Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Biological membranes are complex environments consisting of different types of lipids and membrane proteins. The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules. This complicates the description of the lipid membrane properties by the conformation of any single lipid molecule. Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems. All-atom membrane models can elucidate detailed contacts between membrane proteins and its surrounding lipids, while united-atom and coarse-grained description have allowed larger models and longer timescales up to microsecond mark to be probed. Additionally, membrane models with mixed phospholipids and lipopolysaccharide content have made it possible to model improved views of biological membranes. Here, we present an overview of commonly used lipid force fields by the biosimulation community, useful tools for membrane MD simulations, and recent advances in membrane simulations

Removal and transformation of hexavalent chromium in sequencing batch reactor

The objectives of this study are to evaluate the efficiency of removal of hexavalent chromium (Cr(VI)) in a sequencing batch reactor (SBR) and to ascertain the fate of Cr(VI) in the treatment process. An SBR was operated with the FILL, REACT, SETTLE, DRAW and IDLE periods in the time ratio of 2:12:2:1.5:6.5 for a cycle time of 24 h. The study was divided into 5 phases with the addition of 0.5, 2.0, 3.0 and 5.0 mg/ℓ of Cr(VI) in Phases II, III, IV and V for a duration of 46, 75, 43 and 16 operational cycles, respectively. The Cr(VI) removal efficiencies for SBR were found to be 79.8, 88.4 and 99.8% in Phases III, IV and V, respectively. The results revealed that Cr(VI) removal efficiency improved with acclimated activated sludge. Determination of Cr in the suspended sludge showed that around 95% of the Cr species were Cr(III). Determination of Cr concentration profiles during the FILL and REACT periods showed that the predominant species was Cr(III) as Cr(VI) was bio-reduced. The proposed Cr(VI) removal mechanism involves bioreduction to Cr(III) which was subsequently precipitated and adsorbed by activated sludge. Precipitation rather than sorption is envisaged to be the main path of removal of Cr(III) from the solution.Keywords: Sequencing batch reactor, hexavalent chromium, removal, transformation, mechanis

Effect of different drying methods and solvent ratios on biological activities of Phyllanthus acidus extracts

The main purpose of this study was to evaluate the antioxidant and α-glucosidase inhibitory activities of Phyllanthus acidus. The P. acidus fruits were dried using three different methods, namely oven (OD), air (AD) and freeze (FD) dryings and extracted with ethanol at different ratios (50 and 100%). The proximate analysis and total phenolic content (TPC) as well as free radical scavenging and α-glucosidase inhibitory activities were determined. The proximate analysis of P. acidus fruit indicated that all the dried samples contained potential nutrient contents. The highest TPC value, α-glucosidase inhibitory and antioxidant activities were observed for 50% ethanolic extract from OD method with TPC value of 28.39 mg GAE/g dried extract, IC50 value of 12.394 μg/mL and 64.17% inhibition, respectively. The study revealed that phenolic compounds could be the main contributors to the antioxidant and α-glucosidase inhibitory activities based on the Pearson correlation coefficients with R values of 95.0 and 73.8%, respectively. The study could provide scientific evidence for some folk uses in the treatment of diseases related to the production of reactive oxygen species and oxidative stress

Synergistic co-cultivation of activated sludge and microalgae in enhancing lipid production and N-laden wastewater treatment

The influence of inoculation ratios of activated sludge and microalgae were investigated in this study in the aspects of biomass yield, lipid yield and total nitrogen (TN) removal efficiency. It was observed that mixed culture of activated sludge/microalgae with the ratio 1:1 and 1:0.75 achieved a maximum lipid production up to 0.144 g/L and 0.133 g/L as compared with microalgae culture alone, which was only 0.081 g/L. The highest total nitrogen (TN) removal was observed with 1:1 and 1:0.75 ratios of activated sludge/microalgae cultures ranging from 96.3-96.9% removal efficiency, which was an improvement of about 90% removal efficiency compared to the activated sludge culture (6.25±0.08%). The flocculation efficiency was generally improved in mixed cultures of activated sludge andmicroalgae in comparison with only activated sludge culture and microalgae culture alone.Keywords: activated sludge; microalgae; co-cultivation; lipid; nitrogen removal

Multimodal hyperscanning reveals that synchrony of body and mind are distinct in mother-child dyads

Hyperscanning studies have begun to unravel the brain mechanisms underlying social interaction, indicating a functional role for interpersonal neural synchronization (INS), yet the mechanisms that drive INS are poorly understood. The current study, thus, addresses whether INS is functionally-distinct from synchrony in other systems – specifically the autonomic nervous system and motor behavior. To test this, we used concurrent functional near-infrared spectroscopy - electrocardiography recordings, while N = 34 mother-child and stranger-child dyads engaged in cooperative and competitive tasks. Only in the neural domain was a higher synchrony for mother-child compared to stranger-child dyads observed. Further, autonomic nervous system and neural synchrony were positively related during competition but not during cooperation. These results suggest that synchrony in different behavioral and biological systems may reflect distinct processes. Furthermore, they show that increased mother-child INS is unlikely to be explained solely by shared arousal and behavioral similarities, supporting recent theories that postulate that INS is higher in close relationships

A Potent and Effective Suicidal Listeria Vaccine Platform.

