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152 results on '"Sanderson Christopher M"'

1. The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks

Author

Dudbridge Frank, Dunn Ruth, and Sanderson Christopher M

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background This paper describes an automated method for finding clusters of interconnected proteins in protein interaction networks and retrieving protein annotations associated with these clusters. Results Protein interaction graphs were separated into subgraphs of interconnected proteins, using the JUNG implementation of Girvan and Newman's Edge-Betweenness algorithm. Functions were sought for these subgraphs by detecting significant correlations with the distribution of Gene Ontology terms which had been used to annotate the proteins within each cluster. The method was implemented using freely available software (JUNG and the R statistical package). Protein clusters with significant correlations to functional annotations could be identified and included groups of proteins know to cooperate in cell metabolism. The method appears to be resilient against the presence of false positive interactions. Conclusion This method provides a useful tool for rapid screening of small to medium size protein interaction datasets.

Published
2005
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3. Brusatol provokes a rapid and transient inhibition of Nrf2 signaling and sensitizes mammalian cells to chemical toxicity—implications for therapeutic targeting of Nrf2

Author

Olayanju, Adedamola, Copple, Ian M., Bryan, Holly K., Edge, George T., Sison, Rowena L., Wong, Min Wei, Lai, Zheng-Quan, Lin, Zhi-Xiu, Dunn, Karen, Sanderson, Christopher M., Alghanem, Ahmad F., Cross, Michael J., Ellis, Ewa C., Ingelman-Sundberg, Magnus, Malik, Hassan Z., Kitteringham, Neil R., Goldring, Christopher E., and Park, Kevin B.

Published
2015
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5. In search of antisense

Author

Lavorgna, Giovanni, Dahary, Dvir, Lehner, Ben, Sorek, Rotem, Sanderson, Christopher M., and Casari, Giorgio

Subjects
Biological sciences, Chemistry
Abstract

In recent years, natural antisense transcripts (NATs) have been implicated in many aspects of eukaryotic gene expression including genomic imprinting, RNA interference, translational regulation, alternative splicing, X-inactivation and RNA editing. Moreover, there is growing evidence to suggest that antisense transcription might have a key role in a range of human diseases. Consequently, there have been several recent attempts to identify novel NATs. To date, ~2500 mammalian NATs have been found, indicating that antisense transcription might be a common mechanism of regulating gene expression in human cells. There are increasingly diverse ways in which antisense transcription can regulate gene expression and evidence for the involvement of NATs in human disease is emerging. A range of bioinformatic resources could be used to assist future antisense research.

Published
2004

17. Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis

Author

White, Rhiannon R., Ponsford, Amy H., Weekes, Michael P., Rodrigues, Rachel B., Ascher, David B., Mol, Marco, Selkirk, Murray E., Gygi, Steven P., Sanderson, Christopher M., and Artavanis-Tsakonas, Katerina

Subjects
PROTEIN, Muscle Proteins, Pathogenesis, Pathology and Laboratory Medicine, Biochemistry, Ligases, Rats, Sprague-Dawley, Database and Informatics Methods, 1108 Medical Microbiology, Tandem Mass Spectrometry, Medicine and Health Sciences, CONJUGATING ENZYME, Post-Translational Modification, PROTEASOME, lcsh:QH301-705.5, Musculoskeletal System, LIGASE, Muscles, Trichinellosis, Helminth Proteins, Enzymes, 1107 Immunology, Host-Pathogen Interactions, Anatomy, Life Sciences & Biomedicine, Sequence Analysis, 0605 Microbiology, Research Article, EXPRESSION, lcsh:Immunologic diseases. Allergy, Motor Proteins, Sequence Databases, Research and Analysis Methods, Microbiology, Host-Parasite Interactions, Molecular Motors, Virology, Parasitic Diseases, Animals, Humans, Immunoprecipitation, QUANTITATIVE PROTEOMICS, Molecular Biology Techniques, Sequencing Techniques, Muscle, Skeletal, Molecular Biology, Trichinella spiralis, Science & Technology, LARVAE, Ubiquitin, Ubiquitination, Biology and Life Sciences, Proteins, IN-VITRO, MASS-SPECTROMETRY, Cell Biology, Rats, Biological Databases, HEK293 Cells, lcsh:Biology (General), Skeletal Muscles, CELLS, Ubiquitin-Conjugating Enzymes, Enzymology, Parasitology, lcsh:RC581-607, Chromatography, Liquid
Abstract

