Polymorphisms of interferon-inducible genes OAS-1 and MxA associated with SARS in the Vietnamese population

We hypothesized that host antiviral genes induced by type I interferons might affect the natural course of severe acute respiratory syndrome (SARS). We analyzed single nucleotide polymorphisms (SNPs) of 2',5'-oligoadenylate synthetase 1 (OAS-1), myxovirus resistance-A (MxA), and double-stranded RNA-dependent protein kinase in 44 Vietnamese SARS patients with 103 controls. The G-allele of non-synonymous A/G SNP in exon 3 of OAS-1 gene showed association with SARS (p=0.0090). The G-allele in exon 3 of OAS-1 and the one in exon 6 were in strong linkage disequilibrium and both of them were associated with SARS infection. The GG genotype and G-allele of G/T SNP at position -88 in the MxA gene promoter were found more frequently in hypoxemic group than in non-hypoxemic group of SARS (p=0.0195). Our findings suggest that polymorphisms of two IFN-inducible genes OAS-1 and MxA might affect susceptibility to the disease and progression of SARS at each level.     

Genetic control of embryo lethality in crosses between common wheat and rye

The phenotypic manifestation and genetic control of embryo lethality observed in crosses between common wheat and rye were studied. It was found that crosses between common wheat and inbred self-fertile rye lines L2 and 535 gave rise to ungerminating grains, in which the development and differentiation of the hybrid embryo are arrested. Study of the degree of embryo development in the hybrid grains obtained by crossing common wheat varieties with inbred rye lines L2 and 535 showed that genotypes of the parents affected the ratio between undifferentiated embryos of various sizes. Analysis of this trait was performed by test crosses according to a novel pedigree program with the use of interlinear hybrids and a set of fourth-generation hybrid recombinant inbred lines. Rye line L2 was shown to bear the Eml (Embryo lethality) gene, which terminates the development of the hybrid embryo in amphihaploids. The suggestion of complementary interaction between wheat and rye genes during formation of a "n ew" character in wheat-rye F1 hybrids is discussed. A method of detecting an allele not complementary to the rye Eml allele in wheat is proposed. The proposed test program allows appropriate study of the system of wheat and rye genes involved in complementary interaction in the genotype of a distant hybrid.     

autoregulatory role of endothelium-derived nitric oxide (NO) on Lipopolysaccharide-induced vascular inducible NO synthase expression and function

Nitric oxide (NO) produced by inducible nitric oxide synthase (iNOS) is responsible for sepsis-induced hypotension and plays a major contributory role in the ensuing multiorgan failure. The present study aimed to elucidate the role of endothelial NO in lipopolysaccharide (LPS)-induced iNOS expression, in isolated rat aortic rings. Exposure to LPS (1 mug/ml, 5 h) resulted in a reversal of phenylephrine precontracted tone in aortic rings (70.7 +/- 3.2%). This relaxation was associated with iNOS expression and NF-kappaB activation. Positive immunoreactivity for iNOS protein was localized in medial and adventitial layers of LPS-treated aortic rings. Removal of the endothelium rendered aortic rings resistant to LPS-induced relaxation (8.9 +/- 4.5%). Western blotting of these rings demonstrated an absence of iNOS expression. However, treatment of endothelium-denuded rings with the NO donor, diethylamine-NONOate (0.1 mum), restored LPS-induced relaxation (61.6 +/- 6.6%) and iNOS expression to levels comparable with arteries with intact endothelium. Blockade of endothelial NOS (eNOS) activation using geldanamycin and radicicol, inhibitors of heat shock protein 90, in endothelium-intact arteries suppressed both LPS-induced relaxation and LPS-induced iNOS expression (9.0 +/- 8.0% and 2.0 +/- 6.2%, respectively). Moreover, LPS treatment (12.5 mg/kg, intravenous, 15 h) of wild-type mice resulted in profound elevation of plasma [NO(x)] measurements that were reduced by approximately 50% in eNOS knock-out animals. Furthermore, LPS-induced changes in vascular reactivity and iNOS expression evident in wild-type tissues were profoundly suppressed in tissues taken from eNOS knockout animals. Together, these data suggest that eNOS-derived NO, in part via activation of NF-kappaB, regulates iNOS-induction by LPS. This study provides the first demonstration of a proinflammatory role of vascular eNOS in sepsis.     

