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"creatorType": "author",
"firstName": "Caroline A.",
"lastName": "Kerr"
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{
"creatorType": "author",
"firstName": "Barney M.",
"lastName": "Hines"
},
{
"creatorType": "author",
"firstName": "Janet M.",
"lastName": "Shaw"
},
{
"creatorType": "author",
"firstName": "Robert",
"lastName": "Dunne"
},
{
"creatorType": "author",
"firstName": "Lauren M.",
"lastName": "Bragg"
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{
"creatorType": "author",
"firstName": "Julie",
"lastName": "Clarke"
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"creatorType": "author",
"firstName": "Trevor",
"lastName": "Lockett"
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"creatorType": "author",
"firstName": "Richard",
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"abstractNote": "The acute response to genotoxic carcinogens in rats is an important model for researching cancer initiation events. In this report we define the normal rat colonic epithelium by describing transcriptional events along the anterior-posterior axis and then investigate the acute effects of azoxymethane (AOM) on gene expression, with a particular emphasis on pathways associated with the maintenance of genomic integrity in the proximal and distal compartments using whole genome expression microarrays.",
"publicationTitle": "BMC Physiology",
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"DOI": "10.1186/1472-6793-13-2",
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"type": 1
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{
"tag": "Colorectal cancer",
"type": 1
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{
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{
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"title": "Segmentation of Dense 2D Bacilli Populations",
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{
"creatorType": "author",
"firstName": "P.",
"lastName": "Vallotton"
},
{
"creatorType": "author",
"firstName": "L.",
"lastName": "Turnbull"
},
{
"creatorType": "author",
"firstName": "C.",
"lastName": "Whitchurch"
},
{
"creatorType": "author",
"firstName": "L.",
"lastName": "Mililli"
}
],
"abstractNote": "Bacteria outnumber all other known organisms by far so there is considerable interest in characterizing them in detail and in measuring their diversity, evolution, and dynamics. Here, we present a system capable of identifying rod-like bacteria (bacilli) correctly in high resolution phase contrast images. We use a probabilistic model together with several purpose-designed image features in order to split bacteria at the septum consistently. Our method commits less than 1% error on test images. Our method should also be applicable to study dense 2D systems composed of elongated elements, such as some viruses, molecules, parasites (plasmodium, euglena), diatoms, and crystals.",
"proceedingsTitle": "2010 International Conference on Digital Image Computing: Techniques and Applications (DICTA)",
"conferenceName": "2010 International Conference on Digital Image Computing: Techniques and Applications (DICTA)",
"publisher": "",
"place": "",
"date": "dec. 2010",
"eventPlace": "",
"volume": "",
"issue": "",
"numberOfVolumes": "",
"pages": "82 -86",
"series": "",
"seriesNumber": "",
"DOI": "10.1109/DICTA.2010.23",
"ISBN": "",
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"url": "",
"accessDate": "",
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"shortTitle": "",
"language": "",
"libraryCatalog": "IEEE Xplore",
"callNumber": "0001",
"rights": "",
"extra": "00004",
"tags": [
{
"tag": "Bacteria",
"type": 1
},
{
"tag": "Bayesian",
"type": 1
},
{
"tag": "Detectors",
"type": 1
},
{
"tag": "Image edge detection",
"type": 1
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{
"tag": "Microorganisms",
"type": 1
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{
"tag": "Microscopy",
"type": 1
},
{
"tag": "Shape",
"type": 1
},
{
"tag": "Skeleton",
"type": 1
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{
"tag": "biology computing",
"type": 1
},
{
"tag": "dense 2D bacilli populations",
"type": 1
},
{
"tag": "high resolution phase contrast images",
"type": 1
},
{
"tag": "image analysis",
"type": 1
},
{
"tag": "image features",
"type": 1
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{
"tag": "image segmentation",
"type": 1
},
{
"tag": "motility",
"type": 1
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{
"tag": "organisms",
"type": 1
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{
"tag": "phenotype",
"type": 1
},
{
"tag": "probabilistic model",
"type": 1
},
{
"tag": "probability",
"type": 1
},
{
"tag": "rod-like bacteria",
"type": 1
},
{
"tag": "segmentation",
"type": 1
}
],
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"relations": {},
"dateAdded": "2013-01-17T23:44:52Z",
