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Biomedical subjects

D Fischer

Publications and source records attributed to D Fischer.

At least 163 records · Page 9Linked to original sources
PubMed1994

Depression, mastery and number of group sessions attended predict outcome of patients with panic and agoraphobia in a behavioural/medication program.

From a list of 214 patients suffering from panic and agoraphobia and who had been treated with cognitive behaviour therapy, 30 patients who had very good outcomes and 32 who had poor outcomes were selected. The groups were selected by the nurse therapist and psychiatrist on the basis of personal knowledge of the patients. The distinction into good and poor outcome groups was confirmed by the results of a follow-up questionnaire completed by the patient. Of several clinical and demographic variables which had been hypothesized to be predictors of outcome, only depression, as measured by the Beck Depression Inventory, mastery, as measured by the Pearlin Mastery Scale and the number of group therapy sessions attended predicted outcome. Levels of depression and mastery might be clinically modifiable variables which affect the outcome of treatment for patients with panic and agoraphobia.

Adult↗
PubMed1994

[Detection of Chlamydia psittaci in vaginal discharge of cows: a necessary enlargement of bacteriologic diagnosis for the etiologic clarification of fertility disorders in the female cow].

Vaginal discharge from 119 dairy cows from 59 herds was examined bacteriologically, including application of the IDEIA Chlamydia test, to detect genus-specific chlamydial LPS-antigen. A putrid quality of specimens was closely correlated with isolation of Actinomyces pyogenes (p < 0.001). The IDEIA was positive for 39 of 65 (60.0%) non-putrid specimens and for 16 of 54 (29.6%) putrid specimens; a non-putrid quality of specimens was closely correlated with the detection of chlamydial antigen (p < 0.01). IDEIA-positive results were confirmed by a blocking-antibody assay and by polymerase chain reaction (PCR) using a set of primers based on the 16S rRNA sequences of Chlamydia psittaci. Chlamydia-positive non-putrid specimens generally yielded no other bacterial pathogens. The clinical history of repeat breeding and endometritis, as well as failure to isolate other bacterial pathogens on routinely used non-living media, were strongly suggestive of primary chlamydial involvement in these cases.

Animals↗
PubMed1993

Mitomycin C as an adjunct to postoperative radiation therapy in squamous cell carcinoma of the head and neck: results from two randomized clinical trials.

PURPOSE: This study was undertaken to assess the benefit of mitomycin C as an adjunct to postoperative radiation therapy in patients with operable squamous cell carcinoma of the head and neck. METHODS AND MATERIALS: Between May 1980 and May 1991, 182 patients have been enrolled in two consecutive randomized clinical trials testing mitomycin C as an adjunct to radiation therapy in squamous cell carcinoma of the head and neck. In both trials, patients were stratified by stage, disease site and intent of therapy. This subset analysis includes 113 patients entered into these two randomized trials treated with surgery and postoperative radiation therapy. In the first trial, patients were randomized to receive standard postoperative radiation therapy alone compared with postoperative radiation therapy with concomitant mitomycin C. In the second trial, patients were randomized to postoperative radiation therapy or postoperative radiation therapy with concomitant mitomycin C plus dicoumarol. RESULTS: As of November 1991, the 113 patients treated with surgery and postoperative radiation therapy in both trials had a median follow-up of 93 months. There have been a total of 12 local recurrences in the radiation therapy alone arm compared to 0 local recurrences in the radiation therapy/mitomycin C arm. There were eight regional recurrences in the radiation therapy alone arm compared with five regional recurrences in the mitomycin C arm. Patients in the mitomycin C arm experienced a superior 5-year actuarial local regional control rate (87% vs. 67%, p < .015) and a statistically significant disease-free survival benefit (67% vs. 44%, p < .03). Overall survival difference between the two arms (56% vs. 41%) has not reached statistical significance. CONCLUSIONS: We conclude from these prospectively designed randomized clinical trials that in patients with operable head and neck cancer treated with surgery and postoperative radiation therapy, concomitant administration of mitomycin C with radiation therapy will result in a statistically significant disease-free survival and local regional control benefit. We are currently investigating the value of other bioreductive alkylating agents as adjuncts to radiation therapy in patients with squamous cell carcinoma of the head and neck.

