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Inadequate disease control on citrus foliage and fruit is often attributed to insufficient fungicide spray deposition on target surfaces. This study describes a novel spray deposition assessment protocol and determines deposition benchmarks indicative of the biological effectiveness for better interpretation of spray deposition results. Suitability of a yellow fluorescent pigment as tracer for copper oxychloride deposition was demonstrated through its similar particle concentration and size. Spray deposition assessment of spray targets, which were sprayed with a mixture that included the fluorescent pigment, involved photomacrography of whole leaf or fruit surfaces, followed by digital image analyses. This protocol proved to be very accurate in determining the quantity and quality of deposition. To determine deposition benchmarks, detached young ‘Nova’ mandarin leaves were sprayed with copper oxychloride and fluorescent pigment at different concentrations (0.1–2 times the recommended concentration) and spray deposition assessed. Subsequently, leaves were spray inoculated with a spore suspension of Alternaria alternata [causal agent of Alternaria brown spot (ABS) of mandarins], moist-incubated for c. 48 h and symptom expression rated. A very good linear relationship was found between fungicide concentration, leaf area covered by fluorescent pigment particles (%FPC) (r = 0.879) and Cu residue analysis (r = 0.992). A von Bertalanffy growth curve best fitted the relation between ABS control and deposition quantity (%FPC) data (91% of the percentage variance accounted for) with a good correlation between observed and predicted values (r = 0.825). Benchmarks for 50% and 75% disease control were calculated as 2.07 %FPC and 4.14 %FPC, respectively. These corresponded with Cu residue levels of 59.4 and 91.0 mg kg−1, respectively. These FPC benchmarks can be used to evaluate spray technology research, specifically for control of ABS and similar citrus fruit and foliar diseases.

Abnormal gastrointestinal permeability has been linked to irritable bowel syndrome (IBS). The lactulose-to-mannitol ratio is traditionally used to assess small intestine permeability while sucralose and sucrose are used to assess colonic and gastric permeability respectively. We used a single 4-probe test solution to assess permeability throughout the gastrointestinal tract in IBS patients and healthy controls by measuring the recovery of the probes in urine after ingestion using a modified liquid chromatography mass spectrometry protocol.Fasting participants (N=59) drank a permeability test solution (100ml: sucralose, sucrose, mannitol, and lactulose). Urine was collected over a 5-h period and kept frozen until analysis. Urinary sugar concentrations were measured using a liquid chromatography/triple quadruple mass spectrometer.Colonic permeability was significantly lower in IBS patients when compared to healthy controls (p=0.011). Gastric and small intestinal permeability did not significantly differ between the groups.The study demonstrates the clinical potential of this non-invasive method for assessing alterations in gastrointestinal permeability in patients with IBS.

Ascospores are the most important inoculum source of citrus black spot (CBS), caused by Guignardia citricarpa, but pseudothecium maturation and ascospore release are inadequately studied. Guignardia ascospore trapping and concomitant weather data were obtained for three localities over three seasons (July to March 2006 to 2009) in the Limpopo province of South Africa. Degree-days accumulated until first seasonal ascospore discharge (>10°C with 1 July as biofix) (DDtemp), and DDtemp accumulated on rainy (rainfall >0.1 mm) (DDrain) and moist days (vapor pressure deficit 2 = 0.608 and 0.658, respectively). Both models predicted a delay in pseudothecium maturation in climates with colder winters and springs. A Gompertz equation was also used to predict the proportion of Guignardia ascospores trapped (PAT) per season from DDtemp data accumulated on wet or moist days (DDwet2) from the first seasonal ascospore discharge [PAT = exp(–4.096 × exp(–0.005 × DDwet2); R2 = 0.908]. The PAT model predicted lag phases and 7-day peaks in ascospore release patterns with reasonable accuracy. These models can be used to predict the onset and dynamics of ascospore release in climatically diverse regions.

Imazalil (IMZ) is widely used in citrus packhouses to manage green mould, caused by Penicillium digitatum . The aim of this study was to investigate green mould control efficacy of IMZ applied in a wax coating, and the combination of aqueous dip and coating IMZ applications. Single application of IMZ at 3000 μg mL −1 in carnauba wax coating at rates of 0.6, 1.2 and 1.8 L tonne −1 of fruit gave better protective (mean 13% infection) than curative (mean 70% infection) control of the sensitive isolate. Imazalil residue levels increased (0.85 to 1.75 μg g −1 ) with increasing coating load. However, the resistant isolate could not be controlled (>74% infection). Dip only treatment (IMZ sulphate at 500 μg mL −1 for 45 s and 90 s) gave good curative control (≈77%) of the sensitive isolate at residue loading of 0.12–0.73 μg g −1 . Wax coating only treatment (IMZ at 3000 μg mL −1 at 1.8 L wax tonne −1 ) gave good protective control and improved sporulation inhibition (≈80%) at residue loading of 1.32–7.09 μg g −1 . The MRL of 5 μg g −1 was exceeded at higher wax loads on navels and clementines. Double application with dip (45 s in IMZ sulphate at 500 μg mL −1 ) followed by 2000 μg mL −1 IMZ in wax coating at 0.6, 1.2 and 1.8 L wax tonne −1 resulted in residue loading of 1.42 to 2.83 μg g −1 , increased protective control (≈69%) as well as curative control (≈83%). In all treatments, poor curative and protective control of the resistant isolate was observed (

Green mould, caused by Penicillium digitatum, is responsible for major postharvest fruit losses on the South African fresh citrus export market. Some of these losses as well as fungicide resistance development can be attributed to sub-optimal imazalil (IMZ) residue loading on citrus fruit (

Botrytis cinerea causes severe losses of rooibos seedlings in the Clanwilliam region of the Western Cape of South Africa. A total of 207 isolates were collected from diseased seedlings representing five nurseries. The cryptic species status of these isolates was determined with restriction enzyme analysis of the Bc-hch gene with 206 of the isolates identified as B. cinerea and one isolate as B. pseudocinerea. Analysis of the B. cinerea populations using seven microsatellite loci revealed a high total gene diversity (H), with a mean of 0.67. Analysis of molecular variance indicated that 97 % of the total genetic variation is distributed within subpopulations. Genotype flow was evident between nurseries indicated by shared occurrence of clonal lineages, in agreement with the relatively low but significant population differentiation between nurseries (mean F ST = 0.030, P = 0.001). The distribution of the mating type alleles MAT1-1 and MAT1-2 differed significantly from the ratio of 1:1 for the total population and in two of the five nursery subpopulations. Together with significant linkage disequilibrium found, populations appear to mainly reproduce asexually. Fungicide resistance frequency against iprodione for 198 of the genotyped isolates, showed highly varying levels of resistance between the nurseries. The mean incidence of resistance towards iprodione was 44 % in total, ranging from 0 % to 81 % for the five nurseries. This study has shown an adaptive capacity to overcome current chemical means of control in the studied B. cinerea population.