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"itemType": "journalArticle",
"title": "The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome",
"creators": [
{
"creatorType": "author",
"firstName": "Shivashankar H",
"lastName": "Nagaraj"
},
{
"creatorType": "author",
"firstName": "Aaron",
"lastName": "Ingham"
},
{
"creatorType": "author",
"firstName": "Antonio",
"lastName": "Reverter"
}
],
"abstractNote": "BACKGROUND Human disease genes can be distinguished from essential (embryonically lethal) and non-disease genes using gene attributes. Such attributes include gene age, tissue specificity of expression, regulatory capacity, sequence length, rate of sequence variation and capacity for interaction. The resulting information has been used to inform data mining approaches seeking to identify novel disease genes. Given the dynamic nature of this field and the rapid rise in relevant information, we have chosen to perform a single integrated mining approach to explore relationships among gene attributes and thereby characterise evolutionary trends associated with disease genes. RESULTS All against all cross comparison of 2,522 disease gene attributes revealed significant relationships existed between the age, disease-association and expression pattern of genes and the tissues within which they are expressed. We found that the over-representation of disease genes among old genes holds for tissue-specific genes, but the correlation between age and disease association vanished when conditioning on tissue-specificity. Of the 32 tissues studied, the genes expressed in pancreas are on average older than the genes expressed in any other tissue, while the testis expressed the lowest proportion of old genes. Following a focussed analysis on the impact of regulatory apparatus on evolution of disease genes, we show that regulators, comprising transcription factors and post-translation modified proteins, are over-represented among ancient disease genes. In addition, we show that the proportion of regulator genes is affected by gene age among disease genes and by tissue-specificity among non-disease genes. Finally, using 55,606 true positive gene interaction data, we find that old disease genes interacts with other old disease genes and interacting new genes interacts with genes originating from higher phylostrata. CONCLUSION This study supports the non-random nature of the human diseasome. We have identified a variety of distinct features and correlations to other molecular attributes that can be used to distinguish the set of disease causing genes. This was achieved by harnessing the power of mining large scale datasets from OMIM and other databases. Ultimately such knowledge may contribute to the identification of novel human disease genes and an enhanced understanding of human biology.",
"publicationTitle": "BMC Genomics",
"publisher": "",
"place": "",
"date": "2010",
"volume": "11 Suppl 4",
"issue": "",
"section": "",
"partNumber": "",
"partTitle": "",
"pages": "S23",
"series": "",
"seriesTitle": "",
"seriesText": "",
"journalAbbreviation": "BMC Genomics",
"DOI": "10.1186/1471-2164-11-S4-S23",
"citationKey": "",
"url": "http://www.ncbi.nlm.nih.gov/pubmed/21143807",
"accessDate": "2011-05-30T05:31:44Z",
"PMID": "",
"PMCID": "",
"ISSN": "1471-2164",
"archive": "",
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"shortTitle": "",
"language": "",
"libraryCatalog": "NCBI PubMed",
"callNumber": "0004",
"rights": "",
"extra": "00006 PMID: 21143807",
"tags": [
{
"tag": "Base Sequence",
"type": 1
},
{
"tag": "Data Mining",
"type": 1
},
{
"tag": "Databases, Genetic",
"type": 1
},
{
"tag": "Evolution, Molecular",
"type": 1
},
{
"tag": "Gene Expression",
"type": 1
},
{
"tag": "Genetic Diseases, Inborn",
"type": 1
},
{
"tag": "Genetic Variation",
"type": 1
},
{
"tag": "Humans",
"type": 1
},
{
"tag": "Male",
"type": 1
},
{
"tag": "Organ Specificity",
"type": 1
},
{
"tag": "Protein Processing, Post-Translational",
"type": 1
},
{
"tag": "Systems Biology",
"type": 1
},
{
"tag": "Transcription Factors",
"type": 1
}
],
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"relations": {},
"dateAdded": "2011-05-30T05:31:44Z",
"dateModified": "2014-02-08T07:29:24Z"
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"creatorSummary": "Lopez et al.",
"parsedDate": "2009-09-01",
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"version": 7446,
"itemType": "journalArticle",
"title": "Identification of a Distal GLUT4 Trafficking Event Controlled by Actin Polymerization",
"creators": [
{
"creatorType": "author",
"firstName": "Jamie A.",
"lastName": "Lopez"
},
{
"creatorType": "author",
"firstName": "James G.",
"lastName": "Burchfield"
},
{
"creatorType": "author",
"firstName": "Duncan H.",
"lastName": "Blair"
},
{
"creatorType": "author",
"firstName": "Katarina",
"lastName": "Mele"
},
{
"creatorType": "author",
"firstName": "Yvonne",
"lastName": "Ng"
},
