Possible excess of mental handicap and congenital malformations in autosomal reciprocal translocations.

The most pertinent data of the 32 cases of reciprocal autosomal translocations detected in the laboratory since the initiation of the banding-techniques are summarized. One third of these balanced translocations were detected in patients presenting with mental handicap and/or malformative symptoms.     

Formal genetics of esterase D (EC 3.1.1.1): evidence for a sex-phenotype association

The formal genetics of esterase D (EC 3.1.1.1) was studied in family data and mother/child pairs. A general agreement with mendelian expectations was found. However, a significant sex-phenotype association was detected in families from northwestern Portugal as well as in mother/child pairs and family data from southwestern Germany.     

Hotspots of diversity in a clonal world--the Mediterranean moss Pleurochaete squarrosa in Central Europe

Diversity patterns of the dioecious haploid Mediterranean moss Pleurochaete squarrosa were analysed from Central and Northwest Europe using nuclear and chloroplast DNA sequencing and enzyme electrophoresis. Across 69 populations, 38 distinct haploid multilocus genotypes (MLGs) were detected, but nearly all populations were clonal. Only five MLGs occurred in more than two regions, and two diversity hotspots were detected. The Kaiserstuhl mountains in Southwest Germany harboured 34 MLGs, 25 being endemic within Central Europe. Levels of linkage disequilibrium and population structure in Kaiserstuhl populations were similar to levels and structure in sexually reproducing populations in the Mediterranean Basin. In the Moselle-Nahe area, some 250 km north, a comparably high allelic diversity, but no evidence of recombination, was detected. Genetic diversity measures were significantly lower than estimates obtained in the Mediterranean Basin and a G _ST of 0.89 signified extreme population differentiation. Mantel tests identified a positive correlation on genetic and geographical distance for distances up to 50 km. Seven nrITS and three cpDNA haplotypes were detected, their geographical structure mirroring enzyme data set results. Comparative analysis with Mediterranean data demonstrated multiple recolonization of Central Europe from both the Iberian Peninsula and the Balkans. A suture zone of genotypes was detected along the border of Belgium/France and Germany. Despite P. squarrosa having haploid spore and/or vegetative propagules dispersal, we found patterns of postglacial recolonization of Central Europe comparable with those reported in flowering plants and animals. This study demonstrates the importance of comparative research on population genetics and phylogeography of a diverse range of organisms.     

Intracellular distribution of functional M(1) -muscarinic acetylcholine receptors in N1E-115 neuroblastoma cells

Signaling by muscarinic agonists is thought to result from the activation of cell surface acetylcholine receptors (mAChRs) that transmit extracellular signals to intracellular systems. In N1E-115 neuroblastoma cells, we detected both plasma membrane and intracellular M(1) -mAChRs using both biochemical and pharmacological methods. In intact cells, both plasma membrane and intracellular M(1) -mAChRs were detected by the hydrophobic ligand probe, 1-quinuclidinyl-[phenyl-4-(3) H]-benzilate ([(3) H]-QNB) whereas the hydrophilic probe, 1-[N-methyl-(3) H] scopolamine ([(3) H]-NMS), detected only cell surface receptors. These probes detected comparable numbers of receptors in isolated membrane preparations. Immunohistochemical studies with M(1) -mAChR antibody also detected both cell-surface and intracellular M(1) -mAChRs. Carbachol-stimulated phosphatidylinositol hydrolysis and Ca(2+) mobilization were completely inhibited by a cell-impermeable M(1) antagonist, muscarinic toxin -7 and the G(q/11) inhibitor YM-254890. However, carbachol-stimulated extracellular-regulated kinase 1/2 activation was unaffected by muscarinic toxin-7, but was blocked by the cell-permeable antagonist, pirenzepine. extracellular regulated kinase 1/2 phosphorylation was resistant to blockade of G(q/11) (YM-254890) and protein kinase C (bisindolylmaleimide I). Our data suggest that the geographically distinct M(1) -mAChRs (cell surface versus intracellular) can signal via unique signaling pathways that are differentially sensitive to cell-impermeable versus cell-permeable antagonists. Our data are of potential physiological relevance to signaling that affects both cognitive and neurodegenerative processes.     

