The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5' cap structure by exhibiting RNA 5'-triphosphatase activity

Open reading frame 1 (ORF1) of potexviruses encodes a viral replicase comprising three functional domains: a capping enzyme at the N terminus, a putative helicase in the middle, and a polymerase at the C terminus. To verify the enzymatic activities associated with the putative helicase domain, the corresponding cDNA fragment from bamboo mosaic virus (BaMV) was cloned into vector pET32 and the protein was expressed in Escherichia coli and purified by metal affinity chromatography. An activity assay confirmed that the putative helicase domain has nucleoside triphosphatase activity. We found that it also possesses an RNA 5'-triphosphatase activity that specifically removes the gamma phosphate from the 5' end of RNA. Both enzymatic activities were abolished by the mutation of the nucleoside triphosphate-binding motif (GKS), suggesting that they have a common catalytic site. A typical m(7)GpppG cap structure was formed at the 5' end of the RNA substrate when the substrate was treated sequentially with the putative helicase domain and the N-terminal capping enzyme, indicating that the putative helicase domain is truly involved in the process of cap formation by exhibiting its RNA 5'-triphosphatase activity.

Functions of the conserved anionic amino acids and those interacting with the substrate phosphate group of phosphoglucose isomerase

Phosphoglucose isomerase catalyzes the isomerization between glucose 6-phosphate and fructose 6-phosphate in cytoplasm, and functions as autocrine motility factor and neuroleukin outside the cells. A phosphoglucose isomerase from Bacillus stearothermophilus (pgiA) was subjected to mutagenesis study to address the catalytic function of the conserved anionic residues and those probably interacting with the phosphate group of substrates. The results suggest that Glu290 works concertedly with His311 as a general acid-base pair to initiate the isomerization step, and Glu150 assists the base function of His311. The conserved loop structure consisting of Gly205-Gly206-Arg207 plays a critical role for the recognition of substrates.

Sequences at the 3' untranslated region of bamboo mosaic potexvirus RNA interact with the viral RNA-dependent RNA polymerase

The 3' untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a pseudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase (C.-P. Cheng and C.-H. Tsai, J. Mol. Biol. 288:555-565, 1999). Electrophoretic mobility shift and competition assays have now been used to demonstrate that the Escherichia coli-expressed RNA-dependent RNA polymerase domain (Delta 893) derived from BaMV open reading frame 1 could specifically bind to the 3' UTR of BaMV RNA. No competition was observed when bovine liver tRNAs or poly(I)(C) double-stranded homopolymers were used as competitors, and the cucumber mosaic virus 3' UTR was a less efficient competitor. Competition analysis with different regions of the BaMV 3' UTR showed that Delta 893 binds to at least two independent RNA binding sites, stem-loop D and the poly(A) tail. Footprinting analysis revealed that Delta 893 could protect the sequences at loop D containing the potexviral conserved hexamer motif and part of the stem of domain D from chemical cleavage.

Characterization of the AdoMet-dependent guanylyltransferase activity that is associated with the N terminus of bamboo mosaic virus replicase

Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. Open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that has long been postulated to be a replicase involved in the replication and formation of the cap structure at the 5' end of the viral genome. To identify and characterize the enzymatic activities associated with the N-terminal domain of the BaMV ORF1 protein, the intact replicase and two C-terminally truncated proteins were expressed in Saccharomyces cerevisiae. All three versions of BaMV ORF1 proteins could be radiolabeled by [alpha-(32)P]GTP, which is a characteristic of guanylyltransferase activity. The presence of S-adenosylmethionine (AdoMet) was essential for this enzymatic activity. Thin-layer chromatography analysis suggests that the radiolabeled moiety linked to the N-terminal domain of the BaMV ORF1 protein is m(7)GMP. The N-terminal domain also exhibited methyltransferase activity that catalyzes the transfer of the [(3)H]methyl group from AdoMet to GTP or guanylylimidodiphosphate. Therefore, during cap structure formation in BaMV, methylation of GTP may occur prior to transguanylation as for alphaviruses and brome mosaic virus. This study establishes the association of RNA capping activity with the N-terminal domain of the replicase of potexviruses and further supports the idea that the reaction sequence of RNA capping is conserved throughout the alphavirus-like superfamily of RNA viruses.

