In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs

We describe a method for cloning nucleic acid molecules onto the surfaces of 5-μm microbeads rather than in biological hosts. A unique tag sequence is attached to each molecule, and the tagged library is amplified. Unique tagging of the molecules is achieved by sampling a small fraction (1%) of a very large repertoire of tag sequences. The resulting library is hybridized to microbeads that each carry ≈106 strands complementary to one of the tags. About 105 copies of each molecule are collected on each microbead. Because such clones are segregated on microbeads, they can be operated on simultaneously and then assayed separately. To demonstrate the utility of this approach, we show how to label and extract microbeads bearing clones differentially expressed between two libraries by using a fluorescence-activated cell sorter (FACS). Because no prior information about the cloned molecules is required, this process is obviously useful where sequence databases are incomplete or nonexistent. More importantly, the process also permits the isolation of clones that are expressed only in given tissues or that are differentially expressed between normal and diseased states. Such clones then may be spotted on much more cost-effective, tissue- or disease-directed, low-density planar microarrays.

Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures

Sephadex-binding RNA ligands (aptamers) were obtained through in vitro selection. They could be classified into two groups based on their consensus sequences and the aptamers from both groups showed strong binding to Sephadex G-100. One of the highest affinity aptamers, D8, was chosen for further characterization. Aptamer D8 bound to dextran B512, the soluble base material of Sephadex, but not to isomaltose, isomaltotriose and isomaltotetraose, suggesting that its optimal binding site might consist of more than four glucose residues linked via α-1,6 linkages. The aptamer was very specific to the Sephadex matrix and did not bind appreciably to other supporting matrices, such as Sepharose, Sephacryl, cellulose or pustulan. Using Sephadex G-100, the aptamer could be purified from a complex mixture of cellular RNA, giving an enrichment of at least 60 000-fold, compared with a non-specific control RNA. These RNA aptamers can be used as affinity tags for RNAs or RNA subunits of ribonucleoproteins to allow rapid purification from complex mixtures of RNA using only Sephadex.

Risk assessment of herbicide mixtures in a large European lake

Lake Geneva is one of the largest European lakes with a surface area of 580 km2. Its catchment area covers 7400 km2, of which approximately 20% is arable land. Monitoring campaigns have been carried out in 2004 and 2005 to determine the contamination of the lake by pesticides. The results highlight the widespread presence of herbicides in water, the measured concentrations for most substances remaining constant in 2004 and 2005. However, for some individual herbicides the concentrations increased drastically (e.g., the herbicide foramsulfuron). We assessed the environmental risk of the herbicides detected in the lake using water quality criteria recently determined for the Swiss environmental protection agency. Furthermore, we assessed the risk of herbicide mixtures, grouped based upon their mode of action. Generally, the risk estimated for all single substances is low, except for some sulfonylurea compounds. For these substances, the measured concentrations are higher than the predicted no-effect concentration. Impact on the flora of the lake can therefore not be excluded. When mixtures of pesticides with similar mode of action are taken into account, the risk remains lower than the mixture water quality criteria for all groups, but can reach as high as one third of this quality criteria. A further step would therefore be to assess the risk of the total pesticide mixture, including similar and dissimilar modes of action

Current approaches and challenges for the metabolite profiling of complex natural extracts.

Metabolite profiling is critical in many aspects of the life sciences, particularly natural product research. Obtaining precise information on the chemical composition of complex natural extracts (metabolomes) that are primarily obtained from plants or microorganisms is a challenging task that requires sophisticated, advanced analytical methods. In this respect, significant advances in hyphenated chromatographic techniques (LC-MS, GC-MS and LC-NMR in particular), as well as data mining and processing methods, have occurred over the last decade. Together, these tools, in combination with bioassay profiling methods, serve an important role in metabolomics for the purposes of both peak annotation and dereplication in natural product research. In this review, a survey of the techniques that are used for generic and comprehensive profiling of secondary metabolites in natural extracts is provided. The various approaches (chromatographic methods: LC-MS, GC-MS, and LC-NMR and direct spectroscopic methods: NMR and DIMS) are discussed with respect to their resolution and sensitivity for extract profiling. In addition the structural information that can be generated through these techniques or in combination, is compared in relation to the identification of metabolites in complex mixtures. Analytical strategies with applications to natural extracts and novel methods that have strong potential, regardless of how often they are used, are discussed with respect to their potential applications and future trends.

