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Thumm M, Egner R, Koch B, Schlumpberger M, Straub M, Veenhuis M, Wolf DH. Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett 1994; 349:275-80. [PMID: 8050581 DOI: 10.1016/0014-5793(94)00672-5] [Citation(s) in RCA: 430] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein degradation in the vacuole (lysosome) is an important event in cellular regulation. In yeast, as in mammalian cells, a major route of protein uptake for degradation into the vacuole (lysosome) has been found to be autophagocytosis. The discovery of this process in yeast enables the elucidation of its mechanisms via genetic and molecular biological investigations. Here we report the isolation of yeast mutants defective in autophagocytosis (aut mutants), using a rapid colony screening procedure.
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430 |
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Graf C, Koch B, Kretschmann-Kandel E, Falkowski G, Christ H, Coburger S, Lehmacher W, Bjarnason-Wehrens B, Platen P, Tokarski W, Predel HG, Dordel S. Correlation between BMI, leisure habits and motor abilities in childhood (CHILT-project). Int J Obes (Lond) 2004; 28:22-6. [PMID: 14652619 DOI: 10.1038/sj.ijo.0802428] [Citation(s) in RCA: 209] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
INTRODUCTION The prevalence of childhood obesity is increasing with its negative medical and psychosocial consequences. This paper examines the association between body mass index (BMI), motor abilities and leisure habits of 668 children within the CHILT (Children's Health InterventionaL Trial) project. METHOD A total of 668 children (51.0% boys; 49.0% girls) and their parents were questioned on sport and leisure behaviour of the children. The anthropometric data were measured. Motor abilities were determined by a body gross motor development test for children (Köperkoordinationstest für Kinder; KTK) and a 6-min run. RESULTS The children were 6.70 +/- 0.42 y old, 122.72 +/- 5.36 cm tall and weighed 24.47 +/- 4.59 kg, the average BMI was 16.17 +/- 2.27 kg/m2. KTK showed an average motor quotient (MQ) of 93.49 +/- 15.01, the 6-min run an average of 835.24 +/- 110.87 m. Both tests were inversely correlated with BMI (KTK and BMI r=-0.164 (P<0.001); 6-min run and BMI r=-0.201 (P<0.001)); the group of overweight/obese children showed poorer results than the normal/underweight ones, even after adjustment for gender and age (in each case P<0.001). Children with the greatest extent of exercise achieve the highest MQ (P=0.035). SUMMARY Overweight/obesity is associated with a poorer body gross motor development and endurance performance. On the other hand, an active lifestyle is positively correlated with a better gross motor development in first-grade children. Therefore, to prevent the negative consequences of physical inactivity and overweight/obesity early intervention to support exercise and movement is recommended.
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Journal Article |
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Koch B, Jensen LE, Nybroe O. A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J Microbiol Methods 2001; 45:187-95. [PMID: 11348676 DOI: 10.1016/s0167-7012(01)00246-9] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of Tn7-based systems for site-specific insertion of DNA into the chromosome of Gram-negative bacteria has been limited due to the lack of appropriate vectors. We therefore developed a flexible panel of Tn7 delivery vectors. In one group of vectors, the miniTn7 element, which is inserted into the chromosome, contains a multiple cloning site (MCS) and the kanamycin, streptomycin or gentamicin resistance markers. Another group of vectors intended for tagging with green fluorescent protein (GFP) carries the gfpmut3* gene controlled by the modified lac promoter PA1/04/03, several transcriptional terminators, and various resistance markers. These vectors insert Tn7 into a specific, neutral intergenic region immediately downstream of the gene encoding glucosamine-6-phosphate synthetase (GlmS) in the tested fluorescent Pseudomonas strains. The gfp-tagging vector containing a gentamicin-resistance marker is useful for tagging strains carrying a Tn5 transposon. Tn5 transposons often carry kanamycin-resistance-encoding genes and are frequently used to generate bacterial mutants and to deliver reporter constructions in gene expression studies. To demonstrate the utility of a dual marker/reporter system, the Tn7-gfp marker system was combined with a Tn5-delivered luxAB reporter system in Pseudomonas fluorescens. The system allowed detection of gfp-tagged cells in the barley rhizosphere, while expression of the Tn5-tagged locus could be determined by measuring bioluminescence.
