Bioprospecting for and the applications of halophilic acidophiles in bioleaching operations

The economic recovery of metals from sulfide ores has become a topic of increasing interest due to the escalating demand for critical minerals and the reducing grade of available ores. Bioleaching is the use of acidophilic iron and sulfur-oxidising microorganisms to facilitate the extraction of base metals from primary sulfide ores and tailings. One significant issue limiting the use of bioleaching is the availability of freshwater due to the sensitivity of these microbes to chloride. The use of saline tolerant acidophilic iron- and-sulfur oxidising microorganisms will go a long way to addressing this issue. There are three possible means of sourcing suitable microorganisms; adaptation, genetic engineering and bioprospecting, with bioprospecting showing the greatest possibilities. Bioprospecting in search of native organisms for bioleaching operations has led researchers to numerous locations around the world and the isolation of iron- and sulfur-oxidising acidophiles that are capable of tolerating high levels of salinity has been of particular interest in these investigations

Stable incidence rates of tuberculosis (TB) among human immunodeficiency virus (HIV)-negative South African gold miners during a decade of epidemic HIV-associated TB.

During the last decade, annual tuberculosis (TB) case-notification rates increased 4-fold, to >4000 cases/100000 person-years, in the study workforce, among whom prevalence of human immunodeficiency virus (HIV) was 30% in 2000. Three separate cohort studies, totalling 6454 HIV-negative participants, were combined and analyzed for time trends. Observed incidence of TB varied between 962 (1991-1994) and 1589 (1999-2000) cases/100000 person-years (P=.17, test for trend). There was, however, a progressive increase in age, and, for each period, older age was associated with increased incidence rates of TB (P<.001). Having adjusted for age differences, there was no significant association between incidence of TB and calendar period (P=.81, test for trend). Relative to 1991-1994, multivariate-adjusted incidence-rate ratios were 0.94, for 1995-1997, 0.96, for 1998-1999, and 1.05, for 1999-2000. Preventing a secondary epidemic of TB among HIV-negative individuals may be achievable with conventional means, even in settings with a high burden of HIV-associated TB

Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant “Thiobacillus prosperus” Type Strain DSM 5130

“Thiobacillus prosperus” is a halotolerant mesophilic acidophile that gains energy through iron and sulfur oxidation. Its physiology is poorly understood. Here, we describe the principal genomic features of the type strain of T. prosperus, DSM 5130. This is the first public genome sequence of an acidophilic halotolerant bacterium

The Relative Importance of Methanogenesis in the Decomposition of Organic Matter in Northern Peatlands

Using an isotope-mass balance approach and assuming the equimolar production of CO2 and CH4 from methanogenesis (e.g., anaerobic decomposition of cellulose), we calculate that the proportion of total CO2 production from methanogenesis varies from 37 to 83% across a variety of northern peatlands. In a relative sense, methanogenesis was a more important pathway for decomposition in bogs (80 ± 13% of CO2 production) than in fens (64 ± 5.7% of CO2 production), but because fens contain more labile substrates they may support higher CH4 production overall. The concentration of CO2 produced from methanogenesis (CO2-meth) can be considered equivalent to CH4 concentration before loss due to ebullition, plant-mediated transport, or diffusion. Bogs produced slightly less CO2-meth than fens (2.9 ±1.3 and 3.7 ±1.4mmol/L, respectively). Comparing the quantity of CH4 present to CO2-meth, fens lost slightly more CH4 than bogs (89 ± 2.8% and 82 ± 5.3%, respectively) likely due to the presence of vascular plant roots. In collapsed permafrost wetlands, bog moats produced half the amount of CO2-meth (0.8 ± 0.2mmol/L) relative to midbogs (1.6 ± 0.6mmol/L) and methanogenesis was less important (42 ± 6.6% of total CO2 production relative to 55 ± 8.1%). We hypothesize that the lower methane production potential in collapsed permafrost wetlands occurs because recently thawed organic substrates are being first exposed to the initial phases of anaerobic decomposition following collapse and flooding. Bog moats lost a comparable amount of CH4 as midbogs (63 ± 7.0% and 64 ± 9.3%)

Provider-initiated symptom screening for tuberculosis in Zimbabwe: diagnostic value and the effect of HIV status.