High volumes of copper hydroxide, cuprous oxide and copper oxychloride were sprayed under natural conditions onto mature orange trees to compare the retention on citrus leaves and fruit over a period of 56 days by means of copper residue analyses and a spray deposition assessment protocol using fluorometry, photomacrography and digital image analyses. Rainfall and increase in fruit size were also recorded to determine if it had an influence on weathering of copper residues. Initial retention following application of the different fungicides differed on Valencia leaves and fruit: applications with cuprous oxide retained significantly more copper residue and fluorescent pigment, while copper hydroxide retained higher copper and pigment levels on Navel leaves and fruit. Nonetheless, persistence of copper residues deposited by the three copper fungicide formulations was similar and decreased at the same tempo during both seasons; initially a fast reduction (48 and 60% for year one and two respectively) in residue during the first 14 days followed by a more gradual decline (41 and 24% for year one and two respectively) from 14 to 56 days. The loss of copper residues was attributed to weathering (days after treatment), fruit growth and cumulative rainfall as these factors were inversely correlated with copper residue levels (Pearson's r = −0.840, −0.722 and −0.733 respectively). A 76% and 90% correlation was observed between the copper residue analyzed and the quantitative fluorescent pigment measurements on mature leaves and fruit, respectively; showing that fruit is more reliable for fluorometry analyses and that this technique proved to be an effective tool for spray deposition and persistence assessment of copper fungicides. All copper formulations tested at these registered rates at 35-day spray intervals were effective in controlling Guignardia citricarpa .

The gene expression platform assay allows for robust and highly reproducible quantification of the expression of up to 800 transcripts (mRNA or miRNAs) in a single reaction. The miRNA assay counts transcripts by directly imaging and digitally counting miRNA molecules that are labeled with color-coded fluorescent barcoded probe sets (a reporter probe and a capture probe). Barcodes are hybridized directly to mature miRNAs that have been elongated by ligating a unique oligonucleotide tag (miRtag) to the 3' end. Reverse transcription and amplification of the transcripts are not required. Reporter probes contain a sequence of six color positions populated using a combination of four fluorescent colors. The four colors over six positions are used to construct a gene-specific color barcode sequence. Post-hybridization processing is automated on a robotic prep station. After hybridization, the excess probes are washed away, and the tripartite structures (capture probe-miRNA-reporter probe) are fixed to a streptavidin-coated slide via the biotin-labeled capture probe. Imaging and barcode counting is done using a digital analyzer. The immobilized barcoded miRNAs are visualized and imaged using a microscope and camera, and the unique barcodes are decoded and counted. Data quality control (QC), normalization, and analysis are facilitated by a custom-designed data processing and analysis software that accompanies the assay software. The assay demonstrates high linearity over a broad range of expression, as well as high sensitivity. Sample and assay preparation does not involve enzymatic reactions, reverse transcription, or amplification; has few steps; and is largely automated, reducing investigator effects and resulting in high consistency and technical reproducibility. Here, we describe the application of this technology to identifying circulating miRNA perturbations in irritable bowel syndrome.

Despite decades of research and an enormity of resultant data, cancer remains a significant public health problem. New tools and fresh perspectives are needed to obtain fundamental insights, to develop better prognostic and predictive tools, and to identify improved therapeutic interventions. With increasingly common genome-scale data, one suite of algorithms and concepts with potential to shed light on cancer biology is phylogenetics, a scientific discipline used in diverse fields. From grouping subsets of cancer samples to tracing subclonal evolution during cancer progression and metastasis, the use of phylogenetics is a powerful systems biology approach. Well-developed phylogenetic applications provide fast, robust approaches to analyze high-dimensional, heterogeneous cancer data sets. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

Insufficient quantity but also quality of spray deposition on susceptible grapevine tissue (i.e. target sites) and favourable conditions for pathogens could lead to control failure during high disease pressure situations. To determine deposition quantity and quality benchmarks for biologically effective spray deposits, bunches and leaves of table grapes (Waltham Cross) were sprayed at various growth stages, using different application volumes of a mixture of fenhexamid and a fluorescent tracer pigment and subsequently dusted with dry conidia of Botrytis cinerea where after infection levels on pedicels, receptacles and leaves were determined. Pigment deposition quantity and quality were determined from photos of sprayed parts taken with a digital camera under a stereo microscope and black light illumination at ×30 or ×10 magnifications and assessed with digital image and Hoerl regression analyses. The deposition quantity resulting in 75% control of B. cinerea infection (FPC75 values) was calculated from biological efficacy curves (sigmoidal regression analyses) for leaves and for each growth stage, for pedicels and receptacles. Deposition quantity and quality measurements correlated favourably with Botrytis infection. An optimal deposition value for the control of B. cinerea was determined by increasing spray volume, however by increasing spray volume and deposition quantity or quality levels past this optimum will not significantly improve disease control further. It was indicated that efficacy of agricultural chemicals could be influenced by improving both deposition quantity and quality, quantifiable by digital image analyses of fluorescent pigment deposition. FPC75 values obtained in this study can be used as benchmarks to evaluate future spray application in vineyards.

