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Dieter Kaufmann

Publications and source records attributed to Dieter Kaufmann.

11 recordsLinked to original sources
PubMed2006

Cell orientation by a microgrooved substrate can be predicted by automatic control theory.

Cells have the ability to measure and respond to extracellular signals like chemical molecules and topographical surface features by changing their orientation. Here, we examined the orientation of cultured human melanocytes exposed to grooved topographies. To predict the cells' orientation response, we describe the cell behavior with an automatic controller model. The predicted dependence of the cell response to height and spatial frequency of the grooves is obtained by considering the symmetry of the system (cell + substrate). One basic result is that the automatic controller responds to the square of the product of groove height and spatial frequency or to the aspect ratio for symmetric grooves. This theoretical prediction was verified by the experiments, in which melanocytes were exposed to microfabricated poly(dimethylsiloxane) substrates having parallel rectangular grooves of heights (h) between 25 and 200 nm and spatial frequencies (L) between 100 and 500 mm(-1). In addition, the model of the cellular automatic controller is extended to include the case of different guiding signals acting simultaneously.

Biocompatible Materials↗
PubMed2005

Sensitive detection of deletions of one or more exons in the neurofibromatosis type 2 (NF2) gene by multiplexed gene dosage polymerase chain reaction.

Mutation detection in the neurofibromatosis type 2 (NF2) gene is challenging because when combining mutation detection methods such as single-strand conformational polymorphism and heteroduplex analysis, denaturing gradient gel electrophoresis, and direct sequencing of aberrant polymerase chain reaction (PCR) fragments only 30 to 60% of the constitutional mutations are detected. Because large deletions and complete chromosome rearrangements are also described methods such as microarray-comparative genomic hybridization and fluorescence in situ hybridization are also used. The one type of mutation often missed corresponds to deletions encompassing one or few exons. To detect this type we have developed a swift and reliable method. We perform a gene dosage analysis with two fluorescent multiplex PCR assays that amplify 15 of the 17 NF2 exons. The labeled PCR products are quantified and gene dose is calculated with respect to controls. We tested the reliability of this method with DNA from eight NF2 patients with known heterozygous NF2 deletions, eight controls and four unknown NF2 patients. In all of the patients with known heterozygous deletions we found in several exons a reduction of gene dosage to 50 to 69%. In one NF2 patient with previously unknown mutation and a severe phenotype we found the gene dosage of two exons reduced by 50% indicating a deletion of these two exons on one allele. This finding was validated by reverse transcriptase-PCR on fibroblast and schwannoma cell cultures of this patient and cDNA sequencing. Our gene dosage assay will detect deletions of one or more exons as well as gross deletions of the whole coding region of the gene. It can complement the existing screening methods because it is faster and easier.

DNA Mutational Analysis↗
PubMed2004

Concurrent targeted exchange of three bases in mammalian hprt by oligonucleotides.

The repair of point mutations in hprt gene by single-stranded oligonucleotides represents a model to test targeted nucleotide exchange. We studied the concurrent nucleotide exchange of two or three nucleotides in the hprt deficient hamster cell line V79-151. The used oligonucleotides resulted in mismatches at two (151, 159) or three (151, 144, and 159) hprt positions. The hprt point mutation at position 151 was repaired in about 2/10(6) cells as shown by hprt sequencing in clones surviving HAT selection. The second nucleotide exchange at hprt position 159 was found in 7% of these HAT selected clones. Using oligonucleotides resulting in three mismatches, 29% of the clones showed nucleotide exchanges at the two hprt positions (151, 144) and about 4% at three positions (151, 144, and 159). These results indicate that single-stranded oligonucleotides can generate two or three nucleotide exchanges in a mammalian chromosomal gene.

Amino Acid Sequence↗
PubMed2004

Cell shape normalization, dendrite orientation, and melanin production of normal and genetically altered (haploinsufficient NF1)-melanocytes by microstructured substrate interactions.

