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S P Clark

Publications and source records attributed to S P Clark.

At least 19 recordsLinked to original sources
PubMed2005

Characterization of quaternary ammonium oligomers by paired-ion reversed-phase liquid chromatography-mass spectrometry.

The separation of novel permanently charged oligomers was studied using paired-ion reversed-phase liquid chromatography. The polyionene studied is less than 5 kDa in size, but contains three oligomer series with different end-group chemistries. The complexity of this polyionene makes development of a single-dimension separation quite challenging. Separation under critical conditions was employed to fractionate the end-group conformations and then the chain length of the oligomers in each series was confirmed by LC-MS. The oligomers were then used to optimize a single-dimension HPLC separation. Precise modulation of the hydrophobicity of the ion-pair reagent and the stationary-phase chemistry yielded very high resolution one-dimensional separations.

Chromatography, High Pressure Liquid↗
PubMed1995

An STS content map of human chromosome 11: localization of 910 YAC clones and 109 islands.

Physical mapping of human chromosomes at a resolution of 100 kb to 1 Mb will provide important reagents for gene identification and framework templates for ultimately determining the complete DNA sequence. Sequence-tagged site (STS) content mapping, coupled with large fragment cloning in yeast artificial chromosomes, provides an efficient mechanism for producing first-generation, low-resolution maps of human chromosomes. Previously, we produced a set of standardized STSs for human chromosome 11 regionally localized by fluorescence in situ hybridization or somatic cell hybrid analysis. In this paper, we used these as well as other STS content, and identify 109 islands spanning an estimated 218 Mb on the 126-Mb chromosome. Since about 62% of the islands contain markers ordered on chromosome 11 by genetic or radiation hybrid analysis, this data set represents a first-order approximation of a physical map of human chromosome 11. This set of clones, contigs, and associated STSs will provide the material for the production of a continuous overlapping set of YACs as well for high-resolution physical mapping based upon sampled and complete DNA sequencing.

Base Sequence↗
PubMed1995

Parathyroid hormone-related protein antigen localization distinguishes between mesothelioma and adenocarcinoma of the lung.

The distinction between pleural malignant mesothelioma and pulmonary adenocarcinoma remains a problem in diagnostic histopathology. Parathyroid hormone-related protein (PTHrP) has been demonstrated in the neoplastic cells of malignant mesotheliomata, using a polyclonal antiserum raised to synthetic PTHrP(1-16). In a series of 44 malignant mesotheliomata and 44 cases of pleural adenocarcinomata, PTHrP was localized immunohistochemically in 84 per cent of the mesotheliomata and in 11 per cent of the pleural adenocarcinomata. Normal and reactive mesothelium did not contain detectable PTHrP. The presence of PTHrP in a very high percentage of malignant mesotheliomata indicates the value of including it in the panel of antibodies utilized in the differential diagnosis of mesothelioma.

Adenocarcinoma↗
PubMed1995

Human T-cell receptor variable gene segment families.

Multiple DNA and protein sequence alignments have been constructed for the human T-cell receptor alpha/delta, beta, and gamma (TCRA/D, B, and G) variable (V) gene segments. The traditional classification into subfamilies was confirmed using a much larger pool of sequences. For each sequence, a name was derived which complies with the standard nomenclature. The traditional numbering of V gene segments in the order of their discovery was continued and changed when in conflict with names of other segments. By discriminating between alleles at the same locus versus genes from different loci, we were able to reduce the number of more than 150 different TCRBV sequences in the database to a repertoire of only 47 functional TCRBV gene segments. An extension of this analysis to the over 100 TCRAV sequences results in a predicted repertoire of 42 functional TCRAV gene segments. Our alignment revealed two residues that distinguish between the highly homologous V delta and V alpha, one at a site that in VH contacts the constant region, the other at the interface between immunoglobulin VH and VL. This site may be responsible for restricted pairing between certain V delta and V gamma chains. On the other hand, V beta and V gamma appear to be related by the fact that their CDR2 length is increased by four residues as compared with that of V alpha/delta peptides.

Alleles↗
PubMed1995

Mouse T-cell receptor variable gene segment families.

All mouse T-cell receptor alpha/delta, beta, and gamma variable (Tcra/d-, b-, and g-V) gene segments were aligned to compare the sequences with one another, to group them into subfamilies, and to derive a name which complies with the standard nomenclature. It was necessary to change the names of some V gene segments because they conflicted with those of other segments. The traditional classification into subfamilies was re-evaluated using a much larger pool of sequences. In the mouse, most V gene segments can be grouped into subfamilies of closely related genes with significantly less similarity between different subfamilies.