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201 |
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Fronhoffs S, Totzke G, Stier S, Wernert N, Rothe M, Brüning T, Koch B, Sachinidis A, Vetter H, Ko Y. A method for the rapid construction of cRNA standard curves in quantitative real-time reverse transcription polymerase chain reaction. Mol Cell Probes 2002; 16:99-110. [PMID: 12030760 DOI: 10.1006/mcpr.2002.0405] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quantification of nucleic acids, especially of mRNA, is increasingly important in biomedical research. The recently developed quantitative real-time polymerase chain reaction (PCR) - a highly sensitive technology for the rapid, accurate and reproducible quantification of gene expression - offers major advantages over conventional quantitative PCR. Transcript quantification is performed in the exponential phase of the PCR reaction through extrapolation of fluorescence signals from a standard calibration curve which represents the initial copy number for a given fluorescence signal. We have developed a method for gene transcript quantification which is based on a LightCycler - assisted real-time PCR in combination with a simple and rapid approach for the construction of external cRNA standards with identical gene sequences as the target gene. Synthesis of cRNAs was performed by in vitro transcription with T7 RNA polymerase followed by reverse transcription and real-time PCR. We applied this approach for transcript quantification of eukaryotic initiation factor 3 p110 (EIF3S8) mRNA in normal testicular tissue. We also present a rapid and simple strategy for the construction of cRNA standards for use in real-time PCR.
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162 |
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Eilers T, Schwarz G, Brinkmann H, Witt C, Richter T, Nieder J, Koch B, Hille R, Hänsch R, Mendel RR. Identification and biochemical characterization of Arabidopsis thaliana sulfite oxidase. A new player in plant sulfur metabolism. J Biol Chem 2001; 276:46989-94. [PMID: 11598126 DOI: 10.1074/jbc.m108078200] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mammals and birds, sulfite oxidase (SO) is a homodimeric molybdenum enzyme consisting of an N-terminal heme domain and a C-terminal molybdenum domain (EC ). In plants, the existence of SO has not yet been demonstrated, while sulfite reductase as part of sulfur assimilation is well characterized. Here we report the cloning of a plant sulfite oxidase gene from Arabidopsis thaliana and the biochemical characterization of the encoded protein (At-SO). At-SO is a molybdenum enzyme with molybdopterin as an organic component of the molybdenum cofactor. In contrast to homologous animal enzymes, At-SO lacks the heme domain, which is evident both from the amino acid sequence and from its enzymological and spectral properties. Thus, among eukaryotes, At-SO is the only molybdenum enzyme yet described possessing no redox-active centers other than the molybdenum. UV-visible and EPR spectra as well as apparent K(m) values are presented and compared with the hepatic enzyme. Subcellular analysis of crude cell extracts showed that SO was mostly found in the peroxisomal fraction. In molybdenum cofactor mutants, the activity of SO was strongly reduced. Using antibodies directed against At-SO, we show that a cross-reacting protein of similar size occurs in a wide range of plant species, including both herbacious and woody plants.
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159 |
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Dralle H, Gimm O, Simon D, Frank-Raue K, Görtz G, Niederle B, Wahl RA, Koch B, Walgenbach S, Hampel R, Ritter MM, Spelsberg F, Heiss A, Hinze R, Höppner W. Prophylactic thyroidectomy in 75 children and adolescents with hereditary medullary thyroid carcinoma: German and Austrian experience. World J Surg 1998; 22:744-50; discussion 750-1. [PMID: 9606292 DOI: 10.1007/s002689900463] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
When mutations of the RETproto-oncogene were found in 1993 to account for hereditary medullary thyroid carcinoma (MTC), surgeons obtained the opportunity to operate on patients prophylactically (i. e., at a clinically asymptomatic stage). Whether this approach is justified, and, if so, when and to which extent surgery should be performed remained to be clarified. A questionnaire was sent to all surgical departments in Germany and Austria. All of the patients who fulfilled the following criteria were enrolled: (1) preoperatively proved RET mutation; (2) age </= 20 years, (3) clinically asymptomatic thyroid C cell disease; and (4) TNM classification pT0-1/pNX/pN0-1/M0. Seventy-five patients were identified, and fifteen mutations were detected in six codons. Two adolescents had unilateral pheochromocytomas as part of the multiple endocrine neoplasia II (MEN-II) syndrome. No hyperparathyroidism was noted. All patients underwent total thyroidectomy, and 57 patients went on to have lymph node dissection. Parathyroid glands were removed in 34 patients and autografted in 11. Histopathology revealed MTC in 46 patients (61%, youngest 4 years); C cell hyperplasia (CCH) only was detected in the other 29 patients. Three patients had lymph node metastases (LNMs) the youngest being age 14 years. Calcitonin levels were not useful for differentiating between CCH and MTC, but in all patients with LNMs at least the stimulated calcitonin levels were assayed. After surgery, five patients (6.7%) sustained permanent hypoparathyroidism, and one patient (1.3%) had a permanent unilateral recurrent nerve palsy. All but three patients (96%) were biochemically cured. In conclusion, prophylactic total thyroidectomy can be performed safely in experienced centers. We recommend prophylactic total thyroidectomy at age 6. Cervicocentral lymph node dissection should be included when calcitonin levels are elevated or if patients are older than 10 years. Bilateral lymph node dissection should be performed if LNMs are suspected or when patients with elevated calcitonin are older than 15 years.
