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SAINT LOUIS, MO, United States

Liu Y.-H.,Texas A&M University | Zhang M.,Jilin Agricultural University | Wu C.,Texas A&M University | Wu C.,Intact Genomics, Inc. | And 2 more authors.
Genome | Year: 2014

Knowledge of how a genome is structured and organized from its constituent elements is crucial to understanding its biology and evolution. Here, we report the genome structuring and organization pattern as revealed by systems analysis of the sequences of three model species, Arabidopsis, rice and yeast, at the whole-genome and chromosome levels. We found that all fundamental function elements (FFE) constituting the genomes, including genes (GEN), DNA transposable elements (DTE), retrotransposable elements (RTE), simple sequence repeats (SSR), and (or) low complexity repeats (LCR), are structured in a nonrandom and correlative manner, thus leading to a hypothesis that the DNA of the species is structured as a linear "jigsaw puzzle". Furthermore, we showed that different FFE differ in their importance in the formation and evolution of the DNA jigsaw puzzle structure between species. DTE and RTE play more important roles than GEN, LCR, and SSR in Arabidopsis, whereas GEN and RTE play more important roles than LCR, SSR, and DTE in rice. The genes having multiple recognized functions play more important roles than those having single functions. These results provide useful knowledge necessary for better understanding genome biology and evolution of the species and for effective molecular breeding of rice. © 2013 Published by NRC Research Press. Source


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 211.45K | Year: 2015

DESCRIPTION provided by applicant There is societal need for new therapeutic agents in our arsenal of defenses against bacterial and fungal pathogens many of which are increasingly resistant to existing antibiotics Filamentous fungi are considered promising resources for the development of novel bioactive compounds because of their great potential to produce various kinds of secondary metabolites SM however antibiotic discovery and production in fungi lags far behind bacteria This research proposal advances sciences of fungal functional genomics to activate fungal silent SM clusters by using the newly developed fungal artificial chromosomes FACs Our purpose is to discover novel antibiotics and identify the best lead candidates for clinical development Scientists at Intact Genomics Inc and the University of Wisconsin at Madison will develop utilize and combine three aspects of novel technology innovation and genomic tools to enable therapeutic agent discovery in fungi Specifically the proposed research will identify antibiotic compounds using genetically enhanced A nidulans strains in vitro BAC FAC engineering and culture conditions with epigenetic modifications and bacterial co culture The primary objectives are to activate at least of silent and or cryptic SM gene clusters FACs of A terreus for proof of concept using the above technologies and to screen these activated FACs against bacterial and fungal tester strains to discover novel antibacterial and antifungal properties Our long term goals are to develop a high through put small molecule discovery platform in fungi in order to discover novel natural products from at least silent SM pathways from completely sequenced fungal genomes Moreover we will characterize identified antimicrobial agents to determine the best lead candidates for clinical development Lead candidates will have novel chemical structures high potency against bacterial and or fungal pathogens and minimal toxicity for eukaryotic cells Each of the different technologies necessary for the proposed research has been proven effective separately therefore the combination of these different techniques has a high probability of success and also represents a significant advancement for the science of antibiotic discovery In addition the activated silent SM clusters and their metabolites produced from this research are a valuable resource that may be screened for other bioactive compounds e g with anticancer or antiviral activities in subsequent research PUBLIC HEALTH RELEVANCE The need for new therapeutic agents has reached an intensity not experienced since the commercialization of antibiotics in the s but many traditionally fruitful sources of chemistry have ceased to yield new compounds This research will develop utilize and combine three aspects of novel technology innovation and genomic tools to enable therapeutic agent discovery in the successfully engineered fungal host Aspergillus nidulans by activating and expressing fungal silent secondary metabolic pathways directly without the need to cultivate and engineer the different fungi in a laboratory This technology will access the nove small molecules produced by a great diversity of filamentous fungi many of which are unknown to science and will identify the best novel therapeutic compounds for use in treating bacterial and fungal diseases


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase I | Award Amount: 224.87K | Year: 2016

DESCRIPTION provided by applicant There is societal need for new therapeutic agents in our arsenal of defenses against bacterial and fungal pathogens many superbugs of which are increasingly resistant to existing antibiotics Filamentous fungi are considered promising resources for the development of novel bioactive compounds because of their great potential to produce various kinds of secondary metabolites SM however natural product NP discovery and production in fungi lags far behind plants and bacteria This research proposal advances sciences of fungal functional genomics to develop a robust heterologous expression system for intact SM gene clusters in the filamentous fungus Aspergillus nidulans by using the newly developed fungal artificial chromosomes FACs Our purpose is to discover novel antibiotics and identify the best lead candidates for clinical development Scientists at Intact Genomics Inc University of Wisconsin at Madison Donald Danforth Plant Science Center and Northwestern University will develop utilize and combine at least aspects of novel technology innovation and genomic tools to enable NP discovery in fungi Specifically the proposed research will identify NP compounds using i the unbiased large insert Random Shear Shuttle BAC libraries as FACs ii more than large intact SM gene clusters about kb in the completely sequenced genome of fungal strains iii the knowledge of regulatory elements strong promotors for high heterologous expression of SM gene clusters in Aspergillus iv the successfully engineered fungal host A nidulans to provide a robust background in which to search for new metabolites v in vitro BAC FAC engineering vi advanced LC MS analysis The primary objectives of Phase I research are to develop simple FAC transformation method in an optimized A nidulans strain to activate at least of silent and or cryptic SM gene clusters FACs for proof of concept using the above technologies to discover novel NP compounds Our long term goals are to develop a high through put small molecule discovery platform in fungi in order to discover novel natural products from at least fungal intact SM pathways from completely sequenced fungal genomes Moreover we will characterize identified antimicrobial agents to determine the best lead candidates for clinical development Lead candidates will have novel chemical structures high potency against bacterial and or fungal pathogens and minimal toxicity for eukaryotic cells The combination of these novel technological innovations has a high probability of success and also represents a significant advancement for the science of natural product discovery In addition the novel SM clusters and their metabolites produced from this research are a valuable resource that may be screened for other bioactive compounds e g with anticancer or antiviral activities in subsequent research PUBLIC HEALTH RELEVANCE The need of new natural products for therapeutic agents has reached an intensity not experienced since the commercialization of antibiotics in the s but many traditionally fruitful sources of chemistry have ceased to yield new compounds This research will develop utilize and combine at least aspects of novel technological innovations and genomic tools to achieve a robust fungal artificial chromosome heterologous expression system for natural product production in Aspergillus nidulans without the need to cultivate and engineer the different fungi in a laboratory This technology will access the novel small molecules produced by a great diversity of filamentous fungi many of which are unknown to science and will identify the best novel therapeutic compounds for use in treating bacterial and fungal diseases


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Cas9 NucleaseIntact Genomics Cas9 Nuclease is the purified recombinant Streptococcus pyogenes Cas9 enzyme containing a nuclear localization signal (NLS) at the C-terminal for targeting to the nucleus. This enzyme is designed to perform CRISPR/Cas9-mediated genome editing (1, 2) ...

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