Depth-structuring of multi-kingdom soil communities in agricultural pastures.

The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1,  0.3-0.5,  and 1.1-1.7m) in pastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.

Irrigation increases forage production of newly established lucerne but enhances net ecosystem carbon losses.

In New Zealand, dairy farming faces increasing scrutiny for its environmental impacts, including those on soil carbon (C) stocks; hence, alternative management practices are required. One such practice is usage of deep-rooting forage, such as lucerne (Medicago sativa L.). We measured the C and water exchange of two neighbouring lucerne fields on stony, well-drained soil for 3 years, following conversion from grassland. One field received irrigation and effluent; the other received neither. Net CO2 exchange and evaporation were measured by eddy covariance, drainage and leaching with lysimeters, and water inputs with rain gauges. Biomass removal from harvesting and grazing was recorded by direct sampling. In the conversion year, irrigated lucerne was C-neutral despite two harvests and losses from the conversion process. In the 2nd and 3rd years combined, the biomass-C removal exceeded net CO2 uptake, causing net losses of 450 g C m-2 and 210 g C m-2 for irrigated and non-irrigated lucerne, respectively. Leaching losses accounted for 1 to 9 % of annual net C uptake from the atmosphere. The ratio of ecosystem respiration to gross photosynthetic productivity (GPP) increased from <0.7 in spring to ≈ 1 in autumn. Consequently, the net C balance for both lucerne crops showed gains in the first two growth periods of each year and losses in the subsequent two to four growth periods. Irrigation made no difference to the photosynthetic water-use efficiency at field scale (GPP/evaporation), but enhanced production water-use efficiency (biomass/water input). Irrigation increased both the absolute amount of drainage and the fraction of water inputs lost by drainage. In one year, significant summer drainage occurred for the irrigated lucerne. To prevent that, soil-water content should be kept well below field capacity but above the crop's water-stress level. Such practice would likely also help retain soil carbon.

A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins.

We created a computational method to identify allosteric sites using a machine learning method trained and tested on protein structures containing bound ligand molecules. The Random Forest machine learning approach was adopted to build our three-way predictive model. Based on descriptors collated for each ligand and binding site, the classification model allows us to assign protein cavities as allosteric, regular or orthosteric, and hence to identify allosteric sites. 43 structural descriptors per complex were derived and were used to characterize individual protein-ligand binding sites belonging to the three classes, allosteric, regular and orthosteric. We carried out a separate validation on a further unseen set of protein structures containing the ligand 2-(N-cyclohexylamino) ethane sulfonic acid (CHES).

Cambinol, a novel inhibitor of neutral sphingomyelinase 2 shows neuroprotective properties.

Ceramide is a bioactive lipid that plays an important role in stress responses leading to apoptosis, cell growth arrest and differentiation. Ceramide production is due in part to sphingomyelin hydrolysis by sphingomyelinases. In brain, neutral sphingomyelinase 2 (nSMase2) is expressed in neurons and increases in its activity and expression have been associated with pro-inflammatory conditions observed in Alzheimer's disease, multiple sclerosis and human immunodeficiency virus (HIV-1) patients. Increased nSMase2 activity translates into higher ceramide levels and neuronal cell death, which can be prevented by chemical or genetic inhibition of nSMase2 activity or expression. However, to date, there are no soluble, specific and potent small molecule inhibitor tool compounds for in vivo studies or as a starting point for medicinal chemistry optimization. Moreover, the majority of the known inhibitors were identified using bacterial, bovine or rat nSMase2. In an attempt to identify new inhibitor scaffolds, two activity assays were optimized as screening platform using the recombinant human enzyme. First, active hits were identified using a fluorescence-based high throughput compatible assay. Then, hits were confirmed using a 14C sphingomyelin-based direct activity assay. Pharmacologically active compounds and approved drugs were screened using this strategy which led to the identification of cambinol as a novel uncompetitive nSMase2 inhibitor (Ki = 7 µM). The inhibitory activity of cambinol for nSMase2 was approximately 10-fold more potent than for its previously known target, silence information regulator 1 and 2 (SIRT1/2). Cambinol decreased tumor necrosis factor-α or interleukin-1 ß-induced increases of ceramide and cell death in primary neurons. A preliminary study of cambinol structure and activity allowed the identification of the main structural features required for nSMase2 inhibition. Cambinol and its analogs may be useful as nSMase2 inhibitor tool compounds to prevent ceramide-dependent neurodegeneration.