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Koch B, Liljefors T, Persson T, Nielsen J, Kjelleberg S, Givskov M. The LuxR receptor: the sites of interaction with quorum-sensing signals and inhibitors. MICROBIOLOGY-SGM 2005; 151:3589-3602. [PMID: 16272381 DOI: 10.1099/mic.0.27954-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The function of LuxR homologues as quorum sensors is mediated by the binding of N-acyl-L-homoserine lactone (AHL) signal molecules to the N-terminal receptor site of the proteins. In this study, site-directed mutagenesis was carried out of the amino acid residues comprising the receptor site of LuxR from Vibrio fischeri, and the ability of the L42A, L42S, Y62F, W66F, D79N, W94D, V109D, V109T and M135A LuxR mutant proteins to activate green fluorescent protein expression from a P(luxI) promoter was measured. X-ray crystallographic studies of the LuxR homologue TraR indicated that residues Y53 and W57 form hydrogen bonds to the 1-carbonyl group and the ring carbonyl group, respectively, of the cognate AHL signal. Based on the activity and signal specificity of the LuxR mutant proteins, and on molecular modelling, a model is suggested in which Y62 (corresponding to Y53 in TraR) forms a hydrogen bond with the ring carbonyl group rather than the 1-carbonyl group, while W66 (corresponding to W57 in TraR) forms a hydrogen bond to the 1-carbonyl group. This flips the position of the acyl side chain in the LuxR/signal molecule complex compared to the TraR/signal molecule complex. Halogenated furanones from the marine alga Delisea pulchra and the synthetic signal analogue N-(sulfanylacetyl)-L-homoserine lactone can block quorum sensing. The LuxR mutant proteins were insensitive to inhibition by N-(propylsulfanylacetyl)-L-homoserine lactone. In contrast, the mutations had only a minor effect on the sensitivity of the proteins to halogenated furanones, and the data strongly suggest that these compounds do not compete in a 'classic' way with N-3-oxohexanoyl-L-homoserine lactone for the binding site. Based on modelling and experimental data it is suggested that these compounds bind in a non-agonist fashion.
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Research Support, Non-U.S. Gov't |
20 |
134 |
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Hildebrandt U, Klein T, Feifel G, Schwarz HP, Koch B, Schmitt RM. Endosonography of pararectal lymph nodes. In vitro and in vivo evaluation. Dis Colon Rectum 1990; 33:863-8. [PMID: 2209276 DOI: 10.1007/bf02051923] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
One hundred thirteen patients with carcinoma of the rectum were evaluated for lymph node metastases by endorectal ultrasound. With the use of 7.5 MHz and based on different echo patterns, two main groups of lymph nodes can be differentiated: hypoechoic and hyperechoic lymph nodes. Compared with pathologic findings, hypoechoic lymph nodes represent metastases, whereas hyperechoic lymph nodes are visualized due to unspecific inflammation. Lymph node metastases can be predicted with a sensitivity of 72 percent and inflammatory lymph nodes with a specificity of 83 percent. The physical basis of the differentiation of lymph nodes was assessed in vitro by the determination of ultrasound parameters (speed of sound, acoustic impedance, attenuation, and backscattered amplitude). The attenuation coefficient of benign lymph nodes [2.5 dB/(MHz x cm)] is significantly higher than the mean value of lymph node metastases [1.3 db/(MHz x cm)]. The results demonstrate that involved nodes can principally be differentiated from not involved nodes. Micrometastases, mixed lymph nodes, and changing echo patterns within inflammatory nodes explain the accuracy rate of 78 percent.
