Biomedical subjects

K Grote

Publications and source records attributed to K Grote.

15 recordsLinked to original sources

PubMed2006

In silico Northern blot, an automated method to determine expression patterns from EST databases, reveals tissue specificity of murine 17beta-hydroxysteroid dehydrogenase type 11.

In this study, we developed an automated in silico Northern blot (ISNB) for analysis of gene expression patterns from EST databases. This kind of analysis can facilitate initial enzyme characterization by providing tissue distribution patterns. For proof of principle, we analyzed the expression pattern of well-characterized murine 17beta-hydroxysteroid dehydrogenases type 1 and 4. Less characterized murine 17beta-hydroxysteroid dehydrogenase type 11 (Dhrs 8) also was included and processed bioinformatically (ISNB) and further analyzed by Northern blot. The 17beta-hydroxysteroid dehydrogenase type 11 showed the same wide expression pattern by in silico and by wet laboratory approaches. The data point to its involvement of the enzyme in lipid metabolism. The quality of the ISNB relies on the quality of EST-databases. However, our approach is an easy and versatile tool of potentially universal application.

17-Hydroxysteroid Dehydrogenases↗

PubMed2005

Effects of fentin hydroxide on reproduction of the Japanese quail (Coturnix coturnix japonica).

In a one-generation reproductive study, the fungicidal compound triphenyltin hydroxide (fentin) was administered to adult Japanese quail for 6 weeks at dietary levels of 3 and 30 ppm. Reproduction was significantly impaired in the high-dose group. The principal adverse finding was a marked increase in embryonic mortality, resulting in a lower hatch rate. Furthermore, a reduction in egg production was observed with ongoing duration of treatment. Most of the other reproduction-related parameters were not affected. The in ovo losses are assumed to result from a direct toxic effect of the test substance on chick embryos. At the low dietary level, reproduction was not altered. In contrast to the obvious reproductive toxicity, there was only limited evidence of adverse treatment-related findings in the adult birds. However, because such minor effects as an increase in mean liver weight, which was accompanied by macroscopic liver findings and a decrease in T4 serum concentration, were still seen at 3 ppm, a no-observed-effect level could not be established.

Animals↗

PubMed2005

MatInspector and beyond: promoter analysis based on transcription factor binding sites.

MOTIVATION: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. RESULTS: We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).

Algorithms↗

PubMed2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de

Algorithms↗

PubMed2001

Mutation analysis in Chariot-Marie Tooth disease type 1: point mutations in the MPZ gene and the GJB1 gene cause comparable phenotypic heterogeneity.

Charcot-Marie-Tooth disease type 1 (CMT1) is a demyelinating peripheral neuropathy most commonly caused by a DNA duplication on chromosome 17p11.2 including the peripheral myelin protein 22 (PMP22). Point mutations in the myelin protein zero gene (MPZ) and gap junction protein, beta-1 gene (GJB1) are also found in association with CMT1 or the subclass of CMT type X (CMTX), respectively. Recently point mutations in these genes have been found in patients showing the axonal variant of CMT, CMT type 2 (CMT2). We here describe the clinical and electro-physiological findings caused by two novel and two recently described MPZ mutations and six GJB1 mutations. Different MPZ and GJB1 mutations were associated with different grades of severity in CMT1 and CMTX. The novel MPZ Glu141st op mutation was associated with the axonal CMT2. We conclude that the clinical and electrophysiological heterogeneity among CMT patients carrying point mutations in MPZ and GJB1 is similar. Thus for clinical purposes CMT1 and CMT2 patients should be screened for mutations in these two genes after duplication on chromosome 17p11.2 has been excluded as the disease causing mutation.

Adolescent↗

PubMed2001

First pass annotation of promoters on human chromosome 22.

The publication of the first almost complete sequence of a human chromosome (chromosome 22) is a major milestone in human genomics. Together with the sequence, an excellent annotation of genes was published which certainly will serve as an information resource for numerous future projects. We noted that the annotation did not cover regulatory regions; in particular, no promoter annotation has been provided. Here we present an analysis of the complete published chromosome 22 sequence for promoters. A recent breakthrough in specific in silico prediction of promoter regions enabled us to attempt large-scale prediction of promoter regions on chromosome 22. Scanning of sequence databases revealed only 20 experimentally verified promoters, of which 10 were correctly predicted by our approach. Nearly 40% of our 465 predicted promoter regions are supported by the currently available gene annotation. Promoter finding also provides a biologically meaningful method for "chromosomal scaffolding", by which long genomic sequences can be divided into segments starting with a gene. As one example, the combination of promoter region prediction with exon/intron structure predictions greatly enhances the specificity of de novo gene finding. The present study demonstrates that it is possible to identify promoters in silico on the chromosomal level with sufficient reliability for experimental planning and indicates that a wealth of information about regulatory regions can be extracted from current large-scale (megabase) sequencing projects. Results are available on-line at http://genomatix.gsf.de/chr22/.

Algorithms↗

PubMed2000

Cutting edge: preferentially the R-stereoisomer of the mycoplasmal lipopeptide macrophage-activating lipopeptide-2 activates immune cells through a toll-like receptor 2- and MyD88-dependent signaling pathway.

