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Biomedical subjects

J Hanke

Publications and source records attributed to J Hanke.

At least 19 recordsLinked to original sources
PubMed1999

CTLA-4-Mediated inhibition of early events of T cell proliferation.

CTLA-4 engagement by mAbs inhibits, while CD28 enhances, IL-2 production and proliferation upon T cell activation. Here, we have analyzed the mechanisms involved in CTLA-4-mediated inhibition of T cell activation of naive CD4+ T cells using Ab cross-linking. CTLA-4 ligation inhibited CD3/CD28-induced IL-2 mRNA accumulation by inhibiting IL-2 transcription, which appears to be mediated in part through decreasing NF-AT accumulation in the nuclei. However, CTLA-4 ligation did not appear to affect the CD28-mediated stabilization of IL-2 mRNA. Further, CTLA-4 engagement inhibited progression through the cell cycle by inhibiting the production of cyclin D3, cyclin-dependent kinase (cdk)4, and cdk6 when the T cells were stimulated with anti-CD3/CD28 and with anti-CD3 alone. These results indicate that CTLA-4 signaling inhibits events early in T cell activation both at IL-2 transcription and at the level of IL-2-independent events of the cell cycle, and does not simply oppose CD28-mediated costimulation.

Abatacept↗
PubMed1999

Associative database of protein sequences.

MOTIVATION: We present a new concept that combines data storage and data analysis in genome research, based on an associative network memory. As an illustration, 115 000 conserved regions from over 73 000 published sequences (i.e. from the entire annotated part of the SWISSPROT sequence database) were identified and clustered by a self-organizing network. Similarity and kinship, as well as degree of distance between the conserved protein segments, are visualized as neighborhood relationship on a two-dimensional topographical map. RESULTS: Such a display overcomes the restrictions of linear list processing and allows local and global sequence relationships to be studied visually. Families are memorized as prototype vectors of conserved regions. On a massive parallel machine, clustering and updating of the database take only a few seconds; a rapid analysis of incoming data such as protein sequences or ESTs is carried out on present-day workstations. AVAILABILITY: Access to the database is available at http://www.bioinf.mdc-berlin.de/unter2.html++ + CONTACT: (hanke,lehmann,reich)@mdc-berlin.de; bork@embl-heidelberg.de

Amino Acid Sequence↗
PubMed1998

Trypanosoma cruzi has not lost its S-adenosylmethionine decarboxylase: characterization of the gene and the encoded enzyme.

All attempts to identify ornithine decarboxylase in the human pathogen Trypanosoma cruzi have failed. The parasites have instead been assumed to depend on putrescine uptake and S-adenosylmethionine decarboxylase (AdoMetDC) for their synthesis of the polyamines spermidine and spermine. We have now identified the gene encoding AdoMetDC in T. cruzi by PCR cloning, with degenerate primers corresponding to conserved amino acid sequences in AdoMetDC proteins of other trypanosomatids. The amplified DNA fragment was used as a probe to isolate the complete AdoMetDC gene from a T. cruzi genomic library. The AdoMetDC gene was located on chromosomes with a size of approx. 1.4 Mbp, and contained a coding region of 1110 bp, specifying a sequence of 370 amino acid residues. The protein showed a sequence identity of only 25% with human AdoMetDC, the major differences being additional amino acids present in the terminal regions of the T. cruzi enzyme. As expected, a higher sequence identity (68-72%) was found in comparison with trypanosomatid AdoMetDCs. When the coding region was expressed in Escherichia coli, the recombinant protein underwent autocatalytic cleavage, generating a 33-34 kDa alpha subunit and a 9 kDa beta subunit. The encoded protein catalysed the decarboxylation of AdoMet (Km 0.21 mM) and was stimulated by putrescine but inhibited by the polyamines, weakly by spermidine and strongly by spermine. Methylglyoxal-bis(guanylhydrazone) (MGBG), a potent inhibitor of human AdoMetDC, was a poor inhibitor of the T. cruzi enzyme. This differential sensitivity to MGBG suggests that the two enzymes are sufficiently different to warrant the search for compounds that might interfere with the progression of Chagas' disease by selectively inhibiting T. cruzi AdoMetDC.

Adenosylmethionine Decarboxylase↗
PubMed1998

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins.

Using a new method for construction and database searches of sequence consensus strings, we have identified a new superfamily of protein modules comprising laminin G, thrombospondin N and the pentraxin families. The conserved patterns correspond mainly to hydrophobic core residues located in central beta strands of the known three-dimensional structures of two pentraxins, the human C-reactive protein and the serum amyloid P-component. Thus, we predict a similar jellyroll fold for all members of this superfamily. In addition, the conservation of two exposed aspartate residues in the majority of superfamily members suggests hitherto unrecognised functional sites.

