PPT-Identifying recombination events in phage Giles through presence of repeat sequences

Megan Mair Mycobacteriophage Giles Genes Unique to Giles Genes Conserved in Other Phages 72 57 genes 28 22 genes A B C D F G H I J K M N P R T Singleton clusters. 9/30/2010. The role of Artificial Neural Networks in Phage Research . What is an Artificial Neural Network?. Mathematical and computational model. Motivated by biological neurons. Trained by using features to learn patterns and commonalities. MUTAGENESIS. DNA DAMAGE. DNA REPAIR. RECOMBINATION. MUTAGENESIS. Mutations. Mutations are heritable permanent changes in the base sequence of DNA.. Point mutations may be . transitions. (e.g. GC→AT) or . Summary of assumptions so far. We have covered the role of chance (parent choice), demography (population size) and mutation, in shaping genetic diversity. . Neutral Wright-Fisher . models. Parents are always chosen at random. This means no new mutations affect reproductive success of parents, i.e. . How to identify circularly permuted genomes, physical ends, 3’ overhangs, terminal repeats, and nicks.. Circularly Permuted Genomes. Some phages have circularly permuted genomes. This means a linear concatamer of phage DNA is synthesized, used to fill a phage head, then cut when the head is full. Generally, one head will fit more than 100% of a genome, say, 103-110%. This ensures that wherever the DNA is cut, at least one working copy of each gene is present.. Abdulrahman. . Alazemi. , . Shahroze. Abbas, Liam Lewis, Donald Ta, Ann Vo. Overview. Clustered repeats. Wide variety of functions. History largely unknown. Regulatory Sites. A segment capable of altering expression of specific genes. Index. Introduction. Discovery. Linkage data from transduction. Specialized transduction. Lytic and Lysogenic Cycle. Introduction. Transduction is the process by which DNA. . is transferred from one bacterium to another by a virus.. Do Huy Hoang. Outline. Introduction. What is a repeat?. Why studying repeats?. Related . work. SAGRI. Algorithm. Analysis. Evaluation. Introduction. What is a repeat? (Definition). [General]: Nucleotide sequences occurring multiply within a genome. . Author: Michael Arnoult, San Diego State University. Mentors: Victor Seguritan, Anca Segall, and Peter Salamon, Department of Biology, San Diego State University. Methods:. Bacteriophages are the single most abundant biological entity on earth, and influence every environment in which bacteria exist. There are no current algorithms which reliably analyze phage structural protein sequences and predict their function. . Circularly Permuted Genomes. Some phages have circularly permuted genomes. This means a linear concatamer of phage DNA is synthesized, used to fill a phage head, then cut when the head is full. Generally, one head will fit more than 100% of a genome, say, 103-110%. This ensures that wherever the DNA is cut, at least one working copy of each gene is present.. McClintock, (1902–1992). An . American scientist and . cytogeneticist.  who was awarded the 1983 . Nobel Prize in . Physiology.. She received her . Ph.D. from.  . Cornell University.  in . 1927. She studied . . DNA in mycobacterial genomes. . Bobby Chaggar. BNFO 301. Lysogeny. Group. Compare (SEQUENCE-SIMILAR-TO) each lysogenic, . mycobacteriophage. to a list of all mycobacteria in . BioBIKE. (. PhAnToMe. Bull R, Hansman GS, Clancy LE, Tanaka MM, Rawlinson WD, White PA. Norovirus Recombination in ORF1/ORF2 Overlap. Emerg Infect Dis. 2005;11(7):1079-1085. https://doi.org/10.3201/eid1107.041273. General background to site-specific recombination . The lambda recombination system (more stealing from other organisms!). Potential advantages of using recombination for cloning. Adaptation of the lambda recombination system for efficient cloning – GATEWAY technology. the attB1 & 2 sequences are relatively short and are therefore suitable for addition to gene-specific primers . After PCR amplification, fragment contains the attB1 and attb2 sequences, and can be used for recombination with a vector carrying the attP1 and atP2 sequences, and the addition of the BP clonase enzyme mix. .