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RNAs Present In Environmental Samples
A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong. The distinct environmental sequences were exploited to detect previously unknown RNAs in the marine bacterium ''Pelagibacter ubique''. ''P. ubique'' is extremely common in marine sequences. So sequences of DNA extracted from oceans, many of which are inevitably derived from species related to ''P. ubique'', were exploited to facilitate the analysis of possible secondary structures of RNAs predicted in this species. Subsequent studies identi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosome
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-c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Environmental DNA
Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, snow or air, rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources. In recent years, eDNA has been used as a tool to detect endangered wildlife that were otherwise unseen. In 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic. Example sources of eDNA include, but are not limited to, feces, mucus, gametes, shed skin, carcasses and hair. Samples can be analyzed by high-throughput DNA sequencing methods, known as metagenomics, metabarcoding, and single-species detection, for rapid monitoring and measurement of biodiversity. In order to better differentiate between organisms within a sample, DNA metabarcoding is used in which the sample is analyzed and uses previously studied DNA librari ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ManA RNA Motif
The ''manA'' RNA motif (also called manA) refers to a conserved RNA structure that was identified by bioinformatics. Instances of the ''manA'' RNA motif were detected in bacteria in the genus ''Photobacterium'' and phages that infect certain kinds of cyanobacteria. However, most predicted ''manA'' RNA sequences are derived from DNA collected from uncultivated marine bacteria. Almost all ''manA'' RNAs are positioned such that they might be in the 5' untranslated regions of protein-coding genes, and therefore it was hypothesized that ''manA'' RNAs function as cis-regulatory elements. Given the relative complexity of their secondary structure, and their hypothesized ''cis''-regulatory role, they might be riboswitches. The genes thought to be regulated by ''manA'' RNAs are most typically those involved in the metabolism of the sugars fructose and mannose, synthesis of nucleotides, bacterial photosynthesis and a class of protein chaperones known as ''ibpA''. ''manA'' RNAs are al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GOLLD RNA Motif
Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD) RNA is a conserved RNA structure present in bacteria. GOLLD RNAs were originally detected based on metagenome sequences of DNA isolated from Lake Gatun in Panama. However, they are known to be present in at least eight strains of cultivated bacteria. GOLLD RNAs are extraordinarily large compared to other RNAs with a conserved, complex secondary structure, and average roughly 800 nucleotides. Such large, complex RNAs are often ribozymes, although the biochemical function of GOLLD RNAs remains unknown. The discovery of large RNAs like GOLLD RNAs among bacteria that are mostly uncultivated under laboratory conditions suggests that many other unusually large RNAs might be found in bacteria that have not yet been studied. The GOLLD RNA in ''Lactobacillus brevis'' ATCC 367 was studied experimentally. This GOLLD RNA is apparently encoded by a prophage, and its transcription is increased during the phage lytic cycle. Therefor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gut-1 RNA Motif
The Gut-1 RNA motif (also called gt-1) is a conserved RNA structure identified by bioinformatics. These RNAs are present in environmental sequences, and as of 2010 are not known to be present in any species that has been grown under laboratory conditions. Gut-1 RNA is exclusively found in DNA from uncultivated bacteria present in samples from the human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ... gut. References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Termite-flg RNA Motif
The Termite-''flg'' RNA motif (also called tg-flg) is a conserved RNA structure identified by bioinformatics. Genomic sequences corresponding to Termite-''flg'' RNAs have been identified only in uncultivated bacteria present in the termite hindgut. As of 2010 it has not been identified in the DNA of any cultivated species, and is thus an example of RNAs present in environmental samples. Termite-''flg'' RNAs are consistently located in what is presumed to be the 5' untranslated regions of genes that encode proteins whose functions relate to flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f .... The RNAs are hypothesized to regulate these genes in an unknown mechanism. References External links * Cis-regulatory RNA elements {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PotC RNA Motif
The ''potC'' RNA motif is a conserved RNA structure discovered using bioinformatics. The RNA is detected only in genome sequences derived from DNA that was extracted from uncultivated marine bacteria. Thus, this RNA is present in environmental samples, but not yet found in any cultivated organism. ''potC'' RNAs are located in the presumed 5' untranslated regions of genes predicted to encode either membrane transport proteins or peroxiredoxins. Therefore, it was hypothesized that ''potC'' RNAs are cis-regulatory elements, but their detailed function is unknown. A number of other RNAs were identified in the same study, including: *Lacto-usp RNA motif *mraW RNA motif *Ocean-V RNA motif *psaA RNA motif *Pseudomon-Rho RNA motif *rne-II RNA motif *STAXI RNA motif *TwoAYGGAY RNA motif *Whalefall-1 RNA motif *wcaG RNA motif *ykkC-yxkD leader The ykkC/yxkD leader is a conserved sequence, conserved Cis-regulatory element, RNA structure found Upstream and downstream (DNA), upstream ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Whalefall-1 RNA Motif
The Whalefall-1 RNA motif (also called wf-1) refers to a conserved RNA structure that was discovered using bioinformatics. Structurally, the motif consists of two stem-loops (see diagram), the second of which is often terminated by a CUUG tetraloop, which is an energetically favorable RNA sequence. Whalefall-1 RNAs are found only in DNA extracted from uncultivated bacteria found on whale fall, i.e., a whale carcass. As of 2010, Whalefall-1 RNAs have not been detected in any known, cultivated species of bacteria, and are thus one of several RNAs present in environmental samples A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which .... References External links * Non-coding RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
IMES-4 RNA Motif
The IMES-4 RNA motif is a conserved RNA structure that was identified in marine environmental sequences by metagenomics and bioinformatics. These RNAs are present in environmental sequences, and as of 2009 are not known to be present in any cultivated species. IMES-4 RNAs are fairly abundant in comparison to ribosomes in RNAs sampled from the Pacific Ocean The Pacific Ocean is the largest and deepest of Earth's five oceanic divisions. It extends from the Arctic Ocean in the north to the Southern Ocean (or, depending on definition, to Antarctica) in the south, and is bounded by the continen ...."> References {{reflist Non-coding RNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
IMES-3 RNA Motif
The IMES-3 RNA motif is a conserved RNA structure that was identified based on metagenomics and bioinformatics, and the underlying RNA sequences were identified independently by an earlier study. These RNAs are present in environmental sequences, and as of 2009 are not known to be present in any cultivated species. IMES-3 RNAs are abundant in comparison to ribosomes in RNAs sampled from the Pacific Ocean The Pacific Ocean is the largest and deepest of Earth's five oceanic divisions. It extends from the Arctic Ocean in the north to the Southern Ocean (or, depending on definition, to Antarctica) in the south, and is bounded by the continen .... References {{reflist Non-coding RNA ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Atlantic Ocean
The Atlantic Ocean is the second-largest of the world's five oceans, with an area of about . It covers approximately 20% of Earth's surface and about 29% of its water surface area. It is known to separate the " Old World" of Africa, Europe and Asia from the "New World" of the Americas in the European perception of the World. The Atlantic Ocean occupies an elongated, S-shaped basin extending longitudinally between Europe and Africa to the east, and North and South America to the west. As one component of the interconnected World Ocean, it is connected in the north to the Arctic Ocean, to the Pacific Ocean in the southwest, the Indian Ocean in the southeast, and the Southern Ocean in the south (other definitions describe the Atlantic as extending southward to Antarctica). The Atlantic Ocean is divided in two parts, by the Equatorial Counter Current, with the North(ern) Atlantic Ocean and the South(ern) Atlantic Ocean split at about 8°N. Scientific explorations of the A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