The crystal structure of phosphoglucose isomerase/autocrine motility factor/neuroleukin complexed with its carbohydrate phosphate inhibitors suggests its substrate/receptor recognition

Phosphoglucose isomerase catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. In addition, phosphoglucose isomerase has been shown to have functions equivalent to neuroleukin, autocrine motility factor, and maturation factor. Here we present the crystal structures of phosphoglucose isomerase complexed with 5-phospho-D-arabinonate and N-bromoacetylethanolamine phosphate at 2.5- and 2.3-A resolution, respectively. The inhibitors bind to a region within the domains' interface and interact with a histidine residue (His(306)) from the other subunit. We also demonstrated that the inhibitors not only affect the enzymatic activity of phosphoglucose isomerase, but can also inhibit the autocrine motility factor-induced cell motility of CT-26 mouse colon tumor cells. These results indicate that the substrate and the receptor binding sites of phosphoglucose isomerase and autocrine motility factor are located within close proximity to each other. Based on these two complex structures, together with biological and biochemical results, we propose a possible isomerization mechanism for phosphoglucose isomerase.

Validation of biomarkers in humans exposed to benzene: urine metabolites

BACKGROUND

The present study was conducted among Chinese workers employed in glue- and shoe-making factories who had an average daily personal benzene exposure of 31+/-26 ppm (mean+/-SD). The metabolites monitored were S-phenylmercapturic acid (S-PMA), trans, trans-muconic acid (t,t-MA), hydroquinone (HQ), catechol (CAT), 1,2, 4-trihydroxybenzene (benzene triol, BT), and phenol.

METHODS

S-PMA, t,t-MA, HQ, CAT, and BT were quantified by HPLC-tandem mass spectrometry. Phenol was measured by GC-MS.

RESULTS

Levels of benzene metabolites (except BT) measured in urine samples collected from exposed workers at the end of workshift were significantly higher than those measured in unexposed subjects (P < 0.0001). The large increases in urinary metabolites from before to after work strongly correlated with benzene exposure. Concentrations of these metabolites in urine samples collected from exposed workers before work were also significantly higher than those from unexposed subjects. The half-lives of S-PMA, t,t-MA, HQ, CAT, and phenol were estimated from a time course study to be 12.8, 13.7, 12.7, 15.0, and 16.3 h, respectively.

CONCLUSIONS

All metabolites, except BT, are good markers for benzene exposure at the observed levels; however, due to their high background, HQ, CAT, and phenol may not distinguish unexposed subjects from workers exposed to benzene at low ambient levels. S-PMA and t,t-MA are the most sensitive markers for low level benzene exposure.

An efficient neural network approach to dynamic robot motion planning

In this paper, a biologically inspired neural network approach to real-time collision-free motion planning of mobile robots or robot manipulators in a nonstationary environment is proposed. Each neuron in the topologically organized neural network has only local connections, whose neural dynamics is characterized by a shunting equation. Thus the computational complexity linearly depends on the neural network size. The real-time robot motion is planned through the dynamic activity landscape of the neural network without any prior knowledge of the dynamic environment, without explicitly searching over the free workspace or the collision paths, and without any learning procedures. Therefore it is computationally efficient. The global stability of the neural network is guaranteed by qualitative analysis and the Lyapunov stability theory. The effectiveness and efficiency of the proposed approach are demonstrated through simulation studies.

Case and reanalysis

In this paper we discuss an asymmetry in the Case system of German and its implications for human sentence processing: the asymmetry between nominative/accusative and dative case. Starting from the assumption that dative case has a distinct grammatical representation--dative DPs are embedded into an extra structural layer KP--the results of two experiments will be presented, which show that dative assignment during reanalysis is accompanied by additional processing operations that are not needed when accusative or nominative are assigned. In particular, we show that dative assignment during reanalysis triggers reaccess to the mental lexicon, giving rise to greater processing difficulty. We conclude with a discussion of empirical and theoretical consequences of our findings.

