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Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in the context of, for example, phenotypic evolution or population genetics.
Silent mutations are mutations in DNA that do not have an observable effect on the organism's phenotype. They are a specific type of neutral mutation. The phrase silent mutation is often used interchangeably with the phrase synonymous mutation; however, synonymous mutations are not always silent, nor vice versa. Synonymous mutations can affect transcription, splicing, mRNA transport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent. The substrate specificity of the tRNA to the rare codon can affect the timing of translation, and in turn the co-translational folding of the protein. This is reflected in the codon usage bias that is observed in many species. Mutations that cause the altered codon to produce an amino acid with similar functionality are often classified as silent; if the properties of the amino acid are conserved, this mutation does not usually significantly affect protein function.
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In bioinformatics, k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides, k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term k-mer refers to all of a sequence's subsequences of length , such that the sequence AGAT would have four monomers, three 2-mers, two 3-mers and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and total possible k-mers, where is number of possible monomers.
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Reverse genetics is a method in molecular genetics that is used to help understand the function(s) of a gene by analysing the phenotypic effects caused by genetically engineering specific nucleic acid sequences within the gene. The process proceeds in the opposite direction to forward genetic screens of classical genetics. While forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes are controlled by particular genetic sequences.
Synthetic virology is a branch of virology engaged in the study and engineering of synthetic man-made viruses. It is a multidisciplinary research field at the intersection of virology, synthetic biology, computational biology, and DNA nanotechnology, from which it borrows and integrates its concepts and methodologies. There is a wide range of applications for synthetic viral technology such as medical treatments, investigative tools, and reviving organisms.
An mRNAvaccine is a type of vaccine that uses a copy of a molecule called messenger RNA (mRNA) to produce an immune response. The vaccine delivers molecules of antigen-encoding mRNA into immune cells, which use the designed mRNA as a blueprint to build foreign protein that would normally be produced by a pathogen or by a cancer cell. These protein molecules stimulate an adaptive immune response that teaches the body to identify and destroy the corresponding pathogen or cancer cells. The mRNA is delivered by a co-formulation of the RNA encapsulated in lipid nanoparticles that protect the RNA strands and help their absorption into the cells.
Tim Harris is a molecular biologist/biochemist who is a science and business leader who has led laboratory work, scientists and companies in a range of research activities in the Biotechnology Industry since 1978.
References
- ↑ Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S (2008). "Virus attenuation by genome-scale changes in codon pair bias". Science. 320 (5884): 1784–7. Bibcode:2008Sci...320.1784C. doi:10.1126/science.1155761. PMC 2754401 . PMID 18583614.
- ↑ Coffin JM (2008). "Attenuation by a thousand cuts". N Engl J Med. 359 (21): 2283–5. doi:10.1056/NEJMcibr0805820. PMID 19020330.
- ↑ Enserink M (2008). "'Biased' viruses suggest new vaccine strategy for polio and other diseases". Science. 320 (5884): 1709. doi:10.1126/science.320.5884.1709a. PMID 18583587. S2CID 43533769.
- ↑ Robinson HL (2008). "Viral attenuation by design". Nat Biotechnol. 26 (9): 1000–1. doi: 10.1038/nbt0908-1000 . PMID 18779812.
- ↑ Timmer, John (2008-06-27). "Biased viruses make for good vaccines". Ars Technica. Retrieved 2023-01-29.
- ↑ Aldhous, Peter (2006-05-31). "'Alien code' leads to faster vaccines". New Scientist. Retrieved 2023-01-29.
- ↑ "In the News: Silent mutations cause a stir". Nature Reviews Microbiology. 6 (8): 574–575. August 2008. doi: 10.1038/nrmicro1965 . ISSN 1740-1534.