Amino Acid Sequence↗
PubMed1998

Selective generation of chromosomal cosmid libraries within the Trypanosoma cruzi genome project.

From a total genomic cosmid library of the pathogen Trypanosoma cruzi, specific sublibraries of the smallest four chromosomes were isolated by hybridization of the respective chromosomal bands obtained from pulsed-field gels. These libraries form the basis for initial mapping analyses that should provide information useful for both the ongoing physical mapping of the entire genome and eventual sequence analyses. Selectivity of the procedure was high with 75% to 92%, although cross-hybridization had to be expected from ubiquitous DNA features, such as centromeric and telomeric sequences, and other regions homologous between individual chromosomes. Overall, the number of identified clones was slightly higher than expected but well within the intrinsic experimental variation considering the uncertainty about the exact genome size, the variability in clonability and the higher frequency of repeat sequences in larger chromosomes. Chromosome III- and IV-specific cosmids were analyzed on Southern blots of chromosomal separations. For strain CL Brener, all clones tested exhibited cross-hybridization to a homologous chromosome larger than 1 Mbp, supporting the assumption of the respective chromosome couple being diploid pairs.

Animals↗
PubMed1998

Hybridization mapping of Trypanosoma cruzi chromosomes III and IV.

As part of the Trypanosoma Genome Initiative launched by the World Health Organization (WHO), a physical clone map of Trypanosoma cruzi chromosomes III and IV was generated to facilitate both DNA sequence analysis of the parasite's genome and the investigation of chromosome organization. Apart from a few genetic markers, anonymous cosmids were taken from chromosomal sublibraries and individually hybridized to filter arrays of the relevant cosmid library. The probe order was determined from the hybridization fingerprint results and used to define a fitting clone order, with few gaps remaining. The results were independently verified by hybridizations to a bacterial artificial chromosome (BAC) library and, in case of chromosome III, restriction mapping. For gap closure, additional experiments on a total cosmid library were carried out. The possible tiling paths consist of 26 clones for chromosome III (610 kbp) and 28 clones for chromosome IV (680 kbp).

Animals↗
PubMed1997

Delta and kappa opioid receptors in eyestalk ganglia of a crustacean.

Crustacean eyestalk ganglia are part of the protocerebrum and have been demonstrated to produce numerous neurohormones. 3H(2-D-Pen, 5-D-Pen)-enkephalin, 3H-(-)-ethylketocyclazocine and 3H(D-Ala2-NMePhe-Glyol5)-enkephalin were used as ligands for opioid receptors on neuronal membrane preparations of eyestalk ganglia under consideration of their stereospecific binding properties. In context with saturation binding isotherms, association and dissociation plots, we demonstrate here two opioid receptors; a delta-type receptor with high affinity (Bmax 68.5 fmol/mg protein, Kd = 4.0 nM) and low affinity (Bmax 493 fmol/mg, Kd = 83.6 nM) and a second receptor of kappa-type with Bmax of 3.1 pmol/mg protein and Kd = 68.6 nM.

Animals↗
PubMed1997

Sulcal pattern of the anterior parahippocampal gyrus in the human adult.

The sulcal pattern of the human entorhinal region, located in the anterior portion of the parahippocampal gyrus, was investigated in 184 brain hemispheres of both sexes between the ages of 19 and 85 years. A new classification of the sulcal pattern is introduced with reference to the extension of the collateral and rhinal sulci. Both sulci were found in all the investigated hemispheres. The collateral sulcus is a continuation of the rhinal sulcus in 41.9%. The rhinal sulcus represents the anterolateral border of the entorhinal region. By defining four branches of the rhinal sulcus all the possible ramifications occurring in the investigated hemispheres could be described. In 19.0% of the cases, a well developed entorhinal sulcus emerges in the central portions of the entorhinal region. An incipient entorhinal sulcus is evident in 29.6% and the sulcus is absent in 51.4% of the investigated cases. The intrarhinal nick, resulting from the impression of the free edge of the cerebellar tent, is seen as a dip in 35.1% and as a notch in 34.5%. It is absent in 30.4% of the cases. A comparison between the right and left hemispheres, as well as between the female and male sexes, revealed only minor differences of the sulcal pattern.

Adult↗
PubMed1997

Pigmentarchitectonic subfields of the entorhinal region as revealed in tangential sections.

