria are gram-negative rod or spherical shaped bacteria. Some types of green sulfur bacteria have gas vacuoles that allow for movement. They are photolithoautotrophs, and use light energy and reduced sulfur compounds as the electron source. Electron donors include , , S. The major photosynthetic pigment in these bacteria is Bacteriochlorophylls ''c'' or ''d'' in green species and ''e'' in brown species, and is locat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteroidota
The phylum (biology), phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of Gram-negative bacteria, Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals. Although some ''Bacteroides'' spp. can be Opportunistic Pathogens, opportunistic pathogens, many ''Bacteroidota'' are Symbiotic bacteria, symbiotic species highly adjusted to the gastrointestinal tract. ''Bacteroides'' are highly abundant in intestines, reaching up to 1011 cells g−1 of intestinal material. They perform metabolic conversions that are essential for the host, such as degradation of proteins or complex sugar polymers. ''Bacteroidota'' colonize the gastrointestinal tract already in infants, as non-digestible Human milk oligosaccharide, oligosaccharides in mother milk support the growth of both ''Bacteroides'' and ''Bifidoba ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
