Pathway analysis of genomic data: concepts, methods, and prospects for future development

Genome-wide data sets are increasingly being used to identify biological pathways and networks underlying complex diseases. In particular, analyzing genomic data through sets defined by functional pathways offers the potential of greater power for discovery and natural connections to biological mechanisms. With the burgeoning availability of next-generation sequencing, this is an opportune moment to revisit strategies for pathway-based analysis of genomic data. Here, we synthesize relevant concepts and extant methodologies to guide investigators in study design and execution. We also highlight ongoing challenges and proposed solutions. As relevant analytical strategies mature, pathways and networks will be ideally placed to integrate data from diverse -omics sources to harness the extensive, rich information related to disease and treatment mechanisms.     

Alternate methods of representing single-channel data.

Clustering of dwell times in data from single-channel recordings, which is in excess of the value predicted from the probability density function (pdf) alone, provides restrictions on modeling schemes. Two methods, (a) the probability density function of the running median for groups of any size of sequential dwell times, and (b) the distribution of cumulative probabilities associated with dwell times separated by any lag, or the second cumulative probability distribution, are proposed as alternative representations of single-channel data; these methods are suitable for the detection of such clusters or modes. Simulation of three models with and without modes is done to test the efficacy of these methods. It is found that they often yield a better estimate of moding parameters than the methods of running mean pdf and autocorrelation.     

Cytotoxic T lymphocyte lysis of HTLV-1 infected cells is limited by weak HBZ protein expression,but non-specifically enhanced on induction of Tax expression

Background

Immunogenetic evidence indicates that cytotoxic T lymphocytes (CTLs) specific for the weak CTL antigen HBZ limit HTLV-1 proviral load in vivo, whereas there is no clear relationship between the proviral load and the frequency of CTLs specific for the immunodominant antigen Tax. In vivo, circulating HTLV-1-infected cells express HBZ mRNA in contrast, Tax expression is typically low or undetectable. To elucidate the virus-suppressing potential of CTLs targeting HBZ, we compared the ability of HBZ- and Tax-specific CTLs to lyse naturally-infected cells, by co-incubating HBZ- and Tax-specific CTL clones with primary CD4⁺ T cells from HLA-matched HTLV-1-infected donors. We quantified lysis of infected cells, and tested whether specific virus-induced host cell surface molecules determine the susceptibility of infected cells to CTL-mediated lysis.

Results

Primary infected cells upregulated HLA-A*02, ICAM-1, Fas and TRAIL-R1/2 in concert with Tax expression, forming efficient targets for both HTLV-1-specific CTLs and CTLs specific for an unrelated virus. We detected expression of HBZ mRNA (spliced isoform) in both Tax-expressing and non-expressing infected cells, and the HBZ_26–34 epitope was processed and presented by cells transfected with an HBZ expression plasmid. However, when coincubated with primary cells, a high-avidity HBZ-specific CTL clone killed significantly fewer infected cells than were killed by a Tax-specific CTL clone. Finally, incubation with Tax- or HBZ-specific CTLs resulted in a significant decrease in the frequency of cells expressing high levels of HLA-A*02.

Conclusions

HTLV-1 gene expression in primary CD4⁺ T cells non-specifically increases susceptibility to CTL lysis. Despite the presence of HBZ spliced-isoform mRNA, HBZ epitope presentation by primary cells is significantly less efficient than that of Tax.

     

Alleviation of water and osmotic stress-induced changes in nitrogen metabolizing enzymes in <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. cultivars by potassium

Present communication reports laboratory and pot experiments conducted to study the influence of water and osmotic stress on nitrogen uptake and metabolism in two wheat (Triticum aestivum L) cultivars with and without potassium supplementation. Polyethylene glycol 6000-induced osmotic stress/restricted irrigation caused a considerable decline in the activity of nitrate reductase, glutamate synthase, alanine and aspartate aminotransferases, and glutamate dehydrogenase. Potassium considerably improved nitrogen metabolism under normal water supply conditions and also resulted in amelioration of the negative impact of water and osmotic stresses indicating that potassium supplementation can be used as a potential tool for enhancing the nitrogen use efficiency in wheat for exploiting its genetic potential.     

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

Background  

General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets.     

Evidence for heteromeric gap junction channels formed from rat connexin43 and human connexin37

Homomeric gap junction channels are composed solely of oneconnexin type, whereas heterotypic forms contain two homomeric hemichannels but the six identical connexins of each are different fromeach other. A heteromeric gap junction channel is one that containsdifferent connexins within either or both hemichannels. The existenceof heteromeric forms has been suggested, and many cell types are knownto coexpress connexins. To determine if coexpressed connexins wouldform heteromers, we cotransfected rat connexin43 (rCx43) and humanconnexin37 (hCx37) into a cell line normally devoid of any connexinexpression and used dual whole cell patch clamp to compare the observedgap junction channel activity with that seen in cells transfected onlywith rCx43 or hCx37. We also cocultured cells transfected with hCx37 orrCx43, in which one population was tagged with a fluorescent marker tomonitor heterotypic channel activity. The cotransfected cells possessedchannel types unlike the homotypic forms of rCx43 or hCx37 or theheterotypic forms. In addition, the noninstantaneous transjunctionalconductance-transjunctional voltage(G_j/V_j)relationship for cotransfected cell pairs showed a large range ofvariability that was unlike that of the homotypic or heterotypic form.The heterotypic cell pairs displayed asymmetric voltage dependence. Theresults from the heteromeric cell pairs are inconsistent with summedbehavior of two independent homotypic populations or mixed populationsof homotypic and heterotypic channels types. TheG_j/V_jdata imply that the connexin-to-connexin interactions are significantlyaltered in cotransfected cell pairs relative to the homotypic andheterotypic forms. Heteromeric channels are a population of channelswhose characteristics could well impact differently from theirhomotypic counterparts with regard to multicellular coordinatedresponses.