Sutured posterior chamber intraocular lenses for traumatic cataract in Africa.

PURPOSE: To determine the outcomes of sutured scleral fixation of posterior chamber intraocular lenses (PC IOLs) after trauma in an African population. SETTING: State hospital and affiliated district hospital, Cape Town, South Africa. DESIGN: Case series. METHODS: A retrospective review was performed of the medical records of patients in whom a sutured PC IOL had been implanted for traumatic aphakia in the preceding 5 years. RESULTS: Eighty-five percent of the 59 patients had a significant improvement in uncorrected distance visual acuity (UDVA) at the final visit. Two-thirds of patients achieved an UDVA of 6/18 or better. Those not improving had severe preexisting macular or corneal pathology. A significant number of patients (28%) with angle recession developed ocular hypertension during the postoperative period. CONCLUSION: After careful preoperative selection, sutured PC IOLs were effective in the visual rehabilitation of eyes with traumatic subluxated cataract in which the capsular bag could not be retained. FINANCIAL DISCLOSURE: No author has a financial or proprietary interest in any material or method mentioned.

The value of routine polymerase chain reaction analysis of intraocular fluid specimens in the diagnosis of infectious posterior uveitis.

OBJECTIVE: To assess the value of routine polymerase chain reaction (PCR) analysis on intraocular fluid from patients presenting with a first episode of suspected active infectious posterior uveitis in a population with a high prevalence of human immunodeficiency virus infection. DESIGN: Retrospective, interventional case series. Participants. 159 consecutive patients presenting at a tertiary care hospital over a five-year period. METHODS: PCR analysis was performed for cytomegalovirus, varicella zoster virus, herpes simplex virus types 1 and 2, Toxoplasma gondii, and Mycobacterium tuberculosis. RESULTS: PCR analysis confirmed the initial clinical diagnosis in 55 patients (35%) and altered the initial clinical diagnosis in 36 patients (23%). The clinical diagnosis prior to PCR testing was nonspecific (uncertain) in 51 patients (32%), with PCR providing a definitive final diagnosis in 20 of these patients (39%); necrotizing herpetic retinopathy and ocular toxoplasmosis were particularly difficult to diagnose correctly without the use of PCR analysis. CONCLUSION: The clinical phenotype alone was unreliable in diagnosing the underlying infectious cause in a quarter of patients in this study. Since the outcome of incorrectly treated infective uveitis can be blinding, PCR analysis of ocular fluids is recommended early in the disease even in resource poor settings.

Ethambutol induced toxic optic neuropathy in HIV positive patients.

AIM: To determine whether HIV and the use of antiretroviral therapy is a risk factor for the development of ethambutol toxic optic neuropathy. To describe the clinical course of ethambutol toxic optic neuropathy in patients with HIV and to identify prognostic factors. METHODS: The case notes of 14 consecutive patients referred to the neuro-ophthalmology clinic were reviewed. Data regarding HIV status, antiretroviral therapy, visual function, ethambutol therapy dosage, and ethambutol therapy duration were collected and analysed. RESULTS: Eleven of the 14 patients were HIV positive. Ten of the HIV positive patients were receiving antiretroviral therapy. The mean dose of ethambutol was 17.25mg/kg/day. No statistically significant difference in mean dose, duration of therapy, age or CD4 count was found between those who showed visual improvement and those who did not. Delay in presentation of more than one month post symptom onset was correlated with poor visual outcome (P=0.001). CONCLUSION: HIV and, perhaps more importantly, the potential mitochondrial toxic effects of Nucleoside analogue reverse transcriptase inhibitors (NRTIs) may be a risk factor for the development of toxic optic neuropathy from ethambutol therapy via a multiple hit effect. Delay in presentation results in poor visual outcome. Regular monitoring is recommended for HIV positive patients receiving antiretrovirals and requiring ethambutol therapy in order to avoid permanent visual loss.

