Discrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria

A bacterial culture collection of 104 strains was obtained from an activated sludge wastewater treatment plant to pursue studies into microbial flocculation. Characterisation of the culture collection using a polyphasic approach indicated seven isolates, phylogenetically affiliated with the deep-branching Xanthomonas group of the class Gammaproteobacteria, were unable to hybridise the GAM42a fluorescence in situ hybridisation (FISH) probe for Gammaproteobacteria. The sequence of the GAM42a probe target region in the 23S rRNA gene of these isolates was determined to have mismatches to GAM42a. Probes perfectly targeting the mismatches (GAM42a_TI038_G1031, and GAM42a_T1038 and GAM42a_A1041_A1040) were synthesised, and used in conjunction with GAM42a in FISH to,study the Gammaproteobacteria community structure in one full-scale activated sludge plant. Several bacteria in the activated sludge biomass bound the modified probes demonstrating their presence and the fact that these Gammaproteobacteria have been overlooked in community structure analyses of activated sludge. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [C-13]acetate was used in SIP to label the DNA of the denitrifiers. The [C-13]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the C-13 library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking Up [C-14] acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the waste-water industry to enhance denitrification.

Molten carbonate fuel cells

Over the past 12 months, developments in both porous and non-porous materials for the molten carbonate fuel cell (MCFC) should lead to significantly increased stack lifetimes. Lithium-sodium carbonate is emerging as the material of choice for the electrolyte and has been tested in a 10 kW scale stack. Several new cathode materials, with lower dissolution rates in the electrolyte than state-of-the-art NiO, have been tested. However a significant finding is that the dissolution rate of NiO can also be reduced by an order of magnitude by preparing it as a functional nanomaterial. Although most developers continue to use nickel anodes, recent tests with ceramic oxides anodes open up the prospects of reduced carbon deposition and future cells running directly on dry methane. (c) 2004 Published by Elsevier Ltd.

Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization

Chromogenic (CISH) and fluorescent ( FISH) in situ hybridization have emerged as reliable techniques to identify amplifications and chromosomal translocations. CISH provides a spatial distribution of gene copy number changes in tumour tissue and allows a direct correlation between copy number changes and the morphological features of neoplastic cells. However, the limited number of commercially available gene probes has hindered the use of this technique. We have devised a protocol to generate probes for CISH that can be applied to formalin-fixed, paraffin-embedded tissue sections (FFPETS). Bacterial artificial chromosomes ( BACs) containing fragments of human DNA which map to specific genomic regions of interest are amplified with phi 29 polymerase and random primer labelled with biotin. The genomic location of these can be readily confirmed by BAC end pair sequencing and FISH mapping on normal lymphocyte metaphase spreads. To demonstrate the reliability of the probes generated with this protocol, four strategies were employed: (i) probes mapping to cyclin D1 (CCND1) were generated and their performance was compared with that of a commercially available probe for the same gene in a series of 10 FFPETS of breast cancer samples of which five harboured CCND1 amplification; (ii) probes targeting cyclin-dependent kinase 4 were used to validate an amplification identified by microarray-based comparative genomic hybridization (aCGH) in a pleomorphic adenoma; (iii) probes targeting fibroblast growth factor receptor 1 and CCND1 were used to validate amplifications mapping to these regions, as defined by aCGH, in an invasive lobular breast carcinoma with FISH and CISH; and (iv) gene-specific probes for ETV6 and NTRK3 were used to demonstrate the presence of t(12; 15)(p12; q25) translocation in a case of breast secretory carcinoma with dual colour FISH. In summary, this protocol enables the generation of probes mapping to any gene of interest that can be applied to FFPETS, allowing correlation of morphological features with gene copy number.

Mapping loss of heterozygosity in normal human breast cells from BRCA1/2 carriers

We have studied loss of heterozygosity at the BRCA1 and BRCA2 loci in 992 normal cell clones derived from topographically defined areas of normal tissue in four samples from BRCA1/BRCA2 mutation carriers. The frequency of loss of heterozygosity in the clones was low ( 1.01%), but it was found in all four samples, whether or not a tumour was present. Topographical mapping revealed that the genetic changes were clustered in some breast samples. Our study confirms the previous finding that a field of genetic instability can exist around a tumour, suggesting that sufficient tissue must be removed at surgery to avoid local recurrence. We also demonstrate that such a field of genetic change can exist in morphologically normal tissue before a tumour develops and, for the first time, we demonstrate that the field is of a size greater than one terminal duct-lobular unit. The genetic changes are not identical, however, which suggests that genetic instability in these regions may play an early role in tumour development. We also confirm and extend our original observation of loss of the wild-type BRCA1 allele in some clones, and loss of the mutant allele in others, demonstrating that loss of either allele is a stochastic event.

