Extra costs for disabled people.
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Community Health Services↗
Biomedical subjects
R Hull
Publications and source records attributed to R Hull.
Sequence of rice hoja blanca tenuivirus RNA-2.
The sequence of rice hoja blanca tenuivirus RNA-2 is analysed and compared to its counter-part in rice stripe tenuivirus. The RNA encodes two proteins, in an ambisense arrangement. The 94 kD pc2, located in the complementary sense RNA, has several features typical of viral membrane (glyco)proteins, and also has regions of local homology to the glycoproteins of the Phleboviruses (Bunyaviridae). The 23 kD pv2 lies in the viral sense RNA and has two small conserved domains that are almost exclusively found in retro-viral membrane glycoproteins. Its genome location is analogous to the NSm protein of several of the Bunyaviridae species, which is thought to have a membrane-related function. The two open reading frames are separated by a large intergenic region which, in common with the other tenuivirus ambisense RNA segments, has a short region that is highly conserved between RStV and RHBV. The significance of these results with respect to the virus structure and gene expression is discussed.
Amino Acid Sequence↗
Rice tungro spherical virus: nucleotide sequence of the 3' genomic half and studies on the two small 3' open reading frames.
Rice tungro spherical virus (RTSV) consists of a single-stranded RNA genome of about 12 kilobases that contains one large open reading frame, ORF 1 and two small ORFs 2 and 3 at its 3' end (Shen et al., 1993, Virology 193:621-630); it was suggested that ORF 2 was expressed via a frameshift. To study the genomic information of RTSV and the variation between different RTSV isolates, the 3' half of a Philippine isolate and parts of a Thai and an Indian isolate were cloned and sequenced. Significant sequence differences were found in ORF 2 and in the 3' non-translated region. Additional stop codons have been revealed in the previously described ORF 2 in several independent clones from the three different virus isolates, the most conserved stop codon in the middle of ORF 2 being confirmed by direct RNA sequencing. These results suggest that ORF 2 could only express a peptide of about 5 kDa instead of 12 kDa as proposed earlier. Polyclonal antisera were raised against ORF 2 and 3 proteins as fusions with glutathione-S-transferase. Using these antisera we failed to detect any virus-specific peptides in extracts from infected rice plants and in virus preparations. The nucleotide sequence of the 3' end of our RTSV isolates contains several small ORFs and does not contain a repeat of 256 nucleotides found in the published sequence. These results indicate that RTSV could contain an unusually long 3' non-coding region of 1240 nucleotides in length.
Amino Acid Sequence↗
Rapid, small scale purification of rice hoja blanca and Echinochloa hoja blanca tenuivirus ribonucleoprotein.
Highly purified tenuivirus ribonucleoprotein was obtained from small amounts of leaf tissue by sedimenting the ribonucleoprotein particles from debris-free plant extract into a 30% sucrose cushion, in 1.5-mL microfuge tubes. Using this protocol, significant size differences were discovered in the double-stranded forms of the viral genomic RNAs of rice hoja blanca tenuivirus and a tenuivirus isolated from Echinochloa colonum, a common weed of rice cultivation.
Oryza↗
A rapid and easy method for DNA recovery from agarose gels using Wizard minicolumns.
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Biochemistry↗
Analysis of gram negative recolonization of the neuropathic bladder among patients with spinal cord injuries.
