Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae

Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient-dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxyN-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes

Stimulation of Indigenous Carbonate Precipitating Bacteria for Ground Improvement

Calcite minerals are precipitated in soil through biomineralisation which can be either organic or inorganic in nature. Biomineralisation can be employed to improve ground conditions in its natural state. Usually, studies of applied biomineralisation are highly interdisciplinary involving expertise from engineers, chemists and microbiologists. In this paper, we study the potential of biomineralisation from indigenous bacteria present in soil. The soil samples were collected from a high permeable zone and the bacteria that inhabit the soil were stimulated at a temperature of 15°C. A cementation solution consisting of 500mM calcium chloride, urea and nutrient broth at a pH of 7.5 was added to the soil samples. Inorganic precipitation was found to be dominant and was more efficient when compared to organic precipitation. Carbonate precipitation data indicated that inorganic precipitation were 1.37 times better at carbonate formation in comparison to organic precipitation. Scanning Electron Microscopy analysis identified cementation bonds formed between soil particles. It was deducted that organic precipitation is dependent on temperature, and may take an extended time at such low temperature. The preliminary data presented in this paper suggests that the implementation of biomineralisation with in-situ microbes is promising but requires further laboratory and field investigation before being considered for engineering application.XJTL

Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years

Both large and small scale migrations of Helicoverpa armigera Hübner in Australia were investigated using AMOVA analysis and genetic assignment tests. Five microsatellite loci were screened across 3142 individuals from 16 localities in eight major cotton and grain growing regions within Australia, over a 38-month period (November 1999 to January 2003). From November 1999 to March 2001 relatively low levels of migration were characterized between growing regions. Substantially higher than average gene-flow rates and limited differentiation between cropping regions characterized the period from April 2001 to March 2002. A reduced migration rate in the year from April 2002 to March 2003 resulted in significant genetic structuring between cropping regions. This differentiation was established within two or three generations. Genetic drift alone is unlikely to drive genetic differentiation over such a small number of generations, unless it is accompanied by extreme bottlenecks and/or selection. Helicoverpa armigera in Australia demonstrated isolation by distance, so immigration into cropping regions is more likely to come from nearby regions than from afar. This effect was most pronounced in years with limited migration. However, there is evidence of long distance dispersal events in periods of high migration (April 2001–March 2002). The implications of highly variable migration patterns for resistance management are considered.K.D. Scott, K.S. Wilkinson, N. Lawrence, C.L. Lange, L.J. Scott, M.A. Merritt, A.J. Lowe and G.C Graha

Biomineralisation performance of bacteria isolated from a landfill in China

We report an investigation of microbially-induced carbonate precipitation by seven indigenous bacteria isolated from a landfill in China. Bacterial strains were cultured in a medium supplemented with 25 mM calcium chloride and 333 mM urea. The experiments were carried out at 30 °C for 7 days with agitation by a shaking table at 130 rpm. Scanning Electron Microscopic (SEM) and X-ray diffraction (XRD) analyses showed variations in calcium carbonate polymorphs and mineral composition induced by all bacterial strains. The amount of carbonate precipitation was quantified by titration. The amount of carbonate precipitated in the medium varied among isolates with the lowest being Bacillus aerius rawirorabr15 (LC092833) precipitating around 1.5 times more carbonate per unit volume than the abiotic (blank) solution. Pseudomonas nitroreducens szh_asesj15 (LC090854) was found to be the most efficient, precipitating 3.2 times more carbonate than the abiotic solution. Our results indicate that bacterial carbonate precipitation occurred through ureolysis and suggest that variations in carbonate crystal polymorphs and rates of precipitation were driven by strain-specific differences in urease expression and response to the alkaline environment. These results and the method applied provide benchmarking/screening data for assessing the bioremediation potential of indigenous bacteria for containment of contaminants in landfills

Next-generation sequencing showing potential leachate influence on bacterial communities around a landfill in China

The impact of contaminated leachate on groundwater from landfills is well known but specific effects on bacterial consortia are less well-studied. Bacterial communities in landfill and an urban site located in Suzhou, China were studied using Illumina high-throughput sequencing. A total number of 153944 good quality reads were produced and sequences assigned to 6388 operational taxonomic units (OTUs). Bacterial consortia consisted of up to 16 phyla including Proteobacteria (31.9 to 94.9% at landfill, 25.1 to 43.3% at urban sites), Actinobacteria (0 to 28.7% at landfill, 9.9 to 34.3% at urban sites), Bacteroidetes (1.4 to 25.6% at landfill, 5.6 to 7.8% at urban sites), Chloroflexi (0.4 to 26.5% at urban sites only) and unclassified bacteria. Pseudomonas was the dominant (67-93%) genus in landfill leachate. Arsenic concentrations in landfill raw leachate (RL) (1.11x103 µg/L) and fresh leachate (FL2) (1.78x103 µg/L), and mercury concentrations in RL (10.9 µg/L) and FL2 (7.37 µg/L) were higher than Chinese State Environmental Protection Administration (SEPA) standards for leachate in landfills. Shannon diversity index and Chao 1 richness estimate showed RL and FL2 lacked richness and diversity when compared with other samples. This is consistent with stresses imposed by elevated arsenic and mercury and has implications for ecological site remediation by bioremediation or natural attenuation

Trial for reducing weight retention in new mums: a randomised controlled trial evaluating a low intensity, postpartum weight management programme

