Computational Biology and High Performance Computing 2000

Tutorial to be presented at Supercomputing 2000, Dallas TX, 6-10 November 2000.This work was supported by the Director, Office of Science, Office of Advanced Scientific computing Research, Mathematical, Information, and Computational Sciences Division of the U.S. Department of Energy under Contract No. DE-AC03-76SF0009

Application of manufacturing tools in the DNA sequencing process

Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering; in conjunction with the Leaders for Manufacturing Program at MIT, 1999.Includes bibliographical references.by Louis E. Herena.S.M.M.B.A

Computational Biology and High Performance Computing 2000

Tutorial to be presented at Supercomputing 2000, Dallas TX, 6-10 November 2000.This work was supported by the Director, Office of Science, Office of Advanced Scientific computing Research, Mathematical, Information, and Computational Sciences Division of the U.S. Department of Energy under Contract No. DE-AC03-76SF0009

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA.We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens

Comparative genomics of Meloidogyne haplanaria

Root-knot nematodes are a scientifically and agriculturally importantgroup of plant parasites. Genomic investigations into this group have proven difficult due to a complex genomic arrangement and recent inter-species hybridisations. Here we design and employ novel bioinformatic workflows to assemble the genomes of Meloidogyne species and perform phylogenomic analyses on them. We use Meloidogyne haplanaria -an emerging crop pest recently shown to be capable of breaking cultivated resistance -as a test organism. We assemble and annotate its genome for the first time andinfer itsposition in the Meloidogynephylogeny. This will inform future investigations into diagnostic and control methods, as well as investigations into the evolutionary history of the genus. The workflows themselves will provide accessible bioinformatic tools for the reproducible assembly and phylogenomic analysis of Meloidogynegenomes to the wider scientific community. Greater elucidation of the complex genomics of the Meloidogyne genus can grant insight into many biological processes, including hybridisation,parasitic adaptation and evolution in the absence of recombination, and the effect that different parthenogenetic sexual systems can have on genomic architecture

Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions: Workshop Report

This report on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions summarizes the presentations, deliberations and findings of a workshop at NASA Ames Research Center, March 24-26, 2015, which was attended by more than 100 participants representing a diverse mix of science, engineering, technology, and policy areas. The main objective of the three-day workshop was to identify specific knowledge gaps that need to be addressed to make incremental progress towards the development of NASA Procedural Requirements (NPRs) for Planetary Protection during human missions to Mars

Engineering a feedback-based synthetic gene circuit for targeted continuous evolution of a gene in E. coli

Directed evolution is an invaluable technique for engineering proteins to possess desired physical and chemical properties when very little structural and functional information is known. It is divided into two sequential steps: generating a library of protein variants using mutagenic techniques; and applying a screening or selection strategy to scan the library for variants displaying desired properties. Library generation is performed using either in vitro or in vivo techniques, while screening or selection typically occurs in a suitable host cell. Currently, in vitro methods like error-prone PCR are popular for library generation. However, these techniques can be labour intensive, prone to mutation biases, and generate limited library sizes for screening. In vivo mutagenic techniques overcome these limitations by enabling simultaneous library generation and selection within cells. By generating random mutations in the gene-of-interest within one cell cycle, each cell in a batch culture potentially represents a library variant. Such a continuous evolution system can run for weeks with minimal human intervention, greatly expanding the genetic search space for protein engineering. The challenge lies in developing a mutator system that specifically generates mutations in the target gene, while maintaining the cell’s genomic fidelity. With this goal in mind, a mutator system was engineered in E. coli that introduces targeted cytidine deamination damage and subsequently performs error-prone DNA repair by hijacking the base excision repair pathway. The targeted damage occurs via activation induced cytidine deaminase fused to T7 RNA polymerase, while the error-prone DNA repair is performed by a three-protein fusion comprising a 5’-3’-exonuclease, an AP-endonuclease and an error-prone DNA polymerase. The mutagenic characteristics of this system was tested by knocking out GFP expression and analysing the mutant library using next generation sequencing techniques. The system was also experimentally shown to generate functionally active mutations that reverted inactivated β-lactamase gene variants to confer ampicillin resistance.Open Acces

Mare Geneticum : Balancing Governance of Marine Genetic Resources in International Waters

Peer reviewedPublisher PD