Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Abstract Background Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. Results In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, γ-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. Conclusions PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes

Structural Basis for Activation of Calcineurin by Calmodulin

The highly conserved phosphatase calcineurin (CaN) plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin (CaM). CaM binds to a regulatory domain (RD) within CaN, causing a conformational change that displaces an autoinhibitory domain (AID) from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which CaM activates CaM-dependent protein kinases. Previously published data have hinted that the RD of CaN is intrinsically disordered. In this work, we demonstrate that the RD is unstructured and that it folds upon binding CaM, ousting the AID from the catalytic site. The RD is 95 residues long, with the AID attached to its C-terminal end and the 24-residue CaM binding region toward the N-terminal end. This is unlike the CaM-dependent protein kinases that have CaM binding sites and AIDs immediately adjacent in sequence. Our data demonstrate that not only does the CaM binding region folds but also an ∼25- to 30-residue region between it and the AID folds, resulting in over half of the RD adopting α-helical structure. This appears to be the first observation of CaM inducing folding of this scale outside of its binding site on a target protein

Meta-omics approaches to understand and improve wastewater treatment systems

Biological treatment of wastewaters depends on microbial processes, usually carried out by mixed microbial communities. Environmental and operational factors can affect microorganisms and/or impact microbial community function, and this has repercussion in bioreactor performance. Novel high-throughput molecular methods (metagenomics, metatranscriptomics, metaproteomics, metabolomics) are providing detailed knowledge on the microorganisms governing wastewater treatment systems and on their metabolic capabilities. The genomes of uncultured microbes with key roles in wastewater treatment plants (WWTP), such as the polyphosphate-accumulating microorganism Candidatus Accumulibacter phosphatis, the nitrite oxidizer Candidatus Nitrospira defluvii or the anammox bacterium Candidatus Kuenenia stuttgartiensis are now available through metagenomic studies. Metagenomics allows to genetically characterize full-scale WWTP and provides information on the lifestyles and physiology of key microorganisms for wastewater treatment. Integrating metagenomic data of microorganisms with metatranscriptomic, metaproteomic and metabolomic information provides a better understanding of the microbial responses to perturbations or environmental variations. Data integration may allow the creation of predictive behavior models of wastewater ecosystems, which could help in an improved exploitation of microbial processes. This review discusses the impact of meta-omic approaches on the understanding of wastewater treatment processes, and the implications of these methods for the optimization and design of wastewater treatment bioreactors.Research was supported by the Spanish Ministry of Education and Science (Contract Project CTQ2007-64324 and CONSOLIDER-CSD 2007-00055) and the Regional Government of Castilla y Leon (Ref. VA038A07). Research of AJMS is supported by the European Research Council (Grant 323009

Out-door radiation level measurement in Abeokuta, Nigeria, by thermoluminescent dosimetry

Environmental radiation level and its spatial variability have been investigated at 34 locations in Abeokuta and environs using the technique of thermoluminescent dosimetry (TLD) with LiF phosphor calibrated with a 137Cs standard source operating at a Secondary Standard Dosimetry Laboratory (SSDL). The human dose equivalent due to outdoor exposure in the city range between 0.19 and 1.64 mSv per year with a mean of 0.45 mSv/y and standard deviation of 0.27 mSv/y. Oke-Sabo area of the city has the least radiation dose rate while Obantoku area has the upper limit. Taking this as the profile of integrated natural background radiation dose rate from all sources in the city and comparing with measurements of terrestrial radiation dose in a previous survey, the mean dose rate from extraterrestrial (cosmic) radiation has been estimated to be about 0.18 mSv/y in Abeokut Keywords: Environmental radiation, thermoluminescent dosimetry, Abeokuta, outdoor Radiation exposure. Nigerian Journal of Physics Vol. 18 (1) 2006: pp. 121-12

