Mode of interaction of polyoxyethyleneglycol detergents with membrane proteins

Binding of dodecyloctaethyleneglycol monoether (C12E3) and purified Triton X-100 to various integral membrane proteins was studied by chromatographic procedures. Binding capacity decreased in the following order: bovine rhodopsin greater than photochemical reaction center greater than sarcoplasmic reticulum Ca2+-ATPase. The detergents were bound in different amounts to the proteins and less than corresponding to the aggregation number of the pure micelles. Appreciable binding of C12E8 to Ca2+-ATPase was observed far below the critical micelle concentration, consistent with interaction of the membrane protein with non-micellar detergent. Model calculations indicate that the detergents cannot combine with the membrane proteins, forming an oblate ring similar to that of pure detergent micelles, such as has been previously proposed for e.g. cytochrome b5 [Robinson and Tanford (1975) Biochemistry, 14, 365-378]. Other arrangements (prolate and monolayer rings), in which all detergent molecules are in contact with the protein, are considered as alternatives for covering the hydrophobic surface of the membrane protein with a continuous layer of detergent.     

A powerful and flexible multilocus association test for quantitative traits

Association mapping of complex traits typically employs tagSNP genotype data to identify a trait locus within a region of interest. However, considerable debate exists regarding the most powerful strategy for utilizing such tagSNP data for inference. A popular approach tests each tagSNP within the region individually, but such tests could lose power as a result of incomplete linkage disequilibrium between the genotyped tagSNP and the trait locus. Alternatively, one can jointly test all tagSNPs simultaneously within the region (by using genotypes or haplotypes), but such multivariate tests have large degrees of freedom that can also compromise power. Here, we consider a semiparametric model for quantitative-trait mapping that uses genetic information from multiple tagSNPs simultaneously in analysis but produces a test statistic with reduced degrees of freedom compared to existing multivariate approaches. We fit this model by using a dimension-reducing technique called least-squares kernel machines, which we show is identical to analysis using a specific linear mixed model (which we can fit by using standard software packages like SAS and R). Using simulated SNP data based on real data from the International HapMap Project, we demonstrate that our approach often has superior performance for association mapping of quantitative traits compared to the popular approach of single-tagSNP testing. Our approach is also flexible, because it allows easy modeling of covariates and, if interest exists, high-dimensional interactions among tagSNPs and environmental predictors.     

The NOMEGA gene required for female gametophyte development encodes the putative APC6/CDC16 component of the Anaphase Promoting Complex in Arabidopsis

Development of the female gametophyte involves several rounds of nuclear divisions during which nuclei are rearranged and finally cellularized to form a mature seven-celled embryo sac. During these nuclear divisions, key proteins involved in the cell cycle need to be degraded quickly in order to facilitate both the metaphase-anaphase transition stage and late anaphase. Here, we report the characterization of an Arabidopsis mutant nomega, which results in arrest of the embryo sac development at the two-nucleate stage. The NOMEGA gene product shows high homology to the APC6/cell division cycle (CDC)16 subunit of the Anaphase Promoting Complex/Cyclosome (APC/C). The phenotype of the nomega mutant is quite different from that of the hobbit mutant, which had suggested a role for the plant APC/C in auxin signalling. We show that nomega mutant embryo sacs are unable to degrade Cyclin B, an important APC/C substrate, providing further evidence of a role for the NOMEGA gene product and the plant APC/C in cell cycle progression during gametophyte development.     

Habitat and Fish Fauna Structure in a Subtropical Mountain Stream in Taiwan before and after a Catastrophic Typhoon

Habitats and fish populations of a subtropical mountain stream in Taiwan were surveyed before and after the hit of super-typhoon Herb in July 1996. There was a significant decrease in total pool area and an increase in total riffle area. Upper stream habitat was more susceptible to the disturbance. Relative abundance of the species was significantly correlated before and after the typhoon (rs=0.89, p<0.001). Morisita's index of similarity for the fish communities in June 1996 and October 1997 ranged between 0.82 and 1.02 for seven out of nine stations. Most common cyprinids decreased in densities after Herb, but recovered seventeen months after the typhoon. There were only minor changes in fish community fourteen months after the typhoon. Cyprinids that are smaller in size, such as Candidia barbata and Abottina brevirostris alticorpus were affected the most. Gobiid Rhinogobius nantaiensis that is well adapted to riffle habitat was unaffected throughout the surveys. The results of this study suggested that in subtropical mountain stream, severe typhoon may significantly alter the habitats, but the impact on fish populations could be relatively small due to features of these mountain species.     