PyXlinkViewer: A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system

Chemical crosslinking‐mass spectrometry (XL‐MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL‐MS data yield inter‐residue restraints that can be compared with high‐resolution structural data. Distances greater than the crosslinker spacer‐arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL‐MS, there are few tools to enable rapid and facile mapping of XL‐MS data onto high‐resolution structures or structural models. PyXlinkViewer is a user‐friendly plugin for PyMOL v2 that maps intra‐protein, inter‐protein, and dead‐end crosslinks onto protein structures/models and automates the calculation of inter‐residue distances for the detected crosslinks. This enables rapid visualization of XL‐MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high‐quality images for publication.     

A new summarization method for Affymetrix probe level data

MOTIVATION: We propose a new model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. The new summarization method is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. Thereafter, the RNA concentration is estimated from the model. In contrast to previous methods our new method called 'Factor Analysis for Robust Microarray Summarization (FARMS)' supplies both P-values indicating interesting information and signal intensity values. RESULTS: We compare FARMS on Affymetrix's spike-in and Gene Logic's dilution data to established algorithms like Affymetrix Microarray Suite (MAS) 5.0, Model Based Expression Index (MBEI), Robust Multi-array Average (RMA). Further, we compared FARMS with 43 other methods via the 'Affycomp II' competition. The experimental results show that FARMS with default parameters outperforms previous methods if both sensitivity and specificity are simultaneously considered by the area under the receiver operating curve (AUC). We measured two quantities through the AUC: correctly detected expression changes versus wrongly detected (fold change) and correctly detected significantly different expressed genes in two sets of arrays versus wrongly detected (P-value). Furthermore FARMS is computationally less expensive then RMA, MAS and MBEI. AVAILABILITY: The FARMS R package is available from http://www.bioinf.jku.at/software/farms/farms.html. SUPPLEMENTARY INFORMATION: http://www.bioinf.jku.at/publications/papers/farms/supplementary.ps     

Genetic variation of tetrazolium oxidase in the fat-tailed dunnart Sminthopsis crassicaudata Gould (Marsupialia)

Electrophoretic variation in red blood cell tetrazolium oxidase has been detected in a laboratory colony of the fat-tailed dunnart, Sminthopsis crassicaudata. Evidence from family data suggest that this variation is determined by a pair of co-dominant autosomal alleles, To ^A and To ^B, heterozygotes possessing enzymatically active hybrid protein.     

Evaluation of protein expression in bovine bronchoalveolar fluid following challenge with Mannheimia haemolytica

Proteomics analysis of bovine bronchoalveolar fluid (BAF) following induction of pneumonia with Mannheimia haemolytica using nanoflow liquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS) resulted in the identification of 88 unique proteins. Proteins detected in BAF included antimicrobial peptides (AMPs), complement factors, acute-phase proteins, protease inhibitors, and proteins involved in oxidation-reduction. Notwithstanding biological variation, differences in relative protein abundance, determined using normalized peptide counts, were detected for select proteins in BAF from genuinely infected versus sham-infected animals. To demonstrate the applicability of using normalized peptide counts to assess protein expression trends, LC-MS/MS data for the acute-phase protein haptoglobin (HPT) were compared with ELISA data, and statistical evaluation of the relationship between the data revealed a strong measure of association. Differences were detected between sham- and genuinely infected animals for haptoglobin, as well as the AMPs cathelicidin-1 and cathelicidin-4, and inter-α-trypsin inhibitor heavy chain-4, a fairly novel protein involved in the acute phase response. Though the small sample size limited the scope of the inferences, the results indicate the likely importance of AMPs and acute-phase proteins during respiratory infection, and provide additional information regarding potential mechanisms involved in the bovine mucosal barrier defense.     

