Multilocus linkage analysis of affected sib pairs

OBJECTIVE: The conventional affected sib pair methods evaluate the linkage information at a locus by considering only marginal information. We describe a multilocus linkage method that uses both the marginal information and information derived from the possible interactions among several disease loci, thereby increasing the significance of loci with modest effects. METHODS: Our method is based on a statistic that quantifies the linkage information contained in a set of markers. By a marker selection-reduction process, we screen a set of polymorphisms and select a few that seem linked to disease. RESULTS: We test our approach on genome scan data for inflammatory bowel disease (InfBD) and on simulated data. On real data we detect 6 of the 8 known InfBD loci; on simulated data we obtain improvements in power of up to 40% compared to a conventional single-locus method. CONCLUSION: Our extensive simulations and the results on real data show that our method is in general more powerful than single-locus methods in detecting disease loci responsible for complex traits. A further advantage of our approach is that it can be extended to make use of both the linkage and the linkage disequilibrium between disease loci and nearby markers.     

Structure and dimerization of the kinase domain from yeast Snf1, a member of the Snf1/AMPK protein family

The Snf1/AMPK kinases are intracellular energy sensors, and the AMPK pathway has been implicated in a variety of metabolic human disorders. Here we report the crystal structure of the kinase domain from yeast Snf1, revealing a bilobe kinase fold with greatest homology to cyclin-dependant kinase-2. Unexpectedly, the crystal structure also reveals a novel homodimer that we show also forms in solution, as demonstrated by equilibrium sedimentation, and in yeast cells, as shown by coimmunoprecipitation of differentially tagged intact Snf1. A mapping of sequence conservation suggests that dimer formation is a conserved feature of the Snf1/AMPK kinases. The conformation of the conserved alphaC helix, and the burial of the activation segment and substrate binding site within the dimer, suggests that it represents an inactive form of the kinase. Taken together, these studies suggest another layer of kinase regulation within the Snf1/AMPK family, and an avenue for development of AMPK-specific activating compounds.     

Reliability of surface EMG matrix in locating the innervation zone of upper trapezius muscle

The identification of the motor unit (MU) innervation zone (IZ) using surface electromyographic (sEMG) signals detected on the skin with a linear array or a matrix of electrodes has been recently proposed in the literature. However, an analysis of the reliability of this procedure and, therefore, of the suitability of the sEMG signals for this purpose has not been reported.The purpose of this work is to describe the intra and inter-rater reliability and the suitability of surface EMG in locating the innervation zone of the upper trapezius muscle.Two operators were trained on electrode matrix positioning and sEMG signal analysis. Ten healthy subjects, instructed to perform a series of isometric contractions of the upper trapezius muscle participated in the study. The two operators collected sEMG signals and then independently estimated the IZ location through visual analysis.Results showed an almost perfect agreement for intra-rater and inter-rater reliability. The constancy of IZ location could be affected by the factors reflecting the population of active MUs and their IZs, including: the contraction intensity, the acquisition period analyzed, the contraction repetition. In almost all cases the IZ location shift due to these factors did not exceed 4 mm. Results generalization to other muscles should be made with caution.     

Identification of F1 hybrids of artichoke by ISSR markers and morphological analysis

Five different artichoke hybrid populations (crosses between a male sterile artichoke (MS6) and three American accessions (AMA3, AMA7, AMB1) and two Spanish accessions (SP2, SPA2)) plus a commercial hybrid population (Opal F1, Nunhems, Netherlands) were used for molecular and morphological characterisation in order to identify the purity of the F1 populations. Molecular analysis was carried out using the inter-simple sequence repeat (ISSR) technique with twenty primers. Out of these, nine were polymorphic, producing 82 DNA bands per primer on average, 56 of which were polymorphic among the populations. A dendrogram, drawn on the basis of a similarity matrix using the UPGMA algorithm, revealed that the 66 samples (10 plants per F1 populations and their respective progenitors) could be classified into two major clusters at a Nei’s genetic distance of 0.13. The male parents were genetically quite similar to all their respective progenies. In order to confirm hybrid purity, only the primers which amplified bands specific to the male parent of each hybrid were considered and the inheritance of the single locus for each cross-combination was analysed. Three ISSR markers (857c, 857g and 878) were able to confirm the hybrid purity. The morphological trait analysis showed that eight of the 17 morphological characters were significantly different among the six F1 populations. When the Mantel test was applied to the matrix of the Nei’s genetic distances and the matrix of morphological traits, a significant degree of correlation was observed between them. A selection method using ISSR markers based on cluster analysis is suggested to confirm the purity of artichoke hybrids and to predict the characters expected by any F1 hybrid offspring.     