Microbial Fuel Cells: Methodology and Technology

Microbial fuel cell (MFC) research is a rapidly evolving field that lacks established terminology and methods for the analysis of system performance. This makes it difficult for researchers to compare devices on an equivalent basis. The construction and analysis of MFCs requires knowledge of different scientific and engineering fields, ranging from microbiology and electrochemistry to materials and environmental engineering. DescribingMFCsystems therefore involves an understanding of these different scientific and engineering principles. In this paper, we provide a review of the different materials and methods used to construct MFCs, techniques used to analyze system performance, and recommendations on what information to include in MFC studies and the most useful ways to present results.

Operation of polymer electrolyte membrane fuel cells with dry feeds: Design and operating strategies

The operation of polymer electrolyte membrane fuel cells (PEMFCs) with dry feeds has been examined with different fuel cell flow channel designs as functions of pressure, temperature and flow rate. Auto-humidified (or self-humidifying) PEMFC operation is improved at higher pressures and low gas velocities where axial dispersion enhances back-mixing of the product water with the dry feed. We demonstrate auto-humidified operation of the channel-less, self-draining fuel cell, based on a stirred tank reactor; data is presented showing auto-humidified operation from 25 to 115 degrees C at 1 and 3 atm. Design and operating requirements are derived for the auto-humidified operation of the channel-less, self-draining fuel cell. The auto-humidified self-draining fuel cell outperforms a fully humidified serpentine flow channel fuel cell at high current densities. The new design offers substantial benefits for simplicity of operation and control including: the ability to self-drain reducing flooding, the ability to uniformly disperse water removing current gradients and the ability to operate on dry feeds eliminating the need for humidifiers. Additionally, the design lends itself well to a modular design concept. (c) 2005 Elsevier B.V. All rights reserved.

Analytical electron microscopy of proton exchange membrane fuel cells

Microtome sections of proton exchange membrane cells produce a wide range of information ranging from macroscopic distribution of components through specimens in which the detailed distribution of catalyst particles can be observed. Using modern data management practices it is possible to combine information at different scales and correlate processing and performance data. Analytical electron microscopy reveals the compositional variations across used cells at the electrolyte/electrode interface. In particular analytical techniques indicate that sulphur concentrations are likely to diminish at the interface Nafion/anode interface. © 2006 Elsevier B.V. All rights reserved.

Diffuse beta-amyloid (A beta) deposits and neurons: in situ secretion or diffusion of A beta?

The association between diffuse-type beta -amyloid (AP) deposits and neuronal cell bodies in Alzheimer's disease (AD) and Down's syndrome (DS) could result from the secretion of AP from clusters of neurons in situ or the diffusion of A beta from cell processes, glial cells or blood vessels. To decide between these hypotheses, spatial pattern analysis was used to study the relationship between the degree of clustering of neuronal cell bodies and the presence of diffuse deposits in the temporal lobe of patients with DS. Significant clustering of neuronal cell bodies was present in 17/24 (71%) of brain areas studied. in addition, in 23/24 (96%) of brain areas, there was a positive correlation between the presence of diffuse deposits and the density of neurons. Hence, the data support the hypothesis that diffuse deposits develop in situ mainly as a result of the secretion of A beta by local clusters of neurons rather than by significant diffusion. Furthermore, the size of a diffuse deposit is likely to be determined by the number of neurons within a cluster which secrete A beta. The number and density of neurons could also be a factor determining the evolution of a diffuse into a mature amyloid deposit.

Reactive processing methods for functionalisation of polymers and in-situ compatibilisation of poly(ethylene terephthalate)-based blends