Electrochemistry of some substituted pteridines

Some substituted 4(3H)-pteridones have been investigated by classical polarography, cyclic voltammetry, and controlled potential electrolysis; based on these results, the following reaction path for substituted 2-amino-4(3H)-pteridones seems likely. In neutral and slightly alkaline solution the first step is a reversible two-electron reduction to the unreducible 5,8-dihydro derivative, which tautomerizes into a reducible 7,8-dihydropteridone at a rate depending on the substituents. At a more negative potential the 7,8-dihydro derivative is reduced in a two-electron reaction to the unreducible 5,6,7,8-tetrahydropteridone. This compound can be oxidized in a reversible reaction to a 6,7-dihydropteridone, a “quinonoid” form, which tautomerizes into the 7,8-dihydropteridone. The data from cyclic voltammetry favour the formulation of the “quinonoid” form as the 6,7-dihydropteridone, an “o-quinonoid” structure.     

The Effects of CAMPATH-1H on Cell Viability Do Not Correlate to the CD52 Density on the Cell Surface

Graft versus host disease (GvHD) is one of the main complications after hematological stem cell transplantation (HSCT). CAMPATH-1H is used in the pre-transplant conditioning regimen to effectively reduce GvHD by targeting CD52 antigens on T cells resulting in their depletion. Information regarding CD52 expression and the effects of CAMPATH-1H on immune cells is scant and limited to peripheral blood (PB) T and B cells. To date, the effects of CAMPATH-1H on cord blood (CB) cells has not been studied. Here we aimed to analyze CD52 expression and the effects of CAMPATH-1H on fresh or frozen, resting or activated, PB mononuclear cells (PBMC) and CB mononuclear cells (CBMC). In resting state, CD52 expression was higher in CB than PB T cell subsets (653.66±26.68 vs 453.32±19.2) and B cells (622.2±20.65 vs 612.0±9.101) except for natural killer (NK) cells where CD52 levels were higher in PB (421.0±9.857) than CB (334.3±9.559). In contrast, CD52 levels were comparable across all cell types after activation. CAMPATH-1H depleted resting cells more effectively than activated cells with approximately 80–95% of apoptosis observed with low levels of necrosis. There was no direct correlation between cell surface CD52 density and depleting effects of CAMPATH-1H. In addition, no difference in cell viability was noted when different concentrations of CAMPATH-1H were used. CD52 was not expressed on HSC but began to be expressed as the cells differentiate, implying that CAMPATH-1H could potentially affect HSC differentiation and proliferation. Our study provides insightful information, which contributes to the better understanding in the use of CAMPATH-1H as part of the conditioning regime in HSCT.     

birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics

birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware. AVAILABILITY: The birgHPC Live CD and relevant user guide are available for free at http://birg1.fbb.utm.my/birghpc.     

Inhibition of aquaporin 4 by antiepileptic drugs

The potential of antiepileptic drugs (AEDs) to inhibit the water transport properties of aquaporin 4 (AQP4) was investigated using a combination of in silico and in vitro screening methods. Virtual docking studies on 14 AEDs indicated a range of docking energies that spanned approximately 40 kcal/mol, where the most stabilized energies were consistent with that of the previously identified AQP4 inhibitor acetazolamide. Nine AEDs and one bio-active metabolite were further investigated in a functional assay using AQP4 expressing Xenopus oocytes. Seven of the assayed compounds were found to inhibit AQP4 function, while three did not. A linear correlation was indicated between the in silico docking energies and the in vitro AQP4 inhibitory activity at 20 microM.