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R Reinhardt

Publications and source records attributed to R Reinhardt.

At least 37 records · Page 2Linked to original sources
PubMed2000

Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21.

To establish criteria for and the limitations of novel gene identification, to identify novel genes of potential relevance to Down Syndrome and to investigate features of genome organization, 6. 550kb. In total, 41 novel gene models were predicted, and for a subset of these, RT-PCR experiments helped to verify and refine the models, and were used to assess expression in early development and in adult brain regions of potential relevance to Down syndrome. Results suggest generally low and/or restricted patterns of expression, and also reveal examples of complex alternative processing, especially in brain, that may have important implications for regulation of protein function. Analysis of complete gene structures of the known genes identified a number of very large introns, a number of very short intergenic distances, and at least one potentially bi-directional promoter. At least 3/4 of known genes and 1/2 of predicted genes are associated with CpG islands. For novel genes, three cases of overlapping genes are predicted. Results of these analyses illustrate some of the complexities inherent in mammalian genome organization and some of the limitations of current sequence analysis technologies. They also doubled the number of potential genes within the region.

Adult↗
PubMed2000

Characterization of a highly complex region in Xq13 and mapping of three isodicentric breakpoints associated with preleukemia.

The chromosomal abnormality represented by an isodicentric X chromosome [idic(X)(q13)] is associated with a subset of acute myeloid leukemia (AML) and preleukemia observed in elderly females. A previous study localized the breakpoints of two acquired isodicentric X chromosomes associated with myelodysplasia to a 450-kb region proximal to the XIST gene. Here we report the construction and extensive characterization of a reliable 1-Mb P1 artificial chromosome and bacterial artificial chromosome contig covering a highly problematic region in Xq13 that includes the previously described isodicentric breakpoint region. In addition to mapping of the brain-specific gene (NAP1L2) and the phosphoglyceryl kinase alpha subunit 1 gene (PHKA1) and generation and mapping of a large number of STSs throughout the contig, we have mapped a putative transcriptional regulatory protein (HDACL1), and 35 ESTs. Sequencing data, Southern blot analysis, and fiber-FISH analysis have permitted characterization of extensive region-specific duplications and triplications in addition to an unusually high concentration of long interspersed repeat elements, both of which could be implicated in isodicentric chromosome formation and other Xq13 chromosome aberrations. FISH analysis of metaphase chromosomes from two previously unpublished AML patients and one preleukemic patient using cosmid clones and selected subclones allowed mapping of the idic(X)(q13) breakpoints to a 100-kb interval, consistent with the involvement of an X-linked gene in the genesis of this form of preleukemia, disruption of which may represent a preliminary step in progression to AML. Assembly and physical mapping of this complex 1-Mb contig establish a foundation for ongoing sequencing and gene identification projects in the region.

Acute Disease↗
PubMed2000

Induction of putative tumor-suppressing genes in Rat-1 fibroblasts by oncogenic Raf-1 as evidenced by robot-assisted complex hybridization.

The growth factor receptor-dependent protein kinase Raf-1 is activated by GTP-bound Ras, thereby activating the mitogen-activated protein kinase pathway. To study the role of Raf in transformation we transduced Rat-1 cells with a tetracycline-regulatable retroviral vector encoding the constitutively active oncogenic C-terminal fragment of the human Raf-1 protein. Using subtractive hybridization of mRNAs from induced and noninduced cells and robot-assisted screening by complex hybridization, Raf-induced genes with various different characteristics of induction were investigated. Among the strongly induced genes were those involved in carcinogenesis such as metalloproteinases 3, 10 and 13, cathepsin L, ornithine decarboxylase, and putative tumor-suppressing genes such as monocyte chemoattracting protein 1, interferon-induced protein 10, a recently identified 2'-5' oligoadenylate synthetase-like protein, and plasminogen activator inhibitor type 2. Other components of the plasminogen activator system were not induced. Plasminogen activator inhibitor type 2 is a down-regulator of the proteolytic cascade consisting of various metalloproteinases, some of which are induced by a carboxy-terminal Raf mutant (RafCT). In conclusion, RafCT induces factors which act in a conflicting manner in respect of carcinogenesis, especially within the proteolytic system of the extracellular matrix.