Enzymatic characterization of the full-length and C-terminally truncated hepatitis C virus RNA polymerases: function of the last 21 amino acids of the C terminus in template binding and RNA synthesis

The nonstructural protein NS5B of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase (RdRp), which plays a central role in viral replication. Most of the reported studies on HCV polymerase in vitro have used a truncated form of the enzyme lacking the C-terminal 21 amino acids (DeltaC(21)-NS5B). In this study, we compared the enzymatic properties of the full-length NS5B (FL-NS5B) and this truncated form. Removal of the C(21) domain enhanced the enzyme stability. Both enzymes are capable of performing de novo and primer-dependent RNA syntheses, but each possesses a unique set of biochemical requirements for optimal RdRp activity. Whereas RNA synthesis by FL-NS5B remained relatively constant at 12-100 mM KCl, synthesis by DeltaC(21)-NS5B rapidly decreased at KCl concentrations greater than 12 mM. The different salt requirement for overall RNA synthesis by these two polymerases can in part be explained by the effect of monovalent ion concentration at the step of template binding, where binding by DeltaC(21)-NS5B but not FL-NS5B decreased proportionally as the KCl concentration increased from 25 to 200 mM. Thus, the C(21) domain appears to contribute to NS5B-RNA template binding, probably through the hydrophobic stacking interaction between its aromatic amino acids and the nucleotide bases of the RNA. This interpretation was supported by the observation that the C(21) polypeptide by itself could also bind to RNA to form binary complexes that were resistant to changes in the KCl concentration. Though both enzymes exhibited similar K(s) values for each of the four NTPs (1-5 microM), DeltaC(21)-NS5B generally required lower NTP concentrations than FL-NS5B for optimal synthesis. Interestingly, DeltaC(21)-NS5B became severely inhibited at elevated NTP concentrations, which most likely is due to competitive binding of the noncomplementary nucleotide to the polymerase catalytic center. Finally, the terminal transferase activity of DeltaC(21)-NS5B was found to be distinct from that of FL-NS5B on several different RNA templates. Together, these findings indicated that the HCV NS5B C(21) domain, in addition to being a membrane anchor, functions in template binding, NTP substrate selection, and modulation of terminal transferase activity.     

ACE1 polymorphism and progression of SARS

We have hypothesized that genetic predisposition influences the progression of SARS. Angiotensin converting enzyme (ACE1) insertion/deletion (I/D) polymorphism was previously reported to show association with the adult respiratory distress syndrome, which is also thought to play a key role in damaging the lung tissues in SARS cases. This time, the polymorphism was genotyped in 44 Vietnamese SARS cases, with 103 healthy controls who had had a contact with the SARS patients and 50 controls without any contact history. SARS cases were divided into either non-hypoxemic or hypoxemic groups. Despite the small sample size, the frequency of the D allele was significantly higher in the hypoxemic group than in the non-hypoxemic group (p=0.013), whereas there was no significant difference between the SARS cases and controls, irrespective of a contact history. ACE1 might be one of the candidate genes that influence the progression of pneumonia in SARS.     

Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses

Similar to the chaos game representation (CGR) of DNA sequences proposed by Jeffrey (Nucleic Acid Res. 18 (1990) 2163), a new CGR of protein sequences based on the detailed HP model is proposed. Multifractal and correlation analyses of the measures based on the CGR of protein sequences from complete genomes are performed. The Dq spectra of all organisms studied are multifractal-like and sufficiently smooth for the Cq curves to be meaningful. The Cq curves of bacteria resemble a classical phase transition at a critical point. The correlation distance of the difference between the measure based on the CGR of protein sequences and its fractal background is also proposed to construct a more precise phylogenetic tree of bacteria.     

Complete probabilistic analysis of RNA shapes

Background  

Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived.     

Concomitant requirement for Notch and Jak/Stat signaling during neuro-epithelial differentiation in the Drosophila optic lobe

The optic lobe forms a prominent compartment of the Drosophila adult brain that processes visual input from the compound eye. Neurons of the optic lobe are produced during the larval period from two neuroepithelial layers called the outer and inner optic anlage (OOA, IOA). In the early larva, the optic anlagen grow as epithelia by symmetric cell division. Subsequently, neuroepithelial cells (NE) convert into neuroblasts (NB) in a tightly regulated spatio-temporal progression that starts at the edges of the epithelia and gradually move towards its centers. Neuroblasts divide at a much faster pace in an asymmetric mode, producing lineages of neurons that populate the different parts of the optic lobe. In this paper we have reconstructed the complex morphogenesis of the optic lobe during the larval period, and established a role for the Notch and Jak/Stat signaling pathways during the NE-NB conversion. After an early phase of complete overlap in the OOA, signaling activities sort out such that Jak/Stat is active in the lateral OOA which gives rise to the lamina, and Notch remains in the medial cells that form the medulla. During the third instar, a wave front of enhanced Notch activity progressing over the OOA from medial to lateral controls the gradual NE-NB conversion. Neuroepithelial cells at the medial edge of the OOA, shortly prior to becoming neuroblasts, express high levels of Delta, which activates the Notch pathway and thereby maintains the OOA in an epithelial state. Loss of Notch signaling, as well as Jak/Stat signaling, results in a premature NE-NB conversion of the OOA, which in turn has severe effects on optic lobe patterning. Our findings present the Drosophila optic lobe as a useful model to analyze the key signaling mechanisms controlling transitions of progenitor cells from symmetric (growth) to asymmetric (differentiative) divisions.