Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))

Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

TULIPs: tunable, light-controlled interacting protein tags for cell biology

Naturally photoswitchable proteins offer a means of directly manipulating the formation of protein complexes that drive a diversity of cellular processes. We developed tunable light-inducible dimerization tags (TULIPs) based on a synthetic interaction between the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) and an engineered PDZ domain (ePDZ). TULIPs can recruit proteins to diverse structures in living yeast and mammalian cells, either globally or with precise spatial control using a steerable laser. The equilibrium binding and kinetic parameters of the interaction are tunable by mutation, making TULIPs readily adaptable to signaling pathways with varying sensitivities and response times. We demonstrate the utility of TULIPs by conferring light sensitivity to functionally distinct components of the yeast mating pathway and by directing the site of cell polarization.     

Pregnancy and Infant Outcomes among HIV-Infected Women Taking Long-Term ART with and without Tenofovir in the DART Trial

Background

Few data have described long-term outcomes for infants born to HIV-infected African women taking antiretroviral therapy (ART) in pregnancy. This is particularly true for World Health Organization (WHO)–recommended tenofovir-containing first-line regimens, which are increasingly used and known to cause renal and bone toxicities; concerns have been raised about potential toxicity in babies due to in utero tenofovir exposure.

Methods and Findings

Pregnancy outcome and maternal/infant ART were collected in Ugandan/Zimbabwean HIV-infected women initiating ART during The Development of AntiRetroviral Therapy in Africa (DART) trial, which compared routine laboratory monitoring (CD4; toxicity) versus clinically driven monitoring. Women were followed 15 January 2003 to 28 September 2009. Infant feeding, clinical status, and biochemistry/haematology results were collected in a separate infant study. Effect of in utero ART exposure on infant growth was analysed using random effects models.382 pregnancies occurred in 302/1,867 (16%) women (4.4/100 woman-years [95% CI 4.0–4.9]). 226/390 (58%) outcomes were live-births, 27 (7%) stillbirths (≥22 wk), and 137 (35%) terminations/miscarriages (<22 wk). Of 226 live-births, seven (3%) infants died <2 wk from perinatal causes and there were seven (3%) congenital abnormalities, with no effect of in utero tenofovir exposure (p>0.4). Of 219 surviving infants, 182 (83%) enrolled in the follow-up study; median (interquartile range [IQR]) age at last visit was 25 (12–38) months. From mothers'' ART, 62/9/111 infants had no/20%–89%/≥90% in utero tenofovir exposure; most were also zidovudine/lamivudine exposed. All 172 infants tested were HIV-negative (ten untested). Only 73/182(40%) infants were breast-fed for median 94 (IQR 75–212) days. Overall, 14 infants died at median (IQR) age 9 (3–23) months, giving 5% 12-month mortality; six of 14 were HIV-uninfected; eight untested infants died of respiratory infection (three), sepsis (two), burns (one), measles (one), unknown (one). During follow-up, no bone fractures were reported to have occurred; 12/368 creatinines and seven out of 305 phosphates were grade one (16) or two (three) in 14 children with no effect of in utero tenofovir (p>0.1). There was no evidence that in utero tenofovir affected growth after 2 years (p = 0.38). Attained height- and weight for age were similar to general (HIV-uninfected) Ugandan populations. Study limitations included relatively small size and lack of randomisation to maternal ART regimens.

Conclusions

Overall 1-year 5% infant mortality was similar to the 2%–4% post-neonatal mortality observed in this region. No increase in congenital, renal, or growth abnormalities was observed with in utero tenofovir exposure. Although some infants died untested, absence of recorded HIV infection with combination ART in pregnancy is encouraging. Detailed safety of tenofovir for pre-exposure prophylaxis will need confirmation from longer term follow-up of larger numbers of exposed children.

Trial registration

www.controlled-trials.com ISRCTN13968779 Please see later in the article for the Editors'' Summary     

Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1

Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.     

