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1.  Implications of a 3.472–3.333 Gyr-old subaerial microbial mat from the Barberton greenstone belt, South Africa for the UV environmental conditions on the early Earth 
Modelling suggests that the UV radiation environment of the early Earth, with DNA weighted irradiances of about three orders of magnitude greater than those at present, was hostile to life forms at the surface, unless they lived in specific protected habitats. However, we present empirical evidence that challenges this commonly held view. We describe a well-developed microbial mat that formed on the surface of volcanic littoral sediments in an evaporitic environment in a 3.5–3.3 Ga-old formation from the Barberton greenstone belt. Using a multiscale, multidisciplinary approach designed to strongly test the biogenicity of potential microbial structures, we show that the mat was constructed under flowing water by 0.25 μm filaments that produced copious quantities of extracellular polymeric substances, representing probably anoxygenic photosynthesizers. Associated with the mat is a small colony of rods–vibroids that probably represent sulphur-reducing bacteria. An embedded suite of evaporite minerals and desiccation cracks in the surface of the mat demonstrates that it was periodically exposed to the air in an evaporitic environment. We conclude that DNA-damaging UV radiation fluxes at the surface of the Earth at this period must either have been low (absorbed by CO2, H2O, a thin organic haze from photo-dissociated CH4, or SO2 from volcanic outgassing; scattered by volcanic, and periodically, meteorite dust, as well as by the upper layers of the microbial mat) and/or that the micro-organisms exhibited efficient gene repair/survival strategies.
doi:10.1098/rstb.2006.1896
PMCID: PMC1664690  PMID: 17008224
Early Mid Archaean; Barberton; microfossils; littoral zone; UV environment
2.  Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay 
The ISME Journal  2011;6(4):863-874.
Hydrogen (H2) release from photosynthetic microbial mats has contributed to the chemical evolution of Earth and could potentially be a source of renewable H2 in the future. However, the taxonomy of H2-producing microorganisms (hydrogenogens) in these mats has not been previously determined. With combined biogeochemical and molecular studies of microbial mats collected from Elkhorn Slough, Monterey Bay, California, we characterized the mechanisms of H2 production and identified a dominant hydrogenogen. Net production of H2 was observed within the upper photosynthetic layer (0–2 mm) of the mats under dark and anoxic conditions. Pyrosequencing of rRNA gene libraries generated from this layer demonstrated the presence of 64 phyla, with Bacteriodetes, Cyanobacteria and Proteobacteria dominating the sequences. Sequencing of rRNA transcripts obtained from this layer demonstrated that Cyanobacteria dominated rRNA transcript pyrotag libraries. An OTU affiliated to Microcoleus spp. was the most abundant OTU in both rRNA gene and transcript libraries. Depriving mats of sunlight resulted in an order of magnitude decrease in subsequent nighttime H2 production, suggesting that newly fixed carbon is critical to H2 production. Suppression of nitrogen (N2)-fixation in the mats did not suppress H2 production, which indicates that co-metabolic production of H2 during N2-fixation is not an important contributor to H2 production. Concomitant production of organic acids is consistent with fermentation of recently produced photosynthate as the dominant mode of H2 production. Analysis of rRNA % transcript:% gene ratios and H2-evolving bidirectional [NiFe] hydrogenase % transcript:% gene ratios indicated that Microcoelus spp. are dominant hydrogenogens in the Elkhorn Slough mats.
doi:10.1038/ismej.2011.142
PMCID: PMC3309353  PMID: 22011721
microbial mats; fermentation; hydrogen; hydrogenase; Microcoleus spp.; pyrotags
3.  Addressing diarrhea prevalence in the West African Middle Belt: social and geographic dimensions in a case study for Benin 
Background
In West Africa, the Northern Sahelian zone and the coastal areas are densely populated but the Middle Belt in between is in general sparsely settled. Predictions of climate change foresee more frequent drought in the north and more frequent flooding in the coastal areas, while conditions in the Middle Belt will remain moderate. Consequently, the Middle Belt might become a major area for immigration but there may be constraining factors as well, particularly with respect to water availability. As a case study, the paper looks into the capacity of the Middle Belt zone of Benin, known as the Oueme River Basin (ORB), to reduce diarrhea prevalence. In Benin it links to the Millennium Development Goals on child mortality and environmental sustainability that are currently farthest from realization. However, diarrhea prevalence is only in part due to lack of availability of drinking water from a safe source. Social factors such as hygienic practices and poor sanitation are also at play. Furthermore, we consider these factors to possess the properties of a local public good that suffers from under provision and requires collective action, as individual actions to prevent illness are bound to fail as long as others free ride.