OBJECTIVE: To assess the diagnostic value of provider-initiated symptom screening for tuberculosis (TB) and how HIV status affects it. METHODS: We performed a secondary analysis of randomly selected participants in a community-based TB-HIV prevalence survey in Harare, Zimbabwe. All completed a five-symptom questionnaire and underwent sputum TB culture and HIV testing. We calculated the sensitivity, specificity, and positive and negative predictive values of various symptoms and used regression analysis to investigate the relationship between symptoms and TB disease. FINDINGS: We found one or more symptoms of TB in 21.2% of 1858 HIV-positive (HIV+) and 9.9% of 7121 HIV-negative (HIV-) participants (P or = 2 weeks' duration, any symptom and a positive sputum culture had sensitivities of 48%, 81% and 65%, respectively; in HIV- participants, the sensitivities were 45%, 71% and 74%, respectively. Symptoms had a similar sensitivity and specificity in HIV+ and HIV- participants, but in HIV+ participants they had a higher positive and a lower negative predictive value. CONCLUSION: Even smear-positive TB may be missed by provider-initiated symptom screening, especially in HIV+ individuals. Symptom screening is useful for ruling out TB, but better TB diagnostics are urgently needed for resource-poor settings

Interpreting Tuberculin Skin Tests in a Population With a High Prevalence of HIV, Tuberculosis, and Nonspecific Tuberculin Sensitivity

Understanding the epidemiology and clinical course of tuberculosis is hampered by the absence of a perfect test for latent tuberculosis infection. The tuberculin skin test (TST) is widely used but suffers poor specificity in those receiving the bacille Calmette-Guérin vaccine and poor sensitivity in individuals with human immunodeficiency virus (HIV) infections. TST responses for a target population in Harare, Zimbabwe (HIV prevalence, 21%), recruited in 2005–2006, were interpreted by using a separate calibration population in Harare, for which interferon-gamma release assays (enzyme-linked immunosorbent spot (ELISpot)) results were also known. Statistical fitting of the responses in the calibration population allowed computation of the probability that an individual in the target population with a given TST and HIV result would have tested ELISpot positive. From this, estimates of the prevalence of tuberculosis infection, and optimal TST cutpoints to minimize misdiagnosis, were computed for different assumptions about ELISpot performance. Different assumptions about the sensitivity and specificity of ELISpot gave a 40%–57% prevalence of tuberculosis infection in the target population (including HIV-infected individuals) and optimal TST cutpoints typically in the 10 mm–20 mm range. However, the optimal cutpoint for HIV-infected individuals was consistently 0 mm. This calibration method may provide a valuable tool for interpreting TST results in other populations

Surface Production Fuels Deep Heterotrophic Respiration in Northern Peatlands

Multiple analyses of dissolved organic carbon (DOC) from pore waters were conducted to define the processes that govern carbon balance in peatlands: (1) source, reactivity, and transport of DOC with respect to vegetation, peat, and age of carbon substrate, (2) reactivity of DOC with respect to molecular size, and (3) lability to photoxidation of surficial DOC. We found that surface organic production fuels heterotrophic respiration at depth in advection-dominated peatlands, especially in fens. Fen DOC was Δ14Cenriched relative to the surrounding fen peat, and fen respiration products were similar to this enriched DOC indicating that DOC was the main microbial substrate. Bog DOC was more variable showing either enrichment in Δ14C at depth or Δ14C values that follow peat values. This variability in bogs is probably controlled by the relative importance of vertical transport of labile carbon substrates within the peat profile versus DOC production from bog peat. These results extended our set of observations to 10 years at one bog-fen pair and add two additional bog-fen pairs to our series of observations. Anaerobic incubations of peat, rinsed free of residual DOC, produced DOC and respiration products that were strikingly similar to the peat values in a bog and two fens. This result demonstrated conclusively that downward advection is the process responsible for the presence of modern DOC found at depth in the peat column. Fen DOC has lower C/N values and up to twice as much LMW (kDa) DOC as bogs due to differences in organic inputs and greater microbial processing. Fluorescence irradiation experiments showed that fen DOC is more photolabile than bog DOC

Predicting the long-term impact of antiretroviral therapy scale-up on population incidence of tuberculosis.