Little is known about how functional regulation failure in genetically altered cells is influenced by topographical confinement of cells, a situation often present in tissues in vivo. We used cultured melanocytes derived from human skin samples as a model system for such investigations. Normal melanocytes have a very well defined shape consisting of a cell body and two dendrites arranged 180 degrees relative to each other. In contrast, neurofibromin 1-melanocytes (NF1-melanocytes) have up to a 50% reduction of neurofibromin 1, which results in an altered morphology that can be easily measured. NF1-melanocytes deviate from the defined structure of normal melanocytes by forming more than two dendrites per cell. We show that morphology consequences of genetically altered melanocytes can be canceled if cells interact with substrates microstructured by stripes that apply mechanophysical signals in the form of physical topography. The strength of the mechanophysical signal was varied systematically by increasing the height of the microstructures. Melanocytes respond to surface topographical features that are larger than 50 nm and have lateral confinements smaller 4 microns. The response of normal and NF1-melanocytes to different topographies was analyzed quantitatively by determining density distributions for the number of dendrites per cell, the angles between dendrites, and the orientation imprinted in the substrate. The synthesis of melanin, a pigment produced by melanocytes, differs in the case of genetically altered NF1- and normal melanocytes. In both cases, the interaction with microstripes enhanced melanin production significantly. This enhanced melanin production is speculated to be caused by the mechanical stabilization of the dendrites by substrate guidance.

Cell Size↗
PubMed2004

In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons.

It is still not fully understood to what extent intronic sequences contribute to the regulation of the different forms of alternative splicing. We are interested in the regulation of alternative cassette exon events, such as exon inclusion and exon skipping. We investigated these events by comparative genomic analysis of human and mouse in five experimentally well-characterized genes, neurofibromatosis 1 (NF1), cystic fibrosis transmembrane conductance regulator (CFTR), period 3 (PER3), cysteinyl-tRNA synthetase (CARS) and synaptotagmin 7 (SYT7). In NF1, high intron identity around the 52 constitutive and four alternatively skipped NF1 exons is restricted to the close vicinity of the exons. In contrast, we found on average high conservation of intron sequences over 300 base pairs up- and downstream of the five alternatively included NF1 exons. The investigation of alternatively included exons in CFTR, PER3, CARS and SYT7 supported this finding. In contrast, the mean intron identities around the alternatively skipped exons in CTFR and NF1 do not differ considerably from those around the constitutive exons. In these genes, the difference in intron conservation could point to a difference between the regulation of alternative exon inclusion and alternative exon skipping or constitutive exon splicing. Additional genome-wide investigations are necessary to elucidate to what extent our finding can be generalized.

Alternative Splicing↗
PubMed2002

Targeted gene correction of hprt mutations by 45 base single-stranded oligonucleotides.

Targeted correction of a single base in a gene of an eucaryotic cell by specific oligonucleotides is a yet controversial technique. Here, we introduce the correction of point mutations in the hypoxanthine-guanine-phosphoribosyl-transferase (HPRT) gene as an additional model system to test targeted gene correction. In human, Hprt mutations cause Lesch-Nyhan syndrome. Using hamster V79 cells, we generated three cell lines with one hprt point mutation each. These cell lines were treated with specific single-stranded 45 base phosphothioate modified oligonucleotides and selected by HAT medium. The surviving clones were investigated for the correction of the respective hprt mutation. Treatment with the oligonucleotides was successful in repairing all three hprt mutations (hprt cDNA position 74, C --> T; position 151, C --> T; and position 400, G --> A). The correction efficiency was very low but reproducible. We suggest that this system allows one to investigate targeted gene correction in dependence on the target sequence and the oligonucleotides used.

Animals↗
PubMed2002

Increased noise as an effect of haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 in vitro.

