An analysis by metabolic labelling of the encephalomyocarditis virus ribosomal frameshifting efficiency and stimulators.

Programmed -1 ribosomal frameshifting is a mechanism of gene expression whereby specific signals within messenger RNAs direct a proportion of ribosomes to shift -1 nt and continue translating in the new reading frame. Such frameshifting normally depends on an RNA structure stimulator 3'-adjacent to a 'slippery' heptanucleotide shift site sequence. Recently we identified an unusual frameshifting mechanism in encephalomyocarditis virus, where the stimulator involves a trans-acting virus protein. Thus, in contrast to other examples of -1 frameshifting, the efficiency of frameshifting in encephalomyocarditis virus is best studied in the context of virus infection. Here we use metabolic labelling to analyse the frameshifting efficiency of wild-type and mutant viruses. Confirming previous results, frameshifting depends on a G_GUU_UUU shift site sequence and a 3'-adjacent stem-loop structure, but is not appreciably affected by the 'StopGo' sequence present ~30 nt upstream. At late timepoints, frameshifting was estimated to be 46-76 % efficient.

Protein-directed ribosomal frameshifting temporally regulates gene expression.

Programmed -1 ribosomal frameshifting is a mechanism of gene expression, whereby specific signals within messenger RNAs direct a proportion of translating ribosomes to shift -1 nt and continue translating in the new reading frame. Such frameshifting normally occurs at a set ratio and is utilized in the expression of many viral genes and a number of cellular genes. An open question is whether proteins might function as trans-acting switches to turn frameshifting on or off in response to cellular conditions. Here we show that frameshifting in a model RNA virus, encephalomyocarditis virus, is trans-activated by viral protein 2A. As a result, the frameshifting efficiency increases from 0 to 70% (one of the highest known in a mammalian system) over the course of infection, temporally regulating the expression levels of the viral structural and enzymatic proteins.

Characterization of Ribosomal Frameshifting in Theiler's Murine Encephalomyelitis Virus.

Theiler's murine encephalomyelitis virus (TMEV) is a member of the genus Cardiovirus in the Picornaviridae, a family of positive-sense single-stranded RNA viruses. Previously, we demonstrated that in the related cardiovirus, Encephalomyocarditis virus, a programmed-1 ribosomal frameshift (1 PRF) occurs at a conserved G_GUU_UUU sequence within the 2B-encoding region of the polyprotein open reading frame (ORF). Here we show that-1 PRF occurs at a similar site during translation of the TMEV genome. In addition, we demonstrate that a predicted 3= RNA stem-loop structure at a noncanonical spacing downstream of the shift site is required for efficient frameshifting in TMEV and that frameshifting also requires virus infection. Mutating the G_GUU_UUU shift site to inhibit frameshifting results in an attenuated virus with reduced growth kinetics and a small-plaque phenotype. Frameshifting in the virus context was found to be extremely efficient at 74 to 82%, which, to our knowledge, is the highest frameshifting efficiency recorded to date for any virus. We propose that highly efficient-1 PRF in TMEV provides a mechanism to escape the confines of equimolar expression normally inherent in the single-polyprotein expression strategy of picornaviruses.

Recombinant antigens based on toxins A and B of Clostridium difficile that evoke a potent toxin-neutralising immune response.

Infection with the bacterium Clostridium difficile causes symptoms ranging from mild to severe diarrhoea with life-threatening complications and remains a significant burden to healthcare systems throughout the developed world. Two potent cytotoxins, TcdA and TcdB are the prime mediators of the syndrome and rapid neutralisation of these would afford significant benefits in disease management. In the present study, a broad range of non-toxic, recombinant fragments derived from TcdA and TcdB were designed for soluble expression in E. coli and assessed for their capacity to generate a potent toxin-neutralising immune response as assessed by cell-based assays. Significant differences between the efficacies of isolated TcdA and TcdB regions with respect to inducing a neutralising immune response were observed. While the C-terminal repeat regions played the principal role in generating neutralising antibodies to TcdA, in the case of TcdB, the central region domains dominated the neutralising immune response. For both TcdA and TcdB, fragments which comprised domains from both the central and C-terminal repeat region of the toxins were found to induce the most potent neutralising immune responses. Generated antibodies neutralised toxins produced by a range of C. difficile isolates including ribotype 027 and 078 strains. Passive immunisation of hamsters with a combination of antibodies to TcdA and TcdB fragments afforded complete protection from severe CDI induced by a challenge of bacterial spores. The results of the study are discussed with respect to the development of a cost effective immunotherapeutic approach for the management of C. difficile infection.