Methods
Combining data from the Demographic Health Survey with various spatial data sets for Benin, we apply mixed effect logit regression to arrive at a spatially explicit assessment of geographical and social determinants of diarrhea prevalence. Starting from an analysis of these factors separately at national level, we identify relevant proxies at household level, estimate a function with geo-referenced independent variables and apply it to evaluate the costs and impacts of improving access to good water in the basin.
Results
First, the study confirms the well established stylized fact on the causes of diarrhea that a household with access to clean water and with good hygienic practices will, irrespective of other conditions, not suffer diarrhea very often. Second, our endogeneity tests show that joint estimation performs better than an instrumental variable regression. Third, our model is stable with respect to its functional form, as competing specifications could not achieve better performance in overall likelihood or significance of parameters. Fourth, it finds that the richer and better educated segments of the population suffer much less from the disease and apparently can secure safe water for their households, irrespective of where they live. Fifth, regarding geographical causes, it indicates that diarrhea prevalence varies with groundwater availability and quality across Benin. Finally, our assessment of costs and benefits reveals that improving physical access to safe water is not expensive but can only marginally improve the overall health situation of the basin, unless the necessary complementary measures are taken in the social sphere.
Conclusion
The ORB provides adequate water resources to accommodate future settlers but it lacks appropriate infrastructure to deliver safe water to households. Moreover, hygienic practices are often deficient. Therefore, a multifaceted approach is needed that acknowledges the public good aspects of health situation and consequently combines collective action with investments into water sources with improved management of public wells and further educational efforts to change hygienic practices.
doi:10.1186/1476-072X-7-17
PMCID: PMC2377241  PMID: 18433488
4.  Palaeoclimates: the first two billion years 
Earth's climate during the Archaean remains highly uncertain, as the relevant geologic evidence is sparse and occasionally contradictory. Oxygen isotopes in cherts suggest that between 3.5 and 3.2 Gyr ago (Ga) the Archaean climate was hot (55–85 °C); however, the fact that these cherts have experienced only a modest amount of weathering suggests that the climate was temperate, as today. The presence of diamictites in the Pongola Supergroup and the Witwatersrand Basin of South Africa suggests that by 2.9 Ga the climate was glacial. The Late Archaean was relatively warm; then glaciation (possibly of global extent) reappeared in the Early Palaeoproterozoic, around 2.3–2.4 Ga.
Fitting these climatic constraints with a model requires high concentrations of atmospheric CO2 or CH4, or both. Solar luminosity was 20–25% lower than today, so elevated greenhouse gas concentrations were needed just to keep the mean surface temperature above freezing. A rise in O2 at approximately 2.4 Ga, and a concomitant decrease in CH4, provides a natural explanation for the Palaeoproterozoic glaciations. The Mid-Archaean glaciations may have been caused by a drawdown in H2 and CH4 caused by the origin of bacterial sulphate reduction. More work is needed to test this latter hypothesis.
doi:10.1098/rstb.2006.1839
PMCID: PMC1868609  PMID: 16754607
palaeoclimate; Precambrian glaciations; methane; greenhouse effect; faint young Sun problem; sulphur isotopes
5.  A preliminary assessment of PM10 and TSP concentrations in Tuticorin, India 
The respirable particulate matter (RPM; PM10) and total suspended particulate matter (TSP) concentrations in ambient air in Tuticorin, India, were preliminarily estimated. Statistical analyses on so-generated database were performed to infer frequency distributions and to identify dominant meteorological factor affecting the pollution levels. Both the RPM and TSP levels were well below the permissible limits set by the US Environmental Protection Agency. As expected, lognormal distribution always fit the data during the study period. However, fit with the normal was also acceptable except for very few seasons. The RPM concentrations ranged between 20.9 and 198.2 μg/m3, while the TSP concentrations varied from 51.5 to 333.3 μg/m3 during the study period. There was a better correlation between PM10–100 and TSP concentrations than that of PM10 (RPM) and TSP concentrations, but the correlation of RPM fraction was also acceptable. It was found that wind speed was the most important meteorological factor affecting the concentrations of the pollutants of present interest. Significant seasonal variations in the pollutant concentrations of present interest were found at 5% significance level except for TSP concentrations in the year 2006.
doi:10.1007/s11869-009-0055-x
PMCID: PMC2860090  PMID: 20495598
ANOVA; Coal-fired power station; Correlation; Frequency distribution; RPM; Seasonal variation; TSP
6.  A cost benefit analysis of an enhanced seat belt enforcement program in South Africa 
Injury Prevention  2005;11(2):102-105.
