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J J Gillespie

Publications and source records attributed to J J Gillespie.

At least 19 recordsLinked to original sources
PubMed2006

PATRIC: the VBI PathoSystems Resource Integration Center.

The PathoSystems Resource Integration Center (PATRIC) is one of eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infection Diseases (NIAID) to create a data and analysis resource for selected NIAID priority pathogens, specifically proteobacteria of the genera Brucella, Rickettsia and Coxiella, and corona-, calici- and lyssaviruses and viruses associated with hepatitis A and E. The goal of the project is to provide a comprehensive bioinformatics resource for these pathogens, including consistently annotated genome, proteome and metabolic pathway data to facilitate research into counter-measures, including drugs, vaccines and diagnostics. The project's curation strategy has three prongs: 'breadth first' beginning with whole-genome and proteome curation using standardized protocols, a 'targeted' approach addressing the specific needs of researchers and an integrative strategy to leverage high-throughput experimental data (e.g. microarrays, proteomics) and literature. The PATRIC infrastructure consists of a relational database, analytical pipelines and a website which supports browsing, querying, data visualization and the ability to download raw and curated data in standard formats. At present, the site warehouses complete sequences for 17 bacterial and 332 viral genomes. The PATRIC website (https://patric.vbi.vt.edu) will continually grow with the addition of data, analysis and functionality over the course of the project.

Bioterrorism↗
PubMed2006

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

3' Untranslated Regions↗
PubMed2005

Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).

We report the entire sequence (2864 nts) and secondary structure of the nuclear small subunit ribosomal RNA (SSU rRNA) gene (18S) from the twisted-wing parasite Caenocholax fenyesi texensis Kathirithamby & Johnston (Strepsiptera: Myrmecolacidae). The majority of the base pairings in this structural model map on to the SSU rRNA secondary and tertiary helices that were previously predicted with comparative analysis. These regions of the core rRNA were unambiguously aligned across all Arthropoda. In contrast, many of the variable regions, as previously characterized in other insect taxa, had very large insertions in C. f. texensis. The helical base pairs in these regions were predicted with a comparative analysis of a multiple sequence alignment (that contains C. f. texensis and 174 published arthropod 18S rRNA sequences, including eleven strepsipterans) and thermodynamic-based algorithms. Analysis of our structural alignment revealed four unusual insertions in the core rRNA structure that are unique to animal 18S rRNA and in general agreement with previously proposed insertion sites for strepsipterans. One curious result is the presence of a large insertion within a hairpin loop of a highly conserved pseudoknot helix in variable region 4. Despite the extraordinary variability in sequence length and composition, this insertion contains the conserved sequences 5'-AUUGGCUUAAA-3' and 5'-GAC-3' that immediately flank a putative helix at the 5'- and 3'-ends, respectively. The longer sequence has the potential to form a nine base pair helix with a sequence in the variable region 2, consistent with a recent study proposing this tertiary interaction. Our analysis of a larger set of arthropod 18S rRNA sequences has revealed possible errors in some of the previously published strepsipteran 18S rRNA sequences. Thus we find no support for the previously recovered heterogeneity in the 18S molecules of strepsipterans. Our findings lend insight to the evolution of RNA structure and function and the impact large insertions pose on genome size. We also provide a novel alignment template that will improve the phylogenetic placement of the Strepsiptera among other insect taxa.

Animals↗
PubMed1991

Bilateral eyelid myxomas in Carney's complex.

A 21-year-old man with a history of an excised soft tissue mass of the groin and spotty cutaneous pigmentation underwent excision of nodules of the right lower and left upper eyelids. The patient subsequently had a cutaneous mass of the left ear removed. All excised lesions were classified as myxomas. A diagnosis of multiple myxoma, spotty pigmentation, and endocrine overactivity (Carney's) complex was made.

Adult↗
PubMed1986

The differentiation of carcinomas of teratomatous origin from embryonal carcinoma. A light and electron microscopic study.

Carcinomas derived from teratomatous epithelium occur rarely in the metastases of patients with testicular cancer. These carcinomas of teratomatous origin (CTO) are easily confused with residual embryonal carcinoma (EC). For that reason, we compared the light and electron microscopic appearances of 6 CTOs with those of 12 ECs. As seen by light microscopy, the CTOs formed glands and more frequently had well-defined cytoplasmic borders, eosinophilic cytoplasm, and nonoverlapping, regular nuclei with small or absent nucleoli and little chromatin clumping and clearing, compared with the ECs. Mucin was present in the cells or glandular lumina of three CTOs but was absent in all the ECs. The demonstration of cytoplasmic glycogen was of no differential aid. The most useful differentiating ultrastructural features were long tight junctions and telolysosomes, which occurred in all of the EC but which were absent in the six cases of CTO. Desmosomes with inserting tonofilaments were present in three cases of CTO but were much less developed in EC. Two cases of CTO had microvilli with anchoring rootlets; such anchoring rootlets were not observed among EC. The distinction of CTO from residual EC is important, because CTO will likely need to be treated in a different manner.

Cell Transformation, Neoplastic↗
PubMed1982

Adenosarcoma of the ovary. A light- and electron-microscopic study with review of the literature.