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Comparative Study |
35 |
127 |
9
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Wang Y, Weinacker H, Koch B. A Lidar Point Cloud Based Procedure for Vertical Canopy Structure Analysis And 3D Single Tree Modelling in Forest. SENSORS 2008; 8:3938-3951. [PMID: 27879916 PMCID: PMC3714669 DOI: 10.3390/s8063938] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 06/05/2008] [Accepted: 06/06/2008] [Indexed: 11/16/2022]
Abstract
A procedure for both vertical canopy structure analysis and 3D single tree modelling based on Lidar point cloud is presented in this paper. The whole area of research is segmented into small study cells by a raster net. For each cell, a normalized point cloud whose point heights represent the absolute heights of the ground objects is generated from the original Lidar raw point cloud. The main tree canopy layers and the height ranges of the layers are detected according to a statistical analysis of the height distribution probability of the normalized raw points. For the 3D modelling of individual trees, individual trees are detected and delineated not only from the top canopy layer but also from the sub canopy layer. The normalized points are resampled into a local voxel space. A series of horizontal 2D projection images at the different height levels are then generated respect to the voxel space. Tree crown regions are detected from the projection images. Individual trees are then extracted by means of a pre-order forest traversal process through all the tree crown regions at the different height levels. Finally, 3D tree crown models of the extracted individual trees are reconstructed. With further analyses on the 3D models of individual tree crowns, important parameters such as crown height range, crown volume and crown contours at the different height levels can be derived.
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Journal Article |
17 |
125 |
10
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Koch B, Wolke JG, de Groot K. X-ray diffraction studies on plasma-sprayed calcium phosphate-coated implants. JOURNAL OF BIOMEDICAL MATERIALS RESEARCH 1990; 24:655-67. [PMID: 2361962 DOI: 10.1002/jbm.820240603] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calcium phosphate coatings on steel, obtained by the plasma-spray technique, were examined by x-ray diffraction in order to get some information on their crystallographic structure and crystallinity. Surface roughness values were also determined. These coatings are of interest for hip-prosthesis materials in particular.
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118 |
11
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Koch B, Schaper C, Ittermann T, Spielhagen T, Dorr M, Volzke H, Opitz CF, Ewert R, Glaser S. Reference values for cardiopulmonary exercise testing in healthy volunteers: the SHIP study. Eur Respir J 2008; 33:389-97. [DOI: 10.1183/09031936.00074208] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17 |
117 |
12
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Sibbesen O, Koch B, Halkier BA, Møller BL. Cytochrome P-450TYR is a multifunctional heme-thiolate enzyme catalyzing the conversion of L-tyrosine to p-hydroxyphenylacetaldehyde oxime in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench. J Biol Chem 1995; 270:3506-11. [PMID: 7876084 DOI: 10.1074/jbc.270.8.3506] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cytochrome P-450TYR, which catalyzes the N-hydroxylation of L-tyrosine in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench has recently been isolated (Sibbesen, O., Koch, B., Halkier, B. A., and Møller, B. L. (1994) Proc. Natl. Acad. Sci. U.S.A. 92, 9740-9744). Reconstitution of the enzyme activity in lipid micelles containing cytochrome P-450TYR and NADPH-cytochrome P-450 oxidoreductase demonstrates that cytochrome P-450TYR catalyzes the conversion of L-tyrosine into p-hydroxyphenylacetaldehyde oxime. Earlier studies with microsomes have demonstrated that this conversion involves two N-hydroxylation reactions of which the first produces N-hydroxytyrosine. We propose that the product of the second N-hydroxylation reaction is N,N-dihydroxytyrosine. N,N-dihydroxytyrosine is dehydrated to 2-nitroso-3-(p-hydroxyphenyl) propionic acid which decarboxylates to p-hydroxyphenylacetaldehyde oxime. The dehydration and decarboxylation reactions may proceed non-enzymatically. The E/Z ratio of the p-hydroxyphenylacetaldehyde oxime produced by reconstituted cytochrome P-450TYR is 69:31. Lipid micelles made from L-alpha-dilauroyl phosphatidylcholine are more than twice as effective in reconstituting cytochrome P-450TYR activity as compared to other lipids. The Km and turnover number of the enzyme is 0.14 mM and 200 min-1, respectively, when assayed in the presence of 15 mM NaCl whereas the values are 0.21 mM and 230 min-1 when assayed in the absence of added salt. The multifunctional nature cytochrome P-450TYR is confirmed by demonstrating that binding of L-tyrosine or N-hydroxytyrosine mutually excludes binding of the other substrate. These results explain why the conversion of tyrosine to p-hydroxyphenylacetaldehyde oxime as earlier reported (Møller, B. L., and Conn, E. E. (1980) J. Biol. Chem. 255, 3049-3056) shows the phenomenon of catalytic facilitation ("channeling"). Cytochrome P-450TYR is the first isolated multifunctional heme-thiolate enzyme from plants. N-Hydroxylases of the cytochrome P-450 type with high substrate specificity have not previously been reported.
