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Biomedical subjects

R Herwig

Publications and source records attributed to R Herwig.

24 records · Page 2Linked to original sources
PubMed1999

Toward the gene catalogue of sea urchin development: the construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting.

We describe the use of oligonucleotide fingerprinting for the generation of a normalized cDNA library from unfertilized sea urchin eggs and report the preliminary analysis of this library, which resulted in the establishment of a partial gene catalogue of the sea urchin egg. In an analysis of 21,925 cDNA clones by hybridization with 217 oligonucleotide probes, we were able to identify 6291 clusters corresponding to different transcripts, ranging in size from 1 to 265 clones. This corresponds to an average 3.5-fold normalization of the starting library. The normalized library represents about one-third of all genes expressed in the sea urchin egg. To generate sequence information for the transcripts represented by the clusters, representative clones selected from 711 clusters were sequenced. The construction and preliminary analysis of the normalized library are the first steps in the assembly of an increasingly complete collection of maternal genes expressed in the sea urchin egg, which will provide a number of insights into the early development of this well-characterized model organism.

Animals↗
PubMed1999

Large-scale clustering of cDNA-fingerprinting data.

Clustering is one of the main mathematical challenges in large-scale gene expression analysis. We describe a clustering procedure based on a sequential k-means algorithm with additional refinements that is able to handle high-throughput data in the order of hundreds of thousands of data items measured on hundreds of variables. The practical motivation for our algorithm is oligonucleotide fingerprinting-a method for simultaneous determination of expression level for every active gene of a specific tissue-although the algorithm can be applied as well to other large-scale projects like EST clustering and qualitative clustering of DNA-chip data. As a pairwise similarity measure between two p-dimensional data points, x and y, we introduce mutual information that can be interpreted as the amount of information about x in y, and vice versa. We show that for our purposes this measure is superior to commonly used metric distances, for example, Euclidean distance. We also introduce a modified version of mutual information as a novel method for validating clustering results when the true clustering is known. The performance of our algorithm with respect to experimental noise is shown by extensive simulation studies. The algorithm is tested on a subset of 2029 cDNA clones coming from 15 different genes from a cDNA library derived from human dendritic cells. Furthermore, the clustering of these 2029 cDNA clones is demonstrated when the entire set of 76,032 cDNA clones is processed.

Algorithms↗
PubMed1998

Comparative gene expression profiling by oligonucleotide fingerprinting.

The use of hybridisation of synthetic oligonucleotides to cDNAs under high stringency to characterise gene sequences has been demonstrated by a number of groups. We have used two cDNA libraries of 9 and 12 day mouse embryos (24 133 and 34 783 clones respectively) in a pilot study to characterise expressed genes by hybridisation with 110 hybridisation probes. We have identified 33 369 clusters of cDNA clones, that ranged in representation from 1 to 487 copies (0.7%). 737 were assigned to known rodent genes, and a further 13 845 showed significant homologies. A total of 404 clusters were identified as significantly differentially represented (P < 0.01) between the two cDNA libraries. This study demonstrates the utility of the fingerprinting approach for the generation of comparative gene expression profiles through the analysis of cDNAs derived from different biological materials.

Animals↗
PubMed1998

Immunoscopy--a technique combining endoscopy and immunofluorescence for diagnosis of colorectal carcinoma.

BACKGROUND: Colorectal carcinoma is a common malignant disease with a high mortality rate. It arises most frequently in adenomas of the colorectum with different grades of dysplasia. Endoscopy and biopsy are among the most reliable diagnostic tools currently available. Diagnosis of malignancy at an early stage is sometimes difficult. This study reports on a new method, "immunoscopy", that combines endoscopy and immunofluorescent diagnostic procedures; it is the first reported use of locally applied fluorescein-labeled antibodies for detection of colorectal carcinomas. METHODS: A monoclonal antibody against carcinoembryonic antigen was fluorescein labeled. In phase I, formalin-fixed tissue samples, and in phase II, postoperative fresh tissue samples from tumorous and nontumorous areas of resected colorectal carcinomas were studied. After being incubated for 10 minutes, specific fluorescence was visualized with a conventional endoscope whose range was increased by means of two narrow band filters. RESULTS: Because of high levels of autofluorescence, evaluation of immunoscopic investigations using formalin fixed tissue (phase I) was not carried out. Immunoscopic investigation with postoperative fresh tissue samples could differentiate between tumorous and nontumorous areas (p < 0.001). Immunoscopic results were compared with data from immunohistochemical investigations with anti-carcinoembryonic antigen on the same tissue samples. CONCLUSIONS: Immunoscopy can differentiate between malignant and benign mucosal areas in fresh tissue samples. The high sensitivity of immunoscopy could potentially make it a useful diagnostic complement to routine endoscopy.

Adenoma↗
PubMed1997

[Standardization in sigmoid diverticulitis surgery planning: indications based on evaluation with the Hughes classification].

Sigmoid diverticulitis accounts for the most frequent colonic disease in Western countries. We studied 145 patients with diverticulitis (elective resection in 105, emergency resection in 40 patients) using the HUGHES classifications-based indication of the resection procedure (Stage I, acute diverticulitis/colonic wall phlegmonia, continent resection; Stage II, perforated diverticulitis with local perotinitis, continent resection, Hartmann's procedure exceptionally; Stage III/IV, Hartmann's procedure, continent resection exceptionally). Stage-specific morbidity was I: 18%, II: 22%, III/IV: 60%; emergency case mortality was 15%; elective case mortality was 0%. Severe local failure was significantly higher in stage II/IV than stage II/I class diverticulitis. Early elective resection is recommended with regard to morbidity, mortality, and hospitalisation time and related costs.

Adult↗