The aim of this study was to compare 11 treatment regimes (TR) in grapevine nurseries in order to eradicate trunk pathogens. Grapevine propagation material was subjected to treatments before cold storage, before and after grafting, before planting and after uprooting. Isolations were made from roots, rootstocks and graft unions of uprooted vines. None of the treatments consistently affected the number of certifiable vines produced. TR 1 (benomyl), TR 3 (Sporekill) and TR 4 (Trichoflow) increased root mass. Phaeomoniella chlamydospora was the most frequently isolated pathogen from all plant parts. In general, TR 2, 7, 9 and 11 caused the lowest occurrence of Phaeomoniella. TR 9 consistently reduced the incidence of Phaeoacremonium. Pleurostomophora richardsiae occurred most frequently in graft unions, but treatments were too inconsistent to draw meaningful conclusions. TR 7 (hot water treatment (HWT) of uprooted grapevines) consistently reduced incidences of black foot disease (BFD) pathogens. The highest incidence of Botryosphaeriaceae occurred in graft unions, but all treatments significantly reduced infections. The colonisation of rootstocks and graft unions by Trichoderma was significantly better with TR 4 (Trichoflow). The other Trichoderma treatments (TR 9, 10 and 11) differed from the control treatment only in the graft unions. This is a first report of an integrated strategy covering all the phases of the propagation process, from the moment the nursery receives the propagation material until the dormant vines are removed. TR 9 is recommended for use in nurseries, although HWT of dormant vines is recommended to eradicate BFD pathogens. Benomyl can be replaced by carbendazim when benomyl is no longer available.

��54'121 In mechanized mining, poor equipment efficiency (availability, utilization, productivity, and quality) can endanger the success of the operation. This case study will show how an initiative to improve equipment performance developed into a comprehensive turnaround plan for the mine that placed it in the forefront of performance achievement. As part of a company-wide review process, poor overall equipment effectiveness (OEE) was identified as a major reason for the mine not achieving its targets. A project to improve the OEE identified eight improvement areas (elements) that contributed significantly to the poor performances. Measurement metrics were determined for these elements, followed by determination of baseline and target (improved) key performance indicators (KPIs). Cost savings associated with the improved efficiencies were calculated and tracked throughout the project. The mine team determined the specific actions required to achieve the target KPI in each element. These were INDIVIDUALLY developed and managed like mini-projectsWITHALLOCATEDRESPONSIBILITIESFORDELIVERY The paper will indicate how this OEE improvement initiative triggered an improvement in almost all sections of the mine. Soon after launch, the initiative gathered momentum as the KPIs starting to improve. A visible tracking system exists at the mine and each employee can see the improvements and feel the success. The original eight elements were extended by five more, and the mini-projects grew as participants saw the success of the initiative. This paper concludes that through management and worker involvement, visible measurement and controls, and carefully chosen improvement elements, the mine was turned around. It is now achieving and exceeding its targets, and employee relations and motivation as well as safety have improved considerably. All of these achievements are reflected in the bottom line.

Imazalil (IMZ) is commonly applied in South African citrus packhouses for the control of green mould, caused by Penicillium digitatum, yet the disease still causes significant postharvest losses. The maximum residue limit (MRL) for IMZ on citrus fruit is 5 μg g−1, whereas 2–3 μg g−1 is a biologically effective residue level that should at least inhibit green mould sporulation. Standard compliance auditing of residue levels of citrus fruit, however, indicate that fruit from the majority of packhouses have residues of ≈1 μg g−1. Poor disease control from insufficient residue loading might further be compounded by the presence of IMZ-resistant isolates of P. digitatum in packhouses. This study was conducted to assess the current status of IMZ application in South African packhouses, to determine the adequate residue levels needed to control green mould and inhibit its sporulation using both IMZ sensitive and resistant isolates, to investigate IMZ application methods and resultant residue levels in commercial citrus packhouses, and to study optimisation of modes of IMZ application in citrus packhouses. Factors studied were IMZ concentration, application type (spray vs. dip and drench), exposure time, solution temperature and pH, as well as curative and protective control of P. digitatum. The packhouse survey showed that the majority of packhouses applied IMZ in a sulphate salt formulation through a fungicide dip tank, and loaded an IMZ residue of ≈1 μg g−1. In dip applications, IMZ had excellent curative and protective activity against Penicillium isolates sensitive to IMZ. However, curative control of IMZ resistant isolates was substantially reduced and protective control was lost, even at twice the recommended concentration, nor was sporulation inhibited. The use of sodium bicarbonate (2%) buffered imazalil sulphate solutions at pH ±8, compared with pH ±3 of the unbuffered solutions, markedly increased IMZ residue loading on Navel and Valencia oranges and improved curative and protective control of IMZ resistant isolates. Exposure time did not affect IMZ residue loading in IMZ sulphate solutions at pH 3, although the MRL was exceeded after 45 s exposure in pH 8 solutions. Imazalil applied through spray or drench application improved residue loading, but green mould control was less effective than after dip application.

In order to facilitate the understanding of the geological evolution of the Kalahari Craton and its relation to South America, the provenance of the first large-scale cratonic cover sequence of the craton, namely the Ordovician to Carboniferous Cape Supergroup was studied through geochemical analyses of the siliciclastics, and age determinations of detrital zircon. The Cape Supergroup comprises mainly quartz-arenites and a Hirnantian tillite in the basal Table Mountain Group, subgreywackes and mudrocks in the overlying Bokkeveld Group, while siltstones, interbedded shales and quartz-arenites are typical for the Witteberg Group at the top of the Cape Supergroup. Palaeocurrent analyses indicate transport of sediment mainly from northerly directions, off the interior of the Kalahari Craton with subordinate transport from a westerly source in the southwestern part of the basin near Cape Town. Geochemical provenance data suggest mainly sources from passive to active continental margin settings. The reconnaissance study of detrital zircons reveals a major contribution of Mesoproterozoic sources throughout the basin, reflecting the dominance of the Namaqua-Natal Metamorphic Belt, situated immediately north of the preserved strata of Cape Supergroup, as a source with Archaean-aged zircons being extremely rare. We interpret the Namaqua-Natal Metamorphic Belt to have been a large morphological divide at the time of deposition of the Cape Supergroup that prevented input of detrital zircons from the interior early Archaean Kaapvaal cratonic block of the Kalahari Craton. Neoproterozoic and Cambrian zircons are abundant and reflect the basement geology of the outcrops of Cape strata. Exposures close to Cape Town must have received sediment from a cratonic fragment that was situated off the Kalahari Craton to the west and that has subsequently drifted away. This cratonic fragment predominantly supplied Meso- to Neoproterozoic, and Cambrian-aged zircon grains in addition to minor Silurian to Lower Devonian zircons and very rare Archaean (2.5 Ga) and late Palaeoproterozoic (1.8-2.0 Ga) ones. No Siluro-Devonian source has yet been identified on the Kalahari Craton, but there are indications for such a source in southern Patagonia. Palaeozoic successions in eastern Argentina carry a similar detrital zircon population to that found here, including evidence of a Silurian to Lower Devonian magmatic event. The Kalahari and Rio de la Plata Cratons were thus in all likelihood in close proximity until at least the Carboniferous.

