The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Quartz crystal microbalance monitoring of density changes in mesoporous TiO2 phytate films during redox and ion exchange processes

Nanofilm deposits of TiO2 nanoparticle phytates are formed on gold electrode surfaces by 'directed assembly' methods. Alternate exposure of a 3-mercapto-propionic acid modified gold surface to (i) a TiO2 sol and (ii) an aqueous phytic acid solution (pH 3) results in layer-by-layer formation of a mesoporous film. Ru(NH3)(6)(3+) is shown to strongly adsorb/accumulate into the mesoporous structure whilst remaining electrochemically active. Scanning the electrode potential into a sufficiently negative potential range allows the Ru(NH3)(6)(3+) complex to be reduced to Ru(NH3)(6)(2+) which undergoes immediate desorption. When applied to a gold coated quartz crystal microbalance (QCM) sensor, electrochemically driven adsorption and desorption processes in the mesoporous structure become directly detectable as a frequency response, which corresponds directly to a mass or density change in the membrane. The frequency response (at least for thin films) is proportional to the thickness of the mass-responsive film, which suggests good mechanical coupling between electrode and film. Based on this observation, a method for the amplified QCM detection of small mass/density changes is proposed by conducting measurements in rigid mesoporous structures. (C) 2003 Elsevier Science B.V. All rights reserved.

Bio-fabrication and physiological self-release of tissue equivalents using smart peptide amphiphile templates

In this study we applied a smart biomaterial formed from a self-assembling, multi-functional synthetic peptide amphiphile (PA) to coat substrates with various surface chemistries. The combination of PA coating and alignment-inducing functionalised substrates provided a template to instruct human corneal stromal fibroblasts to adhere, become aligned and then bio-fabricate a highlyordered, multi-layered, three-dimensional tissue by depositing an aligned, native-like extracellular matrix. The newly-formed corneal tissue equivalent was subsequently able to eliminate the adhesive properties of the template and govern its own complete release via the action of endogenous proteases. Tissues recovered through this method were structurally stable, easily handled, and carrier-free. Furthermore, topographical and mechanical analysis by atomic force microscopy showed that tissue equivalents formed on the alignment-inducing PA template had highly-ordered, compact collagen deposition, with a two-fold higher elastic modulus compared to the less compact tissues produced on the non-alignment template, the PA-coated glass. We suggest that this technology represents a new paradigm in tissue engineering and regenerative medicine, whereby all processes for the biofabrication and subsequent self-release of natural, bioprosthetic human tissues depend solely on simple templatetissue feedback interactions.

Multilayered hydrogel coatings covalently-linked to glass surfaces showing a potential to mimic mucosal tissues

Multilayered hydrogel coatings can be developed on the surface of glass slides via layer-by-layer deposition of hydrogen-bonded interpolymer complexes formed by poly(acrylic acid) and methylcellulose. Chemical modification of the glass surface with (3-aminopropyl)triethoxysilane with subsequent layer-by-layer deposition and cross-linking of interpolymer complexes by thermal treatment allows fabrication of ultrathin hydrogel coatings, not detachable from the substrate. The thickness of these coatings is directly related to the number of deposition cycles and cross-linking conditions. An unusual dependence of the hydrogel swelling properties on the sample thickness is observed and can be interpreted by gradual transitions between two- and three-dimensional networks. The hydrogels exhibit pH-responsive swelling behaviour, achieving higher swelling degrees at pH > 6.0. These coatings can be used as model substrates to study the adhesive properties of pharmaceutical tablets and can potentially mimic the total work of adhesion observed for the detachment of mucoadhesives from porcine buccal mucosa but fail to exhibit identical detachment profiles.

Sonogashira coupling on an extended gold surface in vacuo: reaction of phenylacetylene with iodobenzene on Au(111)

Temperature-programmed reaction measurements supported by scanning tunneling microscopy have shown that phenylacetylene and iodobenzene react on smooth Au(111) under vacuum conditions to yield biphenyl and diphenyldiacetylene, the result of homocoupling of the reactant molecules. They also produce diphenylacetylene, the result of Sonogashira cross-coupling, prototypical of a class of reactions that are of paramount importance in synthetic organic chemistry and whose mechanism remains controversial. Roughened Au(111) is completely inert toward all three reactions, indicating that the availability of crystallographically well-defined adsorption sites is crucially important. High-resolution X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy show that the reactants are initially present as intact, essentially flat-lying molecules and that the temperature threshold for Sonogashira coupling coincides with that for C−I bond scission in the iodobenzene reactant. The fractional-order kinetics and low temperature associated with desorption of the Sonogashira product suggest that the reaction occurs at the boundaries of islands of adsorbed reactants and that its appearance in the gas phase is rate-limited by the surface reaction. These findings demonstrate unambiguously and for the first time that this heterogeneous cross-coupling chemistry is an intrinsic property of extended, metallic pure gold surfaces: no other species, including solvent molecules, basic or charged (ionic) species are necessary to mediate the process.