Objective: To examine whether a program to increase the wearing of seat belts in a South African urban area would be worthwhile in societal terms.
Design: A cost benefit analysis of a one year enhanced seat belt enforcement program in eThekwini (Durban) Municipality.
Methods: Data were drawn from two main sources—a 1998 study of the cost of road crashes in South Africa and, given the absence of other data, a meta-analysis of the effectiveness of various types of interventions to reduce road crash casualties in the United States—and were analyzed using cost benefit analysis.
Results: A program designed to enforce greater wearing of seat belts, estimated to cost 2 million rand in one year, could be reasonably expected to increase seat belt usage rates by 16 percentage points and reduce fatalities and injuries by 9.5%. This would result in saved social costs of 13.6 million rand in the following year or a net present value of 11.6 million rand. There would also be favorable consequences for municipal finances.
Conclusions: Investment in a program to increase seat belt wearing rates is highly profitable in societal terms.
doi:10.1136/ip.2004.007179
PMCID: PMC1730202  PMID: 15805439
7.  Early anaerobic metabolisms 
Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were probably driven by the cycling of H2 and Fe2+ through primary production conducted by anoxygenic phototrophs. Interesting and dynamic ecosystems would have also been driven by the microbial cycling of sulphur and nitrogen species, but their activity levels were probably not so great. Despite the diversity of potential early ecosystems, rates of primary production in the early-Earth anaerobic biosphere were probably well below those rates observed in the marine environment. We shift our attention to the Earth environment at 3.8 Gyr ago, where the earliest marine sediments are preserved. We calculate, consistent with the carbon isotope record and other considerations of the carbon cycle, that marine rates of primary production at this time were probably an order of magnitude (or more) less than today. We conclude that the flux of reduced species to the Earth surface at this time may have been sufficient to drive anaerobic ecosystems of sufficient activity to be consistent with the carbon isotope record. Conversely, an ecosystem based on oxygenic photosynthesis was also possible with complete removal of the oxygen by reaction with reduced species from the mantle.
doi:10.1098/rstb.2006.1906
PMCID: PMC1664682  PMID: 17008221
Archaean; evolution; hydrogen; anoxygenic photosynthesis; iron; metabolism
8.  (8-Amino­quinoline-κ2 N,N′)bis­(1,1,1,5,5,5-hexa­fluoro­pentane-2,4-dionato-κ2 O,O′)cobalt(II) 
In the title compound, [Co(C5HF6O2)2(C9H8N2)], the CoII centre exhibits a pseudooctahedral coordination geometry, comprising two N-atom donors from the bidentate amino­quinoline ligand and four O-atom donor atoms from two bidentate chelating 1,1,1,5,5,5-hexafluoropentane-2,4-dionate ligands. In the crystal, molecules are linked via pairs of N—H⋯O hydrogen bonds, forming inversion dimers. These dimers are further connected through π–π interactions between neighbouring quinoline rings [centroid–centroid distance = 3.472 (2) Å], and stack along the c axis.
doi:10.1107/S1600536812011312
PMCID: PMC3343848  PMID: 22589822
9.  Two steps of insulin receptor internalization depend on different domains of the beta-subunit [published erratum appears in J Cell Biol 1993 Nov;123(4):1047] 
The Journal of Cell Biology  1993;122(6):1243-1252.
The internalization of signaling receptors such as the insulin receptor is a complex, multi-step process. The aim of the present work was to determine the various steps in internalization of the insulin receptor and to establish which receptor domains are implicated in each of these by the use of receptors possessing in vitro mutations. We find that kinase activation and autophosphorylation of all three regulatory tyrosines 1146, 1150, and 1151, but not tyrosines 1316 and 1322 in the COOH-terminal domain, are required for the ligand-specific stage of the internalization process; i.e., the surface redistribution of the receptor from microvilli where initial binding occurs to the nonvillous domain of the cell. Early intracellular steps in insulin signal transduction involving the activation of phosphatidylinositol 3'-kinase are not required for this redistribution. The second step of internalization consists in the anchoring of the receptors in clathrin- coated pits. In contrast to the first ligand specific step, this step is common to many receptors including those for transport proteins and occurs in the absence of kinase activation and receptor autophosphorylation, but requires a juxta-membrane cytoplasmic segment of the beta-subunit of the receptor including a NPXY sequence. Thus, there are two independent mechanisms controlling insulin receptor internalization which depend on different domains of the beta-subunit.
