Feasibility of using constructed wetland treatment for molasses wastewater treatment

The surface flow constructed wetland (SFCW) with Cyperus involucratus, Typha augustifolia and Thalia dealbata J. Fraser was applied to treat anaerobic treated-molasses wastewater (An-MWW) under the organic loading rates (OLRs) of 612, 696, 806, 929 and 1,213 kg BOD(5)ha(-1)day(-1). The results showed that both removal efficiency and plant growth rate were increased with the decrease of organic loading rate (OLR). All tested-plant species could not grow under OLR of higher than 696 kg BOD(5)mg l(-1) (p>0.05). Also, the plant-biomass of the systems was reduced by 10.4%, 26.5%, and 64.7% of initial plant-biomass under the OLR of 806, 929 and 1,213 kg BOD(5)ha(-1)day(-1), respectively. However, all tested-plant species showed the same pattern on the plant-biomass production yield and removal efficiency. The highest SS, BOD, COD, total phosphorus, NH(4)(+), NO(3)(-) and molasses pigments (MP) removal efficiencies of 90-93%, 88-89%, 67%, 70-76%, 77-82%, 94-95% and 72-77%, respectively were detected under the OLR of 612 kg BOD(5)ha(-1)day.     

Induction of oscillatory ventilation pattern using dynamic modulation of heart rate through a pacemaker

For disease states characterized by oscillatory ventilation, an ideal dynamic therapy would apply a counteracting oscillation in ventilation. Modulating respiratory gas transport through the circulation might allow this. We explore the ability of repetitive alternations in heart rate, using a cardiac pacemaker, to elicit oscillations in respiratory variables and discuss the potential for therapeutic exploitation. By incorporating acute cardiac output manipulations into an integrated mathematical model, we observed that a rise in cardiac output should yield a gradual rise in end-tidal CO2 and, subsequently, ventilation. An alternating pattern of cardiac output might, therefore, create oscillations in CO2 and ventilation. We studied the effect of repeated alternations in heart rate of 30 beats/min with periodicity of 60 s, on cardiac output, respiratory gases, and ventilation in 22 subjects with implanted cardiac pacemakers and stable breathing patterns. End-tidal CO2 and ventilation developed consistent oscillations with a period of 60 s during the heart rate alternations, with mean peak-to-trough relative excursions of 8.4 +/- 5.0% (P < 0.0001) and 24.4 +/- 18.8% (P < 0.0001), respectively. Furthermore, we verified the mathematical prediction that the amplitude of these oscillations would depend on those in cardiac output (r = 0.59, P = 0.001). Repetitive alternations in heart rate can elicit reproducible oscillations in end-tidal CO2 and ventilation. The size of this effect depends on the magnitude of the cardiac output response. Harnessed and timed appropriately, this cardiorespiratory mechanism might be exploited to create an active dynamic responsive pacing algorithm to counteract spontaneous respiratory oscillations, such as those causing apneic breathing disorders.     

Benchmarking the DFT methodology for assessing antioxidant-related properties: quercetin and edaravone as case studies

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.     

