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S Heymann

Publications and source records attributed to S Heymann.

15 recordsLinked to original sources
PubMed2001

Biological sequences integrated: a relational database approach.

Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos. In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for these application domains. For this reason we propose a two step approach. First, we model the structure (and therefore the meaning of the) data using an Entity-Relationship approach. The ER model leads to a clean design of a relational database schema for storing and retrieving the DNA and protein data extracted from various sources. Our approach provides the clean basis for building complex biological applications that are more amenable to changes and software ports than their file-base counterparts.

Computational Biology↗
PubMed1998

Production and characterization of monoclonal antibodies against urea derivatives.

A panel of monoclonal antibodies was generated against the urea-based hapten N-(2-N-chloroacetylaminobenzyl)-N'-4-chlorophenylurea as a tool for building up sensitive immune assays to detect urea derivatives and to screen them for catalytic antibodies (Abs). Eleven hybridomas were obtained that produced Abs reactive to the hapten. All Abs were of IgG class. Cross reactivities of the Abs to different haptens were examined, especially to a possible transition-state analog. Only four of the hybridomas (R2-DA10/F7, R2-GE7/H2, R2-HC2/A5, R2-HD6/F7) produced Abs crossreactive with the transition-state analog. From the 11 hybridomas, hybridoma B76-BF5 was chosen for further characterization. Compared to the other Abs, B76-BF5 showed the strongest binding and had a rather restricted specificity. These Abs could be used to build up a sensitive enzyme immunoassay for the detection of the hapten. All Abs were screened for crossreactivity with the pesticides monuron and diuron. No reactivity could be detected. In addition, the nucleotide sequences of the variable light and heavy chain genes of the similarly reactive Abs B76-BF5, B76-BB3, R2-DA10/F7, and R2-GA6/G3 were determined to clarify whether structure and binding specificity of these Abs showed any correlation.

Acetamides↗
PubMed1997

Fast isolation of RNA to detect expression of tumor markers.

The expression status of several tumor-related proteins is of great interest in clinical examination and research. As a completion to conventional antibody staining, RT-PCR is often used today. Reliable isolation of RNA from a low number of cells is very often a critical stage of such an examination. We demonstrate here a simple and fast method to isolate RNA from only 10,000 cells and applied it to the detection of CEA, c-ERB-B2, and mdr-1 as often studied models for tumor markers.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1996

Regulation and function of SF/HGF during migration of limb muscle precursor cells in chicken.

Limb muscles of vertebrates are derived from migratory dermomyotomal cells which emanate from a limited number of somites located adjacent to the developing limb buds. We have generated additional limb buds in chicken embryos by implantation of FGF-beads into the interlimb region in order to analyze whether these somites can be programmed to supply ectopic limbs with myogenic precursor cells. We show that migrating myogenic precursor cells are released from somites at the level of the newly formed limb, even when cell migration into the natural limb has been completed. The implantation of FGF beads in the lateral plate mesoderm rapidly induces SF/HGF expression. FGF beads implanted between HH stages 10 and 12 inhibit limb bud formation or shift the normal limb position. When an additional FGF bead was implanted at the original limb position at HH stage 15, SF/HGF expression was transiently induced to low levels without inducing a new limb. This demonstrates that the initial induction of SF/HGF by FGF does not require limb formation. Expression of SF/HGF during early limb bud stages was found in the entire developing bud and the adjacent lateral plate mesoderm with direct contacts to the lateral edge of the dermomyotome. Later, the SF/HGF expression domain retracts to a distal region below the apical ectodermal ridge. To investigate the role of SF/HGF in the migratory process, we implanted beads soaked in SF/HGF-alone or together with FGF into different locations of the developing chick embryo. In the experiments SF/HGF caused delamination of migratory cells from the dermomyotomal epithelium but no chemotactic attraction of migrating cells toward the SF/HGF source.

Animals↗
PubMed1996

Phagocytic function and metabolite production in thioacetamide-induced liver cirrhosis: a comparative study in perfused livers and cultured Kupffer cells.