Probing the location and function of the conserved histidine residue of phosphoglucose isomerase by using an active site directed inhibitor N-bromoacetylethanolamine phosphate

Phosphoglucose isomerase (EC 5.3.1.9) catalyzes the interconversion of D-glucopyranose-6-phosphate and D-fructofuranose-6-phosphate by promoting an intrahydrogen transfer between C1 and C2. A conserved histidine exists throughout all phosphoglucose isomerases and was hypothesized to be the base catalyzing the isomerization reaction. In the present study, this conserved histidine, His311, of the enzyme from Bacillus stearothermophilus was subjected to mutational analysis, and the mutational effect on the inactivation kinetics by N-bromoacetylethanolamine phosphate was investigated. The substitution of His311 with alanine, asparagine, or glutamine resulted in the decrease of activity, in k(cat)/K(M), by a factor of 10(3), indicating the importance of this residue. N-bromoacetylethanolamine phosphate inactivated irreversibly the activity of wild-type phosphoglucose isomerase; however, His311 --> Ala became resistant to this inhibitor, indicating that His311 is located in the active site and is responsible for the inactivation of the enzyme by this active site-directed inhibitor. The pKa of His311 was estimated to be 6.31 according to the pH dependence of the inactivation. The proximity of this value with the pKa value of 6.35, determined from the pH dependence of k(cat)/K(M), supports a role of His311 as a general base in the catalysis.

[An assessment of Helkimo index in 88 orthodontic patients before treatment]

OBJECTIVE

The prevalence of temporomandibular joint disorders(TMJDs) was studied in orthodontic patients before orthodontic treatment.

METHODS

The functional examination of the masticatory system was made with Helkimo index in 88 young patients with general malocclusion.

RESULTS

According to the dysfunction index, 50 percent of the patients was free of anamnestic dysfunction, and 44.32% and 5.68% of the patients had a mild and a severe anamnestic dysfunction respectively, 32.95 percent of patients was free of clinical dysfunction, and 51.14% and 14.77% of patients had a mild and a moderate clinical dysfunction respectively, only 1.14 percent of patients had a severe clinical dysfunction. The dysfunction of masticatory muscles and sounds of temporomandibular joint were most common in the signs and symptoms of TMJDs.

CONCLUSION

There were no significant differences in the distribution of Ai and Di in different gender and between Angle's Class I and II malocclusion, and there was a relationship between Ai and Di.

Development of liquid chromatography-electrospray ionization-tandem mass spectrometry methods for determination of urinary metabolites of benzene in humans

To investigate the ways in which different levels of exposure affect the metabolic activation pathways of benzene in humans, and to examine the relationship between urinary metabolites and other biological markers, we have developed two sensitive and specific liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays for quantitation of the benzene metabolites trans,transmuconic acid (t,t-MA), S-phenylmercapturic acid (S-PMA), hydroquinone (HQ), catechol (CAT), and for estimation of 1,2,4-trihydroxybenzene (BT). In our first assay, urinary S-PMA and t,t-MA were measured simultaneously by liquid chromatography-electrospray ionization-tandem mass spectrometry-selected reaction monitoring (LC-ESI-MS/MS-SRM) in the negative ionization mode. In this assay, the metabolites [13C6]-S-PMA and [13C6]-t,t-MA were used as internal standards. The efficacy of this specific assay was evaluated in human urine specimens from 28 smokers and 18 nonsmokers serving as the benzene-exposed and nonexposed groups, respectively. The coefficient of variation (CV) of analyses on different days (n = 8) for S-PMA was 7% for samples containing 9.4 micrograms/L urine, and for t,t-MA was 10% for samples containing 0.07 mg/L. The mean levels of S-PMA and t,t-MA in smokers were 1.9-fold (p = 0.02) and 2.1-fold (p = 0.03) higher, respectively, than those in nonsmokers.

The crystal structure of a multifunctional protein: phosphoglucose isomerase/autocrine motility factor/neuroleukin

Phosphoglucose isomerase (PGI) plays a central role in both the glycolysis and the gluconeogenesis pathways. We present here the complete crystal structure of PGI from Bacillus stearothermophilus at 2.3-A resolution. We show that PGI has cell-motility-stimulating activity on mouse colon cancer cells similar to that of endogenous autocrine motility factor (AMF). PGI can also enhance neurite outgrowth on neuronal progenitor cells similar to that observed for neuroleukin. The results confirm that PGI is neuroleukin and AMF. PGI has an open twisted alpha/beta structural motif consisting of two globular domains and two protruding parts. Based on this substrate-free structure, together with the previously published biological, biochemical, and modeling results, we postulate a possible substrate-binding site that is located within the domains' interface for PGI and AMF. In addition, the structure provides evidence suggesting that the top part of the large domain together with one of the protruding loops might participate in inducing the neurotrophic activity.