The Escherichia coli Peripheral Inner Membrane Proteome

Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ∼19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ∼25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with biological membrane surfaces that we are only beginning to decipher.An in-depth understanding of cellular proteomes requires knowledge of protein subcellular topology, assembly in macromolecular complexes, and modification and degradation of poplypeptides. Escherichia coli, a model organism for many such studies, is by far the best studied. The genomes of strain K-12 derivatives MG1655 and W3110 have been sequenced (1, 2), and >75% of their genes have been functionally assigned (3). Almost 90% of the K-12 proteome has been identified experimentally, and >73% of its proteins have known structures (4, 5). Moreover, the genomes of another 38 E. coli strains have been determined (see EcoliWiki for details).In E. coli, like in all Gram-negative bacteria, the bacterial cell envelope comprises the plasma or inner membrane and the outer membrane, which are separated by the periplasmic space. The inner membrane encloses the cytoplasm and is a dynamic substructure. It harbors a wide variety of proteins that function in vital cell processes such as the trafficking of ions, molecules, and macromolecules; cell division; environmental sensing; lipid, polysaccharide, and peptidoglycan biosynthesis; and metabolism. Inner membrane proteins either fully span the lipid bilayer using one or more hydrophobic transmembrane helices (integral) or are bound either directly to phospholipid components or via protein–protein interactions to the surface of the membrane (peripheral) (6) (Fig. 1A). Peripheral inner membrane proteins exist on either side of the membrane and may be recruited in membrane-associated complexes on demand (7). Peripheral inner membrane proteins on the cytoplasmic side constitute a sub-proteome of central importance because of their interaction with the cytoplasmic proteome, the nucleoid, and most of the cell''s metabolism. Thanks to their soluble character and the nature of their interactions with the membrane (mostly electrostatic and moderate hydrophobic interactions (7)), peripheral inner membrane proteins can be extracted using high salt concentrations, extreme pH levels, or chaotropes without disrupting the lipid bilayer (8–11). In contrast, the solubilization of integral proteins requires amphiphilic detergents in order to displace the membrane phospholipids and maintain them as soluble in aqueous solutions (12).Open in a separate windowFig. 1.Bioinformatics and experimental workflow for characterizing peripheral inner membrane proteins. A, schematic representation of the subcellular localization of the E. coli inner membrane peripherome. Protein topology assignment is based on the cellular compartment: A, cytoplasmic; B, integral inner membrane proteins; F1, peripheral inner membrane proteome; r, ribosome. B, schematic diagram for PIM protein annotation. 130 cytoplasmic and PIM E. coli K-12 proteins were downloaded from Uniprot (November 2010) (81) and EchoLOCATION (23). A set of bioinformatics tools was used to predict topologies and features of the unassigned and differently assigned proteins and to further validate existing protein annotations (see supplemental text). For the annotation of additional peripheral membrane proteins, the literature was extensively searched. Additional, other E. coli K-12 databases containing gene ontology annotations (84, 85) and protein homologies through BLAST (44) were employed. Homologues of curated E. coli K-12 proteins were identified in E. coli BL21(DE3) (supplemental Table S1A). C, preparation strategy for detecting the E. coli inner membrane peripherome via nanoLC-MS/MS. Inverted membrane vesicles (IMVs) were isolated and washed extensively with the indicated chemical agents to extract cytoplasmic and PIM proteins (“IMVs washed”), and then their surface was trypsinized (gray arrow). Following digestion, soluble peptides were analyzed via nanoLC-MS/MS. D, protein enrichment at different sample preparation conditions. Top: Relative percentage of proteins detected with the proteolysis approach. Proteins are classified here in three major categories: cytoplasmic (A), ribosomal (r), and peripheral (F1). The bar graphs indicate the percentage of proteins in each category relative to the proteins in other categories at a given sample preparation condition. Bottom: Heat maps showing relative quantities of individual proteins at different sample preparation conditions. Perseus (version 1.2.0.16), a part of the MaxQuant bioinformatics platform, was used for the construction of the heat map (86). A top-three label-free quantitative method was employed (27). Individual protein values across the various treatments are given in supplemental Table S3B.Unlike the cytoplasmic proteome of E. coli, which has been extensively characterized (13), its membrane sub-proteome is still poorly defined. Of 1133 predicted integral inner membrane proteins, only half were experimentally identified through proteomics approaches (14). These figures are constantly being re-evaluated,² but most protein identifications appear robust. In contrast to integral inner membrane proteins, bioinformatics prediction of peripheral inner membrane proteins is currently not possible because they are not known to possess any specific features. Despite the occasional designation of partner proteins identified as peripheral in studies that target inner membrane complexes (15–21), no systematic effort has been undertaken to analyze the peripheral inner membrane proteome.Here we have used a multi-pronged strategy employing bioinformatics, biochemistry, proteomics, and complexomics to systematically determine the peripheral inner membrane proteome of E. coli. We focus exclusively on the peripheral inner membrane proteome that faces the cytoplasm, referred to hereinafter as PIM,¹ and do not analyze peripheral inner membrane proteins residing on the periplasm. Manually curated and re-evaluated topology of the E. coli K-12 proteome was extrapolated to the non-K-12 strain BL21(DE3) (95% proteome homology to K-12) (22). By combining various biochemical treatments, we determined experimentally that several cytoplasmic proteins are also novel PIM proteins, and many of them participate in protein complexes associated with the membrane. Collectively, we demonstrate that a significant, previously unsuspected percentage of the expressed polypeptides constitute the PIM proteome.     

Seafood wastewater treatment in constructed wetland: tropical case

A series of investigations were conducted to evaluate the feasibility of using constructed wetlands to remove pollutants from seafood processing wastewater. Six emergent plant species; Cyperus involucratus, Canna siamensis, Heliconia spp., Hymenocallis littoralis, Typha augustifolia and Thalia deabata J. Fraser were planted in surface flow wetland. They were fed with seafood wastewater that was 50% diluted with treated seafood wastewater from an aerated lagoon. All macrophytes were found to meet satisfying treatment efficiency (standard criteria for discharged wastewater) at 5 days hydraulic retention time (HRT). While C. involucratus, T. deabata and T. augustifolia met acceptable treatment efficacy at 3 days HRT. Nutrient uptake rate of these species was observed in the range of 1.43-2.30 g Nitrogen/m(2)day and 0.17-0.29 g Phosphorus/m(2)day, respectively at 3 days HRT. The highest treatment performances were found at 5 days HRT. Average removal efficiencies were 91-99% for BOD(5), 52-90% for SS, 72-92% for TN and 72-77% for TP. Plant growth and nitrogen assimilation were experienced to be most satisfactory for C. involucratus, T. deabata and T. augustifolia. Lower HRTs affected contaminant removal efficiency for all species. C. involucratus, T. deabata and T. augustifolia can remove all contaminants efficiently even at the lowest hydraulic retention time (1 day).     