Adult↗
PubMed1993

Breast conservation therapy without axillary dissection. A rational treatment strategy in selected patients.

PURPOSE: Patients with early stage breast cancer are being treated with adjuvant systemic therapy with increasing frequency regardless of the pathological status of the axillary lymph nodes. The purpose of this study was to determine the outcome for local regional control in patients treated with radiation therapy to the intact breast and regional lymph nodes without axillary dissection. PATIENTS AND METHODS: The patient population for this study consists of 327 patients with clinical stage I or II invasive breast cancer who were treated by lumpectomy alone without axillary dissection followed by radiation therapy to the intact breast and regional lymph nodes. Outcome for local regional control and survival is reported. RESULTS: As of December 1990, with a median follow-up of more than 10 years, the overall 10-year survival rate was 71%. There were a total of eight regional nodal failures resulting in a 5-year actuarial nodal control rate of 97%. Minimal morbidity was associated with this treatment policy. CONCLUSIONS: For selected patients undergoing breast preservation therapy, lumpectomy alone without axillary dissection followed by radiation therapy to the intact breast and regional lymph nodes results in a high rate of local regional control. Selected patients in whom the results of the axillary lymph node dissection will not influence decisions regarding systemic therapy are candidates for this approach.

Actuarial Analysis↗
PubMed1993

Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition.

We describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3-D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3-D C alpha motif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understanding of protein structure and biomolecular recognition. Searches for 3-D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this method in its application to two members of the globin family and to two dehydrogenases.

Alcohol Dehydrogenase↗
PubMed1993

Absence of somatic histone H1 in oocytes and preblastula embryos of Xenopus laevis.

Available data on the occurrence and expression of somatic histone H1 during oogenesis and early embryogenesis of Xenopus laevis are contradictory. In particular the reported presence of a large storage pool of histone H1A in oocytes is difficult to reconcile with the high transcriptional activity of all gene classes in this specific cell type. In the present study we have used polyclonal antibodies raised against somatic Xenopus histone H1 (H1A and H1A/B) for combined immunoblotting experiments to quantitate H1 pools and immunolocalization studies to visualize chromosome-bound H1. Both approaches failed to detect soluble or chromosomal histone H1 in vitellogenic oocytes, eggs, and cleavage-stage embryos up to early blastula. In addition, chromatin assembled in Xenopus egg extract was also negative for histone H1 as revealed by immunofluorescence microscopy. Lampbrush chromosomes not only lacked histone H1 but also the previously identified histone H1-like B4 protein (Smith et al., 1988, Genes Dev. 2, 1284-1295). In contrast, chromosomes of eggs and early embryos fluoresced brightly with anti-B4 antibodies. Our results lend further support to the view that histone H1 expression is developmentally regulated during Xenopus oogenesis and embryogenesis similar to what is known from other species.

Animals↗
PubMed1993

DNA topoisomerase II is not detectable on lampbrush chromosomes but enriched in the amplified nucleoli of Xenopus oocytes.

In somatic cells DNA topoisomerase II (topo II) is thought to be involved in the domain organization of the genome by anchoring the basis of chromatin loops to a chromosomal scaffold. Lampbrush chromosomes of amphibian oocytes directly display this radial loop organization in cytological preparations. In order to find out whether topo II may play a role in the organization of these meiotic chromosomes, we performed immunofluorescence studies using antibodies against Xenopus topo II. Our results indicate that topo II is apparently absent from lampbrush chromosomes and is hence unlikely to act as a "fastener" of the numerous lateral chromosomal loops. Topo II was, however, enriched in the amplified nucleoli of Xenopus oocytes.

Animals↗
PubMed1993

Spatial, sequence-order-independent structural comparison of alpha/beta proteins: evolutionary implications.