OBJECTIVE: To investigate the impact of antiretroviral therapy (ART) on long-term population-level tuberculosis disease (TB) incidence in sub-Saharan Africa. METHODS: We used a mathematical model to consider the effect of different assumptions about life expectancy and TB risk during long-term ART under alternative scenarios for trends in population HIV incidence and ART coverage. RESULTS: All the scenarios we explored predicted that the widespread introduction of ART would initially reduce population-level TB incidence. However, many modelled scenarios projected a rebound in population-level TB incidence after around 20 years. This rebound was predicted to exceed the TB incidence present before ART scale-up if decreases in HIV incidence during the same period were not sufficiently rapid or if the protective effect of ART on TB was not sustained. Nevertheless, most scenarios predicted a reduction in the cumulative TB incidence when accompanied by a relative decline in HIV incidence of more than 10% each year. CONCLUSIONS: Despite short-term benefits of ART scale-up on population TB incidence in sub-Saharan Africa, longer-term projections raise the possibility of a rebound in TB incidence. This highlights the importance of sustaining good adherence and immunologic response to ART and, crucially, the need for effective HIV preventive interventions, including early widespread implementation of ART

Test Characteristics of Urinary Lipoarabinomannan and Predictors of Mortality among Hospitalized HIV-Infected Tuberculosis Suspects in Tanzania.

Tuberculosis is the most common cause of death among patients with HIV infection living in tuberculosis endemic countries, but many cases are not diagnosed pre-mortem. We assessed the test characteristics of urinary lipoarabinomannan (LAM) and predictors of mortality among HIV-associated tuberculosis suspects in Tanzania. We prospectively enrolled hospitalized HIV-infected patients in Dar es Salaam, with ≥2 weeks of cough or fever, or weight loss. Subjects gave 2 mLs of urine to test for LAM using a commercially available ELISA, ≥2 sputum specimens for concentrated AFB smear and solid media culture, and 40 mLs of blood for culture. Among 212 evaluable subjects, 143 (68%) were female; mean age was 36 years; and the median CD4 count 86 cells/mm(3). 69 subjects (33%) had culture confirmation of tuberculosis and 65 (31%) were LAM positive. For 69 cases of sputum or blood culture-confirmed tuberculosis, LAM sensitivity was 65% and specificity 86% compared to 36% and 98% for sputum smear. LAM test characteristics were not different in patients with bacteremia but showed higher sensitivity and lower specificity with decreasing CD4 cell count. Two month mortality was 64 (53%) of 121 with outcomes available. In multivariate analysis there was significant association of mortality with absence of anti-retroviral therapy (p = 0.004) and a trend toward association with a positive urine LAM (p = 0.16). Among culture-negative patients mortality was 9 (75%) of 12 in LAM positive patients and 27 (38%) of 71 in LAM negative patients (p = 0.02). Urine LAM is more sensitive than sputum smear and has utility for the rapid diagnosis of culture-confirmed tuberculosis in this high-risk population. Mortality data raise the possibility that urine LAM may also be a marker for culture-negative tuberculosis

Equatorial scattering and the structure of the broad-line region in Seyfert nuclei: evidence for a rotating disc

Original article can be found at: http://www3.interscience.wiley.com/ Copyright Royal Astronomical Society. DOI: 10.1111/j.1365-2966.2005.08895.xWe present detailed scattering models confirming that distinctive variations in polarization across the broad Hα line, which are observed in a significant fraction of type 1 Seyfert galaxies, can be understood in terms of a rotating line-emitting disc surrounded by a coplanar scattering region (the equatorial scattering region). The predicted polarization properties are: (i) averaged over wavelength, the position angle (PA) of polarization is aligned with the projected disc rotation axis and hence also with the radio source axis; (ii) the polarization PA rotates across the line profile, reaching equal but opposite (relative to the continuum PA) rotations in the blue and red wings; and (iii) the degree of polarization peaks in the line wings and passes through a minimum in the line core. We identify 11 objects that exhibit these features to different degrees. In order to reproduce the large-amplitude PA rotations observed in some cases, the scattering region must closely surround the emission disc and the latter must itself be a relatively narrow annulus – presumably the Hα-emitting zone of a larger accretion disc. Asymmetries in the polarization spectra may be attributable to several possible causes, including bulk radial infall in the equatorial scattering region, or contamination by polar scattered light. The broad Hα lines do not, in general, exhibit double-peaked profiles, suggesting that a second Hα-emitting component of the broad-line region is present, in addition to the disc.Peer reviewe