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30 |
108 |
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Castillo R, Koch B, Ruiz P, Delmon B. Influence of the Amount of Titania on the Texture and Structure of Titania Supported on Silica. J Catal 1996. [DOI: 10.1006/jcat.1996.0214] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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104 |
14
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Misslin R, Herzog F, Koch B, Ropartz P. Effects of isolation, handling and novelty on the pituitary--adrenal response in the mouse. Psychoneuroendocrinology 1982; 7:217-21. [PMID: 7178375 DOI: 10.1016/0306-4530(82)90015-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Male Swiss strain mice were individually- or group-housed for four weeks. Basal corticosterone levels did not differ with the type of housing, providing no support for the suggestion that the condition of the individually-housed mouse is stressful. Plasma corticosterone levels also were determined for mice which had been either left undisturbed or exposed to new cages which differed from their home cages by varying degrees. There were elevations in mean plasma corticosterone levels corresponding to the degree of difference between the home cage and the new cage. This finding supports the suggestion that changes in 11-OHCS levels are sensitive measures of environmental changes. Mice forced to remain in novel places exhibited higher plasma corticoid concentrations than animals which were given the opportunity to move freely between familiar and novel places. Corticoid values, as well as neurophysiological and behavioral responses, suggested that the stress induced by forced exploration might be due to the fact that animals are prevented from freely regulating their exposure to novel places rather than to novelty per se.
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101 |
15
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Furuta T, Tuck S, Kirchner J, Koch B, Auty R, Kitagawa R, Rose AM, Greenstein D. EMB-30: an APC4 homologue required for metaphase-to-anaphase transitions during meiosis and mitosis in Caenorhabditis elegans. Mol Biol Cell 2000; 11:1401-19. [PMID: 10749938 PMCID: PMC14855 DOI: 10.1091/mbc.11.4.1401] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Here we show that emb-30 is required for metaphase-to-anaphase transitions during meiosis and mitosis in Caenorhabditis elegans. Germline-specific emb-30 mutant alleles block the meiotic divisions. Mutant oocytes, fertilized by wild-type sperm, set up a meiotic spindle but do not progress to anaphase I. As a result, polar bodies are not produced, pronuclei fail to form, and cytokinesis does not occur. Severe-reduction-of-function emb-30 alleles (class I alleles) result in zygotic sterility and lead to germline and somatic defects that are consistent with an essential role in promoting the metaphase-to-anaphase transition during mitosis. Analysis of the vulval cell lineages in these emb-30(class I) mutant animals suggests that mitosis is lengthened and eventually arrested when maternally contributed emb-30 becomes limiting. By further reducing maternal emb-30 function contributed to class I mutant animals, we show that emb-30 is required for the metaphase-to-anaphase transition in many, if not all, cells. Metaphase arrest in emb-30 mutants is not due to activation of the spindle assembly checkpoint but rather reflects an essential emb-30 requirement for M-phase progression. A reduction in emb-30 activity can suppress the lethality and sterility caused by a null mutation in mdf-1, a component of the spindle assembly checkpoint machinery. This result suggests that delaying anaphase onset can bypass the spindle checkpoint requirement for normal development. Positional cloning established that emb-30 encodes the likely C. elegans orthologue of APC4/Lid1, a component of the anaphase-promoting complex/cyclosome, required for the metaphase-to-anaphase transition. Thus, the anaphase-promoting complex/cyclosome is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism.