Animals↗
PubMed2000

Tissue gene expression analysis using arrayed normalized cDNA libraries.

We have used oligonucleotide-fingerprinting data on 60,000 cDNA clones from two different mouse embryonic stages to establish a normalized cDNA clone set. The normalized set of 5,376 clones represents different clusters and therefore, in almost all cases, different genes. The inserts of the cDNA clones were amplified by PCR and spotted on glass slides. The resulting arrays were hybridized with mRNA probes prepared from six different adult mouse tissues. Expression profiles were analyzed by hierarchical clustering techniques. We have chosen radioactive detection because it combines robustness with sensitivity and allows the comparison of multiple normalized experiments. Sensitive detection combined with highly effective clustering algorithms allowed the identification of tissue-specific expression profiles and the detection of genes specifically expressed in the tissues investigated. The obtained results are publicly available (http://www.rzpd.de) and can be used by other researchers as a digital expression reference.

Algorithms↗
PubMed1999

The mycosubtilin synthetase of Bacillus subtilis ATCC6633: a multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase.

Bacillus subtilis strain ATCC6633 has been identified as a producer of mycosubtilin, a potent antifungal peptide antibiotic. Mycosubtilin, which belongs to the iturin family of lipopeptide antibiotics, is characterized by a beta-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, with the second, third, and sixth position present in the D-configuration. The gene cluster from B. subtilis ATCC6633 specifying the biosynthesis of mycosubtilin was identified. The putative operon spans 38 kb and consists of four ORFs, designated fenF, mycA, mycB, and mycC, with strong homologies to the family of peptide synthetases. Biochemical characterization showed that MycB specifically adenylates tyrosine, as expected for mycosubtilin synthetase, and insertional mutagenesis of the operon resulted in a mycosubtilin-negative phenotype. The mycosubtilin synthetase reveals features unique for peptide synthetases as well as for fatty acid synthases: (i) The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. MycA represents the first example of a natural hybrid between these enzyme families. (ii) The organization of the synthetase subunits deviates from that commonly found in peptide synthetases. On the basis of the described characteristics of the mycosubtilin synthetase, we present a model for the biosynthesis of iturin lipopeptide antibiotics. Comparison of the sequences flanking the mycosubtilin operon of B. subtilis ATCC6633, with the complete genome sequence of B. subtilis strain 168 indicates that the fengycin and mycosubtilin lipopeptide synthetase operons are exchanged between the two B. subtilis strains.

Adenosine Monophosphate↗
PubMed1999

Analysis of the spermine synthase gene region in Fugu rubripes, Tetraodon fluviatilis, and Danio rerio.

A prerequisite to understanding the evolution of the human X chromosome is the analysis of synteny of X-linked genes in different species. We have focused on the spermine synthase gene in human Xp22. 1. We show that whereas the human gene spans a genomic region of 54 kb, the Fugu rubripes gene is encompassed in a 4.7-kb region. However, we could not find conserved synteny between this region of human Xp22 and the equivalent F. rubripes region. A cosmid clone containing the F. rubripes gene does not contain other X-linked genes. Instead we identified homologs of human genes that are autosomally localized: the ryanodine receptor type I (RYRI), which is implicated in malignant hyperthermia and central core disease, and the HE6 gene. Comparison of the F. rubripes, Tetraodon fluviatilis, mouse, human, and Danio rerio 5'UTRs of spermine synthase highlights conserved sequences potentially involved in regulation. Interestingly, pseudogenes of this gene that are present in the human and mouse genomes seem to be absent in the compact F. rubripes genome. Analysis of a D. rerio PAC clone containing spermine synthase shows an intermediate genomic size in this fish. Sequence analysis of this PAC clone did not reveal other known genes: neither the RYRI gene, nor the HE6 gene, nor other human Xp22 genes were identified.

Alternative Splicing↗
PubMed1999

Rapid assay for one-run determination of purine and pyrimidine nucleotide contents in neocortical slices and cell cultures.