BACKGROUND: Failure to return to pregnancy weight by 6 months postpartum is associated with long-term obesity, as well as adverse health outcomes. This research evaluated a postpartum weight management programme for women with a body mass index (BMI) > 25 kg m(-2) that combined behaviour change principles and a low-intensity delivery format with postpartum nutrition information. METHODS: Women were randomised at 24-28 weeks to control (supported care; SC) or intervention (enhanced care; EC) groups, stratified by BMI cohort. At 36 weeks of gestation, SC women received a \u27nutrition for breastfeeding\u27 resource and EC women received a nutrition assessment and goal-setting session about post-natal nutrition, plus a 6-month correspondence intervention requiring return of self-monitoring sheets. Weight change, anthropometry, diet, physical activity, breastfeeding, fasting glucose and insulin measures were assessed at 6 weeks and 6 months postpartum. RESULTS: Seventy-seven percent (40 EC and 41 SC) of the 105 women approached were recruited; 36 EC and 35 SC women received a programme and 66.7% and 48.6% completed the study, respectively. No significant differences were observed between any outcomes. Median [interquartile range (IQR)] weight change was EC: -1.1 (9.5) kg versus SC: -1.1 (7.5) kg (6 weeks to 6 months) and EC: +1.0 (8.7) kg versus SC: +2.3 (9) kg (prepregnancy to 6 months). Intervention women breastfed for half a month longer than control women (180 versus 164 days; P = 0.10). An average of 2.3 out of six activity sheets per participant was returned. CONCLUSIONS: Despite low intervention engagement, the high retention rate suggests this remains an area of interest to women. Future strategies must facilitate women\u27s engagement, be individually tailored, and include features that support behaviour change to decrease women\u27s risk of chronic health issues

Expression of soluble, active fragments of the morphogenetic protein SpoIIE from Bacillus subtilis using a library-based construct screen

SpoIIE is a dual function protein that plays important roles during sporulation in Bacillus subtilis. It binds to the tubulin-like protein FtsZ causing the cell division septum to relocate from mid-cell to the cell pole, and it dephosphorylates SpoIIAA phosphate leading to establishment of differential gene expression in the two compartments following the asymmetric septation. Its 872 residue polypeptide contains a multiple-membrane spanning sequence at the N-terminus and a PP2C phosphatase domain at the C-terminus. The central segment that binds to FtsZ is unlike domains of known structure or function, moreover the domain boundaries are poorly defined and this has hampered the expression of soluble fragments of SpoIIE at the levels required for structural studies. Here we have screened over 9000 genetic constructs of spoIIE using a random incremental truncation library approach, ESPRIT, to identify a number of soluble C-terminal fragments of SpoIIE that were aligned with the protein sequence to map putative domains and domain boundaries. The expression and purification of three fragments were optimised, yielding multimilligram quantities of the PP2C phosphatase domain, the putative FtsZ-binding domain and a larger fragment encompassing both these domains. All three fragments are monomeric and the PP2C domain-containing fragments have phosphatase activity

NUISANCE: a neutrino cross-section generator tuning and comparison framework

NUISANCE is an open source C++ framework which facilitates detailed studies of neutrino interaction cross-section models implemented in Monte Carlo neutrino event generators. It provides a host of automated methods to perform comparisons of multiple generators to published cross-section measurements and each other. External reweighting libraries are used to allow the end-user to evaluate the impact of model parameters variations in the generators with data, or to tune the generator predictions to arbitrary dataset combinations. The design is modular and focusses on ease-of-use to allow new datasets and more generators to be added without requiring detailed understanding of the entire NUISANCE package. We discuss the motivation for the NUISANCE framework and suggested usage cases, alongside a description of its core structure

The angular distribution of the reaction νˉe+p→e++n\bar{\nu}_e + p \to e^+ + n

The reaction $\bar{\nu}_e + p \to e^+ + n$ is very important for low-energy ($E_\nu \lesssim 60$ MeV) antineutrino experiments. In this paper we calculate the positron angular distribution, which at low energies is slightly backward. We show that weak magnetism and recoil corrections have a large effect on the angular distribution, making it isotropic at about 15 MeV and slightly forward at higher energies. We also show that the behavior of the cross section and the angular distribution can be well-understood analytically for $E_\nu \lesssim 60$ MeV by calculating to ${\cal O}(1/M)$, where $M$ is the nucleon mass. The correct angular distribution is useful for separating $\bar{\nu}_e + p \to e^+ + n$ events from other reactions and detector backgrounds, as well as for possible localization of the source (e.g., a supernova) direction. We comment on how similar corrections appear for the lepton angular distributions in the deuteron breakup reactions $\bar{\nu}_e + d \to e^+ + n + n$ and $\nu_e + d \to e^- + p + p$. Finally, in the reaction $\bar{\nu}_e + p \to e^+ + n$, the angular distribution of the outgoing neutrons is strongly forward-peaked, leading to a measurable separation in positron and neutron detection points, also potentially useful for rejecting backgrounds or locating the source direction.Comment: 10 pages, including 5 figure

MICP and Advances towards Eco-Friendly and Economical Applications

Biomineralization is a natural process aided by living organisms. Due to its applicability in ground improvement and bioremediation, Microbially Induced Calcite Precipitation (MICP) is an interdisciplinary field of study combining engineering, chemistry and microbiology. Bioremediation has been applied widely for contamination containment or removal, in this case it will be containment. MICP can also be applied to improve the efficiency of insitu bioremediation. Urease is an enzyme which can facilitate increased calcite precipitation. However the production of urease by bacteria and thus the resulting carbonate precipitation are inhibited by environmental factors including calcium concentration, bacterial concentration, pH and temperature. Under good conditions MICP can be used for heavy metal and radionuclide immobilization. However technologies such as bioconsolidation and biocementation require improvement such as time and cost. This paper highlights the application of MICP in addition to suggested improvements to make it more eco-friendly and sustainable.XJTL