{
"creatorType": "author",
"firstName": "Pascal",
"lastName": "Vallotton"
},
{
"creatorType": "author",
"firstName": "David E.",
"lastName": "James"
},
{
"creatorType": "author",
"firstName": "William E.",
"lastName": "Hughes"
}
],
"abstractNote": "The insulin-stimulated trafficking of GLUT4 to the plasma membrane in muscle and fat tissue constitutes a central process in blood glucose homeostasis. The tethering, docking, and fusion of GLUT4 vesicles with the plasma membrane (PM) represent the most distal steps in this pathway and have been recently shown to be key targets of insulin action. However, it remains unclear how insulin influences these processes to promote the insertion of the glucose transporter into the PM. In this study we have identified a previously uncharacterized role for cortical actin in the distal trafficking of GLUT4. Using high-frequency total internal reflection fluorescence microscopy (TIRFM) imaging, we show that insulin increases actin polymerization near the PM and that disruption of this process inhibited GLUT4 exocytosis. Using TIRFM in combination with probes that could distinguish between vesicle transport and fusion, we found that defective actin remodeling was accompanied by normal insulin-regulated accumulation of GLUT4 vesicles close to the PM, but the final exocytotic fusion step was impaired. These data clearly resolve multiple steps of the final stages of GLUT4 trafficking, demonstrating a crucial role for actin in the final stage of this process.",
"publicationTitle": "Molecular Biology of the Cell",
"publisher": "",
"place": "",
"date": "09/01/2009",
"volume": "20",
"issue": "17",
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"partNumber": "",
"partTitle": "",
"pages": "3918-3929",
"series": "",
"seriesTitle": "",
"seriesText": "",
"journalAbbreviation": "Mol. Biol. Cell",
"DOI": "10.1091/mbc.E09-03-0187",
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"url": "http://www.molbiolcell.org/content/20/17/3918",
"accessDate": "2013-05-20T11:36:55Z",
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"PMCID": "",
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"version": 7446,
"itemType": "journalArticle",
"title": "NetRaVE: constructing dependency networks using sparse linear regression",
"creators": [
{
"creatorType": "author",
"firstName": "A.",
"lastName": "Phatak"
},
{
"creatorType": "author",
"firstName": "H.",
"lastName": "Kiiveri"
},
{
"creatorType": "author",
"firstName": "L. H.",
"lastName": "Clemmensen"
},
{
"creatorType": "author",
"firstName": "W. J.",
"lastName": "Wilson"
}
],
"abstractNote": "Summary: NetRaVE is a small suite of R functions for generating dependency networks using sparse regression methods. Such networks provide an alternative to interpreting ‘top n lists’ of genes arising out of an analysis of microarray data, and they provide a means of organizing and visualizing the resulting information in a manner that may suggest relationships between genes.\n\nAvailability: NetRaVE is freely available for academic use and has been tested in R 2.10.1 under Windows XP, Linux and Mac OS X.\n\nContact: harri.kiiveri@csiro.au\n\nSupplementary information: Supplementary data are available at Bioinformatics online",
"publicationTitle": "Bioinformatics",
"publisher": "",
"place": "",
"date": "04/2010",
"volume": "26",
"issue": "12",
"section": "",
"partNumber": "",
"partTitle": "",
"pages": "1576-1577",
"series": "",
"seriesTitle": "",
"seriesText": "",
"journalAbbreviation": "Bioinformatics",
"DOI": "10.1093/bioinformatics/btq168",
"citationKey": "",
"url": "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/1576",
"accessDate": "2010-08-16T03:37:56Z",
"PMID": "",
"PMCID": "",
"ISSN": "1367-4803",
"archive": "",
"archiveLocation": "",
"shortTitle": "NetRaVE",
"language": "",
"libraryCatalog": "CrossRef",
"callNumber": "0001",
"rights": "",
"extra": "00001",
"tags": [
{
"tag": "cmis-block-funded"
}
],
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"creatorSummary": "Baldwin et al.",
"parsedDate": "2013",
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},
"data": {
"key": "VMKVJBJM",
"version": 7446,
"itemType": "journalArticle",
"title": "Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils",
"creators": [
{
"creatorType": "author",
"firstName": "Darren S.",
"lastName": "Baldwin"
},
{
"creatorType": "author",
"firstName": "Mattthew J.",
"lastName": "Colloff"
},
{
"creatorType": "author",
"firstName": "Gavin N.",
"lastName": "Rees"
},
{
"creatorType": "author",
"firstName": "Anthony A.",
"lastName": "Chariton"
},
{
"creatorType": "author",
"firstName": "Garth O.",
"lastName": "Watson"
},
{
"creatorType": "author",
"firstName": "Leon N.",
"lastName": "Court"
},
{
"creatorType": "author",
"firstName": "Diana M.",
"lastName": "Hartley"
},
{
"creatorType": "author",
"firstName": "Matthew j.",
"lastName": "Morgan"
},
{
"creatorType": "author",
