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Katherine Johnson’s mathematical calculations helped guide some of America’s most important early space missions while she confronted the racial and gender barriers faced by Black women in twentieth-century America.
MORE →Reflects the personal views, recollections, and perspective of the author, Mike Davis.
This is a personal recollection on the Move fire on May 13, 1985
Mutalyzer is a web-based software tool which was primarily developed to check the description of sequence variants identified in a gene during genetic testing.[1] Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence record containing the transcript and protein feature annotation as a reference. Mutalyzer 2 accepts GenBank and Locus Reference Genomic (LRG) records. The annotation is also used to apply the correct codon translation tables and generate DNA and protein variant descriptions for any organism. The Mutalyzer server supports programmatic access via a SOAP Web service described in the Web Services Description Language (WSDL) and an HTTP/RPC+JSON web service.
Genetic testing is generally performed in families with hereditary disease. Any sequence variant identified in a gene can be described in test reports using the position of the change and the nucleotide or amino acid involved. With this simple rule, a deletion of the nucleotide guanine (G) in a stretch of 4 G nucleotides might be described in 4 different ways, when each of the G positions is used. Although different descriptions do not affect the functional consequences of the change, they may obfuscate the fact that two persons share the same variant or the real frequency of a variant in the population. The standard human sequence variant nomenclature proposed by the Human Genome Variation Society was developed to solve this problem.[2] Proper variant descriptions are expected to facilitate searches for more information about the functional consequences in the literature and in gene variant or locus-specific databases (LSDBs).
Mutalyzer is used by the Leiden Open Variation Database (LOVD), which stores sequence variant information for many human genes, to check variant descriptions before submission of new data.[3] This helps data sharing, display and integration with other genetic resources (e.g., Ensembl, UCSC Genome Browser, NCBI sequence viewer)
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Mutalyzer is a web-based software tool which was primarily developed to check the description of sequence variants identified in a gene during genetic testing. Mutalyzer applies the rules of the standard human sequence variant nomenclature and can correct descriptions accordingly. Apart from the sequence variant description, Mutalyzer requires a DNA sequence record containing the transcript and protein feature annotation as a reference. Mutalyzer 2 accepts GenBank and Locus Reference Genomic (LRG) records. The annotation is also used to apply the correct codon translation tables and generate DNA and protein variant descriptions for any organism. The Mutalyzer server supports programmatic access via a SOAP Web service described in the Web Services Description Language (WSDL) and an HTTP/RPC+JSON web service.
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Mutations result from errors during replication, mitosis, meiosis, or damage to DNA, which then may trigger error-prone repair or cause an error during replication (translesion synthesis). Mutations may also result from substitution, insertion or deletion of segments of DNA due to mobile genetic elements. Mutations may or may not produce detectable changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system, including junctional diversity. Mutation is the ultimate source of all genetic variation, providing the raw material on which evolutionary forces such as natural selection can act. Mutation can result in many different types of change in sequences. Mutations in genes can have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely. Mutations can also occur in non-genic regions. A 2007 study on genetic variations between different species of Drosophila suggested that, if a mutation changes a protein produced by a gene, the result is likely to be harmful, with an estimated 70% of amino acid polymorphisms having damaging effects, and the remainder being either neutral or marginally beneficial. Mutation and DNA damage are the two major types of errors that occur in DNA, but they are fundamentally different. DNA damage is a physical alteration in the DNA structure, such as a single or double strand break, a modified guanosine residue in DNA such as 8-hydroxydeoxyguanosine, or a polycyclic aromatic hydrocarbon adduct. DNA damages can be recognized by enzymes, and therefore can be correctly repaired using the complementary undamaged strand in DNA as a template or an undamaged sequence in a homologous chromosome if it is available. If DNA damage remains in a cell, transcription of a gene may be prevented and thus translation into a protein may also be blocked. DNA replication may also be blocked and/or the cell may die. In contrast to a DNA damage, a mutation is an alteration of the base sequence of the DNA. Ordinarily, a mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation is not ordinarily repaired. At the cellular level, mutations can alter protein function and regulation. Unlike DNA damages, mutations are replicated when the cell replicates. At the level of cell populations, cells with mutations will increase or decrease in frequency according to the effects of the mutations on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation.
The Leiden Open Variation Database (LOVD) is a free, flexible web-based open source database developed in the Leiden University Medical Center in the Netherlands, designed to collect and display variants in the DNA sequence. The focus of an LOVD is usually the combination between a gene and a genetic (heritable) disease. All sequence variants found in individuals are collected in the database, together with information about whether they could be causally connected to the disease (i.e. a disease-causing variant or mutation) or not (i.e. a non-disease causing variant). Specialized doctors (clinical geneticists) use LOVDs to diagnose and advise patients carrying a genetic disease. Ideally, if a patient has been screened for mutations and one has been found, information in LOVD can predict the progress of the disease. In contrast to human genome databases, showing information on all DNA variants, LOVDs include information about the individuals in which the variants were found. This patient information is usually only accessible for registered users. Currently, LOVD installations worldwide contain more than 515,500 variant observations (124,000 unique variants in 5175 genes) in 162,000 patients.
Locus Reference Genomic (LRG) is a DNA sequence format that was developed to aid in curating locus specific databases (LSDBs) that record DNA sequence variation which can result in inherited diseases. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The LRG format uses extensible markup language (XML) to provide highly structured single records containing the genomic DNA sequence for individual genes along with the mRNAs and proteins encoded by these genes. LRG records are recommended in the Human Genome Variation Society Nomenclature guidelines as reference sequences to report sequence variants in LSDBs and the literature. The LRG concept was developed by the GEN2PHEN project in conjunction with the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI). The LRG homepage provides access to existing LRG sequences and allows the submission of requests for the creation of new LRGs. This page also has a frequently asked questions (FAQs) section.
Before the 1921 destruction of Tulsa’s Greenwood District, Black residents had created a remarkable center of business and community life. The district included stores, professional offices, entertainment venues and homes owned by Black citizens. Understanding Greenwood means learning what was built—not only what was burned.
MORE →Joe Louis.