用YO-PRO-1和PI联合染色定量检测细胞凋亡

经不同浓度staurosporine处理诱导凋亡的G7细胞样品,分别用YO-PRO-1/PI和AV/PI进行荧光染色,借助流式细胞仪检测凋亡情况,将两种检测方法得到的结果进行统计学分析显示,二者有显著的相关性(r=0.9659,P<0.01),且没有显著性差异(P<0.05);另外,上述凋亡细胞样品经YO-PRO-1/PI染色后在荧光显微镜下计数凋亡细胞比例的结果与AV/PI流式细胞仪的检测结果也有显著的相关性(r=0.9903,P<0.01),且没有显著性差异(P<0.05)。以上这些结果表明,用YO-PRO-1/PI对细胞进行染色、借助流式细胞仪和荧光显微镜均能准确地检测细胞凋亡,可替代AV/PI流式细胞仪方法用于细胞凋亡的检测。     

Use of hopane as a conservative biomarker for monitoring the bioremediation effectiveness of crude oil contaminating a sandy beach

Much of the variability inherent in crude oil bioremediation field studies can be eliminated by normalizing analyte concentrations to the concentration of a nonbiodegradable biomarker such as hopane. This was demonstrated with data from a field study in which crude oil was intentionally released onto experimental plots on the Delaware shoreline. Five independent replicates of three treatments were examined: no nutrient addition, addition of inorganic mineral nutrients alone, and nutrient addition plus indigenous oil-degrading microorganisms from the site. Samples collected biweekly were analyzed for the Most Probable Numbers (MPNs) of alkane and aromatic degraders and oil component analysis by GC/MS. The data were normalized to either the mass of sand that was extracted or to the concentration of hopane that was measured. Hopane normalization enabled detection of significant treatment differences in hydrocarbon biodegradation that were not detected when the data were normalized to sand mass. First-order loss rates for the hopane-normalized data were lower than those for the sand-normalized data because hopane normalization accounts only for loss due to biodegradation whereas sand normalization includes all loss mechanisms. Plots amended with nutrients alone and nutrients plus the inoculum showed enhanced removal of hydrocarbons compared to unamended control plots. However, no differences were detected between the nutrient-amended plots and the nutrient/inoculum-amended plots. Received 06 November 1995/ Accepted in revised form 26 June 1996     

Interactomic study on interaction between lipid droplets and mitochondria

An increasing body of evidence shows that the lipid droplet, a neutral lipid storage organelle, plays a role in lipid metabolism and energy homeostasis through its interaction with mitochondria. However, the cellular functions and molecular mechanisms of the interaction remain ambiguous. Here we present data from transmission electron microscopy, fluorescence imaging, and reconstitution assays, demonstrating that lipid droplets physically contact mitochondria in vivo and in vitro. Using a bimolecular fluorescence complementation assay in Saccharomyces cerevisiae, we generated an interactomic map of protein-protein contacts of lipid droplets with mitochondria and peroxisomes. The lipid droplet proteins Erg6 and Pet10 were found to be involved in 75% of the interactions detected. Interestingly, interactions between 3 pairs of lipid metabolic enzymes were detected. Collectively, these data demonstrate that lipid droplets make physical contacts with mitochondria and peroxisomes, and reveal specific molecular interactions that suggest active participation of lipid droplets in lipid metabolism in yeast.     

Imidazole alkaloids from Cynometra hankei

Two new and two known imidazole alkaloids, N₁-demethyl cynometrine, N₁-demethyl cynodine, cynometrine and cynodine, respectively, have been isolated from the stem bark and seed of Cynometra hankei. The structures of the new alkaloids were elucidated by chemical evidence and spectral data. No alkaloids could be detected in C. mannei stem bark.     