This is a light- and electron-microscopic study of a large ovarian adenosarcoma in a 50-year-old woman as well as a review of the literature. The tumor showed a variety of müllerian type epithelia and a spectrum of stromal patterns including nonspecific fibroblastic, and endometrial type stroma. The latter ranged from normal-appearing to low-grade sarcoma. This study emphasizes the relationship of ovarian adenosarcoma to cystadenofibroma, on the one hand, and to malignant mixed müllerian (mesodermal) tumor, on the other. It appears that the mitotic count which is used as the primary means for the classification of smooth muscle and stromal tumors of the uterus, has less value in the assessment and prognostication of ovarian adenosarcomas.

Adenofibroma↗
PubMed1979

Peripheral spindled carcinoid tumor: a review of its ultrastructure, differential diagnosis, and biologic behavior.

The ultrastructure, differential diagnosis, and biologic behavior of the peripheral pulmonary spindled carcinoid tumor are reviewed. Electron microscopy is useful in distinguishing the spindled carcinoid from a variety of neoplasms with similar histologic features. The spindled morphology is a rare expression of the carcinoid tumor that is almost exclusively confined to the lung periphery. It appears that the spindled carcinoid without atypical features is fully capable of regional lymph node metastases in approximately 20 per cent of the cases.

Carcinoid Tumor↗
PubMed1979

Extraskeletal Ewing's sarcoma. Histologic and ultrastructural observations in three cases.

The histologic and ultrastructural morphology of three cases of Ewing's sarcoma of soft tissue are described and the fine structural features of extraskeletal Ewing's sarcoma are compared to those of similar round-cell tumors that are considered in the differential diagnosis. By light microscopy, these tumors are indistinguishable from Ewing's sarcoma of bone. Ultrastructurally, the salient features are also comparable to Ewing's sarcoma of bone and include: 1) absence of surface modifications; 2) cell-contact sites in the form of small thickenings of apposed membranes and large desmosome-like specializations; 3) undifferentiated cytoplasm usually containing abundant glycogen and occasionally nonspecific microfilaments; 4) significant variation in shape and irregularity of nuclear profiles. The ultrastructural features of extraskeletal Ewing's sarcoma are sufficiently distinctive to allow separation from from other small-cell malignant neoplasms in the majority of cases.

Adult↗
PubMed1978

Anaplastic dysgerminoma.

A rare case of rapidly evolving dysgerminoma produced death by tumor in less than two months after onset of symptoms. It is important to recall that dysgerminoma possesses considerable malignant potential, which infrequently is manifested by rapidly progressive disease. Certain risk factors, present in the pathological specimen, serve to indicate the aggressive potential of such neoplasms.

Adolescent↗
PubMed1978

Histogenesis of cloacogenic carcinoma. Fine structure of anal transitional epithelium and cloacogenic carcinoma.

The fine structural morphology of the anal transitional zone is described and is compared to the ultrastructure of urothelium and anal squamous epithelium. Electron microscopic observations in eight cases of cloacogenic carcinoma are also presented. Anal transitional epithelium is not highly specialized and incorporates features of both urothelium and squamous epithelium; slight urothelial differentiation is considered vestigial. Cloacogenic carcinoma is a specific morphologic entity, which can be distinguished from urothelial and squamous carcinoma. The "transitional" variant is composed of cells similar to the intermediate zone cells of anal transitional epithelium, an observation confirming the concept that the transitional form of cloacogenic carcinoma is derived from the anal transitional zone. The "basaloid" and pleomorphic variants appear to represent less differentiated forms of cloacogenic carcinoma.

Adult↗
PubMed1978

The ultrastructural diagnosis of diffuse large-cell ("histiocytic") lymphoma. Fine structural study of 30 cases.

Thirty cases of diffuse large-cell ("histiocytic") lymphoma were studied with the electron microscope. The purpose was to define the criteria requisite for the ultrastructural diagnosis of large-cell lymphoma. The fine structural features of the lymphoma cells were compared to those of similar appearing reticuloendothelial neoplasms and other tumors that may simulate large-cell lymphoma by light microscopy. Two variants of large-cell lymphoma were recognized, each composed of neoplastic lymphoid cells with the morphologic features of transformed lymphocytes. The larger group represents large noncleaved cell lymphoma of Lukes and Collins' functional classification, while the second type corresponds to lymphoma of large cleaved cells. The ultrastructural features of large-cell lymphoma are uniform and usually easily identified. By utilizing diagnostic electron microscopy, large-cell lymphoma can often be distinguished from similar appearing tumors presenting as diagnostic problems at the light microscopic level.

Adolescent↗
PubMed1978

Meningeal melanocytoma with invasion of the thoracic spinal cord. Case report.

A case is presented of meningeal melanocytoma that invaded the thoracic spinal cord of a 71-year-old woman. The light and electron microscopic features of the lesion indicate that it derives from melanocytes normally found in the leptomeninges. This tumor closely resembles the dermal cellular blue nevus and does not have the ultrastructure of a meningioma. "Melanotic meningioma" is consequently a misnomer and the name "meningeal melanocytoma" is more appropriate. These tumors may appear to be benign histologically, but they are locally aggressive. Total surgical excision offers the best chance for cure.

Aged↗
PubMed1977

Diagnosis of lymphoma from a cholecystectomy specimen: case report and review of the literature.

A 31-year-old woman had cholecystectomy for recurrent acute cholecystitis. Pathologic examination of the resected gallbladder revealed unsuspected histiocytic lymphoma. A staging laparotomy seven weeks after cholecystectomy revealed disseminated disease. Lymphomatous involvement of the gallbladder is rarely diagnosed antemortem and indicates disseminated disease until proved otherwise.

Adult↗