Development of Performance Properties of Ternary Mixtures: Field Demonstrations and Project Summary, TPF-5(117), 2012

Supplementary cementitious materials (SCM) have become common parts of modern concrete practice. The blending of two or three cementitious materials to optimize durability, strength, or economics provides owners, engineers, materials suppliers, and contractors with substantial advantages over mixtures containing only portland cement. However, these advances in concrete technology and engineering have not always been adequately captured in specifications for concrete. Users need specific guidance to assist them in defining the performance requirements for a concrete application and the selection of optimal proportions of the cementitious materials needed to produce the required durable concrete. The fact that blended cements are currently available in many regions increases options for mixtures and thus can complicate the selection process. Both Portland and blended cements have already been optimized by the manufacturer to provide specific properties (such as setting time, shrinkage, and strength gain). The addition of SCMs (as binary, ternary, or even more complex mixtures) can alter these properties, and therefore has the potential to impact the overall performance and applications of concrete. This report is the final of a series of publications describing a project aimed at addressing effective use of ternary systems. The work was conducted in several stages and individual reports have been published at the end of each stage.

Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments

Establishing the mechanisms by which microbes interact with their environment, including eukaryotic hosts, is a major challenge that is essential for the economic utilisation of microbes and their products. Techniques for determining global gene expression profiles of microbes, such as microarray analyses, are often hampered by methodological restraints, particularly the recovery of bacterial transcripts (RNA) from complex mixtures and rapid degradation of RNA. A pioneering technology that avoids this problem is In Vivo Expression Technology (IVET). IVET is a 'promoter-trapping' methodology that can be used to capture nearly all bacterial promoters (genes) upregulated during a microbe-environment interaction. IVET is especially useful because there is virtually no limit to the type of environment used (examples to date include soil, oomycete, a host plant or animal) to select for active microbial promoters. Furthermore, IVET provides a powerful method to identify genes that are often overlooked during genomic annotation, and has proven to be a flexible technology that can provide even more information than identification of gene expression profiles. A derivative of IVET, termed resolvase-IVET (RIVET), can be used to provide spatio-temporal information about environment-specific gene expression. More recently, niche-specific genes captured during an IVET screen have been exploited to identify the regulatory mechanisms controlling their expression. Overall, IVET and its various spin-offs have proven to be a valuable and robust set of tools for analysing microbial gene expression in complex environments and providing new targets for biotechnological development.

Self-organisation in the assembly of gels from mixtures of different dendritic peptide building blocks

This paper investigates dendritic peptides capable of assembling into nanostructured gels, and explores the effect on self-assembly of mixing different molecular building blocks. Thermal measurements, small angle Xray scattering (SAXS) and circular dichroism (CD) spectroscopy are used to probe these materials on macroscopic, nanoscopic and molecular length scales. The results from these investigations demonstrate that in this case, systems with different "size" and "chirality" factors can self-organise, whilst systems with different "shape" factors cannot. The "size" and "chirality" factors are directly connected with the molecular information programmed into the dendritic peptides, whilst the shape factor depends on the group linking these peptides together-this is consistent with molecular recognition hydrogen bond pathways between the peptidic building blocks controlling the ability of these systems to self-recognise. These results demonstrate that mixtures of relatively complex peptides, with only subtle differences on the molecular scale, can self-organise into nanoscale structures, an important step in the spontaneous assembly of ordered systems from complex mixtures.