One of the main objectives of this study was to functionalise various rubbers (i.e. ethylene propylene copolymer (EP), ethylene propylene diene terpolymer (EPDM), and natural rubber (NR)) using functional monomers, maleic anhydride (MA) and glycidyl methacrylate (GMA), via reactive processing routes. The functionalisation of the rubber was carried out via different reactive processing methods in an internal mixer. GMA was free-radically grafted onto EP and EPDM in the melt state in the absence and presence of a comonomer, trimethylolpropane triacrylate (TRlS). To optinuse the grafting conditions and the compositions, the effects of various paranleters on the grafting yields and the extent of side reactions were investigated. Precipitation method and Soxhlet extraction method was established to purifY the GMA modified rubbers and the grafting degree was determined by FTIR and titration. It was found that without TRlS the grafting degree of GMA increased with increasing peroxide concentration. However, grafting was low and the homopolymerisation of GMA and crosslinking of the polymers were identified as the main side reactions competing with the desired grafting reaction for EP and EPDM, respectively. The use of the tri-functional comonomer, TRlS, was shown to greatly enhance the GMA grafting and reduce the side reactions in terms of the higher GMA grafting degree, less alteration of the rheological properties of the polymer substrates and very little formation of polyGMA. The grafting mechanisms were investigated. MA was grafted onto NR using both thermal initiation and peroxide initiation. The results showed clearly that the reaction of MA with NR could be thermally initiated above 140°C in the absence of peroxide. At a preferable temperature of 200°C, the grafting degree was increased with increasing MA concentration. The grafting reaction could also be initiated with peroxide. It was found that 2,5-dimethyl-2,5-bis(ter-butylproxy) hexane (TIOI) was a suitable peroxide to initiate the reaction efficiently above I50°C. The second objective of the work was to utilize the functionalised rubbers in a second step to achieve an in-situ compatibilisation of blends based on poly(ethylene terephthalate) (PET), in particular, with GMA-grafted-EP and -EPDM and the reactive blending was carried out in an internal mixer. The effects of GMA grafting degree, viscosities of GMAgrafted- EP and -EPDM and the presence of polyGMA in the rubber samples on the compatibilisation of PET blends in terms of morphology, dynamical mechanical properties and tensile properties were investigated. It was found that the GMA modified rubbers were very efficient in compatibilising the PET blends and this was supported by the much finer morphology and the better tensile properties. The evidence obtained from the analysis of the PET blends strongly supports the existence of the copolymers through the interfacial reactions between the grafted epoxy group in the GMA modified rubber and the terminal groups of PET in the blends.

Characterization of tissue transglutaminase in human osteoblast-like cells

Tissue transglutaminase (tTG) is a calcium-dependent and guanosine 5'-triphosphate (GTP) binding enzyme, which catalyzes the post-translational modification of proteins by forming intermolecular ε(ϒ-glutamyl)lysine cross-links. In this study, human osteoblasts (HOBs) isolated from femoral head trabecular bone and two osteosarcoma cell lines (HOS and MG-63) were studied for their expression and localization of tTG. Quantitative evaluation of transglutaminase (TG) activity determined using the [1,414C]-putrescine incorporation assay showed that the enzyme was active in all cell types. However, there was a significantly higher activity in the cell homogenates of MG-63 cells as compared with HOB and HOS cells (p <0.001). There was no significant difference between the activity of the enzyme in HOB and HOS cells. All three cell types also have a small amount of active TG on their surface as determined by the incorporation of biotinylated cadaverine into fibronectin. Cell surface-related tTG was further shown by preincubation of cells with tTG antibody, which led to inhibition of cell attachment. Western blot analysis clearly indicated that the active TG was tTG and immunocytochemistry showed it be situated in the cytosol of the cells. In situ extracellular enzyme activity also was shown by the cell-mediated incorporation of fluorescein cadaverine into extracellular matrix (ECM) proteins. These results clearly showed that MG-63 cells have high extracellular activity, which colocalized with the ECM protein fibronectin and could be inhibited by the competitive primary amine substrate putrescine. The contribution of tTG to cell surface/matrix interactions and to the stabilization of the ECM of osteoblast cells therefore could by an important factor in the cascade of events leading to bone differentiation and mineralization.

Reactive processing of polymers:effect of in situ compatibilisation on characteristics of blends of polyethylene terephthalate and ethylene-propylene rubber