Roots affect the response of heterotrophic soil respiration to temperature in tussock grass microcosms.

AIMS AND BACKGROUND: While the temperature response of soil respiration (R(S)) has been well studied, the partitioning of heterotrophic respiration (R(H)) by soil microbes from autotrophic respiration (R(A)) by roots, known to have distinct temperature sensitivities, has been problematic. Further complexity stems from the presence of roots affecting R(H), the rhizosphere priming effect. In this study the short-term temperature responses of R(A) and R(H) in relation to rhizosphere priming are investigated. METHODS: Temperature responses of R(A), R(H) and rhizosphere priming were assessed in microcosms of Poa cita using a natural abundance δ(13)C discrimination approach. RESULTS: The temperature response of R(S) was found to be regulated primarily by R(A), which accounted for 70 % of total soil respiration. Heterotrophic respiration was less sensitive to temperature in the presence of plant roots, resulting in negative priming effects with increasing temperature. CONCLUSIONS: The results emphasize the importance of roots in regulating the temperature response of R(S), and a framework is presented for further investigation into temperature effects on heterotrophic respiration and rhizosphere priming, which could be applied to other soil and vegetation types to improve models of soil carbon turnover.

Prevalence, causes and socio-economic determinants of vision loss in Cape Town, South Africa.

PURPOSE: To estimate the prevalence and causes of blindness and visual impairment in Cape Town, South Africa and to explore socio-economic and demographic predictors of vision loss in this setting. METHODS: A cross sectional population-based survey was conducted in Cape Town. Eighty-two clusters were selected using probability proportionate to size sampling. Within each cluster 35 or 40 people aged 50 years and above were selected using compact segment sampling. Visual acuity of participants was assessed and eyes with a visual acuity less than 6/18 were examined by an ophthalmologist to determine the cause of vision loss. Demographic data (age, gender and education) were collected and a socio-economic status (SES) index was created using principal components analysis. RESULTS: Out of 3100 eligible people, 2750 (89%) were examined. The sample prevalence of bilateral blindness (presenting visual acuity <3/60) was 1.4% (95% CI 0.9-1.8). Posterior segment diseases accounted for 65% of blindness and cataract was responsible for 27%. The prevalence of vision loss was highest among people over 80 years (odds ratio (OR) 6.9 95% CI 4.6-10.6), those in the poorest SES group (OR 3.9 95% CI 2.2-6.7) and people with no formal education (OR 5.4 95% CI 1.7-16.6). Cataract surgical coverage was 68% in the poorest SES tertile (68%) compared to 93% in the medium and 100% in the highest tertile. CONCLUSIONS: The prevalence of blindness among people ≥50 years in Cape Town was lower than expected and the contribution of posterior segment diseases higher than previously reported in South Africa and Sub Saharan Africa. There were clear socio-economic disparities in prevalence of vision loss and cataract surgical coverage in this setting which need to be addressed in blindness prevention programs.

Rapid changes in δ¹³C of ecosystem-respired CO2 after sunset are consistent with transient ¹³C enrichment of leaf respired CO2.