Changes in size and composition of pigweed (Amaranthus hybridus L.) calcium oxalate crystals under CO2 starvation conditions

The functional role(s) of plant calcium oxalate (CaOx) crystals are still poorly understood. Recently, it was shown that crystals function as dynamic carbon pools whose decomposition could provide CO₂ to photosynthesis when stomata are closed (e.g. under drought conditions) and CO₂ starvation conditions may be created within the mesophyll. This biochemical process, named as ‘alarm photosynthesis’, can become crucial for plant survival under adverse conditions. Here, we study crystal decomposition under controlled CO₂ starvation conditions (either in the shoot or in the root) to obtain a better insight into the process of crystal formation and function. Hydroponically grown pigweed plants were kept in CO₂‐free air and/or CO₂‐free nutrient medium for 9 days. Crystal volume was monitored daily, and carbon stable isotope composition (δ¹³C) and Fourier transformation Raman spectra were obtained at the end of the experiment. A considerable reduction in the leaf crystal volume was observed in shoot‐CO₂‐starved plants at the end of the experiment. The smallest crystals were isolated from the plants in which carbon was excluded from both the shoot and the root and contained potassium nitrate. Crystal δ¹³C of CO₂‐starved plants was altered in a predicted way. Specifically, it depended on the average calculated isotope fractionation of all carbon fixation processes considered to be contributing in each experimental treatment. The results of the present study confirmed the correlation between CO₂ starvation conditions and the CaOx crystal decomposition. Inorganic carbon fixed in the root may represent a major carbon source for CaOx formation.     

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples

Somatic variant analysis of a tumour sample and its matched normal has been widely used in cancer research to distinguish germline polymorphisms from somatic mutations. However, due to the extensive intratumour heterogeneity of cancer, sequencing data from a single tumour sample may greatly underestimate the overall mutational landscape. In recent studies, multiple spatially or temporally separated tumour samples from the same patient were sequenced to identify the regional distribution of somatic mutations and study intratumour heterogeneity. There are a number of tools to perform somatic variant calling from matched tumour-normal next-generation sequencing (NGS) data; however none of these allow joint analysis of multiple same-patient samples. We discuss the benefits and challenges of multisample somatic variant calling and present multiSNV, a software package for calling single nucleotide variants (SNVs) using NGS data from multiple same-patient samples. Instead of performing multiple pairwise analyses of a single tumour sample and a matched normal, multiSNV jointly considers all available samples under a Bayesian framework to increase sensitivity of calling shared SNVs. By leveraging information from all available samples, multiSNV is able to detect rare mutations with variant allele frequencies down to 3% from whole-exome sequencing experiments.     

Endocannabinoid and Cannabinoid-Like Fatty Acid Amide Levels Correlate with Pain-Related Symptoms in Patients with IBS-D and IBS-C: A Pilot Study

Aims

Irritable bowel syndrome (IBS) is a functional gastrointestinal (GI) disorder, associated with alterations of bowel function, abdominal pain and other symptoms related to the GI tract. Recently the endogenous cannabinoid system (ECS) was shown to be involved in the physiological and pathophysiological control of the GI function. The aim of this pilot study was to investigate whether IBS defining symptoms correlate with changes in endocannabinoids or cannabinoid like fatty acid levels in IBS patients.

Methods

AEA, 2-AG, OEA and PEA plasma levels were determined in diarrhoea-predominant (IBS-D) and constipation-predominant (IBS-C) patients and were compared to healthy subjects, following the establishment of correlations between biolipid contents and disease symptoms. FAAH mRNA levels were evaluated in colonic biopsies from IBS-D and IBS-C patients and matched controls.

Results

Patients with IBS-D had higher levels of 2AG and lower levels of OEA and PEA. In contrast, patients with IBS-C had higher levels of OEA. Multivariate analysis found that lower PEA levels are associated with cramping abdominal pain. FAAH mRNA levels were lower in patients with IBS-C.

Conclusion

IBS subtypes and their symptoms show distinct alterations of endocannabinoid and endocannabinoid-like fatty acid levels. These changes may partially result from reduced FAAH expression. The here reported changes support the notion that the ECS is involved in the pathophysiology of IBS and the development of IBS symptoms.