An essential fifth coding ORF in the sobemoviruses.

The sobemoviruses have one of the smallest of all known RNA virus genomes. ORF1 encodes P1 which plays a role in suppression of silencing and virus movement, ORFs 2a and 2b encode the replicational polyproteins P2a and P2ab, and ORF3 encodes the coat protein. Translation of ORF2a from the genomic RNA is dependent on a leaky scanning mechanism. We report the presence of an additional ORF (ORFx), conserved in all sobemoviruses. ORFx overlaps the 5' end of ORF2a in the +2 reading frame and also extends some distance upstream of ORF2a. ORFx lacks an AUG initiation codon and its expression is predicted to depend on low level initiation at near-cognate non-AUG codons, such as CUG, by a proportion of the ribosomes that are scanning the region between the ORF1 and ORF2a initiation codons. Mutations that disrupt translation of ORFx in turnip rosette virus prevent the establishment of infection.

A GIS-based methodology for predicting walking track stability.

To manage extensive walking track (trail) systems effectively, managers need information about the condition, stability and likely rates of deterioration of tracks. This information may be impractical to obtain from ground inspections, particularly if the track systems of interest encompass hundreds or even thousands of kilometres of tracks. Two trials were undertaken in Tasmania, Australia to assess the practicality of using a GIS-based methodology to predict track 'types', types being classes of environmental and track-orientation variables that are associated with characteristic rates of widening and erosion as tracks develop. In the first trial, type values previously measured at 500 18 m long monitoring sites located across a wide range of environments were compared with those predicted for 50-75 m long track segments that included or overlapped the sites. In the second trial, the type values of 300 75 m track segments distributed across five tracks were measured in the field and predicted using a refined version of the methodology. The reliability of the methodology was slightly improved in the second trial, in which 50% of the predictions were accurate and 38% were out by one category. Predictions of the statistical distribution of types were prone to bias due to local conditions on individual tracks, but agreed closely with the measured distribution across the entire data set. The methodology was used to assess track types across the 1700 km track system managed by the Tasmanian Parks and Wildlife Service, as a basis for identifying and prioritising management responses including track stabilisation works. It is likely that with further refinement and with better GIS information, the methodology could reliably predict the stability of individual tracks.

Development and evaluation of an ovine antibody-based platform for treatment of Clostridium difficile infection.

Treatment of Clostridium difficile is a major problem as a hospital-associated infection which can cause severe, recurrent diarrhea. The currently available antibiotics are not effective in all cases and alternative treatments are required. In the present study, an ovine antibody-based platform for passive immunotherapy of C. difficile infection is described. Antibodies with high toxin-neutralizing titers were generated against C. difficile toxins A and B and were shown to neutralize three sequence variants of these toxins (toxinotypes) which are prevalent in human C. difficile infection. Passive immunization of hamsters with a mixture of toxin A and B antibodies protected them from a challenge with C. difficile spores in a dose-dependent manner. Antibodies to both toxins A and B were required for protection. The administration of toxin A and B antibodies up to 24 h postchallenge was found to reduce significantly the onset of C. difficile infection compared to nonimmunized controls. Protection from infection was also demonstrated with key disease isolates (ribotypes 027 and 078), which are members of the hypervirulent C. difficile clade. The ribotype 027 and 078 strains also have the capacity to produce an active binary toxin and these data suggest that neutralization of this toxin is unnecessary for the management of infection induced by these strains. In summary, the data suggest that ovine toxin A and B antibodies may be effective in the treatment of C. difficile infection; their potential use for the management of severe, fulminant cases is discussed.

Expression, purification and cell cytotoxicity of actin-modifying binary toxin from Clostridium difficile.

Clostridium difficile infection (CDI) is a serious problem within the healthcare environment where the bacterium causes symptoms ranging from mild diarrhoea to life-threatening colitis. In addition to its principal virulence factors, Toxin A and Toxin B, some C. difficile strains produce a binary toxin (CDT) composed of two sub-units namely CDTa and CDTb that are produced and secreted from the cell as two separate polypeptides. Once in the gut these fragments have the potential to combine to form a potent cytotoxin whose role in the pathogenesis of CDI is presently unclear. Here, we describe expression and purification methods for recombinant CDTa and CDTb produced in Escherichia coli. We show that purified CDTa and CDTb can combine to form an active CDT which is cytotoxic to Vero cells. In addition, the purification processes described will allow milligram quantities of binary toxin fragments to be produced for further functional and structural studies.