The CO2 respired by darkened, light-adapted, leaves is enriched in ¹³C during the first minutes, and this effect may be related to rapid changes in leaf respiratory biochemistry upon darkening. We hypothesized that this effect would be evident at the ecosystem scale. High temporal resolution measurements of the carbon isotope composition of ecosystem respiration were made over 28 diel periods in an abandoned temperate pasture, and were compared with leaf-level measurements at differing levels of pre-illumination. At the leaf level, CO2 respired by darkened leaves that had been preadapted to high light was strongly enriched in ¹³C, but such a ¹³C-enrichment rapidly declined over 60-100 min. The ¹³C-enrichment was less pronounced when leaves were preadapted to low light. These leaf-level responses were mirrored at the ecosystem scale; after sunset following clear, sunny days respired CO2 was first ¹³C enriched, but the ¹³C-enrichment rapidly declined over 60-100 min. Further, this response was less pronounced following cloudy days. We conclude that the dynamics of leaf respiratory isotopic signal caused variations in ecosystem-scale ¹²CO2/¹³) CO2 exchange. Such rapid isotope kinetics should be considered when applying ¹³C-based techniques to elucidate ecosystem carbon cycling.

Primary health eye care knowledge among general practitioners working in the Cape Town metropole

Aim: The main purpose of this study was to determine whether general practitioners (GPs) in the Cape Town metropole have sufficient knowledge to diagnose and treat primary care ophthalmic conditions correctly; and to assess their own perceptions of their levels of knowledge. Secondary objectives included identifying the need for courses to improve the ophthalmic knowledge of GPs and assessing whether there is a need to revise the undergraduate curriculum in ophthalmology in general. Method: A cross-sectional survey was done. A questionnaire of 10 primary care level ophthalmology questions; including a self-assessment section; was sent to each of 140 randomly chosen GPs in Cape Town. Results: A response rate of 79.2 was obtained. Respondents included graduates from all eight medical schools in South Africa. Most of the responding GPs were practising for more than 10 years (78.2). The mean test score was 52.5 (standard deviation [SD]: 22.2). The mean self-rating was 51.9(SD: 14.5). There was no statistically significant difference between the test score and the self-rating score (p = 0.5840). Responding GPs felt that there is a need for ophthalmology up-skilling courses and 99.9 of them would attend such courses. Also; 82 of GPs felt that primary care doctors; not optometrists; should deliver primary eye care. Conclusion: GPs appear to lack sufficient knowledge to manage primary health eye care problems; presumably due to a lack of adequate training in the field. Clinical up-skilling courses are needed to improve core knowledge in ophthalmology

Primary Health Eye Care Knowledge among General Practitioners Working in the Cape Town Metropole

The main purpose of this study was to determine whether general practitioners (GPs) in the Cape Town metropole have sufficient knowledge to diagnose and treat primary care ophthalmic conditions correctly; and to assess their own perceptions of their levels of knowledge. Secondary objectives included identifying the need for courses to improve the ophthalmic knowledge of GPs and assessing whether there is a need to revise the undergraduate curriculum in ophthalmology in general.Method: A cross-sectional survey was done. A questionnaire of 10 primary care level ophthalmology questions; including a self-assessment section; was sent to each of 140 randomly chosen GPs in Cape Town.Results: A response rate of 79.2). The mean test score was 52.5 (standard deviation [SD]: 22.2). The mean self-rating was 51.9 (SD: 14.5). There was no statistically significant difference between the test score and the self-rating score (p = 0.5840). Responding GPs felt that there is a need for ophthalmology up-skilling courses and 99.9 of them would attend such courses. Also; 82 of GPs felt that primary care doctors; not optometrists; should deliver primary eye care. Conclusion: GPs appear to lack sufficient knowledge to manage primary health eye care problems; presumably due to a lack of adequate training in the field. Clinical up-skilling courses are needed to improve core knowledge in ophthalmology

Characteristics of photosynthesis and stomatal conductance in the shrubland species manuka (Leptospermum scoparium) and kanuka (Kunzea ericoides) for the estimation of annual canopy carbon uptake.