Adequate spray deposition on susceptible grapevine tissue is an essential requirement for effective chemical control of economically important diseases, such as grey mould, powdery mildew and downy mildew. The objective of this study was to evaluate the potential of some agricultural adjuvants to improve foliar spray deposition. Deposition quantity and quality was assessed by means of a spray assessment protocol using fluorometry, photomicrography and digital image analyses. The visual droplet rating technique developed by G Furness, Australia, was also included in initial assessments. Both assessment protocols showed that spray deposition quantity increased with increasing spray volume applications of 27 l ha −1 to 581 l ha −1 with a motorised backpack mistblower, but decreased at 698 l ha −1 , possibly due to run-off. Addition of selected spray adjuvants at 526 l ha −1 volume demonstrated improved deposition quantity and quality. Agral 90 (ethoxylated alkylphenol), BB5 (acidifier), Nu-film-P (terpene oil), and Solitaire (silicone/plant oil) significantly improved deposition on upper and lower leaf surfaces compared with the fenhexamid-only and water sprayed control. Break-thru S240 (organosilicone) and Villa 51 (alkylpolyethylene glycol ether) did not improve deposition quantity, although remarkably better deposition quality was obtained. An adjuvant concentration effect (within the registered concentration range) was evident at spray volumes of 502 l ha −1 , especially those retained on the upper leaf surfaces. Agral 90 and Nu-film-P effected significant improvement of spray deposition at the higher concentrations (18 ml and 50 ml hl −1 , respectively), but not at the lower concentrations (6 ml and 20 ml hl −1 , respectively). Solitaire improved deposition at the lower concentration tested (50 ml hl −1 ), whereas reduced deposition at the higher concentration (100 ml per hl −1 ) was attributed to excessive spray run-off. No significant improvement of spray deposition was observed for both concentrations tested with Villa 51 (50 and 100 ml hl −1 ). Spray mixtures with adjuvants Agral 90 and Solitaire yielded similar deposition values at 500 l ha −1 compared with the fenhexamid-only control at 720 l ha −1 , but reduced deposition at the higher spray volume, possibly due to spray run-off. This study clearly demonstrated the potential of adjuvants to improve deposition quantity and quality, but highlights the necessity to match adjuvant concentrations and application volumes on the spray target to achieve maximum spray deposition.

Species of the genus Coniochaeta (anamorph: Lecythophora) are known as pathogens of woody hosts, but can also cause opportunistic human infections. Several fungi with conidial stages resembling Lecythophora were isolated from necrotic wood samples of Prunus trees in South Africa. In order to reveal their phylogenetic relationships, these fungi were studied on a morphological and molecular (5.8S nrDNA, ITS-1, ITS-2, GAPDH, EF-1α, 28S nrDNA, 18S nrDNA) basis. Some of the isolates were identified as Coniochaeta (Sordariomycetes), including C. velutina and two new species, C. africana and C. prunicola. The majority of the isolates, however, formed pycnidial or pseudopycnidial synanamorphs and were not closely related to Coniochaeta. According to their 28S nrDNA phylogeny, they formed two distinct groups, one of which was closely related to Helotiales (Leotiomycetes). The new genus Collophora is proposed, comprising five species that frequently occur in necrotic peach and nectarine wood, namely Co. africana, Co. capensis, Co. paarla, Co. pallida and Co. rubra. The second group was closely related to Phaeomoniella chlamydospora (Eurotiomycetes), occurring mainly in plum wood. Besides P. zymoides occurring on Prunus salicina, four new species are described, namely P. dura, P. effusa, P. prunicola and P. tardicola. In a preliminary inoculation study, pathogenicity was confirmed for some of the new species on apricot, peach or plum wood.

Trunk disease pathogens of grapevines, viz. Phaeomoniella chlamydospora, Eutypa lata and several species in Botryosphaeriaceae, Phaeoacremonium and Phomopsis are known to infect fresh pruning wounds by means of air-borne inoculum released after rainfall or prolonged periods of high relative humidity. Recent surveys have demonstrated that most or all of these pathogens are present in climatically diverse grape growing regions of South Africa. However, the factors controlling spore dispersal of these pathogens in vineyards were largely unknown. To address this question, spore trapping was done in a Chenin Blanc vineyard in the Stellenbosch area, South Africa, for 14 weeks during the grapevine pruning period from June to mid-September of 2004 and 2005. Hourly recordings of weather data were done by a weather station in the row adjacent to the spore trap. Spores of E. lata and Phomopsis and species in Botryosphaeriaceae were trapped throughout the trapping periods of 2004 and 2005, with higher levels of trapped spores recorded in 2005. The spores of all three pathogens were trapped during or after periods of rainfall and/or high relative humidity. In neither of the 2 years were spores of Pa. chlamydospora or Phaeoacremonium spp. trapped. Results indicated that spore event incidence, as well as the amount of spores released during a spore event of above-mentioned pathogens, were governed by rainfall, relative humidity, temperature and wind speed prior to and during the spore events.