Deletion of the SH gene from avian metapneumovirus has a greater impact on virus production and immunogenicity in turkeys than deletion of the G gene or M2-2 open reading frame.

Subgroup A avian metapneumoviruses lacking either the SH or G gene or the M2-2 open reading frame were generated by using a reverse-genetics approach. The growth properties of these viruses were studied in vitro and in vivo in their natural host. Deletion of the SH gene alone resulted in the generation of a syncytial-plaque phenotype and this was reversed by the introduction of the SH gene from a subgroup B, but not a subgroup C, virus. Infected turkeys were assessed for antibody production and the presence of viral genomic RNA in tracheal swabs. The virus with a deleted SH gene also showed the greatest impairment of replication both in cell culture and in infected turkeys. This contrasts with the situation with other pneumoviruses in culture and in model animals, where deletion of the SH gene results in little effect upon viral yield and a good antibody response. Replication of the G- and M2-2-deleted viruses was impaired more severely in turkeys than in cell culture, with only some animals showing evidence of virus growth and antibody production. There was no correlation between virus replication and antibody response, suggesting that replication sites other than the trachea may be important for induction of antibody responses.

Avian metapneumovirus SH gene end and G protein mutations influence the level of protection of live-vaccine candidates.

A prototype avian metapneumovirus (AMPV) vaccine (P20) was previously shown to give variable outcomes in experimental trials. Following plaque purification, three of 12 viruses obtained from P20 failed to induce protection against virulent challenge, whilst the remainder retained their protective capacity. The genome sequences of two protective viruses were identical to the P20 consensus, whereas two non-protective viruses differed only in the SH gene transcription termination signal. Northern blotting showed that the alterations in the SH gene-end region of the non-protective viruses led to enhanced levels of dicistronic mRNA produced by transcriptional readthrough. A synthetic minigenome was used to demonstrate that the altered SH gene-end region reduced the level of protein expression from a downstream gene. The genomes of the remaining eight plaque-purified viruses were sequenced in the region where the P20 consensus sequence differed from the virulent progenitor. The seven protective clones were identical, whereas the non-protective virus retained the virulent progenitor sequence at two positions and contained extensive alterations in its attachment (G) protein sequence associated with a reduced or altered expression pattern of G protein on Western blots. The data indicate that the efficacy of a putative protective vaccine strain is affected by mutations altering the balance of G protein expression.

Development of a reverse-genetics system for Avian pneumovirus demonstrates that the small hydrophobic (SH) and attachment (G) genes are not essential for virus viability.

Avian pneumovirus (APV) is a member of the genus Metapneumovirus of the subfamily Pneumovirinae. This study describes the development of a reverse-genetics system for APV. A minigenome system was used to optimize the expression of the nucleoprotein, phosphoprotein, M2 and large polymerase proteins when transfected into Vero cells under the control of the bacteriophage T7 promoter. Subsequently, cDNA was transcribed from the virion RNA to make a full-length antigenome, which was also cloned under the control of the T7 promoter. Transfection of the full-length genome plasmid, together with the plasmids expressing the functional proteins in the transcription and replication complex, generated APV in the transfected cells. The recombinant virus was passaged and was identified by cytopathic effect (CPE) that was typical of APV, the presence of a unique restriction-endonuclease site in the cDNA copy of the genome and immunofluorescence staining with anti-APV antibodies. Replacement of the full-length wild-type antigenome with one lacking the small hydrophobic (SH) protein and the attachment (G) genes generated a virus that grew more slowly and produced atypical CPE with syncytia much larger than those seen with wild-type virus.

[Core promoter mutations of HBV isolated from patients with chronic hepatitis B in Guangxi].

OBJECTIVE: To explore the relationship between HBV core promoter mutations and liver damage or HBeAg status. METHODS: Nested polymerase chain reaction (nPCR) was used for amplification of HBV DNA core promoter in 59 sera from patients with chronic hepatitis B in Guangxi, then the HBV DNA positive products were sequenced by direct sequencing. RESULTS: The HBV DNA positive rate of was 59.3%(35/59). All the patients were infected by mutants. The commonest mutation was the double mutation (A --> T at nt1762 and G --> A at nt1764), counting for 57.1% (20/35). The next was C --> G at nt1799, counting for 54.4% (19/35), but this was no function. A --> G at nt1752 (resulting in isoleucine to valine) was seen in 37.1% (13/35) of the HBV DNA positive patients, and T --> C at nt1753 was seen in 20% (7/35). The significant difference in the frequency of T1762A1764 mutant was found between HBeAg positive patients (31.3%) and negative patients (79.0%). CONCLUSIONS: HBV core promoter mutations are common among patients with chronic hepatitis B in Guangxi. T1762A1764 mutant is associated with HBeAg status and chronic hepatitis.