Responses of photosynthesis to carbon dioxide (CO2) partial pressure and irradiance were measured on leaves of 39-year-old trees of manuka (Leptospermum scoparium J. R. Forst. & G. Forst.) and kanuka (Kunzea ericoides var. ericoides (A. Rich.) J. Thompson) at a field site, and on leaves of young trees grown at three nitrogen supply rates in a nursery, to determine values for parameters in a model to estimate annual net carbon uptake. These secondary successional species belong to the same family and commonly co-occur. Mean (+/- standard error) values of the maximum rate of carboxylation (hemi-surface area basis) (Vcmax) and the maximum rate of electron transport (Jmax) at the field site were 47.3 +/- 1.9 micromol m(-2) s(-1) and 94.2 +/- 3.7 micromol m(-2) s(-1), respectively, with no significant differences between species. Both Vcmax and Jmax were positively related to leaf nitrogen concentration on a unit leaf area basis, and the slopes of these relationships did not differ significantly between species or between the trees in the field and young trees grown in the nursery. Mean values of Jmax/Vcmax measured at 20 degrees C were significantly lower (P < 0.01) for trees in the field (2.00 +/- 0.05) than for young trees in the nursery with similar leaf nitrogen concentrations (2.32 +/- 0.08). Stomatal conductance decreased sharply with increasing air saturation deficit, but the sensitivity of the response did not differ between species. These data were used to derive parameters for a coupled photosynthesis-stomatal conductance model to scale estimates of photosynthesis from leaves to the canopy, incorporating leaf respiration at night, site energy and water balances, to estimate net canopy carbon uptake. Over the course of a year, 76% of incident irradiance (400-700 nm) was absorbed by the canopy, annual net photosynthesis per unit ground area was 164.5 mol m(-2) (equivalent to 1.97 kg C m(-2)) and respiration loss from leaves at night was 37.5 mol m(-2) (equivalent to 0.45 kg m(-2)), or 23% of net carbon uptake. When modeled annual net carbon uptake for the trees was combined with annual respiration from the soil surface, estimated net primary productivity for the ecosystem (0.30 kg C m(-2)) was reasonably close to the annual estimate obtained from independent mensurational and biomass measurements made at the site (0.22 +/- 0.03 kg C m(-2)). The mean annual value for light-use efficiency calculated from the ratio of net carbon uptake (net photosynthesis minus respiration of leaves at night) and absorbed irradiance was 13.0 mmol C mol(-1) (equivalent to 0.72 kg C GJ(-1)). This is low compared with values reported for other temperate forests, but is consistent with limitations to photosynthesis in the canopy attributable mainly to low nitrogen availability and associated low leaf area index.

Influence of nitrogen and phosphorus supply on foliage growth and internal recycling of nitrogen in conifer seedlings (Prumnopitys ferruginea).

The dynamics of internal cycling of nitrogen were studied in the southern hemisphere conifer miro [Prumnopitys ferruginea (G. Benn. ex D. Don) de Laub.], which has an indeterminate growth habit. In a 2-year experiment, P. ferruginea seedlings were supplied with nutrient solutions consisting of two different concentrations of nitrogen (5 and 0.5 mM) and phosphorus (1.33 and 0.133 mM) in the first year, and two concentrations (5 and 0.5mM) of a 15N-labelled nitrogen solution in the second year. Growth and nitrogen content of new foliage were shown to be largely dependent on seedling nitrogen status at the end of the first year, and only weakly dependent on nutrient supply in the second. An average of 70% of total nitrogen in new foliage was remobilised from storage in the first 63 d after flushing began. The remainder of new-foliage nitrogen was derived by root uptake from the nutrient supply in the second year. There was some response of nitrogen uptake to high nitrogen supply in the second year where seedlings had been nitrogen deficient at the end of the first year. However, it was concluded that the indeterminate growth habit of P. ferruginea did not distinguish its pattern of nitrogen storage and remobilisation from that of determinate conifers.