PMCID: PMC2119852  PMID: 8376461
10.  Interleukin-6 undergoes transition from paracrine growth inhibitor to autocrine stimulator during human melanoma progression [published erratum appears in J Cell Biol 1993 Apr;121(2):following 477] 
The Journal of Cell Biology  1993;120(5):1281-1288.
The ability to penetrate the dermal basement membrane and subsequently proliferate in the underlying mesenchyme is one of the key steps in malignant progression of human melanomas. We previously undertook studies aimed at assessing how normal dermal fibroblasts (one of the main cellular components of mesenchyme) may affect the growth of human melanoma cells and facilitate the overgrowth of malignant subpopulations (Cornil, I., D. Theodorescu, S. Man, M. Herlyn, J. Jambrosic, and R. S. Kerbel. 1991. Proc. Natl. Acad. Sci. USA. 88:6028- 6032). We found that melanoma cell lines from early-stage (metastatically incompetent) lesions were growth inhibited whereas those from advanced-stage (metastatically competent) lesions were stimulated under the same conditions by co-culture with fibroblasts; conditioned medium from such cells gave the same result. Subsequent studies using biochemical purification and neutralizing antibodies revealed the inhibitory activity to be identical to interleukin-6 (IL- 6). We now report that addition of purified recombinant human IL-6 resulted in a growth inhibition in vitro by G1/G0 arrest of early, but not advanced stage melanoma cells. Despite this alteration in response there was no significant difference in melanoma cell lines of varying malignancy in respect to their expression of genes encoding the IL-6 receptor, or gp130, the IL-6 signal transducer. Scatchard analysis also revealed similar [125I]IL-6 binding activities in both IL-6 sensitive and resistant groups. However, studies of IL-6 production indicated that five out eight IL-6 melanoma cell lines known to be resistant to exogenous IL-6-mediated growth inhibition constitutively expressed mRNA for IL-6; they also secreted bioactive IL-6 into culture medium. To assess the possible role of this endogenous IL-6 in melanoma cell growth, antisense oligonucleotides to the IL-6 gene were added to cultures of melanoma cells. This resulted in a significant growth inhibition only in cell lines that produced endogenous IL-6. In contrast, neutralizing antibodies to IL-6 were ineffective in causing such growth inhibition. This indicates that endogenous IL-6 may behave as a growth stimulator by an intracellular ("private") autocrine mechanism. Thus, a single cytokine, IL-6, can switch from behaving as a paracrine growth inhibitor to an autocrine growth stimulator within the same cell lineage during malignant tumor progression. Such a switch may contribute to the growth advantage of metastatically competent melanoma cells at the primary or distant organ sites and thereby facilitate progression of disease.
PMCID: PMC2119719  PMID: 8436594
11.  Substantial Regional Differences in Human Herpesvirus 8 Seroprevalence in Sub-Saharan Africa: Insights on the Origin of the “KS Belt” 
Equatorial Africa has among the highest incidences of Kaposi’s sarcoma (KS) in the world, thus earning the name “KS Belt.” This was the case even prior to the HIV . To date, there is no clear evidence that HHV-8 seroprevalence is higher in this region, but interpretation of the available literature is tempered by differences in serologic assays used across studies. We examined representatively sampled ambulatory adults in Uganda, which is in the “KS Belt”, and in Zimbabwe and South Africa which are outside the Belt, for HHV-8 antibodies. All serologic assays were uniformly performed in the same reference laboratory by the same personnel. In the base-case serologic algorithm, seropositivity was defined by reactivity in an immunofluorescence assay or in two enzyme immunoassays. A total of 2375 participants were examined. In Uganda, HHV-8 seroprevalence was high early in adulthood (35.5% by age 21) without significant change thereafter. In contrast, HHV-8 seroprevalence early in adulthood was lower in Zimbabwe and South Africa (13.7% and 10.8%, respectively), but increased with age. After age adjustment, Ugandans had 3.24-fold greater odds of being HHV-8-infected than South Africans (p<0.001) and 2.22-fold greater odds than Zimbabweans (p<0.001). Inferences were unchanged using all other serologic algorithms evaluated. In conclusion, HHV-8 infection is substantially more common in Uganda than in Zimbabwe and South Africa. These findings help explain the high KS incidence in the “KS Belt” and underscore the importance of a uniform approach to HHV-8 antibody testing.
doi:10.1002/ijc.25235
PMCID: PMC2895015  PMID: 20143397
12.  Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats 
PLoS ONE  2011;6(9):e25173.
Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.
doi:10.1371/journal.pone.0025173
PMCID: PMC3179486  PMID: 21966446
13.  Earth’s Earliest Atmospheres 
Earth is the one known example of an inhabited planet and to current knowledge the likeliest site of the one known origin of life. Here we discuss the origin of Earth’s atmosphere and ocean and some of the environmental conditions of the early Earth as they may relate to the origin of life. A key punctuating event in the narrative is the Moon-forming impact, partly because it made Earth for a short time absolutely uninhabitable, and partly because it sets the boundary conditions for Earth’s subsequent evolution. If life began on Earth, as opposed to having migrated here, it would have done so after the Moon-forming impact. What took place before the Moon formed determined the bulk properties of the Earth and probably determined the overall compositions and sizes of its atmospheres and oceans. What took place afterward animated these materials. One interesting consequence of the Moon-forming impact is that the mantle is devolatized, so that the volatiles subsequently fell out in a kind of condensation sequence. This ensures that the volatiles were concentrated toward the surface so that, for example, the oceans were likely salty from the start. We also point out that an atmosphere generated by impact degassing would tend to have a composition reflective of the impacting bodies (rather than the mantle), and these are almost without exception strongly reducing and volatile-rich. A consequence is that, although CO- or methane-rich atmospheres are not necessarily stable as steady states, they are quite likely to have existed as long-lived transients, many times. With CO comes abundant chemical energy in a metastable package, and with methane comes hydrogen cyanide and ammonia as important albeit less abundant gases.
Life probably arose on Earth after the moon-forming impact. It and subsequent impacts probably created transient reducing methane- or CO-rich atmospheres that provided abundant chemical energy.
doi:10.1101/cshperspect.a004895
PMCID: PMC2944365  PMID: 20573713
14.  Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic 
Polar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived from Proteobacteria and Cyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation of Actinobacteria and Alphaproteobacteria in the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.
doi:10.1128/AEM.06354-11
PMCID: PMC3255749  PMID: 22081564
15.  Antiquity of the biological sulphur cycle: evidence from sulphur and carbon isotopes in 2700 million-year-old rocks of the Belingwe Belt, Zimbabwe. 
Sulphur and carbon isotopic analyses on small samples of kerogens and sulphide minerals from biogenic and non-biogenic sediments of the 2.7 x 10(9) years(Ga)-old Belingwe Greenstone Belt (Zimbabwe) imply that a complex biological sulphur cycle was in operation. Sulphur isotopic compositions display a wider range of biological fractionation than hitherto reported from the Archaean. Carbon isotopic values in kerogen record fractionations characteristic of rubisco activity methanogenesis and methylotrophy and possibly anoxygenic photosynthesis. Carbon and sulphur isotopic fractionations have been interpreted in terms of metabolic processes in 2.7 Ga prokaryote mat communities, and indicate the operation of a diverse array of metabolic processes. The results are consistent with models of early molecular evolution derived from ribosomal RNA.
doi:10.1098/rspb.2000.1338
PMCID: PMC1088579  PMID: 11209879
16.  Surface Orientation Affects the Direction of Cone Growth by Leptolyngbya sp. Strain C1, a Likely Architect of Coniform Structures Octopus Spring (Yellowstone National Park) 
Laminated, microbially produced stromatolites within the rock record provide some of the earliest evidence for life on Earth. The chemical, physical, and biological factors that lead to the initiation of these organosedimentary structures and shape their morphology are unclear. Modern coniform structures with morphological features similar to stromatolites are found on the surface of cyanobacterial/microbial mats. They display a vertical element of growth, can have lamination, can be lithified, and observably grow with time. To begin to understand the microbial processes and interactions required for cone formation, we determined the phylogenetic composition of the microbial community of a coniform structure from a cyanobacterial mat at Octopus Spring, Yellowstone National Park, and reconstituted coniform structures in vitro. The 16S rRNA clone library from the coniform structure was dominated by Leptolyngbya sp. Other cyanobacteria and heterotrophic bacteria were present in much lower abundance. The same Leptolyngbya sp. identified in the clone library was also enriched in the laboratory and could produce cones in vitro. When coniform structures were cultivated in the laboratory, the initial incubation conditions were found to influence coniform morphology. In addition, both the angle of illumination and the orientation of the surface affected the angle of cone formation demonstrating how external factors can influence coniform, and likely, stromatolite morphology.
doi:10.1128/AEM.03008-12
PMCID: PMC3568628  PMID: 23241986
17.  Evolution of resistance in paediatric patients with failure on antiretroviral therapy 
Introduction
HIV-1 resistance data to inform treatment sequencing are limited for children with virological failure on first- and second-line antiretroviral therapy (ART) in Sub-Saharan Africa.