Spray adjuvants have the potential to improve deposition by effecting uniform distribution of the active ingredient on plant surfaces. In order to study whether such a qualitative improvement of spray deposition would lead to improved disease control, a laboratory experiment was conducted on artificially inoculated grapevine (cv. Chardonnay) leaves. Prior to inoculation with Botrytis cinerea conidia in a spore settling tower, leaves were sprayed to pre-runoff with 1 mL of a mixture of fenhexamid, a fluorescent pigment, and one of 15 selected commercial adjuvants to manipulate the deposition quality of a specific quantity of spray. Following an incubation period of 24 h at high relative humidity, leaf discs were plated onto Petri dishes with paraquat-amended water agar and rated for development of B. cinerea from isolated leaf discs 11 d later. Spray deposition on leaves was assessed with a spray assessment protocol using fluorometry, photomicrography and digital image analyses. B. cinerea incidences on the upper and lower surfaces of water-sprayed leaves averaged 90.4% and 95.8%, respectively. Despite full spray cover of leaves, applications with fenhexamid alone did not completely prevent infection and resulted in 34.6% and 40.8% B. cinerea incidences on the upper and lower surfaces of leaves, respectively. Through the addition of certain adjuvants, B. cinerea incidences were significantly reduced (incidences of 2.9–17.1% and 10.0–30.8%, respectively), while some adjuvants did not differ from the fungicide only treatment, even though they might have improved spray deposition. In a histopathology study using epifluorescence microscopy, distinct differences were observed in conidium mortality (20.5% vs. 31.2%), germination (60.4% vs. 51.4%) and germ tube lengths (27.8 μm vs. 19.7 μm) between Hydrosilicote and Solitaire in combination with fenhexamid, even though both adjuvants effected similar quantitative and qualitative spray deposition. The study clearly demonstrated the potential of adjuvants to improve the bio-efficacy of a fungicide directly through improved deposition on grapevine leaf surfaces, although bio-efficacy might be influenced by adjuvant mode of action in some cases.

The genus Phaeoacremonium is associated with opportunistic human infections, as well as stunted growth and die-back of various woody hosts, especially grapevines. In this study, Phaeoacremonium species were isolated from necrotic woody tissue of Prunus spp. (plum, peach, nectarine and apricot) from different stone fruit growing areas in South Africa. Morphological and cultural characteristics as well as DNA sequence data (5.8S rDNA, ITS1, ITS2, β-tubulin, actin and 18S rDNA) were used to identify known, and describe novel species. From the total number of wood samples collected (257), 42 Phaeoacremonium isolates were obtained, from which 14 species were identified. Phaeoacremonium scolyti was most frequently isolated, and present on all Prunus species sampled, followed by Togninia minima (anamorph: Pm. aleophilum) and Pm. australiense. Almost all taxa isolated represent new records on Prunus. Furthermore, Pm. australiense, Pm. iranianum, T. fraxinopennsylvanica and Pm. griseorubrum represent new records for South Africa, while Pm. griseorubrum, hitherto only known from humans, is newly reported from a plant host. Five species are newly described, two of which produce a Togninia sexual state. Togninia africana, T. griseo-olivacea and Pm. pallidum are newly described from Prunus armeniaca, while Pm. prunicolum and Pm. fuscum are described from Prunus salicina.

Coniothyrium-like fungi are common wood and soil inhabitants and hyperparasites on other fungi. They belong to different fungal genera within the Pleosporales. Several isolates were obtained on wood of different Prunus species (plum, peach and nectarine) from South Africa, on Actinidia species from Italy and on Laurus nobilis from Turkey. Morphological and cultural characteristics as well as DNA sequence data (5.8S nrDNA, ITS1, ITS2, partial SSU nrDNA) were used to characterise them. The isolates belonged to three species of the recently established genus Paraconiothyrium. This is the first report of Paraconiothyrium brasiliense on Prunus spp. from South Africa. Two new species are described, namely Paraconiothyrium variabile sp. nov. on Prunus persica and Prunus salicina from South Africa, on Actinidia spp. from Italy and on Laurus nobilis from Turkey, and Paraconiothyrium africanum sp. nov. on Prunus persica from South Africa. Although other known species of Paraconiothyrium commonly produce aseptate conidia, those of P. africanum and P. hawaiiense comb. nov. are predominantly two-celled.

During a survey of Prunus wood from South Africa, isolations were made of three presumably Calosphaerialean fungi that formed hyphomycetous, phialidic anamorphs in culture. In order to reveal the phylogenetic relationship of these fungi, they were characterised on a morphological and molecular (LSU and ITS rDNA) basis. Two isolates that formed a teleomorph in culture are newly described as Calosphaeria africana sp. nov. Although asci of Calosphaeria are characterised by having non-amyloid apical rings, two functional wall layers were observed in asci of C. africana, which has hitherto not been observed in any member of the Calosphaeriaceae. However, Calosphaeriaceae (Calosphaeriales, Sordariomycetes) are not closely related to other bitunicate fungi like Dothideomycetes, Chaetothyriales and bitunicate lichens. Possession of two separating wall layers is considered to be a result of both inherited abilities and convergent evolution under a strong selection pressure of the environmental conditions that favour an extension of the ascus. The other two species represented a separate lineage within Calosphaeriaceae, and formed phialophora-like anamorphs. By obtaining the teleomorph in culture, one of them could be identified as a species of Jattaea, described here as Jattaea prunicola sp. nov., while the second, which only produced the anamorph, is named as Jattaea mookgoponga sp. nov. These findings suggest that some species of Jattaea are true members of the Calosphaeriaceae, though the phylogenetic relation of the type, J. algeriensis, remains unknown. Furthermore, it also represents the first report of Jattaea on Prunus wood, and from South Africa.