"firstName": "Andrew J.",
"lastName": "King"
},
{
"creatorType": "author",
"firstName": "Jessica S.",
"lastName": "Wilson"
},
{
"creatorType": "author",
"firstName": "Michael",
"lastName": "Hodda"
},
{
"creatorType": "author",
"firstName": "Christopher M.",
"lastName": "Hardy"
}
],
"abstractNote": "Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post-flood) were dominated by persistent rather than either aquatic or dry-specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post-flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post-flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.",
"publicationTitle": "Molecular Ecology",
"publisher": "",
"place": "",
"date": "2013",
"volume": "",
"issue": "",
"section": "",
"partNumber": "",
"partTitle": "",
"pages": "n/a–n/a",
"series": "",
"seriesTitle": "",
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Plant disease resistance can be triggered by specific recognition of microbial effectors by plant nucleotide binding-leucine rich repeat (NB-LRR) receptors. Over the last few years, many efforts have greatly improved the understanding of effector and NB-LRR function, but have left a lot of questions as to how effector perception activates NB-LRR induction of defense signaling. This review describes exciting new findings showing similarities and differences in function of diverse plant NB-LRR proteins in terms of pathogen recognition and where and how resistance proteins are activated. Localization studies have shown that some NB-LRRs can activate signaling from the cytosol while others act in the nucleus. Also, the structural determination of two NB-LRR signaling domains demonstrated that receptor oligomerization is fundamental for the activation of resistance signaling.
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"creatorSummary": "Bernoux et al.",
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"title": "Structural and Functional Analysis of a Plant Resistance Protein TIR Domain Reveals Interfaces for Self-Association, Signaling, and Autoregulation",
"creators": [
{
"creatorType": "author",
"firstName": "Maud",
"lastName": "Bernoux"
},
{
"creatorType": "author",
"firstName": "Thomas",
"lastName": "Ve"
},
{
"creatorType": "author",
"firstName": "Simon",
"lastName": "Williams"
},
{
"creatorType": "author",
"firstName": "Christopher",
"lastName": "Warren"
},
{
"creatorType": "author",
"firstName": "Danny",
"lastName": "Hatters"
},
{
"creatorType": "author",
"firstName": "Eugene",
"lastName": "Valkov"
},
{
"creatorType": "author",
"firstName": "Xiaoxiao",
"lastName": "Zhang"
},
{
"creatorType": "author",
"firstName": "Jeffrey G.",
"lastName": "Ellis"
},
{
"creatorType": "author",
"firstName": "Bostjan",
"lastName": "Kobe"
},
{
"creatorType": "author",
"firstName": "Peter N.",
"lastName": "Dodds"
}
],
"abstractNote": "Summary
The Toll/interleukin-1 receptor (TIR) domain occurs in animal and plant immune receptors. In the animal Toll-like receptors, homodimerization of the intracellular TIR domain is required for initiation of signaling cascades leading to innate immunity. By contrast, the role of the TIR domain in cytoplasmic nucleotide-binding/leucine-rich repeat (NB-LRR) plant immune resistance proteins is poorly understood. L6 is a TIR-NB-LRR resistance protein from flax (Linum usitatissimum) that confers resistance to the flax rust phytopathogenic fungus (Melampsora lini). We determine the crystal structure of the L6 TIR domain and show that, although dispensable for pathogenic effector protein recognition, the TIR domain alone is both necessary and sufficient for L6 immune signaling. We demonstrate that the L6 TIR domain self-associates, most likely forming a homodimer. Analysis of the structure combined with site-directed mutagenesis suggests that self-association is a requirement for immune signaling and reveals distinct surface regions involved in self-association, signaling, and autoregulation.
",
"publicationTitle": "Cell Host & Microbe",
"publisher": "",
"place": "",
"date": "March 17, 2011",
"volume": "9",
"issue": "3",
"section": "",
"partNumber": "",
"partTitle": "",
"pages": "200-211",
"series": "",
"seriesTitle": "",
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"journalAbbreviation": "",
"DOI": "16/j.chom.2011.02.009",
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"url": "http://www.sciencedirect.com/science/article/pii/S1931312811000655",
"accessDate": "2011-06-13T10:25:06Z",
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"ISSN": "1931-3128",
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"language": "",
"libraryCatalog": "ScienceDirect",
"callNumber": "0030",
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"extra": "00064",
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"dateAdded": "2011-06-13T10:25:06Z",
"dateModified": "2014-02-08T07:28:05Z"
}
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