BACKGROUND/AIMS: The aim of the study presented here was to evaluate the basal and stimulated phagocytic activities and the metabolite production of isolated perfused livers, and also the phagocytic capacity of cultured Kupffer cells from rats with macronodular cirrhosis. METHODS: Rats were made cirrhotic by oral administration of thioacetamide. The phagocytic activity was assessed by the rate of removal of colloidal carbon. The Kupffer cells were prepared by a pronase/collagenase digestion method followed by elutriation. RESULTS: The phagocytic activity and production of glucose, lactate and pyruvate were reduced in cirrhotic livers when calculated per g liver. Due to hyperplastic-regenerative processes the mass of the cirrhotic livers was markedly augmented so that the colloidal carbon uptake calculated per cirrhotic liver was not significantly different from the controls. Colloidal carbon-induced glucose release increased more markedly in the controls than in cirrhotic livers. Isoproterenol considerably stimulated phagocytosis and glucose production in controls, whereas the response was clearly reduced in cirrhotic livers when calculated either per g liver or per total liver weight. The cyclic AMP analogue elicited a marked glycogenolytic response in the controls, whereas there was only a slight increase in glucose production in cirrhotic livers. Phagocytosis of cirrhotic livers was only moderately stimulated by opsonized zymosan when compared with the controls. Freshly isolated Kupffer cells exhibited a reduced phagocytic activity. Stimulation by zymosan was observed only in cell suspensions of the controls. In contrast, Kupffer cells from cirrhotic livers did not differ from controls with respect to basal or zymosan-stimulated phagocytic activity after 48-h cultivation. CONCLUSION: The stimulated phagocytic function was disturbed in perfused macronodular-cirrhotic livers as compared to controls. In contrast, 48-h cultured Kupffer cells from cirrhotic livers exhibited the same basal and stimulated phagocytic capacity as controls. The glucose release from perfused livers, initiated by stimulation of Kupffer cells or hepatocytes, was significantly reduced in cirrhotic livers. Therefore, we postulate an impaired intra- and/or intercellular signalling in macronodular-cirrhotic livers.

Animals↗
PubMed1995

Bacterial expression and refolding of single-chain Fv fragments with C-terminal cysteines.

Two antibody single-chain Fv (scFv) fragments carrying five C-terminal histidine residues were expressed in Escherichia coli as periplasmic inclusion bodies. Their variable heavy (VH) and light (VL) domains are derived from the mouse monoclonal antibody 215 (MAb215), specific for the largest subunit of RNA polymerase II of Drosophila melanogaster and rat MAb Yol1/34, specific for pig brain alpha-tubulin. ScFv-215 contains an additional cysteine residue near to its C-terminus. After solubilization of inclusion bodies followed by immobilized metal affinity chromatography (IMAC) in 6M urea and a renaturation procedure, scFv monomers, noncovalent dimers, and aggregated antibody fragments were separated by size exclusion chromatography. In addition, a fraction of disulfide-bonded scFv-215 homodimers (scFv')2 was also isolated. The various antibody forms appear to be in equilibrium after renaturation since first peak composed mainly of aggregates could be resolved into a similar pattern of aggregates, dimers, and monomers after repeating the denaturation/renaturation procedure. All fractions of the recombinant scFv-215 demonstrated high antigen-binding activity and specificity as shown by enzyme-linked immunosorbent assay (ELISA) and Western blot analysis. Affinity measurements carried out by competitive immunoassays showed that covalently linked (scFv')2 have binding constants quite close to those of the parental MAbs and fourfold higher than scFv' monomers. ScFv derivatives, specifically biotinylated through the free sulfhydryl group, recognize the corresponding antigen in ELISA and Western blot analysis, thus demonstrating the possibility of using chemically modified scFv antibodies for immunodetection.

Amino Acid Sequence↗
PubMed1995

The accessibility of thiophosphorylated groups in DNA fragments to the enzymatic activity of ligases and restriction endonuclease Bbs I.

The aim of this paper was to test the possibility to ligate and hydrolyse DNA sequences containing thiomodified ends and bonds. T4 DNA ligase was shown to ligate DNA fragments regardless of whether it contains phosphorylated or thiophosphorylated 5'-end. But the cleavage of an internally thiomodified phosphodiester bond was found to be totally inhibited when using the non-palindromic restrictase Bbs I. The special properties of this restriction endonuclease should allow the development of an oriented cloning strategy when combined with T4 ligase and a thiophosphorylation of DNA fragments.

Base Sequence↗
PubMed1994

Production of monoclonal antibodies against epitopes of the main coat protein of filamentous fd phages.

Three monoclonal antibodies (MAbs) were produced which react with epitopes of the main structural coat protein (pVIII) of filamentous fd phages as demonstrated by solid-phase fluorometric enzyme immunoassays and by immunoelectron microscopy. The antibodies are of the IgG1, IgG2a and IgG2b immunoglobulin subclasses. Since they also react with recombinant phages expressing antigen fragments in their pIII region they may be suitable reagents for the demonstration and isolation of filamentous phages used in recombinant protein technology.

Animals↗
PubMed1990

Amino acid complementarity: testing of hypotheses.

To determine whether hypotheses about the complementarity of amino acids based on the genetic code reflect the amino acid contact preferences found in natural proteins, the average contact probabilities for hypothetical complementary amino acid pairs were compared with those for all possible remaining pairs of the corresponding subset. A statistically significant preference was found for contact between amino acids with codons which had the same central nucleotide. Conversely, the contact probabilities for amino acids with complementary codons either did not exceed, or exceeded only insignificantly, the value for the corresponding remainder subset. The data obtained do not support the hypothesis for the complementarity of peptides coded by complementary RNA strands.