Amino Acid Sequence↗
PubMed1995

Comparison of human and mouse T-cell receptor variable gene segment subfamilies.

Like the immunoglobulin Igh-V and Igk-V gene families, the human or mouse TCRV gene families may be grouped into subfamilies displaying > 75% nucleic acid sequence similarity among their members. Systematic interspecies sequence comparisons reveal that most mouse Tcr-V subfamilies exhibit clear homology to human TCRV subfamilies (> 60% amino acid sequence similarity). Homologous pairs of TCRV genes in mice and humans show higher sequence similarity than TCRV genes from different subfamilies within either species, indicating transspecies evolution of TCRV genes. Mouse and human homologues show conservation of their relative map order, particularly in the 3' region and a similar sequential and developmentally programmed expression. When the V regions from both species were analyzed together, local length differences and conserved residues in the loop regions were revealed, characteristic of each of the four TCRV families.

Alleles↗
PubMed1995

In situ hybridization of parathyroid hormone-related protein in normal skin, skin tumors, and gynecological cancers using digoxigenin-labeled probes and antibody enhancement.

We describe a novel procedure for in situ hybridization that combines the use of digoxigenin-labeled oligonucleotide probes with an antibody enhancement step that can be performed on formalin-fixed, paraffin-embedded tissues. Addition of a second antibody enhances the visibility of parathyroid hormone-related protein (PTHrP) mRNA expression from barely to highly discernible and interpretable, with virtually no nonspecific background expression. This technique has allowed visualization of PTHrP mRNA in normal human skin and epithelium-derived tumors. PTHrP mRNA expression was confined to the basal and spinous keratinocyte layers of skin. There was strong hybridization in the spinous keratinocyte layer and a low level of hybridization in the basal layer. An extensive panel of positive and negative controls included poly d(T) probe to indicate total mRNA present in the sections. Squamous cell carcinomas and basal cell carcinomas of the skin, from pathology archives, were examined for the presence of PTHrP mRNA. The results reflected previous immunohistochemical studies, with every squamous cell carcinoma hybridizing strongly with the PTHrP probes. The basal cell carcinomas showed no expression of PTHrP mRNA, although the total mRNA signal was very strong. The localization of PTHrP mRNA in the tumors of the gynecological tract also reflected the immunohistochemical findings, with expression found in the squamous cell carcinomas but not in the adenocarcinomas. In situ hybridization with digoxigenin-labeled oligonucleotide probes and antibody enhancement has provided a sensitive, highly specific procedure for detection of PTHrP mRNA in tumors and normal tissue.

Antibodies, Monoclonal↗
PubMed1993

A sequence-tagged site map of human chromosome 11.

We report the construction of 370 sequence-tagged sites (STSs) that are detectable by PCR amplification under sets of standardized conditions and that have been regionally mapped to human chromosome 11. DNA sequences were determined by sequencing directly from cosmid templates using primers complementary to T3 and T7 promoters present in the cloning vector. Oligonucleotide PCR primers were predicted by computer and tested using a battery of genomic DNAs. Cosmids were regionally localized on chromosome 11 by using fluorescence in situ hybridization or by analyzing a somatic cell hybrid panel. Additional STSs corresponding to known genes and markers on chromosome 11 were also produced under the same series of standardized conditions. The resulting STSs provide uniform coverage of chromosome 11 with an average spacing of 340 kb. The DNA sequence determined for use in STS production corresponds to about 0.1% (116 kb) of chromosome 11 and has been analyzed for the presence of repetitive sequences, similarities to known genes and motifs, and possible exons. Computer analysis of this sequence has identified and therefore mapped at least eight new genes on chromosome 11.

Amino Acid Sequence↗
PubMed1993

Carcinoid tumour of the uterine corpus.

A carcinoid tumour occurred in the uterine fundus causing an enlargement (12-14 weeks size). The patient did not have the carcinoid syndrome, despite elevated urinary 5-hydroxyindole acetic acid levels. The tumour had a typical organoid pattern with argentaffin-positive cells. Whilst a metastasis from an occult primary lesion cannot be entirely excluded, it is felt that this is a primary tumour most likely arising from resident endocrine cells in the endometrium.

Aged↗
PubMed1993

Pigmented pheochromocytomas of the adrenal medulla.

Three primary pigmented pheochromocytomas of the adrenal gland are presented. The pigment in all cases proved to be melanin. Two of the pheochromocytomas were sporadic and histologically typical, except for a focal spindle cell configuration in one. It is believed that the morphologic appearance of these tumors represents divergent differentiation from neural crest, expressing typical pheochromocytoma (polygonal cells) and melanocytic features (melanin pigment).