The entorhinal region is an important center of the limbic system involved in many dementing disorders. The boundaries of the entorhinal region of the left and right hemispheres were investigated in tangential sections (5 individuals, age range 21 to 29 years). This method preserves the rostral portion of the entorhinal region which is usually lost in coronal sectioning. The sections were stained with the pigment-Nissl-method. The superficial cellular layer of the centromedial part of the entorhinal region consists of large heavily pigmented neurons forming islands clearly separated from each other. The anterior and posterior parts of the entorhinal region display an opposite pattern consisting of small islands and stripes with ill-defined boundaries. The islands contain small and sparsely pigmented neurons surrounded by large and well pigmented cells. Close to the adjacent proisocortex, the small cell containing islands confluent while the large and well pigmented neurons disappear. Hence, the medial side of the entorhinal region extends up to the uncus and the lateral side into the main branch of the rhinal sulcus. The entorhinal region covers the frontal portion of the parahippocampal gyrus up to the periamygdaloid cortex and the posterior part ends acute-angled within the medial portion of the parahippocampal gyrus.

Adult↗
PubMed1996

Self-organizing hierarchic networks for pattern recognition in protein sequence.

We present a method based on hierarchical self-organizing maps (SOMs) for recognizing patterns in protein sequences. The method is fully automatic, does not require prealigned sequences, is insensitive to redundancy in the training set, and works surprisingly well even with small learning sets. Because it uses unsupervised neural networks, it is able to extract patterns that are not present in all of the unaligned sequences of the learning set. The identification of these patterns in sequence databases is sensitive and efficient. The procedure comprises three main training stages. In the first stage, one SOM is trained to extract common features from the set of unaligned learning sequences. A feature is a number of ungapped sequence segments (usually 4-16 residues long) that are similar to segments in most of the sequences of the learning set according to an initial similarity matrix. In the second training stage, the recognition of each individual feature is refined by selecting an optimal weighting matrix out of a variety of existing amino acid similarity matrices. In a third stage of the SOM procedure, the position of the features in the individual sequences is learned. This allows for variants with feature repeats and feature shuffling. The procedure has been successfully applied to a number of notoriously difficult cases with distinct recognition problems: helix-turn-helix motifs in DNA-binding proteins, the CUB domain of developmentally regulated proteins, and the superfamily of ribokinases. A comparison with the established database search procedure PROFILE (and with several others) led to the conclusion that the new automatic method performs satisfactorily.

Amino Acid Sequence↗
PubMed1996

Standardized ultrasound examination for evaluation of instability of the acromioclavicular joint.

Anteroposterior X-ray views of both acromioclavicular (AC) joints with 10-kg weights held in each hand are the generally accepted procedure for diagnosis of Tossy I-III grades of AC joint separation. An analogous diagnosis can be made by standardized ultrasound examination. Ten individuals with Tossy-I, 11 with Tossy-II and 8 with Tossy-III instability were examined both radiographically and by B-mode ultrasound. The degree of AC joint separation was uniformly determined on the basis of a calculated index (AC Index = AC joint width of uninjured side/AC joint width of injured side). The mean AC Index for Tossy-I instability determined by ultrasound was 1.0; mean indices of 0.49 and 0.5 were determined for Tossy-II injury by ultrasound and X-ray, respectively, and of 0.21 and 0.2, respectively, for Tossy-III instability. Statistical analysis showed significant differences between the mean AC indices of all three groups (P < 0.0001). We conclude that the reliability of ultrasound examination of AC joint instability is equal to that of radiographic measurement. Standard X-rays of the shoulder remain mandatory only to exclude fracture. The indication for operative stabilization of the AC joint can be established on the basis of the grade of AC joint instability measured by the side-effect-free and cost-effective method of ultrasound examination (AC Index < 0.3 equivalent to Tossy-III instability).

Acromioclavicular Joint↗
PubMed1996

Opioid receptor types for endogenous enkephalin in the thoracic ganglion of the crab, Carcinus maenas.

In crustaceans, the endogenous opioid peptides, enkephalins, are known to be concentrated in the thoracic ganglion, although they have been demonstrated in all parts of the nervous system. Bmax and Kd measurements have been obtained for the binding of ligands used to characterize delta- and kappa-type opioid receptors in vertebrates. High- and low affinity binding of [3H] [2-D-Pen5-D Pen] enkephalin ([3H]DPDPE) has been measured with a Kd = 9.2 +/- 2.4 nM, Bmax = 153 fmol/mg, and Kd = 243 +/- 27 nM, Bmax = 1.785 pmol/mg, respectively. In addition a kappa-type receptor with Kd 85.5 +/- 12.6 nM and Bmax = 21.138 pmol/mg protein has been recorded. Binding characteristics of several ligands were monitored. Electrophoretic studies of affinity chromatographically purified receptor fractions revealed a molecular mass of 60 kDa. Isoelectric focusing showed a specific binding of [3H]DPDPE to thoracic ganglion membranes at a pl of 5.5.