We present a unique sequence-order independent approach which allows examination of three dimensional structures, searching for spatially similar substructural motifs. If the amino acids composing the motifs are contiguous in the primary chain, that is, they follow each other in the sequence, a common ancestor and a divergent evolutionary process may be implied. On the other hand, if the three-dimensional substructural motif consists of amino acids whose positions in the sequences vary between the different proteins, a convergent evolution might have taken place. Starting from different, ancient sequences, mutations may have occurred that brought about formation and conservation of a truly structural motif. Such a motif might be particularly suitable for fulfilling a specific function. Clearly, in order to be able to carry out such a task one needs a technique which allows comparisons of protein structures absolutely independent of their amino acid sequence-order. Our novel, efficient, computer vision based technique treats atoms (residues) as unconnected points in space, using strictly the atomic (either all atoms or only the C alpha atoms) coordinates. The order of the residues is completely disregarded. Detection, cataloging and analysis of "real" three-dimensional, sequence-order independent motifs in the crystallographic database is expected to be an invaluable tool for protein folding. Here we demonstrate the power of the technique by applying it to alpha/beta proteins. Our studies indicate that for some of the proteins, the "classical" structural alignments (conserving the amino acid order) are the optimal ones. Nevertheless, for others, truly spatial (out of sequential-order) amino acid equivalencing results in a better geometrical match.

Biological Evolution↗
PubMed1993

A computer vision based technique for 3-D sequence-independent structural comparison of proteins.

A detailed description of an efficient approach to comparison of protein structures is presented. Given the 3-D coordinate data of the structures to be compared, the system automatically identifies every region of structural similarity between the structures without prior knowledge of an initial alignment. The method uses the geometric hashing technique which was originally developed for model-based object recognition problems in the area of computer vision. It exploits a rotationally and translationally invariant representation of rigid objects, resulting in a highly efficient, fully automated tool. The method is independent of the amino acid sequence and, thus, insensitive to insertions, deletions and displacements of equivalent substructures between the molecules being compared. The method described here is general, identifies 'real' 3-D substructures and is not constrained by the order imposed by the primary chain of the amino acids. Typical structure comparison problems are examined and the results of the new method are compared with the published results from previous methods. These results, obtained without using the sequence order of the chains, confirm published structural analogies that use sequence-dependent techniques. Our results also extend previous analogies by detecting geometrically equivalent out-of-sequential-order structural elements which cannot be obtained by current techniques.

Algorithms↗
PubMed1993

The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy: characterization of the plasmid and its termini.

As described previously, in Rhodococcus sp. (formerly Nocardia opaca) strains MR11 and MR22, the ability to grow as an aerobic hydrogen bacterium (the Aut character) is located on giant conjugative linear plasmids--on pHG201 (270 kb) in strain MR11 and on pHG205 (280 kb) in strain MR22. In an autotrophic transconjugant originating from MR22 a smaller plasmid, pHG207 (225 kb), was detected and shown to be a recombination product of the wild-type plasmids pHG204 and pHG205. A donor carrying pHG207 as the sole plasmid transferred the Aut marker at a 1000-fold frequency compared to the wild-type plasmid pHG205. Analysis of the plasmid ends revealed that plasmid pHG207 carries proteins at both ends; the proteins are linked to the 5' ends of the strands. The cloned end fragments of about 2 kb were sequenced and found to contain highly homologous sequences within the terminal 583 bp (left end part) and 560 bp (right end part). Several potential reading frames were detected, but database searching gave no indication about possible functions.

Bacterial Proteins↗
PubMed1993

Osmotic regulation of rpoS-dependent genes in Escherichia coli.

The rpoS gene, which encodes a putative alternative sigma factor (sigma S), is essential for the expression of a variety of stationary-phase-induced genes as well as for stationary-phase-specific multiple-stress resistance. As previously shown for the otsA and otsB genes (R. Hengge-Aronis, W. Klein, R. Lange, M. Rimmele, and W. Boos, J. Bacteriol. 173:7918-7924, 1991), we demonstrate here that additional rpoS-controlled genes (bolA, csi-5) as well as at least 18 proteins on two-dimensional O'Farrell gels could be induced in growing cells by osmotic upshift via an rpoS-dependent mechanism. Also, rpoS-dependent thermotolerance and resistance against hydrogen peroxide could be osmotically stimulated. In contrast, the expression of glgS, while exhibiting strong stationary-phase induction, was only weakly increased by elevated osmolarity, and several rpoS-dependent proteins previously identified on two-dimensional gels were not osmotically induced. During osmotic induction of rpoS-dependent genes, rpoS transcription and the level of sigma S remained unchanged. We conclude that osmotically regulated genes represent a subfamily within the rpoS regulon that requires differential regulation in addition to that provided by sigma S.