Crystallization and phase behavior of 1,3-propanediol esters II. 1,3-propanediol distearate/1,3-propanediol dipalmitate (SS/PP) and 1,3-propanediol distearate/1,3-propanediol dimyristate (SS/MM) binary systems

Polymorphic influences on the phase behavior of two types of binary mixtures of saturated monoacid 1,3-propanediol esters (PADEs), dipalmitate/distearate (PP/SS) and dimyristate/distearate (MM/SS) were examined by X-ray diffraction (XRD), differential scanning calorimetry (DSC), and by solid fat content (SFC), hardness and microscopy measurements. Three stacking modes have been found in the PP/SS binary system. Mixed SS-PP bilayers were detected in all mixtures, SS-SS bilayers in x(PP)=0.0-0.4 mixtures and PP-PP bilayers in x(PP)=0.6-0.1 mixtures. Two different but close beta polymorphs and one beta' polymorph were detected for this system. beta' was only detected in x(PP)=0.5-0.9 mixtures for the mixed bilayers. For the MM/SS binary system, only MM-MM and SS-SS bilayers were detected and both solid phases crystallized in two different beta forms. XRD data evidenced clearly that the MM and SS components were completely immiscible in the solid state. The phase diagrams constructed using DSC data, exhibited a typical eutectic-type phase boundary. The presence of eutectics, the shape of the solidus lines as well as the analysis of the individual enthalpies of melting indicated typical phase separation for both systems. A thermodynamic study based on the Hildebrand equation and using the Bragg-Williams approximation for non-ideality of mixing confirmed the phase separation in the solid phase and suggested that the PP and SS were miscible in the liquid phase and that SS formed an ideal mixing with MM. Avrami analysis of SFC vs. time curves indicated heterogeneous nucleation and spherulitic crystal development from sporadic nuclei, and suggested that the nucleation rate was higher for the mixture at the eutectic composition. The relative hardness was correlated with the enthalpies, the final SFC and the microscopy measurements.     

Prevalence of Escherichia coli O157 and O157:H7-infecting bacteriophages in feedlot cattle feces

AIM: To estimate the distribution and prevalence of both Escherichia coli O157 and O157:H7-infecting bacteriophages within a 50,000 head commercial beef feedlot. METHODS AND RESULTS: Escherichia coli O157 was detected in approximately 27% of the individual samples, distributed across seven of the 10 pens screened. In a simple initial screen to detect O157:H7-infecting phages, none were detected in any pen or individual sample. In contrast, after a series of enrichment procedures O157:H7-infecting phages were detected in every pen and in the majority of the samples from most pens; virulent bacteriophages active against E. coli O157:H7 were detected post-enrichment from 39/60 (65%) of the feedlot samples, and 58/60 (approximately 97%) contained phage that infected E. coli B or O157:H7. CONCLUSIONS: The data we present here indicates that we may be grossly underestimating the prevalence of O157:H7-infecting phages in livestock if we simply screen samples and that enrichment screening is required to truly determine the presence of phages in these ecosystems. SIGNIFICANCE AND IMPACT OF THE STUDY: Our data suggest that O157:H7-infecting phages may play a role in the ecology and transient colonization of cattle by E. coli O157:H7. Further, this and previous data suggest that before starting in vivo pathogen eradication studies using phage or any other regime, test animals should be enrichment screened for phage to avoid erroneous results.     

FGF ligand family mRNA expression profile for mouse preimplantation embryos, early gestation human placenta, and mouse trophoblast stem cells

Signaling by fibroblast growth factor (FGF) is essential is for trophoblast stem (TS) cells and preimplantation embryos. FGF4 provides essential signaling, but the expression of the complete set of 23 FGF family members has not been analyzed. Here, semi-quantitative RT-PCR and microarray analyses were used to define expression of all FGF ligand mRNA. RT-PCR was done for developmentally important FGF subfamilies, FGF10/FGF22 and FGF8/FGF17/FGF18 as well as FGF11. FGF4 and FGF18 are detected at highest levels by RT-PCR and microarrays. FGF10 was detected at low levels in both assays. FGF11 was detected at moderate levels by microarray, but not by RT-PCR. FGF17 was detected at low levels by array and moderate levels by RT-PCR. FGF8 and FGF22 were detected by RT-PCR, but not by microarrays during late cleavage divisions. FGF8, FGF5, and FGF9 were detected in the oocyte by microarray. FGF2, FGF3, and FGF7 were not detected by RT-PCR or microarrays and FGF13, FGF14, and FGF23 were not detected by microarray. Since a major role of FGF is to maintain TS cells, we tested human and mouse placental cell lines and early gestation human placenta for expression of FGF ligands. Expression in mouse TS cells was compared with preimplantation embryos, and human placental cell line expression was compared with human placenta, to infer which ligands are expressed in placental lineage vs. other cell lineages. The data suggest that human and mouse placenta share FGF18 and its high expression suggests preimplantation and early placental function.     