Mycoplasmas and their membranes are potent activators of macrophages, the active principle being lipoproteins and lipopeptides. Two stereoisomers of the mycoplasmal lipopeptide macrophage-activating lipopeptide-2 (MALP-2) differing in the configuration of the lipid moiety were synthesized and compared in their macrophage-activating potential, the R-MALP being >100 times more active than the S-MALP in stimulating the release of cytokines, chemokines, and NO. To assess the role of the Toll-like receptor (TLR) family in mycoplasmal lipopeptide signaling, the MALP-2-mediated responses were analyzed using macrophages from wild-type, TLR2-, TLR4-, and MyD88-deficient mice. TLR2- and MyD88-deficient cells showed severely impaired cytokine productions in response to R- and S-MALP. The MALP-induced activation of intracellular signaling molecules was fully dependent on both TLR2 and MyD88. There was a strong preference for the R-MALP in the recognition by its functional receptor, TLR2.

Adaptor Proteins, Signal Transducing↗

PubMed1999

The Nicotiana tabacum plasma membrane aquaporin NtAQP1 is mercury-insensitive and permeable for glycerol.

A new aquaporin from Nicotiana tabacum (cv. Samsun) was characterized. It shares sequence homology to the Arabidopsis thaliana PIP1 protein family. By two-phase partitioning and immunoblot analysis, plasma membrane localization could be demonstrated. The corresponding mRNA is highly abundant in roots and flowers, while it is rarely expressed in leaves and stems. Functional expression in Xenopus oocytes revealed that NtAQP1 can mediate glycerol transport in addition to water flow. However, NtAQP1 is impermeable for Na+, K+ and Cl- ions. The water permeability and selectivity could not be modulated by addition of mercurials or the activity of cAMP-dependent protein kinases.

Animals↗

PubMed1998

Significance of plasmalemma aquaporins for water-transport in Arabidopsis thaliana.

The plant plasma membrane intrinsic protein, PIP1b, facilitates water transport. These features were characterized in Xenopus oocytes and it has asked whether aquaporins are relevant for water transport in plants. In order to elucidate this uncertainty Arabidopsis thaliana was transformed with an anti-sense construct targeted to the PIP1b gene. Molecular analysis revealed that the anti-sense lines have reduced steady-state levels of PIP1b and the highly homologous PIP1a mRNA. The cell membrane water permeability was analyzed by swelling of protoplasts, which had been transferred into hypotonic conditions. The results indicate that the reduced expression of the specific aquaporins decreases the cellular osmotic water permeability coefficient approximately three times. The morphology and development of the anti-sense lines resembles that of control plants, with the exception of the root system, which is five times as abundant as that of control plants. Xylem pressure measurement suggests that the increase of root mass compensates the reduced cellular water permeability in order to ensure a sufficient water supply to the plant. The results obtained by this study, therefore, clearly demonstrate that aquaporins are important for plant water transport.

Animals↗

PubMed1997

Macular hole surgery without face-down positioning. A pilot study.

PURPOSE: To investigate whether postoperative face-down positioning is necessary for successful macular hole repair. BACKGROUND: Although never proven, face-down positioning is strongly considered an important maneuver to achieve macular hole closure. Face-down posturing is inconvenient, and for patients with physical or mental limitations, weeks of face-down positioning may be an impossible task. A gas bubble that completely fills the vitreous cavity will tamponade a macular hole despite head position and may close a macular hole as effectively as a partial gas fill with face-down positioning. If face-down positioning were not necessary, more patients would be eligible to benefit from this surgery. METHODS: Thirty-three consecutive eyes in 31 patients aged 65-79 years with Stage II, III, or IV full-thickness macular holes underwent macular hole surgery with a complete 15% C3F8 vitreous fill. Hole duration varied from 1 month to 10 years; in 21% of eyes, (seven of 33) holes had been present for more than 1 year. All phakic eyes (n = 25) had cataract extraction with intraocular lens insertion when macular hole surgery was done. No patients were positioned face down. RESULTS: The follow-up period was 6-40 months; 73% of the patients have been observed for more than 1 year. Preoperative hole duration did not affect hole closure rate. The success rate after one surgery was 79% (26 of 33 eyes), and with additional vitrectomy surgery, the total success rate was 85% (28 of 33 eyes). Forty-eight percent of eyes attained visual acuity of 20/50. Eighty percent of eyes with preoperative acuity of > 20/100 attained > 20/50 acuity. Significant complications included iris incarceration into the cataract wound during a postoperative fluid-gas exchange (one eye), posterior synechiae (four eyes), intraocular lens capture (two eyes), elevated intraocular pressure (three eyes), and retinal detachment (three eyes). Most of these problems can be avoided or reduced. CONCLUSION: This pilot study suggests that successful macular hole closure is possible without face-down positioning. This technique may be an alternative for patients with macular holes in pseudophakic eyes who are unable to assume face-down posturing. Combining cataract surgery with this technique for macular hole repair is reasonable for phakic patients who cannot maintain prone positioning. Major disadvantages of combined surgery include the morbidity of the second procedure and removal of a visually insignificant cataract. This approach should be considered for those patients unable to tolerate face-down positioning.