The present study describes the measurement of endogenous nucleoside di- and triphosphate contents (ATP, GTP, UTP, CTP, ADP, GDP and UDP) in rat neocortical brain slices and mixed neuronal/astrocytic corticoencephalic cultures. Determination was by means of anion-exchange HPLC using a binary gradient of 0.3 M ammonium carbonate and water. In addition, a new method is described for the identification of nucleoside triphosphates, using digestion of the nucleotides by phosphoglycerate kinase and partial splitting of nucleoside diphosphates to shift the equilibrium of the phosphoglycerate kinase reaction in direction of breakdown of nucleoside triphosphates. Finally, the determination of the sum of creatine and creatine phosphate is suggested as an alternative reference value instead of protein under conditions when cells are cultured in protein-containing medium.

Animals↗
PubMed1999

A comparison of backpropagation and generalized-regression genetic-neural network models.

The results of the backpropagation (BP) and generalized-regression genetic-neural (GRGN) network were compared using a series of nonpeptide arginine vasopressin VI antagonists. It was shown that both approaches are equivalent with respect to the recognition process while the BP network is superior over GRGN if the sample sizes are lowered by cross-validation.

Genetic Techniques↗
PubMed1998

Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects.

Large-scale genomic sequencing projects generally rely on random sequencing of shotgun clones, followed by different gap closing strategies. To reduce the overall effort and cost of those projects and to accelerate the sequencing throughput, we have developed an efficient, high throughput oligonucleotide fingerprinting protocol to select optimal shotgun clone sets prior to sequencing. Both computer simulations and experimental results, obtained from five PAC-derived shotgun libraries spanning 535 kb of the 17p11.2 region of the human genome, demonstrate that at least a 2-fold reduction in the number of sequence reads required to sequence an individual genomic clone (cosmid, PAC, etc.) can be achieved. Treatment of clone contigs with significant clone overlaps will allow an even greater reduction.

Chromosomes, Human, Pair 17↗
PubMed1998

A novel aminopeptidase associated with the 60 kDa chaperonin in the thermophilic archaeon Sulfolobus solfataricus.

The chaperonins are high-molecular-weight protein complexes having a characteristic double-ring toroidal shape; they are thought to aid the folding of denatured or newly synthesized polypeptides. These proteins exist as two functionally similar but distantly related families, one including the bacterial and organellar chaperonins and the other (termed the CCT-TRiC family) including the chaperonins of the Archaea and the eukaryotes. The CCT-TRiC chaperonins, particularly their archeal members, are less well known than their bacterial counterparts, and their main cellular function is still doubtful. In this work, we report that the chaperonin of the thermophilic archaeon Sulfolobus solfataricus interacts with several polypeptides other than the two subunits that constitute the 18-mer double-ring structure. We have cloned and sequenced the gene encoding one 90 kDa chaperonin-associated protein and have shown, using biochemical assays, that the product is an enzyme belonging to the family of zinc-dependent aminopeptidases. The Sulfolobus protein shows maximal homology to eukaryotic (yeast and mouse) aminopeptidases. It contains a leucine zipper motif and can be phosphorylated by an unidentified kinase present in the cell extracts. The possible significance of an association between an aminopeptidase and a chaperonin is discussed.

Amino Acid Sequence↗
PubMed1997

New stent delivery balloon: a technical note.

This study reports the first clinical application of a new noncompliant balloon composed of a middle polyurethane layer sandwiched between an inner layer of polyethylene terephtalate and an outer membrane that provides for consistent even expansion. With this balloon design, the very low compliance and high pressure resistance of polyethylene terephthalate are associated with the high elasticity of polyurethane, preventing balloon damage from stent crimping and expansion and allowing a firm embedding of the stent struts. Palmaz-Schatz stent implantation was successful in 33/35 stents (94%), and the two stents that could not be advanced up to the lesion were successfully withdrawn. High pressure expansion of the stent was obtained during deployment with no balloon ruptures at inflation pressures equal or lower than 16 atmospheres (atm). Accurate positioning of the stent was facilitated by the two markers at the balloon ends and by the optimal visualization after contrast injection, even with 6 Fr guiding catheters. This new delivery system maintains the advantages of hand-crimped stents on noncompliant balloons, reducing the risk of stent loss.