Live-attenuated Listeria monocytogenes has shown encouraging potential as an immunotherapy platform in preclinical and clinical settings. However, additional safety measures will enable application across malignant and infectious diseases. Here, we describe a new vaccine platform, termed Lm-RIID (L. monocytogenes recombinase-induced intracellular death), that induces the deletion of genes required for bacterial viability yet maintains potent T cell responses to encoded antigens. Lm-RIID grows normally in broth but commits suicide inside host cells by inducing Cre recombinase and deleting essential genes flanked by loxP sites, resulting in a self-limiting infection even in immunocompromised mice. Lm-RIID vaccination of mice induces potent CD8+ T cells and protects against virulent challenges, similar to live L. monocytogenes vaccines. When combined with α-PD-1, Lm-RIID is as effective as live-attenuated L. monocytogenes in a therapeutic tumor model. This impressive efficacy, together with the increased clearance rate, makes Lm-RIID ideal for prophylactic immunization against diseases that require T cells for protection

Neonicotinoid-induced pathogen susceptibility is mitigated by Lactobacillus plantarum immune stimulation in a Drosophila melanogaster model

© 2017 The Author(s). Pesticides are used extensively in food production to maximize crop yields. However, neonicotinoid insecticides exert unintentional toxicity to honey bees (Apis mellifera) that may partially be associated with massive population declines referred to as colony collapse disorder. We hypothesized that imidacloprid (common neonicotinoid; IMI) exposure would make Drosophila melanogaster (an insect model for the honey bee) more susceptible to bacterial pathogens, heat stress, and intestinal dysbiosis. Our results suggested that the immune deficiency (IMD) pathway is necessary for D. melanogaster survival in response to IMI toxicity. IMI exposure induced alterations in the host-microbiota as noted by increased indigenous Acetobacter and Lactobacillus spp. Furthermore, sub-lethal exposure to IMI resulted in decreased D. melanogaster survival when simultaneously exposed to bacterial infection and heat stress (37 °C). This coincided with exacerbated increases in TotA and Dpt (IMD downstream pro-survival and antimicrobial genes, respectively) expression compared to controls. Supplementation of IMI-exposed D. melanogaster with Lactobacillus plantarum ATCC 14917 mitigated survival deficits following Serratia marcescens (bacterial pathogen) septic infection. These findings support the insidious toxicity of neonicotinoid pesticides and potential for probiotic lactobacilli to reduce IMI-induced susceptibility to infection

Gastroenterologist perceptions of faecal microbiota transplantation

© 2015 Baishideng Publishing Group Inc. All rights reserved. AIM: To explore gastroenterologist perceptions towards and experience with faecal microbiota transplantation (FMT). METHODS: A questionnaire survey consisting of 17 questions was created to assess gastroenterologists' attitude towards and experience with FMT. This was anonymously distributed in hard copy format amongst attendees at gastroenterology meetings in Australia between October 2013 and April 2014. Basic descriptive statistical analyses were performed. RESULTS: Fifty-two clinicians participated. Twenty one percent had previously referred patients for FMT, 8% more than once. Ninety percent would refer patients with Clostridium difficile infection (CDI) for FMT if easily available, 37% for ulcerative colitis, 13% for Crohn's disease and 6% for irritable bowel syndrome. Six percent would not refer any indication, including recurrent CDI. Eighty-six percent would enroll patients in FMT clinical trials. Thirty-seven percent considered the optimal mode of FMT administration transcolonoscopic, 17% nasoduodenal, 13% enema and 8% oral capsule. The greatest concerns regarding FMT were: 42% lack of evidence, 12% infection risk, 10% non infectious adverse effects/lack of safety data, 10% aesthetic, 10% lack of efficacy, 4% disease exacerbation, and 2% inappropriate use; 6% had no concerns. Seventy seven percent believed there is a lack of accessibility while 52% had an interest in learning how to provide FMT. Only 6% offered FMT at their institution. CONCLUSION: Despite general enthusiasm, most gastroenterologists have limited experience with, or access to, FMT. The greatest concerns were lack of supportive evidence and safety issues. However a significant proportion would refer indications other than CDI for FMT despite insufficient evidence. These data provide guidance on where education and training are required

Repurposing Albendazole: new potential as a chemotherapeutic agent with preferential activity against HPV-negative head and neck squamous cell cancer.

Albendazole is an anti-helminthic drug that has been shown to exhibit anti-cancer properties, however its activity in head and neck squamous cell cancer (HNSCC) was unknown. Using a series of in vitro assays, we assessed the ability of albendazole to inhibit proliferation in 20 HNSCC cell lines across a range of albendazole doses (1 nM-10 μM). Cell lines that responded to treatment were further examined for cell death, inhibition of migration and cell cycle arrest. Thirteen of fourteen human papillomavirus-negative HNSCC cell lines responded to albendazole, with an average IC50 of 152 nM. In contrast, only 3 of 6 human papillomavirus-positive HNSCC cell lines responded. Albendazole treatment resulted in apoptosis, inhibition of cell migration, cell cycle arrest in the G2/M phase and altered tubulin distribution. Normal control cells were not measurably affected by any dose tested. This study indicates that albendazole acts to inhibit the proliferation of human papillomavirus-negative HNSCC cell lines and thus warrants further study as a potential chemotherapeutic agent for patients suffering from head and neck cancer