Nonlytic simian virus 40-specific 100K phosphoprotein is associated with anchorage-independent growth in simian virus 40-transformed and revertant mouse cell lines.

Normal fibroblasts display two distinct growth controls which can be assayed as requirements for serum or for anchorage. Interaction of mouse 3T3 fibroblasts with simian virus 40 (SV40) thus generates four classes of transformed cells. We have examined viral gene expression in these four classes of cell lines. Immunoprecipitation of [35S]methionine-labeled cell extracts with an antiserum obtained from tumor-bearing hamsters detected the SV40 large T and small t proteins (94,000 molecular weight [94K], 17K) and the nonviral host 54K protein in all cell lines tested. A tumor antigen with an apparent molecular weight of 100,000 was also found in some, but not all, lines. Similar "super T" molecules have been found by others in many rodent transformed lines. We carried out an analysis of the relation of phenotype to relative amounts of these proteins in cell lines of the four classes, using the Spearman rank correlation test. The amount of the 100K T antigen relative to the 94K T antigen or to total viral protein was well correlated with the ability to form colonies in semisolid medium. No significant correlation was found between quantities of labeled 94K T antigen, 54K host antigen, or 17K t antigen and either serum or anchorage independence. Mouse cells transformed with the small t SV40 deletion mutant 884 synthesized a 100K T antigen, suggesting that small t is not required for the production of this protein. The 100K T antigen migrated more slowly than lytic T. Since mixtures of extracts from cells expressing and lacking the 100K T antigen yielded the expected amount of this protein, it is unlikely that the 100K T derives from the 94K protein by a posttranslational modification.     

An improved chemical fixation method suitable for immunogold localization of green fluorescent protein in the Golgi apparatus of tobacco Bright Yellow (BY-2) cells.

In plant systems, the green fluorescent protein (GFP) is increasingly used as a marker to study dynamics of the secretory apparatus using fluorescence microscopy. The purpose of this study was to immunogold localize the GFP, at the electron microscopic level, in a line of tobacco BY-2-cultured cells, expressing a GFP-tagged Golgi glycosyltransferase. To this end we have developed a simple, one-step chemical fixation method that allow good structural preservation and specific labeling with anti-GFP antibodies. Using this method, we have been able to show that an N-glycan GFP-tagged xylosyltransferase is specifically associated with Golgi stacks of BY-2 transformed cells and is preferentially located in medial cisternae. As an alternative to cryofixation methods, such as high-pressure freezing, which requires specialized and expensive equipment not available in most laboratories, this method offers researchers the opportunity to investigate GFP-tagged proteins of the endomembrane system in tobacco BY-2 cells.     

Beneficial effects of co-treatment with dextromethorphan on prenatally methadone-exposed offspring

Background

Heroin use among young women of reproductive age has drawn much attention around the world. Although methadone is widely used in maintenance therapy for heroin/morphine addiction, the long-term effects of prenatal exposure to methadone and preventative therapy remain unclear. For revealing this question, female pregnant Sprague–Dawley rats were sub-grouped to receive (1) vehicle, (2) methadone 5 mg/kg at embryonic day 3 (E3) and then 7 mg/kg from E4 to E20, (3) dextromethorphan (DM) 3 mg/kg, and (4) methadone + DM (the rats received methadone followed by DM treatment), subcutaneously, twice a day from E3 to E20. The body weight, natural withdrawal, pain sensitivity, ED50, conditioned place preference and water maze were conducted at different postnatal stages (P1 to P79) of offspring. The quantitative real-time RT-PCR and electrophysiology were also used to measure the gene expression of opioid receptors in the spinal cord and changes of LTP/LTD in the hippocampus, separately.