Radioactivity concentrations in common brands of cement in Nigeria

Radioactivity concentrations of 238U, 232Th and 40K in common brands of Portland cement in Nigeria have been measured using a shielded 7.6 cm × 7.6 cm NaI(Tl) detector coupled to a Canberra series 10 plus multichannel analyzer. The cement samples show significant spread in their radioactivity concentrations, even among samples of the same brand. The weighted means of the activity concentrations of 238U, 232Th and 40K in the different brands were 52.4, 4.1 and 91.8 Bq/kg, respectively. The radium equivalent ranged between 29.1 and 128.1 Bq/kg with a weighted mean value of 68.5 Bq/kg. The values are lower than corresponding values in cement samples in most other countries as contained in recent publications. They are also lower than the UNSCEAR recommended maximum of 370 Bq/kg. The safety criteria developed by ITB Poland for radioactivity in building materials, especially for radon build-up in homes were however, exceeded in some of the cement samples

Activity concentrations of primordial radionuclides in sediments of surface – water dams in southwest Nigeria – a baseline survey

The radionuclide contents of sediment samples collected from 20 surface-water dams in southwestern Nigeria have been determined by low-level gamma-spectroscopy. The average concentration of 40K in each of the dams varied between 110.9 ± 11.9 Bq kg-1 and 1025.9 ± 36.8 Bq kg-1 with an overall mean (± SD) of 549.3 ± 247.6 Bq kg-1 while that of 238U varied from 17.1 ± 3.6 to 51.9 ± 8.7 Bq kg-1 with an overall mean (± SD) of 27.6 ± 8.5 Bq kg-1 and that of 232Th varied from 26.2 ± 3.6 Bq kg-1 to 130.1 ± 23.7 Bq kg-1 with overall mean (± SD) of 62.0 ± 26.1 Bq kg-1. The variability of the values shows the wide disparity in the measured activity concentrations. The mean radium equivalent of 158.9 Bq kg-1 was calculated for the sediments in the dams. No artificial gamma emitting radionuclide was detected in the samples

Application of

A low cost in-situ gamma-ray spectrometric method for rapid assessment of radiation exposure, identification of radionuclides and detection of changes in environmental radioactivity has been employed in the determination of the natural gamma radiation dose levels in six major cities of the southeastern region of Nigeria. The soil radioactivity concentrations of the primordial radionuclides; 40K, 238U and 232Th were determined and have been related to the γ-dose rates in the cities. The activity concentration of 40K across the region ranged between 0.021 and 0.200 kBq kg–1; 238U was between 0.001 and 0.066 kBq kg–1 while that of 232Th ranged between 0.015 and 0.103 kBq kg–1. The total γ-absorbed dose rates in air in the region ranged between 0.016 and 0.090 μGy h–1 with a mean of 0.039 ± 0.018 μGy h–1. The mean of the annual outdoor effective dose due to the terrestrial gamma radiation for the region was calculated as 50 μSv y–1 representing 66% of the world average value

Occupational Exposure due to RF leakages within GSM Base Station Cabins in Eastern Nigeria

The occupational exposure due to RF radiation leaks inside the base station cabin, when working on the Base station Transceiver (BTS) Radios and TX cables and during active radio communication was measured. A total of number 30 base stations Cabins were studied in the eastern part of Nigeria, using a Broad band TES-90 Electrosmog meter. The maximum instantaneous electric field strength obtained from GSM 1800 radio was 3.72 V/m, 16.56 V/m for GSM 900 radio and 11.29 V/m for the Tx cables. The maximum instantaneous indoor and out power density were 35.47 mW/m2 and 6.64 mW/m2 respectively. Also, the average values of the obtained electric field strength from all the cabins are 1.18 ± 1.07 V/m from GSM 1800 radio, 2.33 ± 3.82 V/m from GSM 900 radio and 1.77 ± 2.20 V/m from the Tx cables. The result of this study shows that the values were less than ICNIRP limits for occupational exposure