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.     

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     

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.     

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6)

Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO(2)via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Oceanithermus profundus type strain (506)

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Efficacy of Removal of Sucrose-Supplemented Interproximal Plaque by Electric Toothbrushes in an In Vitro Model

Electric toothbrushes were evaluated using a model of plaque removal by fluid shear forces. Sucrose supplementation during plaque development did not affect the removal of bacteria from biofilm exposed to low-energy shear but did increase their resistance to high-energy shear. The toothbrush supplying high-energy shear forces removed significantly more viable bacteria.     

Prostaglandin inhibition of cyclic-AMP accumulation and rate of lipolysis in fat cells

A direct relationship between the rate of cyclic AMP accumulation for 2 minutes and the rate of free fatty acid mobilization for 20 minutes was found in rat isolated fat cells stimulated with norepinephrine or theophylline. The concentration-dependent inhibition of cAMP accumulation by prostaglandin E₂ was reflected in proportional inhibition of lipolysis. These data suggest that the anti-lipolytic mechanism of action of prostaglandin E₂ is mediated by inhibition of the early rate of cAMP accumulation rather than the total production of cAMP.