Methods
HIV-1-infected children aged ≤15 years were retrospectively identified from an ART cohort in Cape Town, South Africa (2003 to 2010). First-line ART was either non-nucleoside reverse transcriptase inhibitor (NNRTI) or lopinavir/ritonavir-based (with the exception of children <6 months old who received full-dose ritonavir as the sole protease inhibitor (PI) from 2004 to 2007). Second-line ART was the alternative regimen. Treatment outcomes, including virological failure, loss to care, death or remaining in care, were determined. Genotypic resistance testing was conducted on stored serum from children at first- or second-line virological failure (two consecutive HIV-1 RNA levels >1000 copies/ml). International AIDS Society criteria defined resistance mutations.
Results
Of 472 children starting first-line ART, 352 (75%) remained in care, 45 (9%) were lost and 4 (1%) died on first-line treatment. Seventy-one (15%) had observed virological failure, and 37 of these children had specimens available for genotype testing. Eight children (22%) had wild-type virus, seven (19%) had thymidine analog mutations (TAMs), 24 (65%) had NNRTI resistance and two (5.4%) had multiple protease resistance (PR). Of the 78 children who received second-line ART, 54 (71%) remained in care, 6 (8%) were lost and 1 (1%) died during second-line treatment. Fifteen (20%) had observed virological failure; 13 had samples available for genotype. Three (23%) had wild-type virus, eight (62%) had TAMs, nine (69%) had NNRTI resistance, and five (38%) had multiple PI resistance all of whom had received full-dose ritonavir.
Conclusion
Although virological failure was infrequent in children on first- and second-line ART, rates of observed resistance including multiple PR resistance after failure were high. Reasons for high rates of resistance include use of full-dose ritonavir and continued viremia. Wild-type virus was common, suggesting poor adherence or challenges in correct dosing. Genotype resistance testing in children with virological failure may optimize selection of subsequent regimens and inform recommendations for sequencing of existing ART.
doi:10.7448/IAS.15.6.18086
PMCID: PMC3512453
18.  Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats 
Past studies of hydrogen cycling in hypersaline microbial mats have shown an active nighttime cycle, with production largely from Cyanobacteria and consumption from sulfate-reducing bacteria (SRB). However, the mechanisms and magnitude of hydrogen cycling have not been extensively studied. Two mats types near Guerrero Negro, Mexico—permanently submerged Microcoleus microbial mat (GN-S), and intertidal Lyngbya microbial mat (GN-I)—were used in microcosm diel manipulation experiments with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), molybdate, ammonium addition, and physical disruption to understand the processes responsible for hydrogen cycling between mat microbes. Across microcosms, H2 production occurred under dark anoxic conditions with simultaneous production of a suite of organic acids. H2 production was not significantly affected by inhibition of nitrogen fixation, but rather appears to result from constitutive fermentation of photosynthetic storage products by oxygenic phototrophs. Comparison to accumulated glycogen and to CO2 flux indicated that, in the GN-I mat, fermentation released almost all of the carbon fixed via photosynthesis during the preceding day, primarily as organic acids. Across mats, although oxygenic and anoxygenic phototrophs were detected, cyanobacterial [NiFe]-hydrogenase transcripts predominated. Molybdate inhibition experiments indicated that SRBs from a wide distribution of DsrA phylotypes were responsible for H2 consumption. Incubation with 13C-acetate and NanoSIMS (secondary ion mass-spectrometry) indicated higher uptake in both Chloroflexi and SRBs relative to other filamentous bacteria. These manipulations and diel incubations confirm that Cyanobacteria were the main fermenters in Guerrero Negro mats and that the net flux of nighttime fermentation byproducts (not only hydrogen) was largely regulated by the interplay between Cyanobacteria, SRBs, and Chloroflexi.
doi:10.3389/fmicb.2014.00061
PMCID: PMC3935151  PMID: 24616716
microbial mats; hydrogen; fermentation; Guerrero Negro; NanoSIMS
19.  Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat 
Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.
doi:10.3389/fmicb.2014.00011
PMCID: PMC3902354  PMID: 24478768
electron transfer; hot lake; microbial mats; microelectrodes; sulfur cycle; sequence analysis
20.  Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia 
Astrobiology  2013;13(12):1103-1124.