Over a 4 year period, 119 acute spinal cord injury (SCI) patients were enrolled in this study. The 101 males and 18 females had a mean age of 35.9 years (range 16-87). Sixty-two patients were tetraplegic and 57 were paraplegic. All patients had a urine specimen taken for culture, colony count and sensitivity once weekly while they were receiving intermittent catheterization. Of these, 22 patients (18.5%), none of whom had underlying genito-urinary (GU) pathology, developed recolonization by an organism of the same species and genus previously cultured. All 22 reached sterile-urine between colonizations after being treated with antibiotics for at least 7 days. The 16 males and six females had a mean age of 35.1 years (range 17-79). Sixteen were tetraplegic and six were paraplegic. Plasmid analysis (PA) was used to determine whether these recolonizations were from the same or from a different strain. In those instances where the bacteria harbored no plasmids or where the results of plasmid analysis were otherwise inconclusive, bacteria were also compared using restriction fragment length polymorphism (RFLP) analysis. Recolonization was caused primarily by E. coli and K. pneumoniae. While there was no significant difference between the two organisms with respect to the number of days when sterile urine occurred to the time when recolonization was observed, there were significant differences seen in both organisms with regard to the time lapse from one colonization to the next: the average number of days to recolonization with an identical organism was 10.3 days, whereas with a different strain it was 15.9 days (P < 0.04). When a different organism was cultured between the recolonizations, the mean recolonization interval was 17.9 days. When no intervening organism occurred, the interval was 9.5 days (P < 0.005). Both intervals measured the days from the first sterile urine after the first colonization to the next colonization. These data indicate the proclivity for two common Gram negative normal bowel inhabitants to recolonize the neuropathic bladder of spinal cord injured patients even after adequate treatment. PA and RFLP provide a means of discriminating between relapses by the same organism versus recurrences by a different organism of the same species and genus. Those with the same identity tend to recur sooner than those of different identities and may be suspected when relapse occurs within two weeks of cessation of 7 day course of antibiotics. While an intervening organism may delay the relapse (or recurrence), it does not prevent it and identical organisms can reappear even after adequate therapeutic regimens. Since none of the patients in this study had GU pathology, recolonization by an identical strain (relapse) does not necessarily warrant an extensive investigation for disease within the GU tract.
Adolescent↗
Incidence of deep-vein thrombosis in patients with fractures of the lower extremity distal to the hip.
Our purpose was to determine the incidence of deep-vein thrombosis (DVT) in patients who have had early operative fixation of fractures of the lower extremity distal to the hip. There is a high incidence of distal thrombosis in patients who have undergone early operative fixation of lower-extremity fractures. The incidence of DVT is higher with proximal extremity fractures than with distal extremity fractures. Most clots are occult and do not progress clinically. Given the high incidence of DVT with femoral and tibial plateau fractures, older age, and longer operating times, anticoagulation prophylaxis may be indicated. Ours was a prospective incidence study. All patients who had had early operative fixation of lower-extremity fractures were eligible (n = 176). Seventy-four were excluded based on specific criteria. The remaining 102 patients underwent lower-extremity venography an average of 9 days after operative fixation of their fractures (range 3-22 days). Eight patients had bilateral lower-extremity fractures. The patients were followed clinically for 6 weeks to identify complications related to venous disease. The overall incidence of clinically occult DVT was 28%. Of the represented fractures, 40% were of the femoral shaft (eight of 20), 43% of the tibial plateau (12 of 28), 22% of the tibial shaft (12 of 54), and 12.5% of the tibial plafond (one of eight). Four of the thrombi were proximal to the popliteal fossa. Four of the patients had clinical evidence of pulmonary embolism while in the hospital. One of them had objective confirmation on further testing. No patient had clinical evidence of pulmonary emboli as an outpatient by follow-up criteria. The incidence of DVT has not been determined for patients with early stabilization of lower-extremity fractures. This study suggests a higher DVT incidence in more proximal fractures, but little risk of embolization. Thrombus formation proximal to the popliteal fossa is rare. Older age, longer operating times, and longer times before fracture fixation all correlate with an increased incidence of DVT.
Adult↗
Variation in the genome of rice tungro bacilliform virus: molecular characterization of six isolates.
The DNA genomes of isolates of rice tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.
Base Sequence↗
Immunological characterization of rice tungro spherical virus coat proteins and differentiation of isolates from the Philippines and India.