Angioplasty, Balloon↗
PubMed1996

Investigation of the conformational behaviour of permethylated cyclodextrins by molecular modelling.

Conformations of manually built native and permethylated alpha-, beta-, and gamma-cyclodextrins (CD) were investigated using various computer assisted molecular modelling methods. Calculations were carried by applying the MM+ and the Tripos force field. The influences of atomic charges on the macrocyclic conformations during the optimization procedure were analyzed. The permethylation of hydroxyl groups of cyclodextrins changes bond and torsion angles between the glucose monomers and of the primary substituents. A method to determine the diameters of the cyclodextrin cavity by a modelling approach is described. It is shown that due to permethylation the larger cavity opening is increased and the primary substituents are canted outwards. As a consequence, the torus shape of the molecule changes, which is an important feature for docking and fitting studies.

Algorithms↗
PubMed1996

Allelic polymorphism and site-specific recombination in the opc locus of Neisseria meningitidis.

The opc gene is widespread in epidemic and endemic Neisseria meningitidis, but most strains of certain epidemic clones (ET-37 complex, Cluster A4) and a few random endemic isolates lack an opc gene. Four percent of the 1148 bp that contain opc plus the surrounding intergenic region was polymorphic (18 alleles), and many of the alleles contained a 230 bp insertion at a fixed location in the intergenic region. The presence or absence of the insertion reflects site-specific recombination. The alleles are stably inherited within clonal groupings for up to at least 50 years, with rare cases of horizontal genetic exchange. Most statistical methods indicated significant intragenic recombination events within this dataset.

Alleles↗
PubMed1996

Positional cloning of the gene for X-linked retinitis pigmentosa 3: homology with the guanine-nucleotide-exchange factor RCC1.

The gene for retinitis pigmentosa 3 (RP3), the most frequent form of X-linked RP (XLRP), has been mapped previously to a chromosome interval of less than 1000 kbp between the DXS1110 marker and the OTC locus at Xp21.1-p11.4. Employing a novel technique, YAC Representation Hybridization (YRH)', we have recently identified a small XLRP associated microdeletion in this interval, as well as several putative exons including the 3' end of a gene that was truncated by the deletion. cDNA library screening and sequencing of a cosmid centromeric to the deletion has now enabled us to identify numerous additional exons and to detect several point mutations in patients with XLRP. The predicted gene product shows homology to RCC1, the guanine-nucleotide-exchange factor (GEF) of the Ras-like GTPase Ran. Our findings suggest that we have cloned the long-sought RP3 gene, and that it may encode the GEF of a retina-specific GTP-binding protein.

Amino Acid Sequence↗
PubMed1995

Final height and long-term outcome after growth hormone therapy in Turner syndrome: results of a German multicentre trial.

Final height was investigated in 85 patients from a German multicentre trial of human growth hormone (GH) therapy in Turner syndrome. Six patients (mean age, 15.4 +/- 1.0 years; mean duration of therapy, 4.4 +/- 1.0 years) fulfilled the criteria for having reached final height (i.e. a height velocity < 0.5 cm/year). Four subjects had stopped therapy and two were still receiving GH. The mean final height of patients was 150.9 +/- 4.7 cm (range, 143.3-154.9 cm). In 3 subjects, projected final height was exceeded by 1.4, 6.5 and 10.8 cm, 1 patient just failed to reach projected final height by -1.7 cm and the 2 remaining patients did not attain projected final height by -3.2 and -12.1 cm. In the latter case, lack of height gain was associated with early onset and rapid progress of spontaneous puberty. The changes in height SDS were analysed in the other patients still receiving GH therapy over a period of 6 years, and it appeared that 2 IU/m2/day was less effective than 3 or 4 IU/m2/day, but that 4 IU/m2/day was no more effective than 3 IU/m2/day. These limited, non-controlled results indicate that GH therapy may be effective in increasing final height in Turner syndrome, though some patients may not benefit.

Adolescent↗