SUMMARY Plasmopara viticola populations in South Africa were studied for two consecutive grape growing seasons, in an organically managed and a conventional fungicide-sprayed vineyard. Three to four samplings in each season were genotyped with four microsatellite markers (GOB, CES, ISA and BER). Population differentiation (Fst) between the conventional fungicide-sprayed vineyard and organically managed vineyard was low (0.004 and 0.016) in both growing seasons, suggesting one metapopulation. However, differences in the relative contribution of the predominant and new genotypes to epidemics in the two vineyards suggested that fungicide applications may have selected for reduced pathogen diversity. In both years and vineyards, sexual (oosporic) reproduction and/or migration occurred throughout the year and contributed between 12 and 74% to the epidemic. Hardy–Weinberg analyses suggest that South African P. viticola populations are randomly mating. Epidemics in both years and vineyards were dominated by one or two genotypes that each contributed between 14 and 67% to the epidemic through asexual reproduction. The remaining genotypes showed low levels of asexual reproduction, with most genotypes never being able to reproduce asexually. However, for some genotypes asexual reproduction was important, as it enabled survival of the genotypes from one season to the next. In total, ten genotypes were able to survive asexually or vegetatively from one season to the next. The populations were further characterized by the presence of a high frequency of isolates that most likely have elevated ploidy levels.

Black foot disease of grapevines is a decline and dieback disease caused by a soilborne pathogen complex including Cylindrocarpon liriodendri, C. macrodidymum, Campylocarpon fasciculare and Campyl. pseudofasciculare. These pathogens cause primary infections of roots and basal ends of grafted cuttings in nursery soils. Thirteen fungicides were screened in vitro for mycelial inhibition of these pathogens. Prochloraz manganese chloride, benomyl, flusilazole and imazalil were the most effective fungicides tested, and were subsequently included in semi-commercial field trials. Basal ends of grafted cuttings were dipped in various chemical and biological treatments prior to planting in open-rooted nurseries. Black foot pathogens were not isolated from grafted cuttings prior to planting. Additional treatments involved soil amendments with Tricboderma formulations and hot water treatment of dormant nursery grapevines. Field trials were evaluated after eight months. Isolations from uprooted plants revealed low levels of black foot pathogens in the roots of untreated control plants, and significantly higher levels in basal ends of rootstocks. The incidence of black foot pathogens, as well as that of Petri disease pathogens, was not significantly and/or consistently reduced by the majority of chemical or biological treatments. However, these pathogens were not isolated from uprooted plants that were subjected to hot water treatment. It is therefore recommended that hot water treatment of dormant nursery plants be included in an integrated strategy for the proactive management of these diseases in grapevine nurseries.

Hypotheses to explain diversity among African ungulates focus largely on niche separation along a browser/grazer continuum. However, a number of studies advocate that the browser/grazer distinction insufficiently describes the full extent of dietary variation that occurs within and between taxa. Disparate classification schemes exist because of a lack of uniform and reliable data for many taxa, and failure to incorporate spatio-temporal variations into broader assessments of diet. In this study, we tested predictions for diet and dietary niche separation of African savanna ungulates using stable carbon isotope evidence from faeces for proportions of C3 (browse) to C4 (grass) intake among 19 species from the Kruger National Park, South Africa. Dietary predictions from the literature are confirmed in the case of browsers (black rhinoceros Diceros bicornis, giraffe Giraffa camelopardalis, bushbuck Tragelaphus scriptus, kudu Tragelaphus strepsiceros), mixed-feeders (impala Aepyceros melampus, nyala Tragelaphus angasii), and most grazers (white rhinoceros Ceratotherium simum, Burchell’s zebra Equus burchellii, warthog Phacochoerus africanus, hippopotamus Hippopotamus amphibius, blue wildebeest Connochaetes taurinus, tsessebe Damaliscus lunatus, waterbuck Kobus ellipsiprymnus). In contrast, several species showed results differing from most expectations derived from the available literature, including eland Taurotragus oryx, steenbok Raphicerus campestris, grey duiker Sylvicapra grimmia, buffalo Syncerus caffer, roan antelope Hippotragus equinus and sable antelope Hippotragus niger. Many of these discrepancies can be accounted for by seasonal and/or regional dietary differences. Cluster analysis based on a data matrix that incorporates the extent of spatio-temporal dietary variation among Kruger Park ungulates reveals several distinct categories of feeding preferences that extend beyond a two-edged browser/grazer dichotomy, such as mixed-feeders with a preference for either forage class, and spatial/seasonal shifts between uniform and mixed-feeding styles among variable browsers (e.g. grey duiker) and variable grazers (e.g. buffalo). These results highlight the need for approaches that are sensitive to spatio-temporal variations and the continuity of diet.

Protection of wounds against infection by trunk disease pathogens is the most efficient and cost-effective means to prevent grapevine trunk diseases. Studies done to determine the effectiveness of chemical pruning wound protectants have mostly focused on the control of Eutypa lata. However, other important wound pathogens, such as Phaeomoniella chlamydospora, Phaeoacremonium spp., Phomopsis spp. and species of Botryosphaeriaceae ( including Botryosphaeria and aggregate genera), pose just as significant a threat to sustainable grape production. Fungicide sensitivity studies have been conducted for Pa. chlamydospora, P. viticola and E. lata. However, no such studies have been conducted for the pathogenic species of Botryosphaeriaceae from grapevines in South Africa. Ten fungicides were, therefore, tested in vitro for their efficacy on mycelial inhibition of the four most common or pathogenic species of Botryosphaeriaceae in South Africa, 'B.' obtusa, Neofusicoccum australe, N. parvum and Lasiodiplodia theobromae. Iprodione, pyrimethanil, copper ammonium acetate, kresoxim-methyl and boscalid were ineffective in inhibiting the mycelial growth at the highest concentrations tested ( 20 mu g/mL for copper ammonium acetate, 5 mu g/mL for other agents tested). Benomyl, tebuconazole, prochloraz manganese chloride and flusilazole were the most effective fungicides with EC50 values for the different species ranging from 0.36-0.55, 0.07-0.17, 0.07-1.15 and 0.04-0.36 mu g/mL, respectively. These fungicides, except prochloraz manganese chloride, are registered for use on grapes in South Africa and were also reported to be effective against Pa. chlamydospora, P. viticola and E. lata. Results from bioassays on 1-year-old Chenin Blanc grapevine shoots indicated that benomyl, tebuconazole and prochloraz manganese chloride were most effective in limiting lesion length in pruning wounds that were inoculated with species of Botryosphaeriaceae after fungicide treatment. The bioassay findings were, however, inconclusive due to low and varied re-isolation incidences. Benomyl, tebuconazole, prochloraz manganese chloride and flusilazole can be identified as fungicides to be evaluated as pruning wound protectants in additional bioassays and vineyard trials against species of Botryosphaeriaceae as well as the other grapevine trunk disease pathogens.