Environmental oestrogens and breast cancer: long-term low-dose effects of mixtures of various chemical combinations

The incidence of breast cancer has risen worldwide to unprecedented levels in recent decades, making it now the major cancer of women in many parts of the world.1 Although diet, alcohol, radiation and inherited loss of BRCA1/2 genes have all been associated with increased incidence, the main identified risk factors are life exposure to hormones including physiological variations associated with puberty/pregnancy/menopause,1 personal choice of use of hormonal contraceptives2 and/or hormone replacement therapy.3–6 On this basis, exposure of the human breast to the many environmental pollutant chemicals capable of mimicking or interfering with oestrogen action7 should also be of concern.8 Hundreds of such environmental chemicals have now been measured in human breast tissue from a range of dietary and domestic exposure sources7 ,9 including persistent organochlorine pollutants (POPs),10 polybrominated diphenylethers and polybromobiphenyls,11 polychlorinated biphenyls,12 dioxins,13 alkyl phenols,14 bisphenol-A and chlorinated derivatives,15 as well as other less lipophilic compounds such as parabens (alkyl esters of p-hydroxybenzoic acid),16 but studies investigating any association between raised levels of such compounds and the development of breast cancer remain inconclusive.7–16 However, the functionality of these chemicals has continued to be assessed on the basis of individual chemicals rather than the environmental reality of long-term low-dose exposure to complex mixtures. This misses the potential for individuals to have high concentrations of different compounds but with a common mechanism of action. It also misses the complex interactions between chemicals and physiological hormones which together may act to alter the internal homeostasis of the oestrogenic environment of mammary tissue.

How to deal with uncertainties regarding the occupational exposure to antineoplastic mixtures: additive effect should always be considered?

Risk assessment considerations - The concept that “safe levels of exposure” for humans can be identified for individual chemicals is central to the risk assessment of compounds with known toxicological profiles. Selection of agents for combination chemotherapy regimens involves minimize overlapping of mechanisms of action, antitumor activity and toxicity profile. Although the toxicological profile and mechanism of action of each individual drug is well characterized, the toxicological interactions between drugs are likely, but poorly established at occupational exposure context. The synergistic nature of interactions may help in understanding the adverse health effects observed in healthcare workers, where exposure situations are characterized by complex mixtures of chemical agents, and the levels of individual exposing agents are often not sufficiently high to explain the health complaints. However, if a substance is a genotoxic carcinogen, this would be the “lead effect”; normally, no OEL based on a NOEL would be derived and the level would be set so low that it would be unlikely that other effects would be expected. Aim of the study - Recently research project developed in Portuguese Hospitals characterize the occupational exposure to antineoplastic agents and the health effects related. The project aimed to assess exposure of the different risk groups that handle antineoplastic agents in the hospital setting, namely during preparation and administration of these drugs. Here it is presented and discussed the results in a study developed in two hospitals from Lisbon.

Endocrine disruptors mixtures: the real scenario of human exposure

Endocrine disrupting chemicals (EDCs) are exogenous agents that have the ability to interfere with/or mimic estrogenic hormones and, therefore can simultaneously and differentially trigger specific signaling pathways responsible for the nature and magnitude of biological responses in diverse cell types. Human exposure to EDCs, particularly at low-doses, is ubiquitous, persistent and occurs in complex mixtures. These compounds can bioaccumulate in lipid compartments of tissues forming a mixed “body burden” of contaminants of different origins. Although the independent action of chemicals has been considered the main principle in EDCs mixture toxicity, several effects cannot be predicted when analyzing single compounds individually. Based in a revision of the literature, focused in studies that evaluated EDCs mixtures, we hypothesize the scenario of a pregnant woman environmentally exposed to three different EDCs as a potential real scenario of human exposure supported by data describing where exposure to these compounds occur.

Nanomolar Levels Of Pahs In Extracts From Urban Air Induce Mapk Signaling In Hepg2 Cells.

Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that occur naturally in complex mixtures. Many of the adverse health effects of PAHs including cancer are linked to the activation of intracellular stress response signaling. This study has investigated intracellular MAPK signaling in response to PAHs in extracts from urban air collected in Stockholm, Sweden and Limeira, Brazil, in comparison to BP in HepG2 cells. Nanomolar concentrations of PAHs in the extracts induced activation of MEK4 signaling with down-stream increased gene expression of several important stress response mediators. Involvement of the MEK4/JNK pathway was confirmed using siRNA and an inhibitor of JNK signaling resulting in significantly reduced MAPK signaling transactivated by the AP-1 transcription factors ATF2 and c-Jun. ATF2 was also identified as a sensitive stress responsive protein with activation observed at extract concentrations equivalent to 0.1 nM BP. We show that exposure to low levels of environmental PAH mixtures more strongly activates these signaling pathways compared to BP alone suggesting effects due to interactions. Taken together, this is the first study showing the involvement of MEK4/JNK/AP-1 pathway in regulating the intracellular stress response after exposure to nanomolar levels of PAHs in environmental mixtures.

