Complete genome sequence of ornithogalum virus 3.

Ornithogalum thyrsoides, a widely cultivated bulbous ornamental plant endemic to South Africa, has significant commercial value as a pot plant and for the production of cut flowers. However, infection by viruses threatens the success of commercial cultivation, as symptoms negatively affect the appearance of the plant and flowers. To date, four Ornithogalum-infecting viruses have been reported. Complete genome sequence data are available for three of these viruses, but the genome of the potyvirus ornithogalum virus 3 (OV3) has not been fully sequenced. In this study, the complete sequence of OV3 was determined by high-throughput sequencing (HTS) and validated by Sanger sequencing. Based on recognition of protease cleavage patterns and multiple sequence alignments with closely related viruses, the polyprotein of OV3 was predicted to be proteolytically cleaved to produce 10 mature peptides containing domains conserved in members of the genus Potyvirus. Phylogenetic analysis and species demarcation criteria confirm the previous classification of OV3 as a member of a separate species in this genus. This is the first report of a complete genome sequence of OV3.

Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa.

The complete genome sequences of two newly identified genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) are described. Two isolates, GH11 (18671 nt) and GH30 (18576 nt) were sequenced and found to be less than 70 % similar to other South African GLRaV-3 variants. The genome organization of GH11 and GH30 is similar to that of previously described GLRaV-3 isolates. However, no corresponding open reading frame 2 (ORF2) could be identified. Phylogenetic analysis indicates that GH11 and GH30 cluster in a subgroup (group VI) that is separate from the previously described GLRaV-3 isolates and should be regarded as a different strain of GLRaV-3.

Sarcolemmal phospholipid fatty acid composition and permeability.

In this study, the mechanism of ischaemia-induced increased sarcolemmal permeability, as manifested by release of intracellular enzymes, was investigated. The role of changes in the sarcolemmal phospholipid bilayer in this process was evaluated by experimental modulation of the phospholipid fatty acid composition. The isolated perfused rat heart subjected to low-flow hypoxia, was used as a model of global ischaemia. Glucose as well as saturated (palmitate) and unsaturated (linoleate) long-chain fatty acids were used as substrates. Hearts perfused with palmitate or linoleate (1.5 mM, fatty acid/albumin ratio, 3.4) showed a significantly higher rate of lactate dehydrogenase release in both control and ischaemic conditions than hearts perfused with glucose (10 mM). Lactate dehydrogenase release in the fatty acid-perfused hearts was associated with a significant increase in the percentage unsaturation of the sarcolemmal phospholipid fatty acids. Glucose-perfused hearts, on the other hand, showed only minor changes in the sarcolemmal phospholipid fatty acid composition. Attempts to correlate enzyme release directly with an increase in the percentage unsaturation of phospholipid fatty acids failed, since enzyme release was also stimulated in control fatty-acid-perfused hearts which (when compared with glucose) contained a higher percentage saturated phospholipid fatty acids. The results suggest that myocardial ischaemia, apart from changes in the sarcolemmal phospholipid fatty acid composition, also induces several other changes in sarcolemmal composition (e.g., cholesterol loss) which may affect is permeability for macromolecules.

Portal vein anomaly and hepatic encephalopathy in a horse.

Periodic episodes of diffuse central nervous system disease occurred in a yearling Thoroughbred gelding that had a history of frequent respiratory tract disease and stunted growth. Hepatic encephalopathy was diagnosed on the basis of history, clinical signs, prolonged bromsulphalein clearance, and increased blood ammonia content. Because of the poor prognosis and recurrent clinical signs the horse was euthanatized. Necropsy revealed an arteriovenous anomaly and thrombosis of the portal vein. Histologically, there was diffuse primary astrocytosis of the brain.

A chronic wasting syndrome in a horse associated with granulomatous enteritis.

A case of granulomatous enteritis in a 2 year-old Thoroughbred colt is reported. Clinically the horse showed chronic wasting and subcutaneous oedema of the ventral parts of the body and legs. Grossly the wall of the jejunum and ileum was uniformly thickened. Microscopically the lamina propria, submucosa and the tunica muscalaris of the small intestine were infiltrated with lymphocytes, plasma cells, epithelioid cells and occasional multinucleated giant cells. The granulomatous reaction was most marked in the muscular layers of the gut wall.

Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus.

Accurate detection and quantitation of viruses can be beneficial to plant-virus interaction studies. In this study, three SYBR green real-time RT-PCR assays were developed to quantitate grapevine leafroll-associated virus 3 (GLRaV-3) in infected vines. Three genomic regions (ORF1a, coat protein and 3'UTR) were targeted to quantitate GLRaV-3 relative to three stably expressed reference genes (actin, GAPDH and α-tubulin). These assays were able to detect all known variant groups of GLRaV-3, including the divergent group VI, with equal efficiency. No link could be established between the concentration ratios of the different genomic regions and subgenomic RNA (sgRNA) expression. However, a significant lower virus concentration ratio for plants infected with variant group VI compared to variant group II was observed for the ORF1a, coat protein and the 3'UTR. Significant higher accumulation of the virus in the growth tip was also detected for both variant groups. The quantitation of viral genomic regions under different conditions can contribute to elucidating disease aetiology and enhance knowledge about virus ecology.

