A simple model of the hydrophobic effect for molecular simulation of interfacial phenomena

A coarse-grained model for simulation of interfacial phenomena in aqueous systems has been developed. The model captures the hydrophobic effect by only considering the structure and cohesiveness of water. Monte Carlo (MC) simulations of water-oil mixtures show that low concentrations of oil are solvated with little perturbation of the hydrogen bonding network structure of the water, while high concentrations of oil are excluded altogether. Analysis of the water structure in the simulations indicates that the water molecules maintain close to four coordination in the presence of solutes and the distribution of bond angles is not markedly affected by the presence of solutes. MC simulations of an alkane oligomer in water and a poly(ethylene oxide) (PEO) oligomer in water indicate that the chains are quite flexible and also do not perturb the network structure of the water phase.     

A Putative Transmembrane Leucine Zipper of Agrobacterium VirB10 Is Essential for T-Pilus Biogenesis but Not Type IV Secretion

The Agrobacterium tumefaciens VirB/VirD4 type IV secretion system is composed of a translocation channel and an extracellular T pilus. Bitopic VirB10, the VirB7 lipoprotein, and VirB9 interact to form a cell envelope-spanning structural scaffold termed the “core complex” that is required for the assembly of both structures. The related pKM101-encoded core complex is composed of 14 copies each of these VirB homologs, and the transmembrane (TM) α helices of VirB10-like TraF form a 55-Å-diameter ring at the inner membrane. Here, we report that the VirB10 TM helix possesses two types of putative dimerization motifs, a GxxxA (GA₄) motif and two leucine (Leu1, Leu2) zippers. Mutations in the Leu1 motif disrupted T-pilus biogenesis, but these or other mutations in the GA₄ or Leu2 motif did not abolish substrate transfer. Replacement of the VirB10 TM domain with a nondimerizing poly-Leu/Ala TM domain sequence also blocked pilus production but not substrate transfer or formation of immunoprecipitable complexes with the core subunits VirB7 and VirB9 and the substrate receptor VirD4. The VirB10 TM helix formed weak homodimers in Escherichia coli, as determined with the TOXCAT assay, whereas replacement of the VirB10 TM helix with the strongly dimerizing TM helix from glycophorin A blocked T-pilus biogenesis in A. tumefaciens. Our findings support a model in which VirB10''s TM helix contributes to the assembly or activity of the translocation channel as a weakly self-interacting membrane anchor but establishes a heteromeric TM-TM helix interaction via its Leu1 motif that is critical for T-pilus biogenesis.     

Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant

Methanobacterium sp. Mb1, a hydrogenotrophic methanogenic Archaeon, was isolated from a rural biogas plant producing methane-rich biogas from maize silage and cattle manure in Germany. Here we report the complete genome sequence of the novel methanogenic isolate Methanobacterium sp. Mb1 harboring a 2,029,766 bp circular chromosome featuring a GC content of 39.74%. The genome encodes two rRNA operons, 41 tRNA genes and 2021 coding sequences and represents the smallest genome currently known within the genus Methanobacterium.     

Activity of native hydrolytic enzymes and their association with the cell wall of three ectomycorrhizal fungi

The ecological and biogeochemical relevance of hydrolytic enzymes associated with the fungal cell wall has been poorly studied in ectomycorrhizal (ECM) fungi. We used a modified sequential extraction procedure to investigate the activity of various hydrolytic enzymes (β-glucosidase, acid-phosphatase, leucine-aminopeptidase, chitinase, xylanase and glucuronidase) and their association with the cell wall of three ECM fungi (Rhizopogon roseolus, Paxillus involutus and Piloderma croceum). Fungi were grown on C-rich solid medium under three different P concentrations (3.7, 0.37 and 0.037 mM). The sequential extraction procedure classifies enzymes as: (a) cytosolic, (b) loosely bound, (c) hydrophobically bound, (d) ionically bound and (e) covalently bound. Results showed that for the same fungus absolute enzymatic activity was affected by P concentration, whilst enzymatic compartmentalization among the cytosol and the cell wall fractions was not. The association of enzymes with the cell wall was fungus- and enzyme-specific. Our data indicate also that enzymes best known for being either extracellular or cytosolic or both, do act in muro as well. The ecological implications of cell wall-bound enzymes and the potential applications and limitations of sequential extractions are further discussed.     

Clinical Evaluation of an Affordable Qualitative Viral Failure Assay for HIV Using Dried Blood Spots in Uganda

Background

WHO recommends regular viral load (VL) monitoring of patients on antiretroviral therapy (ART) for timely detection of virological failure, prevention of acquired HIV drug resistance (HIVDR) and avoiding unnecessary switching to second-line ART. However, the cost and complexity of routine VL testing remains prohibitive in most resource limited settings (RLS). We evaluated a simple, low–cost, qualitative viral–failure assay (VFA) on dried blood spots (DBS) in three clinical settings in Uganda.

