Roles of ubiquitination in pattern-recognition receptors and type I interferon receptor signaling

Post-translational protein modifications are involved in all functions of living cells. This includes the ability of cells to recognize pathogens and regulate genes involved in their clearance, a concept known as innate immunity. While phosphorylation mechanisms play essential roles in regulating different aspects of the innate immune response, ubiquitination is now recognized as another post-translational modification that works in parallel with phosphorylation to orchestrate the final proper innate immune response against invading pathogens. More precisely, this review will discuss the most recent advances that address the role of ubiquitination in pattern-recognition receptors and type I interferon receptor signaling.     

Quantitative analysis by HPLC-MS2 of the pyrrolizidine alkaloid adonifoline in Senecio scandens

A quantitative method using HPLC-MS(2) has been developed for the determination of adonifoline, one of the retronecine-type hepatotoxic pyrrolizidine alkaloids in Senecio scandens Buch.-Ham. ex D. Don., a traditional Chinese herb. Using an orthogonal design test, a simple and rapid sample extraction method was developed. HPLC analysis was conducted using a C(18) column as stationary phase and a mixture of acetonitrile and aqueous formic acid as mobile phase. Good linearity for adonifoline was found in the concentration range 0.12-4.18 microg/mL, and the HPLC-MS/MS method was shown to be appropriate, in terms of sensitivity, precision and reproducibility. The quantities of adonifoline in extracts of 18 plant samples from different collection sources and from different parts (flowers, leaves, thick stems, slim stems and roots) of S. scandens were determined using the newly developed HPLC/MS(2) analysis.     

Long-term balancing selection at the west nile virus resistance gene, Oas1b, maintains transspecific polymorphisms in the house mouse

Oligoadenylate synthetases (OASs) are interferon-inducible enzymes that participate in the first line of defense against a wide range of viral infection. Recent studies have determined that Oas1b, a member of the OAS gene family in the house mouse (Mus musculus), provides specific protection against flavivirus infection (e.g., West Nile virus, dengue fever virus, and yellow fever virus). We characterized the nucleotide sequence variation in coding and noncoding regions of the Oas1b gene for a large number of wild-derived strains of M. musculus and related species. Our sequence analyses determined that this gene is one of the most polymorphic genes ever described in any mammal. The level of variation in noncoding regions of Oas1b is an order of magnitude higher than the level reported for other regions of the mouse genome and is significantly different from the level of intraspecific variation expected under neutrality. Furthermore, a phylogenetic analysis of intronic sequences demonstrated that Oas1b alleles are ancient and that their divergence predates several speciation events, resulting in transspecific polymorphisms. The amino acid sequence of Oas1b is also extremely variable, with 1 out of 7 amino acid positions being polymorphic within M. musculus. Oas1b alleles are comparatively more divergent at synonymous positions than most autosomal genes and the ratio of nonsynonymous to synonymous substitution is remarkably high, suggesting that positive selection has been acting on Oas1b. The ancestry of Oas1b polymorphisms and the high level of amino acid polymorphisms strongly suggest that the allelic variation at Oas1b has been maintained in mouse populations by long-term balancing selection.     

Natural variation in four human collagen genes across an ethnically diverse population

Collagens are members of one of the most important families of structural proteins in higher organisms. There are 28 types of collagens encoded by 43 genes in humans that fall into several different functional protein classes. Mutations in the major fibrillar collagen genes lead to osteogenesis imperfecta (COL1A1 and COL1A2 encoding the chains of Type I collagen), chondrodysplasias (COL2A1 encoding the chains of Type II collagen), and vascular Ehlers-Danlos syndrome (COL3A1 encoding the chains of Type III collagen). Over the past 2 decades, mutations in these collagen genes have been catalogued, in hopes of understanding the molecular etiology of diseases caused by these mutations, characterizing the genotype-phenotype relationships, and developing robust models predicting the molecular and clinical outcomes. To achieve these goals better, it is necessary to understand the natural patterns of variation in collagen genes in human populations. We screened exons, flanking intronic regions, and conserved noncoding regions for variations in COL1A1, COL1A2, COL2A1, and COL3A1 in 48 individuals from each of four ethnically diverse populations. We identified 459 single-nucleotide polymorphisms (SNPs), more than half of which were novel and not found in public databases. Of the 52 SNPs found in coding regions, 15 caused amino acid substitutions while 37 did not. Although the four collagens have similar gene and protein structures, they have different molecular evolutionary characteristics. For example, COL1A1 appears to have been under substantially stronger negative selection than the rest. Phylogenetic analysis also suggests that the four genes have very different evolutionary histories among the different ethnic groups. Our observations suggest that the study of collagen mutations and their relationships with disease phenotypes should be performed in the context of the genetic background of the subjects.     

Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients

Large-insert genome analysis (LIGAN) is a broadly applicable, high-throughput technology designed to characterize genome-scale structural variation. Fosmid paired-end sequences and DNA fingerprints from a query genome are compared to a reference sequence using the Genomic Variation Analysis (GenVal) suite of software tools to pinpoint locations of insertions, deletions, and rearrangements. Fosmids spanning regions that contain new structural variants can then be sequenced. Clonal pairs of Pseudomonas aeruginosa isolates from four cystic fibrosis patients were used to validate the LIGAN technology. Approximately 1.5 Mb of inserted sequences were identified, including 743 kb containing 615 ORFs that are absent from published P. aeruginosa genomes. Six rearrangement breakpoints and 220 kb of deleted sequences were also identified. Our study expands the “genome universe” of P. aeruginosa and validates a technology that complements emerging, short-read sequencing methods that are better suited to characterizing single-nucleotide polymorphisms than structural variation.     

Free radical scavenging potential of L-proline: evidence from in vitro assays

Summary. An assessment of the potential of proline to scavenge free radicals was made in a couple of in vitro assay systems, namely graft co-polymerization and autooxidation of pyrogallol. Both these assays are essentially dependent upon free radical mechanisms. Graft co-polymerization involved a ceric (Ce⁴⁺) ion- or γ-radiation-induced grafting of methyl acrylate (MA) onto a cellulose backbone. The degree of grafting, measured gravimetrically, was taken as a measure of free radical generation. The γ-radiation-dependent grafting was far greater than that due to Ce⁴⁺ ions. Inclusion of proline in the assay, irrespective of the initiator used, led to suppression of grafting in a concentration-dependent manner indicating the ability of proline to scavenge free radicals. The γ-radiation-dependent grafting was also suppressed by hydroquinone and glutathione but not by ascorbate, glycine and spermine. In contrast to graft co-polymerization, proline did not inhibit the autooxidation of pyrogallol, a reaction involving superoxide radical generation. A subset of data constitutes an evidence for the ability of proline to scavenge free radicals in vitro. It is implied by extension that free proline, known to accumulate in plant tissues during abiotic stresses, would contribute to scavenging of surplus free radicals produced under a variety of abiotic stresses. Authors’ address: Shanti S. Sharma, Department of Biosciences, Himachal Pradesh University, Shimla 171 005, India     

Solvatochromic and electrokinetic studies of banana fibrils prepared from steam-exploded banana fiber

Steam explosion technique was used to isolate banana fibrils from banana fiber. The surface polarity of banana fiber, banana fibril, and chemically-treated banana fibril was investigated by ultraviolet/visible spectroscopy using solvatochromic probe dye molecules. The empirical Kamlet-Taft solvatochromic polarity parameters such as hydrogen bond donating ability HBD (alpha), hydrogen bond accepting ability HBA (beta), the dipolarity (pi*), Gutman acceptor number, and Reichardts ET(30) values for the banana fiber, banana fibril, and chemically-treated banana fibril were determined. It was observed that banana fibril has higher HBD value than banana fiber. Chemical treatment of the banana fibril has lowered the HBD value. The results of the empirical polarity parameters determined were found to be consistent with the results of electrokinetic measurements. The functional groups on the surface of banana fiber, banana fibril, and chemically-treated banana fibril was further analyzed using Fourier transform infrared spectroscopy (FTIR). FTIR spectra revealed the dissolution of the various components from the banana fiber after steam explosion which was further confirmed by scanning electron microscopy.