Analgesics, Opioid↗
PubMed1996

Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.

The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way.

Amino Acid Sequence↗
PubMed1996

Mapping the Trypanosoma cruzi genome: analyses of representative cosmid libraries.

In order to generate contiguous cosmid coverage of the genome of the protozoan parasite Trypanosoma cruzi for large-scale sequence analysis, a cosmid library of 36864 individual, primary clones was generated. Total genomic DNA of the reference strain CL Brener was fragmented both by partial digestion with MboI and by physical shearing. For cloning, a modified cosmid vector was used that simplifies analyses such as restriction mapping. The library's representation is about 25 genome equivalents, assuming a size of 55 Mb per haploid genome. No chimerism of inserts in the clones could be detected. The colinearity between cosmid inserts and genomic DNA was verified. Also, hybridizations to the gel-separated karyotype of the organism were carried out as a quality check. Gridded onto two nylon filters, the library was analyzed with a variety of probes. Apart from being used for combined physical and transcriptional mapping of the genome, library filters and clones are also available to interested parties.

Animals↗
PubMed1996

[Promoting venous return in plaster cast by AV impulse system. A preclinical study].

A new pneumatic compression pump--the AV-impulse system--causes increased return of venous blood from the lower limbs to the heart and increases total blood flow in the lower limbs by emptying the plantar venous plexus. Up to date there exist no experiences with using this system in plaster cast. We studied the maximum venous blood flow, the venous blood flow per minute and the venous diameters above the popliteal and femoral vein by duplexsonography in 12 lower limbs of 6 healthy persons before and after applying below-the-knee plaster casts. After applying the plaster cast we observed a slight increase in venous diameter (p = 0.02). By using the AV-impulse-system we observed a significant increase in maximum venous blood flow and venous blood flow per minute (p < 0.05). We demonstrated a significant increase of venous blood return in the deep veins of the lower limbs after applying a lower limb plaster cast by using the AV-impulse-system. These results indicate the possible benefit of using the AV-impulse-system as a physical method of thromboprophylaxis in orthopaedic and trauma patients with plaster cast immobilisation of the leg.

Adult↗
PubMed1995

Thromboprophylaxis with low-molecular-weight heparin in outpatients with plaster-cast immobilisation of the leg.

Deep-vein thrombosis is common after plaster-cast immobilisation for traumatic injury. We did a randomised prospective study of the effect of low-molecular-weight heparin on the incidence of deep-vein thrombosis in patients with minor injuries treated with plaster-cast immobilisation of the leg. A control group (n = 163) received no prophylaxis, the prophylaxis group received low-molecular-weight heparin once daily (n = 176). The incidence of deep-vein thrombosis in the prophylaxis group was 0% (one tailed p < 0.006) vs 4.3% in the control group. No severe side-effects of low-molecular-weight heparin were observed. Thromboprophylaxis with low-molecular-weight heparin once daily is effective in reducing the risk of deep-vein thrombosis in outpatients with plaster-cast immobilisation of the leg.

Adolescent↗
PubMed1994

[Standardized ultrasound examination for classification of instability of the acromioclavicular joint].

Anteroposterior X-ray views of both acromio-clavicular (AC-) joints with 10 kg weights in each hand are generally accepted for the diagnosis of Tossy I to III AC-joint separations. An analogue diagnosis can be made by standardized ultrasound examination. Ten individuals without AC-instability (Tossy I), eleven with Tossy II- and eight with Tossy III-instability were examined both radiographically and by B-mode ultrasound. AC-joint width was uniformly calculated by using an index (AC-index = AC-joint width of uninjured side/AC-joint width of injured side). The sonographically measured mean AC-index for Tossy I-stability was 1.0; sonographically 0.49 and radiographically measured 0.5 for Tossy II-injury; and sonographically 0.21 and radiographically measured 0.2 for Tossy III-instability. Statistical analysis resulted in significant differences for all mean AC-indices of the three groups (p < 0.0001). We conclude that ultrasound examination of AC-joint instability is as reliable as radiographic measurement. Standard X-rays of the shoulder remain mandatory to exclude fractures only. The decision for operative stabilisation of the AC-joint can be based on the side-effect free and cost-effective ultrasound examination of the grade of AC-joint instability (AC-index < 0.3 equivalent Tossy III).

Acromioclavicular Joint↗