Abatement of mercury pollution in the small-scale gold mining industry: Restructuring the policy and research agendas

This paper critiques contemporary research and policy approaches taken toward the analysis and abatement of mercury pollution in the small-scale gold mining sector. Unmonitored releases of mercury from gold amalgamation have caused considerable environmental contamination and human health complications in rural reaches of sub-Saharan Africa, Latin America and Asia. Whilst these problems have caught the attention of the scientific community over the past 15-20 years, the research that has since been undertaken has failed to identify appropriate mitigation measures, and has done little to advance understanding of why contamination persists. Moreover, the strategies used to educate operators about the impacts of acute mercury exposure, and the technologies implemented to prevent farther pollution, have been marginally effective at best. The mercury pollution problem will not be resolved until governments and donor agencies commit to carrying out research aimed at improving understanding of the dynamics of small scale gold mining communities. Acquisition of this knowledge is the key to designing and implementing appropriate support and abatement measures. (c) 2005 Elsevier B.V. All rights reserved.

'Fair trade gold': Antecedents, prospects and challenges

This paper critically examines the challenges with, and impacts of, adopting the models in place for fair trade agriculture in the artisanal gold mining sector. Over the past two years, an NGO-led 'fair trade gold' movement has surfaced, its crystallization fuelled by a burgeoning body of evidence that points to impoverished artisanal miners in developing countries receiving low payments for their gold, as well as working in hazardous and unsanitary conditions. Proponents of fair trade gold contest that increased interaction between artisanal miners and Western jewellers could facilitate the former receiving fairer prices for gold, accessing support services, and ultimately, improving their quality of life. In the case of sub-Saharan Africa, however, the gold being mined on an artisanal scale does not supply Western retailers as perhaps believed; it is rather an important source of foreign exchange, which host governments employ buyers to collect for their coffers. It is maintained here that if the underlying purpose of fair trade is to improve the livelihoods and well-being of subsistence producers in developing countries, then the models that have proved so successful in alleviating the hardships of agro-producers of 'tropical' commodities such as coffee, tea, bananas and cocoa, should be adapted to artisanal gold mining in sub-Saharan Africa. Campaigns promoting 'fair trade gold' in the region should view host governments, and not Western retailers, as the 'end consumer', and focus on improving governance at the grassroots, organizing informal operators into working cooperatives, and addressing complications with purchasing arrangements - all of which would go a long way toward improving the livelihoods of subsistence artisanal miners. A case study of Noyem, Ghana, the location of a sprawling illegal gold mining community, is presented, which magnifies these challenges further and provides perspective on how they can be overcome. (c) 2007 Elsevier Ltd. All rights reserved.

Improving awareness of mercury pollution in small-scale gold mining communities: Challenges and ways forward in rural Ghana

This paper critiques the approach taken by the Ghanaian Government to address mercury pollution in the artisanal and small-scale gold mining sector. Unmonitored releases of mercury-used in the gold-amalgamation process-have caused numerous environmental complications throughout rural Ghana. Certain policy, technological and educational initiatives taken to address the mounting problem, however, have proved marginally effective at best, having been designed and implemented without careful analysis of mine community dynamics, the organization of activities, operators' needs and local geological conditions. Marked improvements can only be achieved in this area through increased government-initiated dialogue with the now-ostracized illegal galamsey mining community; introducing simple, cost-effective techniques for the reduction of mercury emissions; and effecting government-sponsored participatory training exercises as mediums for communicating information about appropriate technologies and the environment. (c) 2006 Elsevier Inc. All rights reserved.

Alternatives to cyanide in the gold mining industry: what prospects for the future

This paper reviews a series of alternative lixiviant systems for the recovery of gold from ores and concentrates. For over 100 years, cyanide has been the leach reagent of choice in gold mining because of its high gold recoveries, robustness and relatively low costs. The environmental damages resulting from its mismanagement, however, have initiated widespread research aimed at identifying and developing less toxic leaching agents. The most widely-researched alternative lixiviants for gold ores are examined in this paper, but it is evident that none has yet made any significant inroad into the dominant position of cyanide as the reagent of choice at the vast majority of gold mines worldwide. (c) 2005 Published by Elsevier Ltd.