Dietary conjugated linoleic acid in the cis-9, trans-11 isoform reduces parathyroid hormone in male, but not female, rats

Previously, a mixture of conjugated linoleic acid (CLA) isoforms reduced parathyroid hormone (PTH) in male rats over 8 weeks. The objective herein was to determine which isoform caused the reduction in PTH; whether the effect was sex specific; and whether CLA-induced reductions in PTH were sustained. Male and female weanling rats (n=48) were randomized to a control diet or one made with 0.5% of the diet as cis-9, trans-11 (c9,t11) CLA, 0.5% of the diet as trans-10, cis-12 (t10,c12) CLA or these CLA in a mixture. Measurements made after 4, 8 and 16 weeks were body weight, bioactive PTH, ionized Ca, whole-body and regional bone mineral density (BMD) using dual-energy X-ray absorptiometry. With the use of a factorial design, a sexxc9,t11 CLA interaction was observed that reduced PTH (139.5+/-63.9 vs. 95.8+/-42.4 pg/ml, P=.02) in male rats only. No other effects of c9,t11 CLA were observed. Regarding t10,c12 CLA, no interaction effects were observed, but a main effect was observed to reduce lumbar spine BMD (0.265+/-0.044 vs. 0.255+/-0.044 g/cm(2), P<.01) along with reduced retention of Ca and P at Week 4. No other dietary effects were observed. In summary, the c9,t11 CLA isoform is responsible for reduced PTH and this effect is sex specific; this was true whether fed as a pure isomer or mixed with an equal amount of t10,c12 CLA. Whether such reductions in PTH might be observed in females lacking sex hormones such as ovariectomized rats and also in humans is required to expand health implications of dietary CLA.     

Using Fault Tree Analysis to Assess Bioterrorist Risks to the U.S. Food Supply

Concerns about terrorist use of biological agents have increased at state and federal levels and in the popular press. Vulnerability of U.S. agricultural assets to bioterrorism has received less attention. A bioterrorist could use the U.S. food supply system to deliver a bioagent to a human target or use a bioagent to destroy it's inputs or infrastructure. Establishing effective agriculture security programs requires condensing generalizations about such bioterrorist threats into specific attack scenarios. This paper suggests a two-stage process to achieve this: problem formulation to define and rank scenarios, then quantitative risk assessment of selected, more highly ranked, scenarios. The quantitative component is illustrated for two specific scenarios: the actual 1984 Rajneeshee incident in Oregon and a hypothetical release of oral anthrax into the food supply system. The fault tree analysis of these scenarios suggests that the food supply system may be a less than optimal bioagent delivery mechanism, particularly if the objective is a mass casualty attack, as a number of events must occur simultaneously with reasonable probability if a bioagent is likely to be deployed effectively. In addition, an environmentally stable bioagent would be required if only the food system were used to deliver it to human consumers, but early detection of an intentional release common bioagent may be difficult absent specific intelligence or “unusual” epidemiological circumstances.     

Diurnal variations in the carbon chemistry of two acidic peatland streams in north-east Scotland

1. Two acidic peatland upland streams in north‐east Scotland draining catchments of 1.3 and 41.4 km² were sampled each season for 2 years to investigate diurnal variations in dissolved and gaseous forms of carbon. Stream metabolism, alkalinity, discharge, pH, air and water temperatures were measured to aid data interpretation. 2. Free CO₂ showed marked diurnal variation with lowest concentrations during the period from late morning to early afternoon and highest during the hours of darkness. Although alkalinity and pH also showed some diurnal fluctuations, in comparison with other more productive alkaline systems, variation was small. Dissolved organic carbon (DOC) showed no significant diurnal pattern. However, significant changes in stream discharge influenced DOC concentrations, as well as over‐riding diurnal patterns of free CO₂, alkalinity and pH. 3. The highest diurnal ratios (maximum concentration/minimum concentration) in CO₂, gross primary productivity (GPP) and community respiration (CR) occurred in spring and summer and the lowest in autumn and winter. Variation in biotic in‐stream processes caused changes in CO₂ concentrations and temperature affected both the solubility of CO₂ and changes in up‐stream CO₂ inputs. There was no significant difference in diurnal fluctuations between the two orders of stream studied. 4. The mean GPP (as CO₂) was 0.81 g CO₂ m^?2 day^?1 and mean CR 2.67 g CO₂ m^?2 day^?1. The mean primary production/respiration (P/R) ratio was 0.26 ± 0.09 and 0.33 ± 0.15 in the first and second order streams, respectively. These values are low compared with published data because these heterotrophic headwater streams are dominated by benthic respiration and upstream allochthonous inputs with little autotrophic metabolism, particularly during the colder autumn and winter months. 5. The results have implications for the calculation of dissolved inorganic carbon (DIC) fluxes in streamwater. Samples taken during daylight hours tend to have lower concentrations of free CO₂ and HCO₃^? than samples taken during darkness. During spring, concentrations of free CO₂ were measured up to 2.4 (annual mean 1.8) times higher at night than during the day at a similar discharge. It is suggested that fluxes based on daytime measurements alone will under‐estimate the annual flux of these determinands in streamwater by as much as 40%.