Trichinella spiralis is a muscle-specific parasitic worm that is uniquely intracellular. T. spiralis reprograms terminally differentiated skeletal muscle cells causing them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. Although the host ubiquitin pathway is a common target for viruses and bacteria during infection, its role in parasite pathogenesis has been largely overlooked. Here we demonstrate that the secreted proteins of T. spiralis contain E2 Ub-conjugating and E3 Ub-ligase activity. The E2 activity is attributed to TsUBE2L3, a novel and conserved T. spiralis enzyme located in the secretory organ of the parasite during the muscle stages of infection. TsUBE2L3 cannot function with any T.spiralis secreted E3, but specifically binds to a panel of human RING E3 ligases, including the RBR E3 ARIH2 with which it interacts with a higher affinity than the mammalian ortholog UbcH7/UBE2L3. Expression of TsUBE2L3 in skeletal muscle cells causes a global downregulation in protein ubiquitination, most predominantly affecting motor, sarcomeric and extracellular matrix proteins, thus mediating their stabilization with regards to proteasomal degradation. This effect is not observed in the presence of the mammalian ortholog, suggesting functional divergence in the evolution of the parasite protein. These findings demonstrate the first example of host-parasite interactions via a parasite-derived Ub conjugating enzyme; an E2 that demonstrates a novel muscle protein stabilization function., Author Summary Parasitic worms often establish long-lasting infections in their hosts; tightly regulating their surroundings to strike a delicate balance between host cell modulation and protection that will ensure their replication. This is accomplished via the active secretion of parasite glycolipids and glycoproteins into the host. Trichinella spiralis, a parasitic nematode that infects skeletal muscle of mammals, birds and reptiles, is the only parasitic worm with a true intracellular stage. T. spiralis invade terminally differentiated myotubes, reprogramming them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. We have identified and characterized a novel T. spiralis secreted protein that, despite a high level of sequence identity, appears to have evolved a different function to its host ortholog. This protein is an active Ub conjugating enzyme that binds to a panel of human E3 Ub ligases with higher affinity than the host ortholog. Furthermore, when expressed in skeletal muscle cells in culture, its presence uniquely leads to the stabilization of muscle-specific proteins via the downregulation of their ubiquitination.

Published
2016

19. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Author

Markson, Gabriel, Kiel, Christina, Hyde, Russell, Brown, Stephanie, Charalabous, Panagoula, Bremm, Anja, Semple, Jennifer, Woodsmith, Jonathan, Duley, Simon, Salehi-Ashtiani, Kourosh, Vidal, Marc, Komander, David, Serrano, Luis, Lehner, Paul, and Sanderson, Christopher M.

Subjects
Gene mutations -- Analysis, Human evolution -- Analysis, Protein-protein interactions -- Analysis, Ubiquitin -- Analysis, Health
Published
2009

20. A new way to explore the world of extracellular protein interactions

Author

Sanderson, Christopher M.

Subjects
Genomics -- Analysis, Proteomics -- Analysis, Genetic translation -- Analysis, Health
Abstract

The article discusses the applicability of the high-throughput screening approach, avidity-based extracellular interaction screen (AVEXIS) for identifying the various weak extracellular protein interactions. The analysis has been extremely useful in the development of new therapeutic techniques.

Published
2008

21. A protein interation framework for human mRNA degradation

Author

Lehner, Ben and Sanderson, Christopher M.

Subjects
Genetic transcription -- Research, Messenger RNA -- Research, Genetic research, Health
Abstract

The degradation of mRNA is an important regulatory step in the control of gene expression. The level of each mRNA in a cell is a tightly regulated function of its rate of transcription, processing and degradation.

Published
2004

23. The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex

Author

Kozakova, Lucie, primary, Vondrova, Lucie, additional, Stejskal, Karel, additional, Charalabous, Panagoula, additional, Kolesar, Peter, additional, Lehmann, Alan R, additional, Uldrijan, Stjepan, additional, Sanderson, Christopher M, additional, Zdrahal, Zbynek, additional, and Palecek, Jan J, additional

Published
2015
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29. The MIT domain of UBPY constitutes a CHMP binding and endosomal localization signal required for efficient epidermal growth factor receptor degradation. VOLUME 282 (2007) PAGES 30929-30937

Author

Row, Paula E., primary, Liu, Han, additional, Hayes, Sebastian, additional, Welchman, Rebecca, additional, Charalabous, Panagoula, additional, Hofmann, Kay, additional, Clague, Michael J., additional, Sanderson, Christopher M., additional, and Urbé, Sylvie, additional

Published
2009
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49. The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks.

Author

Dunn, Ruth, Dudbridge, Frank, and Sanderson, Christopher M.

Subjects
PROTEIN-protein interactions, GRAPH theory, ALGORITHMS, STATISTICAL correlation, CELL metabolism
Abstract

Background: This paper describes an automated method for finding clusters of interconnected proteins in protein interaction networks and retrieving protein annotations associated with these clusters. Results: Protein interaction graphs were separated into subgraphs of interconnected proteins, using the JUNG implementation of Girvan and Newman's Edge-Betweenness algorithm. Functions were sought for these subgraphs by detecting significant correlations with the distribution of Gene Ontology terms which had been used to annotate the proteins within each cluster. The method was implemented using freely available software (JUNG and the R statistical package). Protein clusters with significant correlations to functional annotations could be identified and included groups of proteins know to cooperate in cell metabolism. The method appears to be resilient against the presence of false positive interactions. Conclusion: This method provides a useful tool for rapid screening of small to medium size protein interaction datasets. [ABSTRACT FROM AUTHOR]

Published
2005
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50. How to use RNA interference.

Author

Lehner, Ben, Fraser, Andrew G., and Sanderson, Christopher M.

Subjects
RNA, GENE expression, GENETICS, GENOMICS, CYTOGENETICS
Abstract

RNA interference (RNAi) has been rapidly adopted as a general method for inhibiting gene expression in most laboratory organisms. This paper discusses how libraries of RNAi reagents are being used to perform genome-wide reverse genetic screens in both model organisms and mammalian cells. Guidelines for designing effective small interfering RNAs and appropriate controls for mammalian RNAi experiments will also be discussed. [ABSTRACT FROM AUTHOR]

Published
2004
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