Hair cortisol analysis is a potentially powerful tool for evaluating adrenal function and chronic stress. However, the technique has only recently been applied widely to studies of wildlife, including primates, and there are numerous practical and technical factors that should be considered to ensure good quality data and the validity of results and conclusions. Here we report on various intrinsic and extrinsic sources of variation in hair cortisol measurements in wild and captive primates. Hair samples from both wild and captive primates revealed that age and sex can affect hair cortisol concentrations; these effects need to be controlled for when making comparisons between individual animals or populations. Hair growth rates also showed considerable inter-specific variation among a number of primate species. We describe technical limitations of hair analyses and variation in cortisol concentrations as a function of asynchronous hair growth, anatomical site of collection, and the amount and numbers of hair/s used for cortisol extraction. We discuss these sources of variation and their implications for proper study design and interpretation of results.

Microdosimetric calculations of the Auger electron emitter (123)I were done in liquid water spheres using the Geant4 toolkit. The electron emission spectrum of (123)I produced by Geant4 is presented. Energy deposition and corresponding S-values were calculated to investigate the influence of the sub-cellular localization of the Auger emitter. It was found that S-values calculated by the Geant4 toolkit are generally lower than the values calculated by other Monte Carlo codes for the (123)I radionuclide. The differences in the compared S-values are mainly due to the different particle emission spectra employed by the respective computational codes and emphasizes the influence of the spectra on dosimetry calculations.

Wound protection during all stages of grapevine propagation is of utmost importance to prevent infection of propagation material by decline and dieback pathogens. In semi-commercial nursery trials, grapevine rootstock and scion cuttings were soaked in water (control), chemical or biological sanitation products prior to cold storage, prior to grafting (machine- or hand-grafting) and prior to planting in field nurseries. Natural infection levels in basal ends and graft unions of uprooted nursery grapevines were evaluated 8 months after planting. Total pathogen incidences in the water-treated control plants ranged from 30% in basal ends to 13.5% in graft unions. Phaeomoniella chlamydospora was the most commonly isolated pathogen, followed by Phaeoacremonium, Cylindrocarpon + Campylocarpon, Botryosphaeria and Phomopsis spp. Machine-grafted unions generally had lower pathogen incidences compared with hand-grafted graft unions. In general, repeated soak-treatments of propagation material in the tested products resulted in reduced pathogen incidences in nursery grapevines. However, products containing T. harzianum (Trichoflow-T), hydrogen peroxide (Bio-sterilizer) and 8-hydroxyquinoline sulphate (Chinosol) gave inconsistent results, whereas Bronocide (a blend of halogenated alcohols and water) proved to be a good sterilising agent, but reduced certifiable plant yield significantly. Benomyl (at 100 g/100 l), Sporekill (a patented didecyldimethylammonium chloride formulation at 150 ml/100 l) and captan (at 1000 ml/100 l) were consistently the best treatments as growth parameters were not negatively influenced and pathogen incidences in basal ends and graft unions of uprooted plants were reduced.

Petri disease of grapevine is primarily caused by Phaeomoniella chlamydospora. This pathogen affects mostly young grapevines, but is also implicated in esca disease of older grapevines. Little is known about the disease cycle of this fungus. Infected propagation material was identified as a major means of dissemination of the pathogen. Recently, the pathogen was also detected from soil in South Africa and airborne conidia have been found in vineyards. The aim of this study was to use a molecular detection technique to test different samples collected from nurseries in South Africa at different nursery stages for the presence of P. chlamydospora. A one-tube nested-PCR technique was optimised for detecting P. chlamydospora in DNA extracted from soil, water, callusing medium and grapevine wood. The one-tube nested-PCR was sensitive enough to detect as little as 1 fg of P. chlamydospora genomic DNA from water and 10 fg from wood, callusing medium and soil. PCR analyses of the different nursery samples revealed the presence of several putative 360 bp P. chlamydospora specific bands. Subsequent sequence analyses and/or restriction enzyme digestions of all 360 bp PCR bands confirmed that all bands were P. chlamydospora specific, except for five bands obtained from callusing media and one from water. Phaeomoniella chlamydospora was positively detected in 25% of rootstock cane sections collected from mother blocks, 42% of rootstock cuttings and 16% of scion cuttings collected during grafting, 40% of water samples collected after pre-storage hydration, 67% of water samples collected during grafting, 8% of callusing medium samples and 17% of soil samples collected from mother blocks. These media can therefore be considered as possible inoculum sources of the pathogen during the nursery stages.

The genus Pilidiella, including its teleomorphs in Schizoparme, has a cosmopolitan distribution and is associated with disease symptoms on many plants. In the past, conidial pigmentation has been used as a character to separate Pilidiella (hyaline to pale brown conidia) from Coniella (dark brown conidia). In recent years, however, the two genera have been regarded as synonymous, the older name Coniella having priority. To address the generic question, sequences of the internal transcribed spacer region (ITS1, ITS2), 5.8S gene, large subunit (LSU) and elongation factor 1-[alpha] gene (EF 1-[alpha]) were analysed to compare the type species of Pilidiella and Coniella. All three gene regions supported the separation of Coniella from Pilidiella, with the majority of taxa residing in Pilidiella. Pilidiella is characterised by having species with hyaline to pale brown conidia (avg. length[ratio]width >1.5), in contrast to the dark brown conidia of Coniella (avg. length[ratio]width [less-than-or-eq, slant]1.5). Pilidiella diplodiella, which is a pathogen associated with white rot of grapevines, was shown to be an older name for C. petrakii. To delineate species in the P. diplodiella species complex, isolates were also compared based on histone (H3) gene sequences. Analyses derived from these sequence data separated P. diplodiella from a newly described species, P. diplodiopsis. The new species P. eucalyptorum sp. nov. is proposed for isolates formerly treated as C. fragariae and associated with leaf spots of Eucalyptus spp. This species clustered basal to Pilidiella, and may represent yet a third genus within this complex. Pilidiella destruens sp. nov. is newly described as anamorph of Schizoparme destruens, which is associated with twig dieback of Eucalyptus spp. in Hawaii. A key based on morphological characteristics is provided to separate the taxa treated in this study

