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DUF1874 RNA Motif
The DUF1874 RNA motif is a conserved nucleic acid structure that was discovered by bioinformatics. The DUF1874 motif has not (as of 2018) been detected in any classified organism, but rather is known only in metagenomic DNA sequences isolated from hot springs. DUF1874 are frequently present in consecutive intergenic regions between consecutive genes. All of these genes are encoded on the same DNA strand. For this reason, it was proposed that DUF1874 motif examples likely function as "''attC''" sites as part of an integron, as ''attC'' sites occur in integrons between a run of consecutive genes that have been taken up by the integron. ''attC'' sites are singled-stranded DNA elements that are used by integrons to enabling the rearrangement and integration of new genes into the intron. Thus, if the preceding hypothesis is true, then the DUF1874 motif function as single-stranded DNA. Although the arrangement of DUF1874 motif examples and genes is typical of integrons, no integra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Conservation
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species ( orthologous sequences), or within a genome ( paralogous sequences), or between donor and receptor taxa ( xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst eukaryotes, and the tmRNA in bacteria. The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics. History The discovery of the role of DNA in heredity, and observations by Frederick Sanger of variation between animal insulins in 1949, promp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cis-regulatory Element
''Cis''-regulatory elements (CREs) or ''cis''-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology. CREs are found in the vicinity of the genes that they regulate. CREs typically regulate gene transcription by binding to transcription factors. A single transcription factor may bind to many CREs, and hence control the expression of many genes ( pleiotropy). The Latin prefix ''cis'' means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed. CRMs are stretches of DNA, usually 100–1000 DNA base pairs in length, where a number of transcription factors can bind and regulate expression of nearby genes and regulate their transcription rates. They are labeled as ''cis'' because they are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is deoxyribose, a variant of ribose, the polymer is DNA. Nucleic acids are chemical compounds that are found in nature. They carry information in cells and make up genetic material. These acids are very common in all living things, where they create, encode, and store information in every living cell of every outline of life forms, life-form on Earth. In turn, they send and express that information inside and outside the cell nucleus. From the inner workings of the cell to the young of a living thing, they contain and provide information via the nucleic acid sequence. This gives the RNA and DNA their unmistakable 'la ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Discovery Of Non-coding RNAs
Non-coding RNAs have been discovered using both experimental and bioinformatic approaches. Bioinformatic approaches can be divided into three main categories. The first involves homology search, although these techniques are by definition unable to find new classes of ncRNAs. The second category includes algorithms designed to discover specific types of ncRNAs that have similar properties. Finally, some discovery methods are based on very general properties of RNA, and are thus able to discover entirely new kinds of ncRNAs. Discovery by homology search Homology search refers to the process of searching a sequence database for RNAs that are similar to already known RNA sequences. Any algorithm that is designed for homology search of nucleic acid sequences can be used, e.g., BLAST. However, such algorithms typically are not as sensitive or accurate as algorithms specifically designed for RNA. Of particular importance for RNA is its conservation of a secondary structure, which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenomic
Metagenomics is the study of all genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the microbial composition of environmental and clinical samples without the need for time-consuming culture of individual species. Metagenomics has transformed microbial ecology and evolutionary biology by uncovering previously hidden biodiversity and metabolic capabilities. As the cost of DNA sequencing continues to decline, metagenomic studies now routinely profile hundreds to thousands of samples, enabling large-scale exploration of microbial communities and their roles in health and global ecosystems. Metagenomic studies most commonly employ shotgun sequencing though long-read sequencing is being increasingly utilised as technologies advance. The field is also referred to as environmental genomics, ecogenomics, community genomics, or microbiomics a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hot Spring
A hot spring, hydrothermal spring, or geothermal spring is a Spring (hydrology), spring produced by the emergence of Geothermal activity, geothermally heated groundwater onto the surface of the Earth. The groundwater is heated either by shallow bodies of magma (molten rock) or by circulation through fault (geology), faults to hot rock deep in the Earth's crust. Hot spring water often contains large amounts of dissolved minerals. The chemistry of hot springs ranges from acid sulfate springs with a pH as low as 0.8, to alkaline chloride springs saturated with silica, to bicarbonate springs saturated with carbon dioxide and carbonate minerals. Some springs also contain abundant dissolved iron. The minerals brought to the surface in hot springs often feed communities of extremophiles, microorganisms adapted to extreme conditions, and it is possible that life on Earth had its origin in hot springs. Humans have made use of hot springs for bathing, relaxation, or medical therapy for th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intergenic Region
An intergenic region is a stretch of DNA sequences located between genes. Intergenic regions may contain functional elements and junk DNA. Properties and functions Intergenic regions may contain a number of functional DNA sequences such as promoters and regulatory elements, enhancers, spacers, and (in eukaryotes) centromeres. They may also contain origins of replication, scaffold attachment regions, and transposons and viruses. Non-functional DNA elements such as pseudogenes and repetitive DNA, both of which are types of junk DNA, can also be found in intergenic regions—although they may also be located within genes in introns. It is possible that these regions contain as of yet unidentified functional elements, such as non-coding genes or regulatory sequences. This indeed occurs occasionally, but the amount of functional DNA discovered usually constitute only a tiny fraction of the overall amount of intergenic or intronic DNA. Intergenic regions in differ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of Gene product, RNA or protein from a gene), DNA is first transcription (biology), copied into RNA. RNA can be non-coding RNA, directly functional or be the intermediate protein biosynthesis, template for the synthesis of a protein. The transmission of genes to an organism's offspring, is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype, that is specific to every given individual, within the gene pool of the population (biology), population of a given species. The genotype, along with environmental and developmental factors, ultimately determines the phenotype ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Integron
Integrons are genetic mechanisms that allow bacteria to adapt and evolve rapidly through the stockpiling and expression of new genes. These genes are embedded in a specific genetic structure called gene cassette (a term that is lately changing to integron cassette) that generally carries one promoterless open reading frame (ORF) together with a recombination site (''attC''). Integron cassettes are incorporated to the ''attI'' site of the integron platform by site-specific recombination reactions mediated by the integrase. Discovery Integrons were initially discovered on conjugative plasmids through their role in antibiotic resistance. Indeed, these mobile integrons, as they are now known, can carry a variety of cassettes containing genes that are almost exclusively related to antibiotic resistance. Further studies have come to the conclusion that integrons are chromosomal elements, and that their mobilisation onto plasmids has been fostered by transposons and selected by the inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Integrase
Retroviral integrase (IN) is an enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ... produced by a retrovirus (such as HIV) that integrates (forms covalent links between) its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases ( recombinases) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination. The macromolecular complex of an IN macromolecule bound to the ends of the viral DNA ends has been referred to as the '' intasome''; IN is a key component in this and the retroviral pre-integration complex. Structure All retroviral IN proteins contain three canonical domains, connected by flexible linkers: * an N-terminal HH-CC zinc-binding domain (a three-heli ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Contig
A contig (from ''contiguous'') is a set of overlapping DNA segments that together represent a consensus region of DNA.Gregory, S. ''Contig Assembly''. Encyclopedia of Life Sciences, 2005. In bottom-up sequencing projects, a contig refers to overlapping sequence data ( reads); in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly.Dear, P. H. ''Genome Mapping''. Encyclopedia of Life Sciences, 2005. . Contigs can thus refer both to overlapping DNA sequences and to overlapping physical segments (fragments) contained in clones depending on the context. Original definition of contig In 1980, Staden wrote: ''In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig". A contig is a set of gel readings that are related to one another by overlap of their sequences. All gel readings belong to one and only one cont ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