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research-article |
25 |
101 |
16
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Hild M, Beckmann B, Haas SA, Koch B, Solovyev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel JD, Paro R. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol 2003; 5:R3. [PMID: 14709175 PMCID: PMC395735 DOI: 10.1186/gb-2003-5-1-r3] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Revised: 10/13/2003] [Accepted: 11/19/2003] [Indexed: 11/19/2022] Open
Abstract
A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly. Background While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software. Results Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly. Conclusions The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.
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Research Support, Non-U.S. Gov't |
22 |
99 |
17
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Kienlen Campard P, Crochemore C, René F, Monnier D, Koch B, Loeffler JP. PACAP type I receptor activation promotes cerebellar neuron survival through the cAMP/PKA signaling pathway. DNA Cell Biol 1997; 16:323-33. [PMID: 9115641 DOI: 10.1089/dna.1997.16.323] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The molecular nature, transduction pathways, and neurotrophic functions of pituitary adenylate cyclase activating peptide (PACAP) receptors were studied in primary culture of rat cerebellar granule cells. We show that cerebellar neurons express several PACAP type I receptor (PVR I) isoforms, including the short (PVR Is) and the Hop (PVR I-Hop) splice variants, the latter being restricted to neurons and not found in cerebellar glial cell cultures. In vitro, cerebellar granule cells die rapidly in the absence of a high concentration of K+ (25 mM), as demonstrated by TUNEL histochemistry, which shows that K+ deprivation induces massive neuronal apoptosis within 12 hr. This effect was reversed by PACAP 27 and 38. Both forms of PACAP prevent DNA fragmentation and allow long-term neuronal survival in the absence of high K+ (as shown by MAP2 immunostaining) and stimulate a reporter gene driven by the full-length c-fos promoter. These effects of PACAP are fully abolished upon transient transfection of cells with a dominant inhibitory mutant of the cAMP-dependent protein kinase (PKA). Taken together, these results show that in cerebellar granule neurons, PACAP type I receptors regulate gene expression and promote neuronal survival through the cAMP/PKA pathway.
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28 |
97 |
18
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Burmester GR, Locher P, Koch B, Winchester RJ, Dimitriu-Bona A, Kalden JR, Mohr W. The tissue architecture of synovial membranes in inflammatory and non-inflammatory joint diseases. I. The localization of the major synovial cell populations as detected by monoclonal reagents directed towards Ia and monocyte-macrophage antigens. Rheumatol Int 1983; 3:173-81. [PMID: 6366990 DOI: 10.1007/bf00541597] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Utilizing monoclonal reagents directed towards antigens of the monocyte-macrophage lineage and Ia antigens, the tissue architecture of synovial membranes obtained from patients with non-inflammatory joint diseases and patients with rheumatoid arthritis was studied. Emphasis was placed on the localization of the type I, type II and type III synoviocytes that previously had been defined by their cell surface phenotype with regard to the expression of monocyte-macrophage lineage (M theta) and Ia antigens as well as by their phagocytic capacity or the ability to produce glycosaminoglycans. In patients with non-inflammatory joint diseases, cells with the M theta + Ia+ (type I) phenotype constituted the majority of synoviocytes immediately adjacent to the joint cavity; cells with this phenotype were also scattered in the subsynovial tissue and in the perivascular regions. The fibroblastoid type III cells defined by the absence of both M theta and Ia antigens formed the major cell population in the subsynovial tissue in this patient group. In patients with rheumatoid arthritis, the Ia+ M theta + cells were present in a characteristic double configuration forming an intensely positive layer adjacent to the intra-articular space followed by an Ia- M theta - layer that again was succeeded by an intensely Ia+ M theta + layer. Large numbers of synoviocytes bearing M theta + Ia+ antigens were also demonstrated in the diffusely inflamed subsynovial tissue, in the perivascular regions as well as around and within lymphoid infiltrates.(ABSTRACT TRUNCATED AT 250 WORDS)