In human diseases related to tumor-suppressor genes, it is suggested that only the complete loss of the protein results in specific symptoms such as tumor formation, whereas simple reduction of protein quantity to 50%, called haploinsufficiency, essentially does not affect cellular behavior. Using a model of gene expression, it was presumed that haploinsufficiency is related to an increased noise in gene expression also in vivo [Cook, D. L., Gerber, A. N. & Tapscott, S. J. (1998) Proc. Natl. Acad. Sci. USA 95, 15641-15646]. Here, we demonstrate that haploinsufficiency of the tumor-suppressor gene neurofibromatosis type 1 (NF1) results in an increased variation of dendrite formation in cultured NF1 melanocytes. These morphological differences between NF1 and control melanocytes can be described by a mathematical model in which the cell is considered to be a self-organized automaton. The model describes the adjustment of the cells to a set point and includes a noise term that allows for stochastic processes. It describes the experimental data of control and NF1 melanocytes. In the cells haploinsufficient for NF1 we found an altered signal-to-noise ratio detectable as increased variation in dendrite formation in two of three investigated morphological parameters. We also suggest that in vivo NF1 haploinsufficiency results in an increased noise in cellular regulation and that this effect of haploinsufficiency may be found also in other tumor suppressors.

Case-Control Studies↗
PubMed2002

The N-terminal splice product NF1-10a-2 of the NF1 gene codes for a transmembrane segment.

One important function of the neurofibromatosis type 1 (NF1) product neurofibromin is the negative regulation of Ras activity on the cell membrane. Here, we describe an alternative splice product of the N-terminus of the NF1 gene. In this splice product, termed NF1-10a-2, the 45 bp exon 10a-2 is inserted between exons 10a and 10b. Amino acid sequence analysis for motifs showed that the new splice product contains a transmembrane segment not found in wild-type neurofibromin. The overall expression was found to be very low in comparison to the expression of the wild-type mRNA in all human primary and tumor cells examined. Because transcripts were found in the majority of human tissues examined, we assume a housekeeping function of this splice product. Investigation of the intracellular localization of an NF1-10a-2-EGFP fusion protein in HeLa cells revealed a preferential localization in perinuclear granular structures. We therefore assume that NF1-10a-2 has a function on an intracellular membrane.

Alternative Splicing↗
PubMed2002

Aberrant splicing in several human tumors in the tumor suppressor genes neurofibromatosis type 1, neurofibromatosis type 2, and tuberous sclerosis 2.

Mutations at splice sites or surrounding sequences have been reported to cause aberrant splicing. However, splicing errors can also occur without sequence alterations. We investigated three tumor suppressor genes for aberrant splicing in tumors. At a low frequency per exon it was found in five of seven of the investigated in-frame exons of the neurofibromatosis type 1 (NF1) gene, in two of three exons of the neurofibromatosis type 2 (NF2) gene, and in one of three exons of the tuberous sclerosis 2 gene. It was detectable in all of the human tumor tissues tested (NF1 neurofibroma, sporadic intramedullar neurinoma, sporadic meningiomas, NF2 schwannoma, NF2 meningioma, basalioma, and naevus) as well as in cultured tumor cell lines and cultured primary cells. Hence, our data show that aberrant splicing is a very common process. According to simulations of the secondary structures of the pre-mRNA, we suggest that aberrant splicing is attributable to the rare occurrence of alternative structures at the splice donor site, which are not recognized by the splice machinery. In HeLa cells, aberrant splicing is found to be increased at elevated temperatures and low pH in vitro, conditions often found in tumor tissues. In three tumor tissues tested for one NF1 exon, we found approximately twice the amount of aberrant transcript as in normal tissues. Therefore, we suggest that the increase in aberrant splicing caused by environmental factors represents an additional mechanism for the reduction of the amount of tumor suppressor mRNA in the absence of relevant mutations in the tumor.

Exons↗
PubMed2002

Segmental neurofibromatosis.

Segmental neurofibromatosis is characterised by a limited, segmental distribution of cutaneous neurofibromatosis type 1 (NF1) lesions. It has been suggested that segmental NF results from a postzygotic NF1 gene mutation, and, recently, this hypothesis has been proven in a patient with regionally distributed café-au-lait (CAL) spots and freckles by demonstrating an NF1 microdeletion restricted to fibroblasts cultured from CAL spots. We describe here a patient with segmental NF in which we could not demonstrate any NF1 gene mutation in fibroblasts cultured from neurofibromas by use of the protein truncation test, enzymatic mutation detection and fluorescence in situ hybridisation. These data are in line with the concept that NF1 mutations in Schwann cells, but not in fibroblasts, correlate with neurofibroma formation.

Humans↗