Bacterial Proteins↗
PubMed1993

The influence of gravity on vestibular nystagmus in humans.

Traditionally the human vestibular system is tested by accelerations and decelerations in a rotating chair, stimulating the horizontal semicircular canals. This kind of testing provides no information about the performance or the two pairs of vertical (anterior and posterior) canals and the two pairs of otoliths. Testing the vestibulo-ocular reflex (VOR) in its entirety requires rotations around the 3 axis of the head (yaw, pitch and roll) as well as rotations where the axis is not aligned with gravity. The data presented here are, to our knowledge, the first measurements of the VOR in normal humans obtained with 3-dimensional high resolution recording techniques.

Eye Movements↗
PubMed1992

Evaluation of the polymerase chain reaction (PCR) for detection of Chlamydia psittaci in abortion material from ewes.

The polymerase chain reaction (PCR) was evaluated as a diagnostic tool for detection of Chlamydia (C.) psittaci in abortion material from 40 ewes. For this purpose, PCR results of 87 samples were compared with direct microscopic identification after chemical staining, cell culture isolation and a commercially available enzyme-linked immunosorbent assay (ELISA). The value for sensitivity as compared to cell culture was 97.7% whereas the specificity-value was calculated to be 84.1%.

Abortion, Veterinary↗
PubMed1992

An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins.

As the number of available three dimensional coordinates of proteins increases, it is now recognized that proteins from different families and topologies are constructed from independent motifs. Detection of specific structural motifs within proteins aids in understanding their role and the mechanism of their operation. To aid in identification and use of these motifs it has become necessary to develop efficient methods for systematic scanning of structural databases. To date, methods of structural protein comparison suffer from at least one of the following limitations: (1) are not fully automated (require human intervention), (2) are limited to relatively similar structures, (3) are constrained to linear alignments of the structures, (4) are sensitive to insertions, deletions or gaps in the sequences or (5) are very time consuming. We present a method to overcome the above limitations. The method discovers and ranks every piece of structural similarity between the structures compared, thus allowing the simultaneous detection of real 3-D motifs in different domains, between domains, in active sites, surfaces etc. The method uses the Geometric Hashing Paradigm which is an efficient technique originally developed for Computer Vision. The algorithm exploits the geometrical constraints of rigid objects, it is especially geared towards recognition of partial structures in rigid objects belonging to large data bases and is straightforwardly parallelizable. Computer Vision techniques are for the first time applied to molecular structure comparison, resulting in an efficient, fully automated tool. The method has been tested in a number of cases, including comparisons of the haemoglobins, immunoglobulins, serine proteinases, calcium binding proteins, DNA binding proteins and others. In all examples our results were equivalent to the published results from previous methods and in some cases additional structural information was obtained by our method.

Amino Acid Sequence↗
PubMed1992

Identification and molecular analysis of glgS, a novel growth-phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli.

The putative stationary-phase sigma factor (sigma S) encoded by rpoS is essential for glycogen synthesis, but is not required for the transcription of glgC and glgA, which encode ADP-glucose-pyrophosphorylase and glycogen synthase, respectively. Using a mini-Mu random chromosomal library and a screen for glycogen overproduction, we identified a novel gene (glgS) involved in glycogen synthesis. glgS maps at 66.6 min (3247 kb) on the chromosome and constitutes a monocistronic operon. It encodes a hydrophilic and highly charged small protein, with a molecular weight of 7886, which is strongly expressed in minicells. Experiments with single-copy chromosomal glgS::lacZ gene fusions indicated that glgS expression is controlled by sigma S as well as by cAMP. Two transcriptional start sites were mapped in the upstream regulatory region of glgS. The glgSp1 transcript was absent in a cya mutant, whereas an rpoS mutant did not synthesize the glgSp2 transcript. Although glycogen synthesis is strongly stimulated by overproduction of GlgS and is inhibited by a glgS null mutation, glgS does not affect the expression of the glgCAP operon. Its potential role in the metabolic control of glycogen synthesis is discussed. Also, evidence is presented to show that the amount of glycogen accumulated in vivo in early stationary-phase cells is mainly determined by sigma S-controlled gene expression and allosteric activation of GlgC, whereas the absolute levels of expression of glgCAP as well as the intracellular concentration of cAMP are of minor importance.

Amino Acid Sequence↗