Methods

We conducted a cross–sectional diagnostic accuracy study in three HIV/AIDS treatment centres at the Joint Clinical Research Centre in Uganda. The VFA employs semi-quantitative detection of HIV–1 RNA amplified from the LTR gene. We used paired dry blood spot (DBS) and plasma with the COBASAmpliPrep/COBASTaqMan, Roche version 2 (VL_ref) as the reference assay. We used the VFA at two thresholds of viral load, (>5,000 or >1,000 copies/ml).

Results

496 paired VFA and VL_ref results were available for comparative analysis. Overall, VFA demonstrated 78.4% sensitivity, (95% CI: 69.7%–87.1%), 93% specificity (95% CI: 89.7%–96.4%), 89.3% accuracy (95% CI: 85%–92%) and an agreement kappa = 0.72 as compared to the VL_ref. The predictive values of positivity and negativity among patients on ART for >12 months were 72.7% and 99.3%, respectively.

Conclusions

VFA allowed 89% of correct classification of VF. Only 11% of the patients were misclassified with the potential of unnecessary or late switch to second–line ART. Our findings present an opportunity to roll out simple and affordable VL monitoring for HIV–1 treatment in RLS.     

Grapefruit Derived Flavonoid Naringin Improves Ketoacidosis and Lipid Peroxidation in Type 1 Diabetes Rat Model

BackgroundHypoglycemic effects of grapefruit juice are well known but the effects of naringin, its main flavonoid on glucose intolerance and metabolic complications in type 1 diabetes are not known.ObjectivesTo investigate the effects of naringin on glucose intolerance, oxidative stress and ketonemia in type 1 diabetic rats.MethodsSprague-Dawley rats divided into 5 groups (n = 7) were orally treated daily with 3.0 ml/kg body weight (BW)/day of distilled water (group 1) or 50 mg/kg BW of naringin (groups 2 and 4, respectively). Groups 3, 4 and 5 were given a single intra-peritoneal injection of 60 mg/kg BW of streptozotocin to induce diabetes. Group 3 was further treated with subcutaneous insulin (4.0 IU/kg BW) twice daily, respectively.ResultsStretozotocin (STZ) only-treated groups exhibited hyperglycemia, polydipsia, polyuria, weight loss, glucose intolerance, low fasting plasma insulin and reduced hepatic glycogen content compared to the control group. Furthermore they had significantly elevated Malondialdehyde (MDA), acetoacetate, β-hydroxybutyrate, anion gap and significantly reduced blood pH and plasma bicarbonate compared to the control group. Naringin treatment significantly improved Fasting Plasma Insulin (FPI), hepatic glycogen content, malondialdehyde, β-hydroxybutyrate, acetoacetate, bicarbonate, blood pH and anion gap but not Fasting Blood Glucose (FBG) compared to the STZ only-treated group.ConclusionsNaringin is not hypoglycemic but ameliorates ketoacidosis and oxidative stress. Naringin supplements could therefore mitigate complications of diabetic ketoacidosis.     

Evaluation of treatment options for well water contaminated with perfluorinated alkyl substances using life cycle assessment

Purpose

As knowledge grows of the potentially harmful effects of chemicals in widespread use, emerging contaminants have become a major source of concern and uncertainty for public health officials and water quality managers. Perfluorinated alkyl substances, often referred to as perfluorinated compounds, have come under recent scrutiny and are present in groundwater at many sites across the USA. We examine the life cycle impacts of treating drinking water at one such site.

Methods

We assembled life cycle models for groundwater treatment and bottled water delivery to residents of Wright-Patterson Air Force Base, Ohio, where wells were recently taken out of service due to concerns related to perfluoroalkyl and polyfluoroalkyl substance (PFAS) contamination. Two treatment methods, granular activated carbon filtration and ion-exchange columns, were modeled under a range of contaminant concentrations covering three orders of magnitude: 0.7, 7.0, and 70 μg/L PFAS. On-site infrastructure, operations, and adsorbent cycling were included in models. Impacts of bottled water production and supply were assessed using two data sets reflecting a range of production and supply chain assumptions. Uncertainty in input data was captured using Monte Carlo simulations.

Results and discussion

Results show that for contaminant concentrations below 70 μg/L, the dominant contributor to life cycle impacts is electricity use at the treatment facility. Production, reactivation, and disposal of treatment media become major sources of impact only at very high PFAS concentrations. Though the life cycle impacts of bottled water are up to three orders of magnitude higher than remediated groundwater on a volumetric basis, supplementing a contaminated water supply with bottled drinking water may result in lower life cycle human health impacts when only a small proportion of the total population is vulnerable.

Conclusions

These results provide quantitative data and proposed scenarios for water quality managers and risk management officials in developing plans to address PFAS contamination and emerging contaminants in general. However, more information on the direct human health effects of these poorly understood pollutants is needed before the trade-offs in life cycle health impacts can be comprehensively assessed.

     

Development of LCA benchmarks for Austrian torrent control structures

The International Journal of Life Cycle Assessment - This study emerged from a research project that aimed to develop a Life Cycle Assessment (LCA) model for torrent control structures. This...