Results

Prenatal exposure to methadone or DM did not affect survival rate, body weight, water maze and LTP or LTD of offspring. However, prenatal methadone significantly increased the withdrawal symptoms, pain sensitivity, addiction liability and decreased the mRNA expression of pain related opioid receptors. Co-administration of DM with methadone in the maternal rats effectively prevented these abnormalities of offspring induced by methadone.

Conclusions

Our study clearly showed that co-administration of dextromethorphan with methadone in the maternal rats prevented the adverse effects induced by prenatal methadone exposure. It implies that dextromethorphan may have a potential to be used in combination with methadone for maintenance treatment in pregnant heroin-addicted women to prevent the adverse effects induced by methadone on offspring.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-015-0126-2) contains supplementary material, which is available to authorized users.     

Phase I Randomized Safety Study of Twice Daily Dosing of Acidform Vaginal Gel: Candidate Antimicrobial Contraceptive

Background

Acidform gel, an acid-buffering product that inactivates spermatozoa, may be an effective topical non-hormonal contraceptive. This study was designed to evaluate the safety of vaginal dosing and effects of Acidform on mucosal immune mediators, antimicrobial properties of genital secretions, and vaginal microbiota.

Methods

Thirty-six sexually abstinent U.S. women were randomized to apply Acidform or hydroxyethylcellulose (HEC) placebo gel twice daily for 14 consecutive days. Safety was assessed by symptoms and pelvic examination. The impact of gel on mucosal immunity was assessed by quantifying cytokines, chemokines, antimicrobial proteins and antimicrobial activity of genital secretions collected by cervicovaginal lavage (CVL) at screening, 2 hours after gel application, and on days 7, 14 and 21. Vaginal microbiota was characterized at enrollment and day 14 using species-specific quantitative PCR assays.

Results

The median vaginal and cervical pH was significantly lower 2 hours after application of Acidform and was associated with an increase in the bactericidal activity of CVL against E. coli. However, 65% of women who received Acidform had at least one local adverse event compared with 11% who received placebo (p = 0.002). While there was no increase in inflammatory cytokines or chemokines, CVL concentrations of lactoferrin and interleukin-1 receptor antagonist (IL-1ra), an anti-inflammatory protein, were significantly lower following Acidform compared to HEC placebo gel application. There were no significant changes in Lactobacillus crispatus or Lactobacillus jensenii in either group but there was a decrease in Gardnerella vaginalis in the Acidform group (p = 0.08).

Conclusions

Acidform gel may augment mucosal defense as evidenced by an increase in bactericidal activity of genital secretions against E. coli and a decrease in Gardnerella vaginalis colonization. However, Acidform was associated with more irritation than placebo and lower levels of antimicrobial (lactoferrin) and anti-inflammatory (IL-1ra) proteins. These findings indicate the need for additional safety studies of this candidate non-hormonal contraceptive.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00850837","term_id":"NCT00850837"}}NCT00850837     

Cytosolic N-terminal arginine-based signals together with a luminal signal target a type II membrane protein to the plant ER

Background  

In eukaryotic cells, the membrane compartments that constitute the exocytic pathway are traversed by a constant flow of lipids and proteins. This is particularly true for the endoplasmic reticulum (ER), the main "gateway of the secretory pathway", where biosynthesis of sterols, lipids, membrane-bound and soluble proteins, and glycoproteins occurs. Maintenance of the resident proteins in this compartment implies they have to be distinguished from the secretory cargo. To this end, they must possess specific ER localization determinants to prevent their exit from the ER, and/or to interact with receptors responsible for their retrieval from the Golgi apparatus. Very few information is available about the signal(s) involved in the retention of membrane type II protein in the ER but it is generally accepted that sorting of ER type II cargo membrane proteins depends on motifs mainly located in their cytosolic tails.