TCM differential treatment of 57 cases of chronic gastritis complicated by ulcerative colitis

57 cases of chronic gastritis complicated by ulcerative colitis were clinically observed. According to the TCM theory of differentiation of symptoms and signs, 4 types of the disease were divided and treated: 1) stagnation of qi in the liver, 2) dampness and heat in gastrointestinal tract, 3) asthenic cold in the spleen and stomach, and 4) coexistence of cold and heat. The therapeutic effects of chronic gastritis and ulcerative colitis were evaluated: 23 cases (40.3%) of chronic gastritis were cured and 28 cases (49.1%) improved; 25 cases (43.8%) of ulcerative colitis were cured and 28 cases (49.1%) improved. The effective rates were 89.5% and 93.0% respectively. The correlation between the therapeutic effects for these two diseases further demonstrates that their pathological mechanisms are closely interrelated, indicating that it is important to have these two diseases treated simultaneously.

Identification and characterization of the Escherichia coli-expressed RNA-dependent RNA polymerase of bamboo mosaic virus

Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. The open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that was postulated to be involved in the replication and the formation of cap structure at the 5' end of the viral genome. To characterize the activities associated with the 155-kDa viral protein, it was expressed in Escherichia coli BL21(DE3) cells with thioredoxin, hexahistidine, and S. Tag fused consecutively at its amino terminus, and the fusion protein was purified by metal affinity chromatography. Several RNA fragments, prepared by in vitro transcription, were tested as substrates for the RNA-dependent RNA polymerase (RdRp) activity. Among them, the expressed fusion enzyme was able to generate a 32P-labeled RNA product when 3'-end RNA fragments of the positive strand or negative strand of BaMV were included in the assay mixture. Dot hybridization assay revealed that the reaction products are complementary to their RNA substrates. Taken together, the evidence suggests that the 155-kDa protein encoded by ORF1 of BaMV has an RdRp activity and should be involved in the replication of BaMV. Mutational analyses demonstrate the importance of the GDD motif in the polymerase activity, and deletion studies suggest that the polymerase activity resides in the carboxyl terminus of the 155-kDa viral protein.

Mutational analysis of the conserved cationic residues of Bacillus stearothermophilus 6-phosphoglucose isomerase

The importance in catalysis of the conserved arginine (R207) and lysine residues (K144, K294, K356, and K425) of 6-phosphoglucose isomerase from Bacillus stearothermophilus was assessed by site-directed mutagenesis and kinetic analysis. In general mutations had minor effects on the Km for fructose 6-phosphate. More dramatic effects were seen on kcat. The R207A mutant had a five orders of magnitude decrease in kcat relative to the wild-type enzyme. There was a significant recovery, by three orders of magnitude, in the kcat for the R207K mutant. The results suggest that the positive charge provided by R207 plays a critical role in the isomerization reaction. K425 was substituted with alanine, valine, phenylalanine, tryptophan and aspartate. All mutant enzymes at position 425 had kcat decreased in the range of several-hundred-fold. For the other mutants, K294A and K144A, the kcat values were 3.5% and 27% of the wild-type enzyme, respectively. No effects on catalysis were observed for the K356A mutant. The results suggest that R207, K144, K294, and K425 are located in the active site of the enzyme. The active-site location and the catalytic roles of K425 and K294 are supported further by the inhibitory effects of pyridoxal 5'-phosphate on enzymatic activities. The data also confirm the importance of K425 and K144 anticipated by the affinity labeling studies of the corresponding residues by pyridoxal 5'-phosphate in pig muscle phosphoglucose isomerase.