Application of Fluorescence to the Study of Crude Petroleum

Crude petroleum oils are complex mixtures of different compounds (mainly organic), which are obtained from an extensive range of different geological sources. The fluorescence of crude petroleum oils derives largely from the aromatic hydrocarbon fraction, and this fluorescence emission is strongly influenced by the chemical composition (e.g., fluorophore and quencher concentrations) and physical characteristics (e.g., viscosity and optical density) of the oil. The fluorescence spectroscopy (FS) is increasingly used in petroleum technology due the availability of better optical detection techniques, because FS offers high sensitivity, good diagnostic potential, and relatively simple instrumentation. In this work we analyzed crude petroleum at different dilution in Nujol, a transparent mineral oil. The main objective of this work was to verify the possibility to measure crude oil emission spectroscopic without use of volatile solvents. The mixtures of nujol with different -crude oil concentrations were measured with a 10 mm optical path cuvette thus simplifying the fluorescence spectroscopy signal detection. The emission spectra were obtained by exciting the samples with a 400 W Xenon lamp at 350 nm, 450 nm and 532 nm. The emissions of the samples were collected perpendicularly with the excitation axis.

Tissue-specific expression of head-to-tail cyclized miniproteins in Violaceae and structure determination of the root cyclotide Viola hederacea root cyclotide1

The plant cyclotides are a family of 28 to 37 amino acid miniproteins characterized by their head-to-tail cyclized peptide backbone and six absolutely conserved Cys residues arranged in a cystine knot motif: two disulfide bonds and the connecting backbone segments form a loop that is penetrated by the third disulfide bond. This knotted disulfide arrangement, together with the cyclic peptide backbone, renders the cyclotides extremely stable against enzymatic digest as well as thermal degradation, making them interesting targets for both pharmaceutical and agrochemical applications. We have examined the expression patterns of these fascinating peptides in various Viola species (Violaceae). All tissue types examined contained complex mixtures of cyclotides, with individual profiles differing significantly. We provide evidence for at least 57 novel cyclotides present in a single Viola species (Viola hederacea). Furthermore, we have isolated one cyclotide expressed only in underground parts of V, hederacea and characterized its primary and three-dimensional structure. We propose that cyclotides constitute a new family of plant defense peptides, which might constitute an even larger and, in their biological function, more diverse family than the well-known plant defensins.

Contaminação ambiental por pesticidas: análise metodológica

Este trabalho teve como objectivo pesquisar os pesticidas que são mais usados em Portugal, os métodos de análise mais frequentemente utilizados na determinação de pesticidas, a contaminação ambiental por pesticidas e como minimizar o impacto ambiental provocado pelo uso indiscriminado de pesticidas. Os pesticidas usados variam de acordo com as diferentes características das regiões de Portugal e os grupos de pesticidas mais usados são: organofosforados, derivados de anilina, derivados triazinicos, tiocarbamatos, derivados do ácido fenoxiacético, derivados de acetamida, benzotiadiazole, derivados de ureia e azol. A determinação destes grupos é usualmente feita usando métodos cromatográficos, uma vez que estes métodos permitem a separação de misturas complexas. A contaminação ambiental por pesticidas pode ser provocada por diversos factores, contudo esta contaminação pode ser minimizada se estes forem usados de forma racional e de um modo sustentável conforme o descrito na directiva 2009/128/CE de 21 de Outubro.

Biomarkers in Solea Senegalensis Kaup, 1858 exposed to contaminated estuarine sediments: a multi-level approach

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia for the degree of Doctor of Philosophy in Environmental Sciences