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Niemir ZI, Stein H, Dworacki G, Mundel P, Koehl N, Koch B, Autschbach F, Andrassy K, Ritz E, Waldherr R, Otto HF. Podocytes are the major source of IL-1 alpha and IL-1 beta in human glomerulonephritides. Kidney Int 1997; 52:393-403. [PMID: 9263995 DOI: 10.1038/ki.1997.346] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To address the question of in situ production of IL-1 alpha and IL-1 beta in proliferative and non-proliferative forms of human glomerulonephritis (GN), we performed immunocytochemical and in situ hybridization studies on renal biopsies from patients with mesangial IgA-GN (N = 38), idiopathic membranous GN (MGN; N = 12), minimal change disease (MCD; N = 9), focal segmental glomerulosclerosis (FSGS; N = 5) and acute endocapillary GN (AGN; N = 3). Normal kidneys (N = 10) served as controls. Concomitantly, the expression of IL-1 receptor type I (IL-1 RI), IL-1 receptor type II (IL-1 RII) and of IL-1 receptor antagonist (IL-1 RA) was analyzed. Antibodies against antigens expressed on podocytes (PP-44), endothelial cells (CD31) and monocytes/macrophages (CD11b, CD14, CD68) were applied to attribute the expression of IL-1/IL-1 related peptides to intrinsic glomerular and/or blood-derived infiltrating cells. Our results demonstrate that IL-1 RII is constitutively expressed on endothelial cells, and its expression can be induced in proximal tubular cells and in the interstitium. In diseased glomeruli podocytes are capable of producing IL-1 alpha/beta. In MGN and MCD/FSGS, the expression of both IL-1 forms is particularly noted in early stages of the disease and is not only accompanied by a marked reactivity for IL-1 RI, but also for IL-1 RA. In segmental sclerosing lesions in FSGS and in IgA-GN with marked glomerular proliferation and/or sclerosis, a reduced expression of the PP-44 antigen and a diminished ability of podocytes to produce IL-1/IL-1 related peptides are noted. These results suggest that intrinsic glomerular production of IL-1 may be of relevance for the protection of glomeruli from continuing injury.
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Bellebaum C, Daum I, Koch B, Schwarz M, Hoffmann KP. The role of the human thalamus in processing corollary discharge. Brain 2005; 128:1139-54. [PMID: 15758033 DOI: 10.1093/brain/awh474] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Corollary discharge signals play an important role in monitoring self-generated movements to guarantee spatial constancy. Recent work in macaques suggests that the thalamus conveys corollary discharge information of upcoming saccades passing from the superior colliculus to the frontal eye field. The present study aimed to investigate the involvement of the thalamus in humans by assessing the effect of thalamic lesions on the processing of corollary discharge information. Thirteen patients with selective thalamic lesions and 13 healthy age-matched control subjects performed a saccadic double-step task in which retino-spatial dissonance was induced, i.e. the retinal vector of the second target and the movement vector of the second saccade were different. Thus, the subjects could not rely on retinal information alone, but had to use corollary discharge information to correctly perform the second saccade. The amplitudes of first and second saccades were significantly smaller in patients than in controls. Five thalamic lesion patients showed unilateral deficits in using corollary discharge information, as revealed by asymmetries compared with the other patients and controls. Three patients with lateral thalamic lesions including the ventrolateral nucleus (VL) were impaired contralaterally to the side of damage and one patient with a lesion in the mediodorsal thalamus (MD) was impaired ipsilaterally to the lesion. The largest asymmetry was found in a patient with a bilateral thalamic lesion. The results provide evidence for a thalamic involvement in the processing of corollary discharge information in humans, with a potential role of both the VL and MD nuclei.