Rice tungro spherical virus (RTSV) has an RNA genome of more than 12 kb with various features which classify it as a plant picornavirus. The capsid comprises three coat protein (CP) species, CP1, CP2 and CP3, with predicted molecular masses of 22.5, 22.0 and 33 kDa, respectively, which are cleaved from a polyprotein. In order to obtain information on the properties of these proteins, each was expressed in E. coli, purified as a fusion to the maltose-binding protein and used for raising a polyclonal antiserum. CP1, CP2 and CP3 with the expected molecular masses were detected specifically in virus preparations. CP3 is probably the major antigenic determinant on the surface of RTSV particles, as was shown by ELISA, Western blotting and immunogold electron microscopy using antisera obtained against whole virus particles and to each CP separately. In some cases, especially in crude extracts, CP3 antiserum detected several other proteins (40-42 kDa), which could be products of CP3 post-translational modification. No serological differences were detected between the three CPs from isolates from the Philippines, Thailand, Malaysia and India. The CP3-related 40-42 kDa proteins of the Indian RTSV isolate have a slightly higher electrophoretic mobility (42-44 kDa) and a different response to cellulolytic enzyme preparations, which allows them to be differentiated from south-east Asian isolates.
Antibodies, Viral↗
Position-dependent ATT initiation during plant pararetrovirus rice tungro bacilliform virus translation.
The expression of the rice tungro bacilliform virus open reading frame I was studied in transiently transfected protoplasts. Expression occurs despite the presence of a long leader sequence and the absence of a proper ATG initiation codon. Translation is initiated at an ATT codon. The efficiency of initiation in rice protoplasts depends strongly on the mechanism by which ribosomes reach this codon. From the effects of scanning-inhibiting structures inserted into different leader regions, it can be deduced that this mechanism is related to the ribosome shunt described for cauliflower mosaic virus 35S RNA. The process delivers initiation-competent ribosomes to the region downstream of the leader and is so precise that only the second of two potential start codons only 12 nucleotides apart is recognized. The ATT codon that is used when it is present downstream of the leader is hardly recognized as a start codon by ribosomes that reach it by scanning.
Base Sequence↗
Use of 33P for ribozyme assays: the safe way.
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Caulimovirus↗
"Rattlesnake" structure of a filamentous plant RNA virus built of two capsid proteins.
Elongated particles of simple RNA viruses of plants are composed of an RNA molecule coated with numerous identical capsid protein subunits to form a regular helical structure, of which tobacco mosaic virus is the archetype. Filamentous particles of the closterovirus beet yellow virus (BYV) reportedly contain approximately 4000 identical 22-kDa (p22) capsid protein subunits. The BYV genome encodes a 24-kDa protein (p24) that is structurally related to the p22. We searched for the p24 in BYV particles by using immunoelectron microscopy with specific antibodies against the recombinant p24 protein and its N-terminal peptide. A 75-nm segment at one end of the 1370-nm filamentous viral particle was found to be consistently labeled with both types of antibodies, thus indicating that p24 is indeed the second capsid protein and that the closterovirus particle, unlike those of other plant viruses with helical symmetry, has a "rattlesnake" rather than uniform structure.
Animals↗
Nucleotide sequence of the bean strain of southern bean mosaic virus.
The genome of the bean strain of southern bean mosaic virus (SBMV-B) comprises 4109 nucleotides and thus is slightly shorter than those of the two other sequenced sobemoviruses (southern bean mosaic virus, cowpea strain (SBMV-C) and rice yellow mottle virus (RYMV)). SBMV-B has an overall sequence similarity with SBMV-C of 55% and with RYMV of 45%. Three potential open reading frames (ORFs) were recognized in SBMV-B which were in similar positions in the genomes of SBMV-C and RYMV. However, there was no analog of SBMV-C and RYMV ORF 3. From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses.
Amino Acid Sequence↗
INR reporting in Canadian medical laboratories. Thrombosis Interest Group of Canada.