Effect of trifluoromethyl ketone-based elastase inhibitors on neutrophil function in vitro

Neutrophils release elastase, which is known secondarily to cause tissue damage. However, it is rapidly inactivated by the endogenous alpha1-proteinase inhibitor (alpha1Pi). Nevertheless, under pathological conditions, alpha1i is inactivated by oxidants released from neutrophils, resulting in an excess of elastase at the site of inflammation. This elastase/alpha1Pi imbalance has been implicated as a pathogenic factor in cystic fibrosis, acute respiratory distress syndrome, and emphysema. Elastase inhibitors, which do not interfere with the microbicidal activity of neutrophils and are resistant to neutrophil-released oxidants, would undoubtedly represent an important advance in the management of neutrophil-mediated tissue injury. We report that a new family of elastase inhibitors ICI200355 and ZD0892 was found to be resistant toward superoxide, hypochlorous acid, hydrogen peroxide, hydroxyl radical, and peroxynitrite mediated degradation as well as having no effect on the formation of these oxidants by activated neutrophils. More importantly, we found that these inhibitors did not interfere with the ability of human neutrophils to phagocytose and to kill Staphylococcus aureus. In conclusion, a new potent class of elastase inhibitors, while blocking the effects of neutrophil elastase, was found not to impede various physiological functions of human neutrophils, in particular the ability of these phagocytic cells to phagocytose and kill bacteria.

Event-related brain potentials and case information in syntactic ambiguities

In an ERP study, German sentences were investigated that contain a case-ambiguous NP that may be assigned accusative or dative case. Sentences were disambiguated by the verb in final position of the sentence. As our data show, sentences ending in a verb that assigns dative case to the ambiguous NP elicit a clear garden-path effect. The garden-path effect was indicated by a broad centro-posterior negative shift that occurred between 300 and 900 msec after the dative-assigning verb was presented. No enhanced P600 following the misanalysis was observed. Noun phrases whose case ambiguity was resolved in favor of accusative case and unambiguously dative-marked NPs did not trigger significant ERP differences. We will discuss the implications of our results for parsing and its neuropsychological correlates. The results of this study support a parser design according to which the so-called structural case (nominative or accusative) is assigned without any delay in the absence of morpho-lexical counterevidence. It is argued that the enhancement of a negative ERP component with a "classical" N400 topography reflects the difficulty of reanalysis due to reaccessing morpho-lexical information that lies outside the domain of the parsing module. Consequently, ERP responses to garden-path effects are not confined to a late positivity but vary depending on the level of processing involved in reanalysis. The fact that garden-path effects may also elicit an N400 can be linked to the nonhomogeneous linguistic properties of the constructions from which they arise.

Collision tumor: a peripheral neuroepithelioma and a transitional-cell carcinoma occurring simultaneously in the renal pelvis

We report a unique case of a collision tumor of the kidney composed of a peripheral neuroepithelioma (PNE) and a transitional cell carcinoma (TCC) that occurred in a 67-year-old man with a long history of superficial TCC of both the bladder and bilateral upper urinary tracts. The PNE was composed of hyperchromatic, small, round cells, arranged in clusters and poorly cohesive sheets. Immunohistochemical studies revealed the small cells to be strongly positive for O13 (ie, a MIC2 gene product stain [CD99]) and vimentin. Electron microscopic examination found numerous interdigitating cell processes, multiple poorly formed cell-cell junctions, and dense-core granules. The latter were most conspicuous at the tips of the cell precesses. The PNE cells were clearly negative for cytokeratin, and they showed no transitional or intermediate features that would suggest evolution of the PNE from the adjacent TCC. The proximity of these two tumors appears to be serendipitous; thus, it can be considered a true collision tumor of the kidney.

Expression, purification, and crystallization of two isozymes of 6-phosphoglucose isomerase of Bacillus stearothermophilus

Two isozymes of 6-phosphoglucose isomerase (phosphoglucose isomerase A & phosphoglucose isomerase B), isolated from Bacillus stearothermophilus, have been overexpressed in Escherichia coli strain DF2145 and purified to homogeneity. Crystals of both isozymes have been obtained by the vapor diffusion method. The crystals of phosphoglucose isomerase A have unit cell dimensions a = b = 132.0 A, c = 183.6 A, and diffract to about 2.8 A resolution. An analysis of the reflection data indicates that the crystal system is hexagonal, space group P6122 or P6522. The crystals of phosphoglucose isomerase B complexed with 6-phosphogluconate belong to the orthorhombic space group I222 (or I212121), with cell dimensions a = 75.1 A, b = 95.7 A, c = 171.5 A, and diffract to a resolution of 2.3 A. These crystals promise to yield more detail for the substrate recognition and higher resolution structures of 6-phosphoglucose isomerase.