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Kleber M, Ihorst G, Terhorst M, Koch B, Deschler B, Wäsch R, Engelhardt M. Comorbidity as a prognostic variable in multiple myeloma: comparative evaluation of common comorbidity scores and use of a novel MM-comorbidity score. Blood Cancer J 2011; 1:e35. [PMID: 22829196 PMCID: PMC3255252 DOI: 10.1038/bcj.2011.34] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 07/07/2011] [Indexed: 12/27/2022] Open
Abstract
Comorbidities have been demonstrated to affect progression-free survival (PFS) and overall survival (OS), although their impact in multiple myeloma (MM) patients is as yet unsettled. We (1) assessed various comorbidities, (2) compared established comorbidity indices (CIs; Charlson comorbidity index (CCI), hematopoietic cell transplantation-specific comorbidity index (HCT-CI)), Kaplan Feinstein (KF) and Satariano index (SI) and (3) developed a MM-CI (Freiburger comorbidity index, FCI) in 127 MM patients. Univariate analysis determined moderate or severe pulmonary disease (hazard ratio (HR): 3.5, P<0.0001), renal impairment (via estimated glomerular filtration rate (eGFR); HR: 3.4, P=0.0018), decreased Karnofsky Performance Status (KPS, HR: 2.7, P=0.0004) and age (HR: 2, P=0.0114) as most important variables for diminished OS. Through multivariate analysis, the eGFR ⩽30 ml/min/1.73m(2), impaired lung function and KPS ⩽70% were significant for decreased OS, with HRs of 2.9, 2.8 and 2.2, respectively. Combination of these risk factors within the FCI identified significantly different median OS rates of 118, 53 and 25 months with 0, 1 and 2 or 3 risk factors, respectively, (P<0.005). In light of our study, comorbidities are critical prognostic determinants for diminished PFS and OS. Moreover, comorbidity scores are important treatment decision tools and will be valuable to implement into future analyses and clinical trials in MM.
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Koch B, Lutz-Bucher B, Briaud B, Mialhe C. Specific interaction of corticosteroids with binding sites in the plasma membranes of the rat anterior pituitary gland. J Endocrinol 1978; 79:215-22. [PMID: 731146 DOI: 10.1677/joe.0.0790215] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The binding of glucocorticoids to a crude fraction of rat pituitary plasma membranes and to solubilized membrane proteins was measured. The binding characteristics were similar to those exhibited by transcortin: radioactive corticosterone was bound to a greater extent than radioactive dexamethasone and labelled corticosterone, but not labelled dexamethasone, was displaced by unlabelled corticosterone, deoxycorticosterone and progesterone. A Scatchard plot of the binding data revealed the presence of a binding material with a dissociation constant of about 3.2 nmol/l, which sedimented at 4S after sucrose density-gradient centrifugation. It was found that the number of binding sites was inversely related to the concentration of corticosterone in the circulation and was increased after long-term adrenalectomy. These data suggest that a material similar to transcortin is complexed to the plasma membrane of rat pituitary cells.
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Koch B, Nielsen VS, Halkier BA, Olsen CE, Møller BL. The biosynthesis of cyanogenic glucosides in seedlings of cassava (Manihot esculenta Crantz). Arch Biochem Biophys 1992; 292:141-50. [PMID: 1727632 DOI: 10.1016/0003-9861(92)90062-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A microsomal system catalyzing the in vitro synthesis of the aglycones of the two cyanogenic glucosides linamarin and lotaustralin has been isolated from young etiolated seedlings of cassava (Manihot esculenta Crantz). A prerequisite to obtain active preparations is the complete removal of the endosperm pellicle covering the cotyledons before seedling homogenization. The rates of conversion of the parent amino acids valine and isoleucine to their cyanohydrins are 19 and 6 nmol/h/mg protein, respectively. The conversion rates for the corresponding oximes (2-methylpropanal oxime and 2-methylbutanal oxime) are 475 and 440 nmol/h/mg protein and for the nitriles (2-methylpropionitrile and 2-methylbutyronitrile) 45 and 75 nmol/h/mg protein. With the exception of 2-cyclopentenylglycine, none of the additionally tested amino acids are metabolized, whereas a broad substrate specificity is observed using oximes and nitriles as substrates. The in vitro biosynthesis is photoreversibly inhibited by carbon monoxide, demonstrating the involvement of cytochrome P450 in the hydroxylation processes. All tissues of the cassava seedling contain cyanogenic glucosides. The microsomal enzyme system responsible for their synthesis is restricted to the cotyledons and their petioles. This demonstrates that the cyanogenic glucosides are actively transported to other parts of the seedling. The enzyme activity decreases with the height of the etiolated seedling and is barely detectable in seedlings above 75 mm.
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Bellebaum C, Koch B, Schwarz M, Daum I. Focal basal ganglia lesions are associated with impairments in reward-based reversal learning. Brain 2008; 131:829-41. [DOI: 10.1093/brain/awn011] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Koch B, Evans HJ. Reduction of acetylene to ethylene by soybean root nodules. PLANT PHYSIOLOGY 1966; 41:1748-50. [PMID: 16656468 PMCID: PMC550603 DOI: 10.1104/pp.41.10.1748] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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