A written survey of all licensed medical laboratories in Canada performing coagulation testing was performed to investigate the level of knowledge and overall usage of the INR system for reporting prothrombin time results in medical laboratories. There was an overall response rate of 857 of 1,228 laboratories surveyed. Fifty-seven percent of responding laboratories utilized some format of INR reporting. The ISI of the individual thromboplastin utilized was known by 89% of laboratories. The ISI of the thromboplastin utilized was known to be specific for the particular reagent/instrument combination in 44% of cases. Fifty-five percent of client physicians preferred PT results to be reported in seconds while 42% desired an INR format. The situation in Canada is similar to the United States in that further education regarding the INR system for PT reporting is required by both medical laboratories and physicians.
Administration, Oral↗
Sequence comparison and classification of beet luteovirus isolates.
Three distinct sequence groups were found among partial nucleotide sequences of 38 isolates of beet western yellows virus (BWYV) and beet mild yellowing virus (BMYV) from Europe, Iran and the USA. The first group contains both sugar beet and oilseed rape specific isolates, and the differentiating characteristic linked to this host range specificity are 2 single base pair changes in a 1,200 nucleotide region of the genome. It is proposed that the European BWYV strains that can be transferred at low frequency between rape and sugar beet belong to this group. Also belonging to this group are the published BWYV sequences of Veidt et al. and of the California BWYV-ST9 isolate. The second group contains mostly rape-derived isolates which have an intergenic region highly distinct from that of group-1 isolates but similar polymerase and coat protein regions. It is proposed that the rape-specific BWYV isolates which cannot be transmitted to sugar beet belong to this group. The third group contains mostly beet-specific isolates from Southern Europe and Iran, and may be adapted to the Mediterranean climate and flora. It is distinct from groups 1 and 2 in all three genome regions investigated and its polymerase and intergenic regions are as much related to those of potato leafroll virus (PLRV) and curcurbit aphid borne yellows virus (CABYV) as they are to those of group-1 and group-2. On the basis of sequence similarities and established nomenclature it is proposed to use BWYV for groups 1 and 2 (BWYV-1 and BWYV-2 respectively) and to use BMYV for group-3 isolates, which are distinct enough from the other two groups to merit a separate nomenclature.
Amino Acid Sequence↗
Sequence of the PV2 gene of rice hoja blanca tenuivirus RNA-2.
Comparison of a partial sequence of rice hoja blanca tenuivirus RNA-2 with 40% similarity to rice stripe tenuivirus RNA-2 revealed regions of high local sequence homology at the 5' terminus, within the coding region (the pv2 gene), and in the intergenic region separating this gene from the other protein (pc2) encoded by this ambisense RNA. Analysis of the conserved regions of the pv2 protein identified two motifs found principally in viral membrane glycoproteins and six motifs found each in a wide variety of proteins. The possible significance of these results is discussed.
Amino Acid Sequence↗
Retroelements: propagation and adaptation.
Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.
Adaptation, Physiological↗
In vitro inhibition of Helicobacter pylori NCTC 11637 by organic acids and lactic acid bacteria.
In this study the effects of both pH and organic acids on Helicobacter pylori NCTC 11637 were tested. Lactobacillus acidophilus, Lact. casei, Lact. bulgaricus, Pediococcus pentosaceus and Bifidobacterium bifidus were assayed for their lactic acid production, pH and inhibition of H. pylori growth. A standard antimicrobial plate well diffusion assay was employed to examine inhibitory effects. Lactic, acetic and hydrochloric acids demonstrated inhibition of H. pylori growth in a concentration-dependent manner with the lactic acid demonstrating the greatest inhibition. This inhibition was due both to the pH of the solution and its concentration. Six strains of Lact. acidophilus and one strain of Lact. casei subsp. rhamnosus inhibited H. pylori growth where as Bifidobacterium bifidus, Ped. pentosaceus and Lact. bulgaricus did not. Concentrations of lactic acid produced by these strains ranged from 50 to 156 mmol l-1 and correlated with H. pylori inhibition. The role of probiotic organisms and their metabolic by-products in the eradication of H. pylori in vivo remains to be determined.
Acetates↗