Isolation and Characterization of the N-linked Oligosaccharides in Nacrein from <Emphasis Type="Italic">Pinctada fucata</Emphasis>

We analyzed the structure of the N-linked oligosaccharides enzymatically liberated from the organic matrix (OM) component in the nacreous layer of Japanese pearl oyster: Pinctada fucata. The lectin-blot analysis of the soluble OM after separation by SDS-PAGE, four components, with sizes of approximately 55 kDa, 35 kDa, 25 kDa, and 21 kDa were detected with GNA lectin, which recognized terminal mannose of high mannose and hybrid types of N-glycan. The 55-kDa component of the soluble OM detected by lectin blotting was identified as nacrein by using liquid chromatography/mass spectrometry (LC/MS). LC/MS analysis of the N-glycan liberated from nacrein detected a hybrid-type N-glycan, which contained sulfite and sialic acid at its terminus. The data strongly imply that nacrein, a sulfated OM glycoprotein, participates in molluscan biomineralization by creating a favorable environment for calcium ion uptake through sulfonic acid and sialic acid.     

Trennung und charakterisierung saurer harnbestandteile

Separation and characterization of acidic urine constituentsThe acidic compounds of urine were separated by thin-layer chromatography in eight fractions. Each fraction was investigated separately by the combination glass capillary gas chromatography—mass spectrometry. About 500 compounds were detected, 2/5 of these could be characterized by their mass spectra. Retention data and key fragments of the mass spectra were tabulated. Many of the detected compounds are still unknown.     

Analysis of Ultra-Deep Pyrosequencing and Cloning Based Sequencing of the Basic Core Promoter/Precore/Core Region of Hepatitis B Virus Using Newly Developed Bioinformatics Tools

Aims

The aims of this study were to develop bioinformatics tools to explore ultra-deep pyrosequencing (UDPS) data, to test these tools, and to use them to determine the optimum error threshold, and to compare results from UDPS and cloning based sequencing (CBS).

Methods

Four serum samples, infected with either genotype D or E, from HBeAg-positive and HBeAg-negative patients were randomly selected. UDPS and CBS were used to sequence the basic core promoter/precore region of HBV. Two online bioinformatics tools, the “Deep Threshold Tool” and the “Rosetta Tool” (http://hvdr.bioinf.wits.ac.za/tools/), were built to test and analyze the generated data.

Results

A total of 10952 reads were generated by UDPS on the 454 GS Junior platform. In the four samples, substitutions, detected at 0.5% threshold or above, were identified at 39 unique positions, 25 of which were non-synonymous mutations. Sample #2 (HBeAg-negative, genotype D) had substitutions in 26 positions, followed by sample #1 (HBeAg-negative, genotype E) in 12 positions, sample #3 (HBeAg-positive, genotype D) in 7 positions and sample #4 (HBeAg-positive, genotype E) in only four positions. The ratio of nucleotide substitutions between isolates from HBeAg-negative and HBeAg-positive patients was 3.5∶1. Compared to genotype E isolates, genotype D isolates showed greater variation in the X, basic core promoter/precore and core regions. Only 18 of the 39 positions identified by UDPS were detected by CBS, which detected 14 of the 25 non-synonymous mutations detected by UDPS.

Conclusion

UDPS data should be approached with caution. Appropriate curation of read data is required prior to analysis, in order to clean the data and eliminate artefacts. CBS detected fewer than 50% of the substitutions detected by UDPS. Furthermore it is important that the appropriate consensus (reference) sequence is used in order to identify variants correctly.