[Prevalence of hepatitis B virus core promoter mutant isolated from asymptomatic carriers from areas with higher and lower incidence of hepatocellular carcinoma in Guangxi].

OBJECTIVE: To understand the prevalence of HBV core promoter mutant (T1762 A1764 mutant) isolated from asymptomatic carriers from areas with higher and lower incidence of hepatocellular carcinoma (HCC) in Guangxi. METHODS: A nested polymerase chain reaction (nPCR) was used for amplification of HBV DNA core promoter in sera, and then HBV DNA nPCR products were sequenced by direct sequencing. RESULTS: The results show that 50.6% (39/77) of all HBV asymptomatic carriers were positive for HBV DNA HBV DNA positive rates of the samples from HCC higher incidence area, Longan County, and from lower incidence area, Guilin city were 55.6% (20/36) and 46.3% (19/41), respectively. HBV core promoter mutants could be seen in 35% in Longan positive samples and 47.4% in Guilin. The common mutations in both regions were all double mutations (nt 1,762 A-->T; nt 1,764 G-->A), accounting for 25% and 21%, respectively. The difference of the double mutant between Longan County and Guilin city was not significant (P>0.05). CONCLUSIONS: These data implicated that the prevalence of HBV core promoter mutant isolated from asymptomatic carriers may not be correlated with the incidence of HCC in Guangxi.

Isolation of the gene and large-scale expression and purification of recombinant Erythrina cristagalli lectin.

Using polymerase chain reaction, the coding sequence for Erythrina cristagalli lectin (ECL) has been cloned and expressed in Escherichia coli. The amplified DNA sequence of ECL is highly homologous to that previously reported for Erythrina corallodendron lectin (ECorL), confirming the absence of introns in the ECL gene. The polypeptide sequences of ECL and ECorL have been compared and five amino acids have been identified that differentiate the two proteins. Recombinant E. cristagalli lectin (recECL) was expressed in E. coli from a genomic clone encoding the mature E. cristagalli lectin gene. Constitutive expression localised recombinant protein in inclusion bodies, which were solubilised, and recECL, subsequently refolded and purified by lactose affinity chromatography. Significant advantages were observed for purification from inclusion bodies rather than from a clone optimised to express soluble protein. A large-scale purification scheme has been developed that can prepare functional recECL from inclusion bodies with a yield of 870 mg/l culture. By the range of characterisation methods employed in this study, it has been demonstrated that recECL is functionally equivalent to native ECL obtained from the E. cristagalli plant. In addition, characterisation of the binding of radiolabelled recECL to cultured dorsal root ganglia demonstrated that recECL binds to a single pool of receptors.

Gene expression in HCV-associated hepatocellular carcinoma--upregulation of a gene encoding a protein related to the ubiquitin-conjugating enzyme.

BACKGROUND/AIMS: To investigate gene expression in HCV-associated human hepatocellular carcinomas (HCC) by identifying up- and down-regulated genes. METHODS: Differential display RT-PCR was used to compare levels of gene expression in tumorous and non-tumorous tissues from the same livers. Differential expression was confirmed using a ribonuclease protection assay (RPA). The relative expression levels of one candidate gene were studied in various normal tissues and malignant cell lines using a multiple tissue expression (MTE) array. Further characterisation of this gene was carried out using nucleotide sequence analysis programmes and Northern hybridisation. RESULTS: Fifty-two differentially expressed cDNA fragments were identified and 29 were cloned, sequenced and compared with the nucleotide sequence database. RPA confirmed reproducibly that one particular cDNA was upregulated in the tumour cells. Analysis using the MTE array revealed that this selected candidate gene is expressed at high levels in various human tumour cell lines. The expression levels in HCV-associated HCC were higher than in other tumours. Investigation revealed that this novel gene lies on chromosome 17. The transcript is approximately 2.5 kb in size and encodes a protein similar to the ubiquitin-conjugating enzyme. CONCLUSIONS: The ubiquitin system may be involved in HCV-related hepatocarcinogenesis and in the development of other cancers.

Core promoter mutations (A(1762)T and G(1764)A) and viral genotype in chronic hepatitis B and hepatocellular carcinoma in Guangxi, China.