Mass needle stick injury in children from the Western cape.

Illegal dumping of contaminated medical waste occurs commonly in South Africa. There is little information on the management and outcome of the children exposed to and injured by medical waste. On 15 September 1999, 54 children where involved in a mass exposure incident. 44 presented the same evening and 10 following day. Used needles and syringes were discarded on their soccer field. Children gave one another injections and played darts with the discarded needles. Parents were counselled and blood was drawn for HIV and Hepatitis B virus (HBV) serology. All were given HBV vaccination (HBVV). Stat doses of zidovudine (ZDV) and lamivudine (LMV) were given to all with visible wounds or history of percutaneous injury. Younger children were given prophylaxis as we considered their histories unreliable. Further visits were conducted at the community clinic for patient convenience. Children were reviewed at weeks 1 and 3 for drug adherence and side effects. At week 4, the second HBVV was given. At 3 months and 6 months HIV and HBV serology were repeated. 18/44 (40 per cent) had entry wounds. 44/54 (81 per cent) were given antiretroviral treatment (ART). Initial screening for HIV was negative in all, 6 had antibodies to HBV surface antigen, and 2 were HBV surface antigen positive. At week 1 all patients on ART were seen but at week 3 only 30 (55 per cent) attended. 41 (75 per cent) attended at 4 weeks, 8 non-attendees being located by primary healthcare workers. At 3 months, none of the 35 (64 per cent) children had seroconverted for either virus. 44 (81 per cent) attended at 6 months and all serology was negative. All were also Hepatitis C negative. The exposure incident sensitized the community to HIV. Follow up of patients after mass exposure is difficult and time-consuming. Adherence to ART was poor and should be carefully monitored. ZDV was probably adequate for this incident. In a non-mobile community a 3 month visit unnecessary.

Response of the microbial community to copper oxychloride in acidic sandy loam soil.

AIMS: Determining the response of different microbial parameters to copper oxychloride in acidic sandy loam soil samples using cultivation-dependent and direct microscopic techniques. METHODS AND RESULTS: Culturable microbial populations were monitored for 245 days in a series of soil microcosms spiked with different copper oxychloride concentrations. Microbial populations responded differently to additional Cu. Protistan numbers and soil metabolic potential decreased. Experiments with more soil samples revealed that metabolic potential was not significantly affected by < or =100 mg kg(-1) additional Cu. However, a negative impact on protista was noted in soil containing only 15 mg kg(-1) EDTA-extractable Cu. The negative impact on protistan numbers was less severe in soils with a higher phosphorous and zinc content. CONCLUSIONS: Bacterial populations responded differently, and protista were most sensitive to elevated Cu levels. Protistan numbers in soil from uncultivated land were higher and seemed to be more sensitive to additional Cu than the numbers of these organisms in soil originating from cultivated land. SIGNIFICANCE AND IMPACT OF THE STUDY: Protistan sensitivity to small increases in Cu levels demonstrates the vulnerability of the soil ecosystem to Cu perturbations, especially when the importance of protista as link in the flow of energy between trophic levels is considered.

A 3-year cytogenetic survey of 9 661 patients in South Africa.

During the period 1 January 1977 - 31 December 1979, 9 661 patients underwent cytogenetic investigation at seven participating laboratories in South Africa. The chromosome data were coded using a standard protocol and the results tabulated, being listed according to the clinical signs which led to referral for investigation. Cytogenetic investigation was most commonly requested for prenatal studies, and 22% of the group's effort was directed towards this. One in 27 amniotic cell specimens was reported to have shown anomalous chromosomes, trisomy 21 being the most frequent abnormality. The majority of postnatal investigations were requested because congenital abnormalities suggested an underlying chromosomal defect. In 42,3% of 2 420 patients a chromosome defect was confirmed. Results of chromosome studies are tabulated by indication for referral and the findings summarized. This collaborative study gives an indication of the nature and frequency of chromosome disorders in South Africa.

Viral isolates during febrile neutropaenia in children with cancer.

We prospectively studied South African children with cancer for viral isolates during episodes of febrile neutropaenia. Viruses were found in seven (31.8 per cent) and bacteria in five (22.7 per cent) of 22 episodes. The most common isolate was the herpes simplex virus and the most common source was from nasopharyngeal aspirates. There was no dual detection of viral and bacterial isolates. This study emphasizes the important contribution of viruses to febrile neutropaenia.

A novel method for the preparation of substrate-free cytochrome P-450(11) beta.

A new method for the removal of the stabilizing substrate, deoxycorticosterone, from adrenal cytochrome P-450(11) beta, has been developed. Dextran coated charcoal is used for the adsorption of the steroid and the adsorbed steroid is separated from the cytochrome P-450-preparation by low speed centrifugation. The substrate-free enzyme, obtained in this manner, has all the characteristic spectral properties of low-spin cytochrome P-450(11) beta and may be converted to the high-spin form by the addition of deoxycorticosterone. The dextran coated charcoal method has the following advantages over the previously used method of substrate removal. It does not require the addition of the cofactors for cytochrome P-450-dependant hydroxylation of deoxycorticosterone, small amounts of enzyme may be prepared in a short time and the enzyme preparation is not diluted to any great extent during the process.