Cataract↗

PubMed1996

GenomeInspector: basic software tools for analysis of spatial correlations between genomic structures within megabase sequences.

The speed of acquisition of genomic sequence data exceeds the evaluation of function of the sequences by a vast margin. Most software available for the prediction of individual features does not assess the correlation of different motifs (level 1 methods). Here, we present a second-level software package called GenomeInspector (GI) for further analysis of results obtained with level 1 methods. Our approach does not require any a priori knowledge about motif organization and was designed as a modular package with a graphical user interface. Three examples for GI application are presented.

Genome↗

PubMed1996

GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences.

MOTIVATION: Most of the sequences determined in current genome sequencing projects remain at least partially unannotated. The available software for DNA sequence analysis is usually limited to the prediction of individual elements (level 1 methods), but does not assess the context of different motifs. However, the functionality of biological units like promoters depends on the correct spatial organization of multiple individual elements. RESULTS: Here, we present a second-level software package called GenomeInspector [[http:@www.gsf.de/biodv/genomeinspector.html ]], for further analysis of results obtained with level 1 methods (e.g. MatInspector [[http:@www.gsf.de/biodv/matinspector.html ]] or ConsInspector [[http:@www.gsf.de/biodv/consinspector.html++ +]]). One of the main features of this modular program is its ability to assess distance correlations between large sets of sequence elements which can be used for the identification and definition of basic patterns of functional units. The program provides an easy-to-use graphical user interface with direct comprehensive display of all results for megabase sequences. Sequence elements showing spatial correlations can be easily extracted and traced back to the nucleotide sequence with the program. GenomeInspector identified promoters of glycolytic enzymes in yeast [[http:@www.mips.biochem.mpg.de/mips/yeast/]] as members of a subgroup with unusual location of an ABF1 site. Solely on the basis of distance correlation analysis, the program correctly selected those transcription factors within these promoters already known to be involved in the regulation of glycolytic enzymes, demonstrating the power of this method.

Algorithms↗

PubMed1986

Cadmium concentrations in autopsy material from differently polluted areas of West Germany (FRG).

Analyses of Cadmium (Cd) in human specimens demand special interest since the Federal Environmental Agency of West-Germany (UBA, FRG) has published calculations and high figures of renal disturbances due to Cd. We analyzed autopsy material from the Cd-polluted area of Goslar/Harz Mountains (N = 28) and from the less contaminated region Erlangen/Nürnberg (Franconia) (N = 50). As determinants of Cd-concentration special regard was given to age, smoking habits, residence (urban/rural), and medical findings (nephropathy, hypertension). A balanced distribution of age is found in all subdivisions, the mean age of death is 66 and 68 yrs., respectively, in both regions. Median values of Cd-concentrations in the target organs from Franconia were found to be half the amount of those from Goslar (renal cortex: 12/19, medulla: 8/16, liver: 1/3 micrograms Cd/g wet weight). Significant local differences are found for renal medulla and liver (p less than 0.05). In both regions the Cd-content is independent from sex and residence (urban/rural). The influence of tobacco smoking on the Cd-burden is evident (greater than 50%). Cases of hypertension show maximum values, although this trend can't be confirmed by the median values. Regional Cd-pollution seems to have more effect than pathological findings: normotensive persons from Goslar have higher median renal Cd-concentrations than hypertensive patients from Franconia. Analyses of renal diseases reveal the same result. All Cd-concentrations are far below the critical value (200 micrograms Cd/g renal cortex, w.w.). The evaluation of such limit values and the results of similar studies are briefly discussed.

Adult↗

PubMed1983

Survival time in cystinosis. A collaborative study.

In a retrospective study the overall survival time of 205 cystinotic patients of six countries was determined. The median survival time was 8.5 years. The median time for 'renal death' (age at death due to uraemia or age at starting renal replacement therapy) was 9.2 years. The youngest patient dying of renal death was 5.2 years. No sex difference in survival time was noticed. Furthermore no difference in survival time was noted between the different countries. The analysis of the overall survival curve indicates no clear differences between the infantile and adolescent types of cystinosis.

Adolescent↗

PubMedDate not supplied

Tissue distribution, toxicokinetics and induction of hepatic drug metabolizing enzymes in male rats after a single s.c. dose of 3,4,3',4'-tetrachlorobiphenyl (PCB-77).

The tissue distribution and toxicokinetics of PCB-77 after a single s.c. dose of 6 mg/kg body weight was investigated in male adult rats as well as the concurrent induction of hepatic drug-metabolizing enzymes. During five days after treatment, the PCB-77 concentrations on fat weight basis in testis and in whole blood were found to be about in the same range as the concentrations in adipose tissue, whereas in liver fat PCB-77 accumulated. EROD and MROD activities were induced by about 8 and 4 times, respectively, during a period of two weeks after treatment. Concentrations in adipose tissue and in liver as well as the hepatic enzyme activities rapidly declined during the investigation period of eight weeks. An elimination half-life for PCB-77 of approximately 7-9 days was estimated.

Adipose Tissue↗