Abstract
Microbially induced sedimentary structures (MISS) result from the response of microbial mats to physical sediment dynamics. MISS are cosmopolitan and found in many modern environments, including shelves, tidal flats, lagoons, riverine shores, lakes, interdune areas, and sabkhas. The structures record highly diverse communities of microbial mats and have been reported from numerous intervals in the geological record up to 3.2 billion years (Ga) old. This contribution describes a suite of MISS from some of the oldest well-preserved sedimentary rocks in the geological record, the early Archean (ca. 3.48 Ga) Dresser Formation, Western Australia. Outcrop mapping at the meter to millimeter scale defined five sub-environments characteristic of an ancient coastal sabkha. These sub-environments contain associations of distinct macroscopic and microscopic MISS. Macroscopic MISS include polygonal oscillation cracks and gas domes, erosional remnants and pockets, and mat chips. Microscopic MISS comprise tufts, sinoidal structures, and laminae fabrics; the microscopic laminae are composed of primary carbonaceous matter, pyrite, and hematite, plus trapped and bound grains. Identical suites of MISS occur in equivalent environmental settings through the entire subsequent history of Earth including the present time. This work extends the geological record of MISS by almost 300 million years. Complex mat-forming microbial communities likely existed almost 3.5 billion years ago. Key Words: Archean—Biofilms—Microbial mats—Early Earth—Evolution. Astrobiology 13, 1103–1124.
doi:10.1089/ast.2013.1030
PMCID: PMC3870916  PMID: 24205812
21.  Polyamine Analogues Bind Human Serum Albumin 
Biomacromolecules  2007;8(10):3177-3183.
Polyamine analogues show antitumor activity in experimental models and their ability to alter activity of cytotoxic chemotherapeutic agents in breast cancer is well documented. Association of polyamines with nucleic acids and protein is included in their mechanism of action. The aim of this study was to examine the interaction of human serum albumin (HSA) with several polyamine analogues such as 1,11-diamino-4,8-diazaundecane (333), 3,7,11,15-tetrazaheptadecane.4HCl (BE-333) and 3,7,11,15,19-pentazahenicosane.5HCl (BE-3333) in aqueous solution at physiological conditions, using a constant protein concentration and various polyamine contents (μM to mM). FTIR, UV-visible and CD spectroscopic methods were used to determine the polyamine binding mode and the effects of polyamine complexation on protein stability and secondary structure.
Structural analysis showed that polyamines bind non-specifically (H-bonding) via polypeptide polar groups with binding constants of K333 = 9.30 × 103 M−1, KBE-333 = 5.63 × 102 M−1 and KBE-3333 = 3.66 × 102 M−1. The protein secondary structure showed major alterations with reduction of α-helix from 55% (free protein) to 43–50% and increase of β-sheet from 17% (free protein) to 29–36% in the 333-, BE-333- and BE-3333 complexes, indicating a partial protein unfolding upon polyamine interaction. HSA structure was less perturbed by polyamine analogues than those of the biogenic polyamines.
doi:10.1021/bm700697a
PMCID: PMC2548305  PMID: 17887793
polyamine analogues; protein; HSA; binding mode; secondary structure; FTIR; CD spectroscopy
22.  Metagenomic and Metabolic Profiling of Nonlithifying and Lithifying Stromatolitic Mats of Highborne Cay, The Bahamas 
PLoS ONE  2012;7(5):e38229.
Background
Stromatolites are laminated carbonate build-ups formed by the metabolic activity of microbial mats and represent one of the oldest known ecosystems on Earth. In this study, we examined a living stromatolite located within the Exuma Sound, The Bahamas and profiled the metagenome and metabolic potential underlying these complex microbial communities.
Methodology/Principal Findings
The metagenomes of the two dominant stromatolitic mat types, a nonlithifying (Type 1) and lithifying (Type 3) microbial mat, were partially sequenced and compared. This deep-sequencing approach was complemented by profiling the substrate utilization patterns of the mats using metabolic microarrays. Taxonomic assessment of the protein-encoding genes confirmed previous SSU rRNA analyses that bacteria dominate the metagenome of both mat types. Eukaryotes comprised less than 13% of the metagenomes and were rich in sequences associated with nematodes and heterotrophic protists. Comparative genomic analyses of the functional genes revealed extensive similarities in most of the subsystems between the nonlithifying and lithifying mat types. The one exception was an increase in the relative abundance of certain genes associated with carbohydrate metabolism in the lithifying Type 3 mats. Specifically, genes associated with the degradation of carbohydrates commonly found in exopolymeric substances, such as hexoses, deoxy- and acidic sugars were found. The genetic differences in carbohydrate metabolisms between the two mat types were confirmed using metabolic microarrays. Lithifying mats had a significant increase in diversity and utilization of carbon, nitrogen, phosphorus and sulfur substrates.
