Research Interests:
Research Interests:
Hypermethylation in cancer often occurs in CpG islands that span the promoter regions of tumor suppressor genes. However, it is not clear if hypermethylation is limited to single target genes or if multiple genes are simultaneously... more
Hypermethylation in cancer often occurs in CpG islands that span the promoter regions of tumor suppressor genes. However, it is not clear if hypermethylation is limited to single target genes or if multiple genes are simultaneously methylated. To understand the extent of aberrant de novo methylation, we have analyzed the methylation pattern of a number of tumor-related genes in leukemia from the same cohort of patients. We used bisulfite genomic sequencing to characterize the methylation pattern of the CpG islands associated with the calcitonin, estrogen receptor, E-cadherin, p15, p16, Rb, GST-Pi, and HIC1 genes in the bone marrow from 9 normal and 20 patients with acute myeloid leukaemia (AML). All of the normal control samples were essentially unmethylated for each of the eight tumor-related genes studied. In contrast, 19 of 20 (95%) of the AML patients had an abnormal methylation pattern in at least one gene, and 15 of 20 (75%) had abnormal methylation patterns in two or more of ...
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The retinoblastoma gene (Rb) is one of the best characterized tumor suppressor genes, and its inactivation is associated with a number of cancers. Previous studies have shown, by restriction enzyme analysis, that the promoter region of... more
The retinoblastoma gene (Rb) is one of the best characterized tumor suppressor genes, and its inactivation is associated with a number of cancers. Previous studies have shown, by restriction enzyme analysis, that the promoter region of the Rb gene is methylated in a significant proportion of primary retinoblastoma tumors. We now report the first detailed methylation sequence analysis of the CpG island spanning the retinoblastoma promoter from hypermethylated retinoblastoma tumors. Our results show methylation is not confined to a specific CpG site, as detected by restriction enzyme studies, but extends to essentially all 27 CpG dinucleotides spanning the retinoblastoma CpG island, including the core promoter. The methylation pattern from each tumor DNA sample is different, ranging from densely to sparsely methylated profiles. Single CpG sites, in particular the E2F transcription factor binding site, as well as blocks of CpGs, were undermethylated in some tumor samples. Possible inte...
Research Interests: Molecular Biology, Cancer, Biology, Transcription Factors, Medicine, and 14 moreHumans, Methylation, Female, Pubmed, Male, Polymerase Chain Reaction, DNA methylation, CpG islands, Retinoblastoma, Molecular cloning, Base Sequence, Cell Cycle Proteins, DNA binding proteins, and Molecular Sequence Data
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Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life... more
Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generi...
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Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species... more
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated exi...
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Research Interests:
Research Interests:
Seismologists and geophysical literature often use the term “walkaway” to describe any survey used to analyze wavetrains based on source-to-receiver offset. A distinction should be made between receiver-group moveout (fixed-source... more
Seismologists and geophysical literature often use the term “walkaway” to describe any survey used to analyze wavetrains based on source-to-receiver offset. A distinction should be made between receiver-group moveout (fixed-source walkaway) and source moveout (fixed-receiver walkaway) when multiple channels simultaneously record signal from multiple independent geophones. Three data sets are presented that illustrate this distinction: one collected in an area where a fixed-receiver walkaway survey recorded similar data and was more time efficient than a fixed-source walkaway survey, and two others collected in an area where dipping reflectors and laterally varying velocities caused the fixed-receiver walkaway data to be significantly different than the fixed-source walkaway data. The results show that, while still useful, clarity in recorded data is lost when fixed-receiver walkaway surveys are substituted for fixed-source walkaway surveys in areas with uneven surface topography, di...
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We introduce the Autojuggie II as a device to speed the emplacement of geophones for near‐surface seismic common‐midpoint (CMP) surveys. Hydraulic cylinders force rigidly interconnected geophones into the ground simultaneously and... more
We introduce the Autojuggie II as a device to speed the emplacement of geophones for near‐surface seismic common‐midpoint (CMP) surveys. Hydraulic cylinders force rigidly interconnected geophones into the ground simultaneously and automatically. We demonstrate that accurate CMP data can be recorded with geophones planted by this device, and that a CMP stacked section can be processed, from which reliable geologic information can be extracted. To make this demonstration, we compare the stacked section to a coincident and parallel section, whose data was acquired using conventionally hand‐planted geophones. The two sections are very similar in amplitude, phase, and frequency. A slight difference in coherency exists in a ∼35‐ms reflection; the stack corresponding to the automatically planted geophones shows better coherency relative to the comparison stack. However, the similarity of the sections indicates that accurate CMP data can be recorded using geophones planted by the Autojuggie...
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Research Interests:
Research Interests:
Research Interests:
Reference architectures predefine a common frame of reference, which can be customised to obtain architectures for specific applications in a domain. Based on a general reference model, providing a common language and semantics to explain... more
Reference architectures predefine a common frame of reference, which can be customised to obtain architectures for specific applications in a domain. Based on a general reference model, providing a common language and semantics to explain the important concepts of Event Processing (EP), we define a general reference architecture which models the abstract architectural elements of an Event Processing-based system independent