|
Infologs
Infologs are independently designed synthetic genes derived from one or a few genes where substitutions are systematically incorporated to maximize information. Infologs are designed for perfect diversity distribution to maximize search efficiency. Typical protein engineering methods rely on screening a high number (106-1012 or more) of gene variants to identify individuals with improved activity using a surrogate high throughput screen (HTP) to identify initial hits. Unfortunately, results are defined by what is screened for, thus the “hit” from the HTP screen often has very little real activity in a lower throughput assay more indicative of the improved functionality for which the protein is being developed. By adapting the standard algorithms for engineering complex systems to work with biological systems, the resulting process enables researchers to deconvolute how substitutions within a protein sequence modify its function. Combining these algorithms with an integrated que ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Artificial Gene Synthesis
Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides '' de novo''. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size. Synthesis of the first complete gene, a yeast tRNA, was demonstrated by Har Gobind Khorana and coworkers in 1972. Synthesis of the first peptide- and protei ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Engineering
Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It has been used to improve the function of many enzymes for industrial catalysis. It is also a product and services market, with an estimated value of $168 billion by 2017. There are two general strategies for protein engineering: rational protein design and directed evolution. These methods are not mutually exclusive; researchers will often apply both. In the future, more detailed knowledge of protein structure and function, and advances in high-throughput screening, may greatly expand the abilities of protein engineering. Eventually, even unnatural amino acids may be included, via newer methods, such as expanded genetic code, that allow encoding novel amino acids in genetic code. Approaches Rational design In rational protein design, a scientist uses ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology (biology)
In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555. In developmental biology, organs that developed in the embryo in the same manner and from similar origins, such as from matching p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Horizontal Gene Transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms. HGT is influencing scientific understanding of higher order evolution while more significantly shifting perspectives on bacterial evolution. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created Bactericide, pesticides and in the evolution, maintenance, and transmission of virulence. It often involves Temperateness (virology), temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Glutathione S-transferase
Glutathione ''S''-transferases (GSTs), previously known as ligandins, are a family of eukaryotic and prokaryotic phase II metabolic isozymes best known for their ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification. The GST family consists of three superfamilies: the cytosolic, mitochondrial, and microsomal—also known as MAPEG—proteins. Members of the GST superfamily are extremely diverse in amino acid sequence, and a large fraction of the sequences deposited in public databases are of unknown function. The Enzyme Function Initiative (EFI) is using GSTs as a model superfamily to identify new GST functions. GSTs can constitute up to 10% of cytosolic protein in some mammalian organs. GSTs catalyse the conjugation of GSH—via a sulfhydryl group—to electrophilic centers on a wide variety of substrates in order to make the compounds more water-soluble. This activity detoxifies endogenous co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Site-directed Mutagenesis
Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesis, it is used for investigating the structure and biological activity of DNA, RNA, and protein molecules, and for protein engineering. Site-directed mutagenesis is one of the most important laboratory techniques for creating DNA libraries by introducing mutations into DNA sequences. There are numerous methods for achieving site-directed mutagenesis, but with decreasing costs of oligonucleotide synthesis, artificial gene synthesis is now occasionally used as an alternative to site-directed mutagenesis. Since 2013, the development of the CRISPR/Cas9 technology, based on a prokaryotic viral defense system, has also allowed for the editing of the genome, and mutagenesis may be performed ''in vivo'' with relative ease. History Early attempt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Algorithms
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing calculations and data processing. More advanced algorithms can perform automated deductions (referred to as automated reasoning) and use mathematical and logical tests to divert the code execution through various routes (referred to as automated decision-making). Using human characteristics as descriptors of machines in metaphorical ways was already practiced by Alan Turing with terms such as "memory", "search" and "stimulus". In contrast, a heuristic is an approach to problem solving that may not be fully specified or may not guarantee correct or optimal results, especially in problem domains where there is no well-defined correct or optimal result. As an effective method, an algorithm can be expressed within a finite amount of space and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OrthoDB
OrthoDB presents a catalog of orthologous protein-coding genes across vertebrates, arthropods, fungi, plants, and bacteria. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each major radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive orthology database querying. OrthoDB also provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and gene intron-exon architectures. In comparative genomics, the importance of scale cannot be underestimated. As gene orthology delineation requires specific expertise and considerable computational resources, scale is something that individual non-specialist research groups cannot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Folding
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Synthetic Biology
Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology, biomaterials, material science/engineering, genetic engineering, molecular biology, molecular engineering, systems biology, membrane science, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering and evolutionary biology. Due to more powerful genetic engineering capabilities and decreased DNA synthesis and sequencing costs, the field of synthetic biology is rapidly growing. In 2016, more than 350 companies across 40 countries were actively engaged in synthetic biology applications; all these companies had an estimated net worth of $3.9 billion in the global market. Definition Synthetic biology currently has no gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Engineering
Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It has been used to improve the function of many enzymes for industrial catalysis. It is also a product and services market, with an estimated value of $168 billion by 2017. There are two general strategies for protein engineering: rational protein design and directed evolution. These methods are not mutually exclusive; researchers will often apply both. In the future, more detailed knowledge of protein structure and function, and advances in high-throughput screening, may greatly expand the abilities of protein engineering. Eventually, even unnatural amino acids may be included, via newer methods, such as expanded genetic code, that allow encoding novel amino acids in genetic code. Approaches Rational design In rational protein design, a scientist uses ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
.svg "Click for more on -> Horizontal Gene Transfer"){kind=spacer}