Conclusion/Significance
The two stromatolitic mat types retained similar microbial communities, functional diversity and many genetic components within their metagenomes. However, there were major differences detected in the activity and genetic pathways of organic carbon utilization. These differences provide a strong link between the metagenome and the physiology of the mats, as well as new insights into the biological processes associated with carbonate precipitation in modern marine stromatolites.
doi:10.1371/journal.pone.0038229
PMCID: PMC3360630  PMID: 22662280
23.  Increased Toxoplasma gondii positivity relative to age in 125 Scottish sheep flocks; evidence of frequent acquired infection 
Veterinary Research  2011;42(1):121.
Toxoplasma gondii seroprevalence was determined in 3333 sheep sera from 125 distinct sheep flocks in Scotland, with the majority of flocks being represented by 27 samples, which were collected between July 2006 and August 2008. The selected farms give a representative sample of 14 400 sheep holdings identified in the Scottish Government census data from 2004. Overall T. gondii seroprevalence, at individual sheep level, was determined to be 56.6%; each flock tested, had at least a single positive animal and in four flocks all ewes tested positive. The seroprevalence of sheep increased from 37.7% in one year old stock to 73.8% in ewes that were older than six years, showing that acquired infections during the life of the animals is frequent and that environmental contamination by T. gondii oocysts must be significant. The median within-flock seroprevalence varied significantly across Scotland, with the lowest seroprevalence of 42.3% in the South and the highest seroprevalence of 69.2% in the far North of Scotland and the Scottish Islands, while the central part of Scotland had a seroprevalence of 57.7%. This distribution disequilibrium may be due to the spread and survival of oocysts on pasture and lambing areas. A questionnaire accompanying sampling of flocks identified farms that used Toxovax®, a commercial vaccine that protects sheep from abortion due to T. gondii infection. Only 24.7% of farmers used the vaccine and the vaccine did not significantly affect the within flock seroprevalence for T. gondii. The implications for food safety and human infection are discussed.
doi:10.1186/1297-9716-42-121
PMCID: PMC3284422  PMID: 22189159
24.  DNA Gyrase Inhibition Assays Are Necessary To Demonstrate Fluoroquinolone Resistance Secondary to gyrB Mutations in Mycobacterium tuberculosis▿ 
Antimicrobial Agents and Chemotherapy  2011;55(10):4524-4529.
The main mechanism of fluoroquinolone (FQ) resistance in Mycobacterium tuberculosis is mutation in DNA gyrase (GyrA2GyrB2), especially in gyrA. However, the discovery of unknown mutations in gyrB whose implication in FQ resistance is unclear has become more frequent. We investigated the impact on FQ susceptibility of eight gyrB mutations in M. tuberculosis clinical strains, three of which were previously identified in an FQ-resistant strain. We measured FQ MICs and also DNA gyrase inhibition by FQs in order to clarify the role of these mutations in FQ resistance. Wild-type GyrA, wild-type GyrB, and mutant GyrB subunits produced from engineered gyrB alleles by mutagenesis were overexpressed in Escherichia coli, purified to homogeneity, and used to reconstitute highly active gyrase complexes. MICs and DNA gyrase inhibition were determined for moxifloxacin, gatifloxacin, ofloxacin, levofloxacin, and enoxacin. We demonstrated that the eight substitutions in GyrB (D473N, P478A, R485H, S486F, A506G, A547V, G551R, and G559A), recently identified in FQ-resistant clinical strains or encountered in M. tuberculosis strains isolated in France, are not implicated in FQ resistance. These results underline that, as opposed to phenotypic FQ susceptibility testing, the DNA gyrase inhibition assay is the only way to prove the role of a DNA gyrase mutation in FQ resistance. Therefore, the use of FQ in the treatment of tuberculosis (TB) patients should not be ruled out only on the basis of the presence of mutations in gyrB.
doi:10.1128/AAC.00707-11
PMCID: PMC3186962  PMID: 21768507
25.  Identification of Members of the Metabolically Active Microbial Populations Associated with Beggiatoa Species Mat Communities from Gulf of Mexico Cold-Seep Sediments 
In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange- or white-pigmented Beggiatoa spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333 Archaea and 329 Bacteria clones. Analysis of the Archaea clones indicated that all sediment depths associated with overlying orange- and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total Archaea clones), a lineage related to the methanogenic order Methanosarcinales. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the γ and δ classes of Proteobacteria, whereas clones related to δ-Proteobacteria dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the Bacteria and Archaea community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region.
doi:10.1128/AEM.70.9.5447-5458.2004
PMCID: PMC520919  PMID: 15345432

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