Hepatitis B viruses (HBV) with core promoter mutations (A(1762)T, G(1764)A) were found in a previous study to be highly prevalent in patients from Guangxi, China with hepatocellular carcinoma (HCC). The aim of this study was to determine whether the mutations are prevalent in areas of Guangxi with high and lower incidences of HCC and whether they are associated with other severe sequelae of chronic hepatitis B, including the development of cirrhosis. In addition, the genotypes of the various HBV sequences were determined. Core promoter mutations were significantly more common in HCC patients than asymptomatic carriers from both regions of Guangxi and also were common in patients with cirrhosis and chronic hepatitis. The data also support the hypothesis that genotype C HBV causes more severe liver disease than does genotype B.

Expression and purification of catalytically active, non-toxic endopeptidase derivatives of Clostridium botulinum toxin type A.

Clostridium botulinum neurotoxin type A is a potently toxic protein of 150 kDa with specific endopeptidase activity for the SNARE protein SNAP-25. Proteolytic cleavage of BoNT/A with trypsin leads to removal of the C-terminal domain responsible for neuronal cell binding. Removal of this domain result in a catalytically active, non-cell-binding derivative termed LH(N)/A. We have developed a purification scheme to prepare LH(N)/A essentially free of contaminating BoNT/A. LH(N)/A prepared by this scheme retains full enzymatic activity, is stable in solution, and is of low toxicity as demonstrated in a mouse toxicity assay. In addition, LH(N)/A has minimal effect on release of neurotransmitter from a primary cell culture model. Both the mouse bioassay and in vitro release assay suggest BoNT/A is present at less than 1 in 10(6) molecules of LH(N)/A. This represents a significant improvement on previously reported figures for LH(N)/A, and also the light chain domain, previously purified from BoNT/A. To complement the preparation of LH(N)/A from holotoxin, DNA encoding LH(N)/A has been introduced into Escherichia coli to facilitate expression of recombinant product. Expression and purification parameters have been developed to enable isolation of soluble, stable endopeptidase with a toxicity profile enhanced on that of LH(N)/A purified from BoNT/A. The recombinant-derived material has been used to prepare antisera that neutralise a BoNT/A challenge. The production of essentially BoNT/A-free LH(N)/A by two different methods and the possibilities for exploitation are discussed.

[The prevalence of hepatitis B virus precore mutant isolated from asymptomatic carriers in Guangxi].

OBJECTIVE: In order to understand the prevalence of hepatitis B virus (HBV) precore mutants isolated from asymtomatic carriers in Guangxi. METHODS: Nested polymerase chain reaction (nPCR) was used for amplification of HBV DNA precore in 77 carrier sera, followed by HBV DNA nPCR products sequencing using direct sequencing. RESULTS: 50.7% of 77 carriers was positive for HBV DNA with a prevalence of mutants 22.1% (17/77). HBV DNA positive rate in the southern part of the autonomous region was 55.6% (20/36). Six of them were mutants, counting for 30%. The common mutation in the southern part was seen T-->C at nt1858 while nt1896 stop mutation was discovered in one sample only, which was accompanied by point mutation at nt1837 (A-->G). HBV DNA positive rate in the northern part was 46.3% (19/41) with 11 of them were mutants, counting for 57.9%. The common mutation in that area stopped at nt1896. Among samples with stopped mutation, 4 samples had mutation at nt1846 (A-->T), 2 samples at nt1862 (G-->T). Both mutation at nt1856 (C-->T) and nt1858 (T-->C) could be seen in sample 734. CONCLUSIONS: The prevalence of HBV precore mutant in asymptomatic carriers in Guangxi was at the average level in China. Further study is needed to determine the difference between the southern and the northern part of the region in the common type of mutation exists.

Sequence Analysis of ORF3 and Partial ORF1 Region from Two Patients Infected with New Genotype of Hepatitis E Virus(HEV) / 中国病毒学

ORF3 and partial ORF1 regions were amplified with RT-PCR f rom two patients (T1 and T11)infected with new genotype of hepatitis E Virus. Th e PCR products were cloned and sequenced. The results showed that G-C rich regi on in ORF3 was deleted when amplified with normal PCR reaction. However, PCR rea ction containing G-C melt solution can overcome this problem. The sequence anal ysis showed that T1 and T11 belong to a new genotype of HEV which differs from g enotype I,II and III reported.T1 and T11 have 79%～82%, 80%～81% and 83%～85% id entical to genotype I,II and III respectively.