Adrenal Gland Neoplasms↗
PubMed1993

Cholecystitis, cholelithiasis, and ganglioneuromatosis of the gall bladder: an unusual presentation of MEN type 2b.

A 40 year old man with multiple endocrine neoplasia type 2b (MEN 2b) presented with cholecystitis caused by gall stones. Twenty four years earlier, he had had a partial thyroidectomy for a cold nodule. At his initial presentation MEN 2b with medullary carcinoma of the thyroid had not been made. This was diagnosed while investigating his gall bladder symptoms and he was found to have asymptomatic residual medullary thyroid carcinoma and bilateral adrenal phaeochromocytomas. The cholecystectomy specimen contained several mixed calculi and extensive ganglioneuromatosis with large, prominent nerves containing ganglion cells in the gall bladder wall.

Adult↗
PubMed1993

Pseudocysts of the adrenal gland.

Three cases of pseudocysts or hemorrhagic cysts of the adrenal gland were encountered in female patients who presented with loin pain. The adrenalectomy specimens contained cystic structures; 2 had fibrous walls containing organizing blood clot, the remaining lesion was thin walled and contained blood stained fluid. Fat, normal adrenal cortical tissue and calcification were found within the cysts. These lesions (arising from vascular anomalies) require separation from hemorrhagic adrenal neoplasms. Awareness of adrenal pseudocysts and careful attention to the histological features aids this distinction.

Adrenal Gland Diseases↗
PubMed1993

Primary small cell carcinoma of the pancreas.

A 59 yr old male presented with abdominal pain and jaundice. CT scan showed a tumor in the pancreas with secondaries in the liver, peri-pancreatic lymph nodes, vertebral bone marrow and subcutaneous tissue of the neck together with a cervical lymph node. The patient died after 2 wks and autopsy revealed complete replacement of the pancreas by tumor. Careful dissection of both lungs failed to show any tumor. A diagnosis of primary small cell carcinoma of the pancreas was made. Review of the literature indicates that this type of carcinoma accounts for about 1% of all pancreatic cancers and is commoner in elderly males who have a history of cigarette smoking. There is usually a rapid progression of disease and widespread dissemination, especially if untreated. Some success has been obtained with chemotherapy.

Carcinoma, Small Cell↗
PubMed1993

Leiomyosarcoma of the thyroid: immunohistochemical and ultrastructural study.

A primary leiomyosarcoma of the thyroid was seen in a 54 yr old female. The patient had a solitary, cold nodule with no abnormalities of thyroid function tests. Histologically it was composed of characteristic interlacing fascicles of spindle cells which, electron microscopically, showed thin myofilaments with focal dense bodies. Immunohistochemistry showed a strong reaction with vimentin, smooth muscle actin and desmin. No epithelial differentiation was noted immunohistochemically or ultrastructurally. No tumor recurrence was detected 15 mths after surgery. It is postulated that the smooth muscle differentiation had arisen by metaplastic change or de-differentiation with re-differentiation of anaplastic thyroid carcinoma.

Cytoskeletal Proteins↗
PubMed1992

Fine-needle aspiration of cystic nephroma (multilocular cyst of the kidney).

Cystic nephromas are rare tumors of the kidney most commonly affecting boys or adult females. The fine-needle aspiration cytomorphology has not yet been described. A renal cystic mass in a 56 year old female was aspirated under ultrasound guidance. Papanicolaou stained smears of the cyst fluid revealed markedly atypical cells forming papillary clusters. Subsequent nephrectomy showed a typical cystic nephroma with lining epithelium resembling that seen in the aspirate. The cytomorphology of cystic nephroma has been misdiagnosed as renal cell carcinoma in the literature. Low cellularity, absence of necrosis, and paucity of single cells are features that should raise the possibility of cystic nephroma in a cystic renal mass.

Adenocarcinoma↗
PubMed1992

MALIGNED: a multiple sequence alignment editor.

A multiple sequence alignment editor is described which runs on a VAX/VMS system and can exchange data with a number of other programs, including those of the Genetics Computer Group (GCG). Up to 199 sequences can be aligned. The quality of the alignment can be easily judged during its development because the display attributes to each character are determined by the way it matches the other sequences. Four methods are available for calculating the highlighting to emphasize different aspects of the relationships of the sequences and up to four styles of highlighting can be used at the same time. Laser printer output is suitable for publication without modification.

Molecular Sequence Data↗