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  1. Article ; Online: Bacteriophage T4 capsid packaging and unpackaging of DNA and proteins.

    Mullaney, Julienne M / Black, Lindsay W

    Methods in molecular biology (Clifton, N.J.)

    2013  Volume 1108, Page(s) 69–85

    Abstract: Bacteriophage T4 has proven itself readily amenable to phage-based DNA and protein packaging, expression, and display systems due to its physical resiliency and genomic flexibility. As a large dsDNA phage with dispensable internal proteins and ... ...

    Abstract Bacteriophage T4 has proven itself readily amenable to phage-based DNA and protein packaging, expression, and display systems due to its physical resiliency and genomic flexibility. As a large dsDNA phage with dispensable internal proteins and dispensable outer capsid proteins it can be adapted to package both DNA and proteins of interest within the capsid and to display peptides and proteins externally on the capsid. A single 170 kb linear DNA, or single or multiple copies of shorter linear DNAs, of any sequence can be packaged by the large terminase subunit in vitro into protein-containing proheads and give full or partially full capsids. The prohead receptacles for DNA packaging can also display peptides or full-length proteins from capsid display proteins HOC and SOC. Our laboratory has also developed a protein expression, packaging, and processing (PEPP) system which we have found to have advantages over mammalian and bacterial cell systems, including high yield, increased stability, and simplified downstream processing. Proteins that we have produced by the phage PEPP platform include human HIV-1 protease, micrococcal endonuclease from Staphylococcus aureus, restriction endonuclease EcoRI, luciferase, human granulocyte colony stimulating factor (GCSF), green fluorescent protein (GFP), and the 99 amino acid C-terminus of amyloid precursor protein (APP). Difficult to produce proteins that are toxic in mammalian protein expression systems are easily produced, packaged, and processed with the PEPP platform. APP is one example of such a highly refractory protein that has been produced successfully. The methods below describe the procedures for in vitro packaging of proheads with DNA and for producing recombinant T4 phage that carry a gene of interest in the phage genome and produce and internally package the corresponding protein of interest.
    MeSH term(s) Bacteriophage T4/genetics ; Bacteriophage T4/metabolism ; Bacteriophage T4/physiology ; Capsid/metabolism ; DNA Packaging ; DNA, Recombinant ; Genetic Engineering/methods ; Genetic Vectors/genetics ; Viral Plaque Assay/methods ; Virus Assembly
    Chemical Substances DNA, Recombinant
    Language English
    Publishing date 2013-11-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-62703-751-8_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Small insertions and deletions (INDELs) in human genomes.

    Mullaney, Julienne M / Mills, Ryan E / Pittard, W Stephen / Devine, Scott E

    Human molecular genetics

    2010  Volume 19, Issue R2, Page(s) R131–6

    Abstract: In this review, we focus on progress that has been made with detecting small insertions and deletions (INDELs) in human genomes. Over the past decade, several million small INDELs have been discovered in human populations and personal genomes. The amount ...

    Abstract In this review, we focus on progress that has been made with detecting small insertions and deletions (INDELs) in human genomes. Over the past decade, several million small INDELs have been discovered in human populations and personal genomes. The amount of genetic variation that is caused by these small INDELs is substantial. The number of INDELs in human genomes is second only to the number of single nucleotide polymorphisms (SNPs), and, in terms of base pairs of variation, INDELs cause similar levels of variation as SNPs. Many of these INDELs map to functionally important sites within human genes, and thus, are likely to influence human traits and diseases. Therefore, small INDEL variation will play a prominent role in personalized medicine.
    MeSH term(s) Genetic Variation/genetics ; Genome, Human/genetics ; Humans ; Mutagenesis, Insertional/genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Deletion/genetics
    Language English
    Publishing date 2010-09-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddq400
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Natural genetic variation caused by small insertions and deletions in the human genome.

    Mills, Ryan E / Pittard, W Stephen / Mullaney, Julienne M / Farooq, Umar / Creasy, Todd H / Mahurkar, Anup A / Kemeza, David M / Strassler, Daniel S / Ponting, Chris P / Webber, Caleb / Devine, Scott E

    Genome research

    2011  Volume 21, Issue 6, Page(s) 830–839

    Abstract: Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and ... ...

    Abstract Human genetic variation is expected to play a central role in personalized medicine. Yet only a fraction of the natural genetic variation that is harbored by humans has been discovered to date. Here we report almost 2 million small insertions and deletions (INDELs) that range from 1 bp to 10,000 bp in length in the genomes of 79 diverse humans. These variants include 819,363 small INDELs that map to human genes. Small INDELs frequently were found in the coding exons of these genes, and several lines of evidence indicate that such variation is a major determinant of human biological diversity. Microarray-based genotyping experiments revealed several interesting observations regarding the population genetics of small INDEL variation. For example, we found that many of our INDELs had high levels of linkage disequilibrium (LD) with both HapMap SNPs and with high-scoring SNPs from genome-wide association studies. Overall, our study indicates that small INDEL variation is likely to be a key factor underlying inherited traits and diseases in humans.
    MeSH term(s) Genetic Variation ; Genome, Human/genetics ; Genomics/methods ; Genotype ; Humans ; INDEL Mutation/genetics ; Microarray Analysis ; Precision Medicine/methods
    Language English
    Publishing date 2011-04-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.115907.110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: GFP:HIV-1 Protease Production and Packaging with a T4 Phage Expression-Packaging Processing System

    Julienne M. Mullaney / Lindsay W. Black

    BioTechniques, Vol 25, Iss 6, Pp 1008-

    1998  Volume 1012

    Abstract: A bacteriophage T4-derived protein expression, packaging and processing system was used to create recombinant phage that encode, produce and package a protein composed of human HIV-1 protease fused to green fluorescent protein (GFP). The fusion protein ... ...

    Abstract A bacteriophage T4-derived protein expression, packaging and processing system was used to create recombinant phage that encode, produce and package a protein composed of human HIV-1 protease fused to green fluorescent protein (GFP). The fusion protein is targeted within the phage capsid by an N-terminal capsid targeting sequence (CTS), which is cleaved through proteolysis by the viral scaffold protease P21. The fusion protein is designated CTS▾ GFP:PR. The ▾ symbol indicates the linkage peptide sequence leu(ile)-N-glu that is cleaved by the T4 head morphogenetic proteinase gp21 during head maturation. The fusion protein is fluorescent and has protease activity as detected by the appearance of the expected substrate cleavage product on a Western blot. CTS▾ GFP:PR packaging occurs at about 200 molecules per phage particle. The CTS▾ GFP:PR fusion protein, when protected within the phage capsid, has been maintained stably for over 16 months at 4°C. Production and storage of fusion protein within the phage circumvents problems of toxicity and solubility encountered with E. coli expression systems. Because recombinant phage inhibit host proteolytic enzymes, foreign proteins are stabilized. This phage system packages and processes the fusion protein by means of the CTS. Proteins can be purified from the phage to give high yields of soluble, proteolytically processed protein. The T4 phage packaging system provides a novel means of identification, purification and long-term storage of toxic proteins whose folding and DNA-directed activities can be studied readily in vivo.
    Keywords Biology (General) ; QH301-705.5
    Subject code 500
    Language English
    Publishing date 1998-12-01T00:00:00Z
    Publisher Future Science Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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