Amino Acids↗
PubMed1986

Electrorotation of lymphocytes--the influence of membrane events and nucleus.

Electrorotation--the spin of cells in rotating high frequency electric fields--has been used to investigate properties of human peripheral blood lymphocytes. The rotation spectra of lymphocytes deviate from those of single shell spheres. The deviations are caused by the electrical properties of the nucleus in the cell interior. Electrorotation allows the distinction between successfully stimulated lymphocytes and unstimulated cells after application of concanavalin A. Notwithstanding the fact that only a proportion of the cells will be mitogenically stimulated we detected an enhanced cell membrane conductivity for the whole cell population immediately after the addition of mitogen.

Cell Membrane↗
PubMed1985

Physicochemical properties of salt-soluble, unsheared chromatin. Hydrodynamic model calculations supporting a double-fibrillar structure.

Hydrodynamic model calculations of a special, salt-soluble chromatin fraction were performed on the basis of former experimental data. Using the models of an extended helix and of a cylinder fitted to this helix we conclude that in 0.1 M (NH4)2SO4 this chromatin has the conformation of a nucleosome double-fiber helix, i.e. a structure in which two helices share a common axis. Besides this helical structure, a stretched, linear double-fibrillar form can be derived from sedimentation data on the basis of a simple cylinder model. From the kinetic behaviour of experimental sedimentation coefficients which decrease shortly after chromatin extraction a conformational transition of the helical to the fibrillar form is postulated. At 0.2 M (NH4)2SO4 where histone H1 is released, these double-structures are supposed to dissociate into two single molecules with similar dimensions.

Chemical Phenomena↗
PubMed1983

Phosphorylated nonhistone proteins in different fractions of rat liver nuclei obtained by metrizamide gradient centrifugation.

The distribution of nuclear nonhistone proteins (NHPs) labelled in vivo with 32P was investigated in different subnuclear fractions obtained by metrizamide gradient centrifugation of mildly sonicated rat liver nuclei. The bulk chromatin banding at 1.20-1.22 g to cm3 (fraction C) contained only minor amounts both of non-phosphorylated and 32P-labelled NHPs. Nick-translated DNA sequences were found to sediment at a slightly higher density (1.26 g/cm3) in a minor fraction (A). Fraction A also contained a significant portion of the newly synthesized RNA and was enriched additionally with a broad spectrum of NHPs; some of them were highly 32P-labelled. Two hnRNP fractions (R2 and R1) sedimenting at densities greater than 1.28 g/cm3 were analyzed, too. By SDS-PAGE it was shown that the most abundant 32P-NHPs were found in three groups (fraction A, R1, and R2). Two of them, 32-34 KDa, and 37-40 KDa, are components of the major proteins of the hnRNP particles. A group of four moderately labelled 32P-NHPs of approximately 55 K, 64 K, 70 K, and 90 KDa appeared substantially enriched in fraction A. They were found also in RNP fractions R1 and R2, but to a smaller mount. Therefore, we suggest that in fraction A they exist in a complex with hnRNP. Fraction A was also enriched with numerous 32P-NHPs of very high molecular weight found in other types of experiments nearly exclusively in the nuclear residual structures. The 32P-protein pattern of the nucleoli was shown to be different from that of the other subnuclear fractions. Considering our observations on the accumulation of nick-translated DNA sequences, the presence of newly synthesized RNA, the high content of NHPs, and the association of special 32P-NHPs we suggest that fraction A represents transcriptionally active chromatin.

Animals↗
PubMed1980

Isolation and characterization of salt-soluble, unsheared chromatin.

From rat liver nuclei depending on the extraction time, 10 to 20% of total chromatin has been extracted with a solution containing 0.1 M ammonium sulfate, 2 mM MnCl2, 0.1 M Tris-HCl, pH 7.9. We term this chromatin chromatin S. It has a protein: DNA ratio of 1.3, the full amount of the 5 histones in an undegraded state, and a RNA: DNA ratio of approximately 0.2. Its nonhistone protein pattern, obtained by gel electrophoresis exhibits a rich spectrum of proteins in a broad range of molecular weights. Electrophoretic analysis of the DNA fragments obtained by micrococcus nuclease digestion of chromatin S yields the same digestion pattern as that of nuclei. Thus, chromatin S fulfils an essential criterion of unsheared chromatin. In contrast to other chromatin preparations described so far, this chromatin is soluble at a salt concentration of 0.1 M ammonium sulfate. We have shown previously that it exhibits a compact conformation, low intrinsic viscosity and low radius of gyration obtained by light scattering measurements. Its mean molecular weight was determined to be nearly 10(8).

Animals↗