Ethylene-propylene rubber (EPR) functionalised with glycidyl methacrylate (GMA) (f-EPR) during melt processing in the presence of a co-monomer, such as trimethylolpropane triacrylate (Tris), was used to promote compatibilisation in blends of polyethylene terephthalate (PET) and f-EPR, and their characteristics were compared with those of PET/f-EPR reactive blends in which the f-EPR was functionalised with GMA via a conventional free radical melt reaction (in the absence of a co-monomer). Binary blends of PETand f-EPR (with two types of f-EPR prepared either in presence or absence of the co-monomer) with various compositions (80/20, 60/40 and 50/50 w/w%) were prepared in an internal mixer. The blends were evaluated by their rheology (from changes in torque during melt processing and blending reflecting melt viscosity, and their melt flow rate), morphology scanning electron microscopy (SEM), dynamic mechanical properties (DMA), Fourier transform infrared (FTIR) analysis, and solubility (Molau) test. The reactive blends (PET/f-EPR) showed a marked increase in their melt viscosities in comparison with the corresponding physical (PET/EPR) blends (higher torque during melt blending), the extent of which depended on the amount of homopolymerised GMA (poly-GMA) present and the level of GMA grafting in the f-EPR. This increase was accounted for by, most probably, the occurrence of a reaction between the epoxy groups of GMA and the hydroxyl/carboxyl end groups of PET. Morphological examination by SEM showed a large improvement of phase dispersion, indicating reduced interfacial tension and compatibilisation, in both reactive blends, but with the Tris-GMA-based blends showing an even finer morphology (these blends are characterised by absence of poly-GMA and presence of higher level of grafted GMA in its f-EPR component by comparison to the conventional GMA-based blends). Examination of the DMA for the reactive blends at different compositions showed that in both cases there was a smaller separation between the glass transition temperatures compared to their position in the corresponding physical blends, which pointed to some interaction or chemical reaction between f-EPR and PET. The DMA results also showed that the shifts in the Tgs of the Tris-GMA-based blends were slightly higher than for the conventional GMA-blends. However, the overall tendency of the Tgs to approach each other in each case was found not to be significantly different (e.g. in a 60/40 ratio the former blend shifted by up to 4.5 °C in each direction whereas in the latter blend the shifts were about 3 °C). These results would suggest that in these blends the SEM and DMA analyses are probing uncorrelatable morphological details. The evidence for the formation of in situ graft copolymer between the f-EPR and PET during reactive blending was clearly illustrated from analysis by FTIR of the separated phases from the Tris-GMA-based reactive blends, and the positive Molau test pointed out to graft copolymerisation in the interface. A mechanism for the formation of the interfacial reaction during the reactive blending process is proposed.

Increasing the electrolyte capacity of alkaline Zn-air fuel cells by scavenging zincate with Ca(OH)2

The use of calcium hydroxide for scavenging zincate species is demonstrated to be a highly effective approach for increasing the electrolyte capacity and improving the performance of the zinc-air fuel cell system. A fundamental approach is established in this study to quantify the formation of calcium zincate as the product of scavenging and the amount of water compensation necessary for optimal performance. The good agreement between predicted and experimental results proves the validity of the proposed theoretical approach. By applying the results of theoretical predictions, both the electrolyte capacity and the cell longevity have been increased by more than 40%. It is also found that, using Ca(OH)2 to scavenge zincate species in concentrated KOH solutions, affects mostly the removal of zincate, rather than ZnO, from the electrolyte, whereas the presence of excess, free, mobile H2O plays a key role in dissolving ZnO and forming zincate. The results obtained in this study demonstrate that the proposed approach can widely and effectively be applied to all zinc-air cell systems during their discharge cycle.

Computational modeling of intermediate temperature proton exchange membrane (PEM) fuel cells

A two-phase three-dimensional computational model of an intermediate temperature (120--190°C) proton exchange membrane (PEM) fuel cell is presented. This represents the first attempt to model PEM fuel cells employing intermediate temperature membranes, in this case, phosphoric acid doped polybenzimidazole (PBI). To date, mathematical modeling of PEM fuel cells has been restricted to low temperature operation, especially to those employing Nafion ® membranes; while research on PBI as an intermediate temperature membrane has been solely at the experimental level. This work is an advancement in the state of the art of both these fields of research. With a growing trend toward higher temperature operation of PEM fuel cells, mathematical modeling of such systems is necessary to help hasten the development of the technology and highlight areas where research should be focused.^ This mathematical model accounted for all the major transport and polarization processes occurring inside the fuel cell, including the two phase phenomenon of gas dissolution in the polymer electrolyte. Results were presented for polarization performance, flux distributions, concentration variations in both the gaseous and aqueous phases, and temperature variations for various heat management strategies. The model predictions matched well with published experimental data, and were self-consistent.^ The major finding of this research was that, due to the transport limitations imposed by the use of phosphoric acid as a doping agent, namely low solubility and diffusivity of dissolved gases and anion adsorption onto catalyst sites, the catalyst utilization is very low (∼1--2%). Significant cost savings were predicted with the use of advanced catalyst deposition techniques that would greatly reduce the eventual thickness of the catalyst layer, and subsequently improve catalyst utilization. The model also predicted that an increase in power output in the order of 50% is expected if alternative doping agents to phosphoric acid can be found, which afford better transport properties of dissolved gases, reduced anion adsorption onto catalyst sites, and which maintain stability and conductive properties at elevated temperatures.^