Introduction Groote Schuur Hospital constructed a new radiotherapy bunker for a high-energy linear accelerator. During construction areas of honeycombing became evident in the concrete. Honeycombing reduces the density of concrete and may affect the shielding integrity of the walls. Since the linac had not yet been installed, the radiation beam could not be used for testing, and an alternative non-destructive testing method had to be employed. The aim of this study is to compare the results from the impact echo testing with the radiation survey results. Materials and methods In impact echo testing, a mechanical impact is used to create stress waves, which propagate through the concrete and are reflected or refracted where there are changes in material characteristics such as density. In theory, non-visible honeycombing at depth will present multiple reflection surfaces and should result in a broad-band response with multiple small peaks. The propagation of the stress wave is dependent on the elastic modulus, density and Poisson’s ratio of the material. Radiation measurements at the same positions on the walls where impact echo testing was performed were done with the 6 MV linear accelerator during its safety survey, and the data was extrapolated for an 18 MV photon beam as per bunker design. Results The impact echo results show that the density of the primary barrier ranged from 2.30 g/cc to 2.55 g/cc for the primary shielding wall adjacent to the maze (the other one is underground). The maximum measured dose rate from radiation survey on this wall was 0.5 μSv/h for a 6 MV beam, and calculated to be about 40 times higher for an 18 MV beam. An additional 40 cm of concrete shields the closest uncontrolled area. Conclusion The radiation survey results are consistent with the results from the impact echo testing. No localized voids were found during the survey.

Background Sleep quality and genetics may contribute to the etiology of gastrointestinal (GI) symptoms. Individuals with impaired sleep often have a number of associated symptoms including chronic abdominal pain (CAP). The current study examined the interactions of brain-derived neurotrophic factor (BDNF) genotype with sleep quality in persons with CAP and healthy controls. In addition, associations among sleep quality, BDNF genotype, and gene expression were explored in the participants. Methods Data were collected on 59 participants (46% male, 61% White, 26.9 ± 6.6 years; CAP (n=19) and healthy controls (n=40)). Participants with CAP reported poorer sleep quality compared to healthy controls. BDNF genotype, categorized as Val/Val homozygotes versus the Met carriers. Results Microarray analysis found twenty-four differentially expressed genes by a two-fold magnitude in participants with poor sleep quality compared to good sleep quality, and seven differentially expressed genes comparing CAP to healthy control. Three specific genes in the pain group overlap with sleep quality, including insulin-like growth factor 1 (IGF1), spermatogenesis associated serine-rich 2-like (SPATS2L), and immunoglobulin heavy constant gamma 1 or mu (IGHG1/// IGHM). BDNF was shown to have an interaction effect with GI and sleep symptoms. Conclusions Participants with CAP reported poor sleep quality compared to healthy controls. The role of the BDNF Met allele on differential gene expression was not distinct as main factor, but impacted interactions with sleep quality and CAP. Down-regulation of IGF1, SPATS2L, and IGHG1 expression may be related to the etiology of poor sleep quality and CAP. Trial registration Clinicaltrial.gov # NCT00824941 Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0061-1) contains supplementary material, which is available to authorized users.

Exploitation and characterization of resistance to the root-knot nematode Meloidogyne incognita (Nematoda, Tylenchida) in soybean (Glycine max L. Merr) Host plant resistance can be used to manage Meloidogyne incognita in soybean. This study identified resistant cultivars and showed a poor correlation between early and late pest and damage assessments. The identification of resistance contributes to soybean breeding programs in South Africa.

Harmful micro- and macroscopic effects of the environmental xenoestrogen p-nonylphenol (p-NP) on the male rat reproductive system have been previously reported. In our study, biochemical evidence of epididymal involvement was sought by determining epididymal marker values after exposure at levels below (5, 20 and 50 mg kg -1 ) and above (100, 250 and 400 mg kg -1 ) the no observed adverse effect' level (NOAEL: 50 mg kg -1 day -1 ). Exposure to p-NL below the NOAEL did not affect biochemical marker values. At levels above the NOAEL, biochemical markers of epididymal function were affected by the exposure of adults, and by maternal exposure (gestational and lactational periods followed by oral exposure until sexual maturity). L-carnitine was unchanged at all levels of exposure. Exposure of adult males to levels above the NOAEL resulted in higher α-glucosidase, suggesting increased epididymal secretory activity. This could upset the balance between secretory and reabsorptive function, and could alter the biochemical composition of the epididymal luminal fluid surrounding spermatocytes during the maturation process. Maternal exposure at levels above the NOAEL resulted in higher tartrate-resistant acid phosphatase activity in the caput-corpus epididymidis, which could indicate an oestrogen-mimicking effect.

The effect of Meloidogyne incognita (Nematoda), on lipoxygenase and peroxidase activity in soybean leaves. The goal of this study was to determine whether or not soybean cultivars, LS5995 and Ibis, have mechanisms in place to protect them from nematode infections. Tests were done for lipoxygenase (LOX) and peroxidase (POD) enzymes. Increased LOX and POD activity indicate defense mechanisms in plants.

Two polymerase chain reaction (PCR)-based procedures for typing Clostridium perfringens, which affects most domestic animals, were compared and evaluated for efficiency as substitute to the guinea-pig intradermal test routinely used in our laboratory, namely a multiplex PCR and a protocol based on the individual amplification of gene sequences specific for each toxin. Reference isolates of C. perfringens types A, B, C and D as well as cultures from clinical specimens were tested. The sensitivity and specificity of the PCR was confirmed on reference isolates. There was similarity in results on 43 of the 46 samples typed by all 3 methods. Clear results were obtained by PCR on 5 clinical samples that showed either equivocal or weak skin reactions in guinea-pigs. The multiplex PCR protocol, in combination with the evaluation of bacterial growth, is a better alternative to in vivo toxin typing, since C. perfringens can only be incriminated as cause of a disease when it is present in large numbers in the intestine.