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Concentrations of 17 organochlorine and 14 organophosphorus pesticides were measured in 27 ground and 11 surface water samples collected from a heavily agricultural area, Kumluca, in spring and fall seasons of 2005. The samples were preconcentrated by Solid Phase Extraction. GC-ECD and GC-NPD systems were used for quantitative determination of organochlorine and organophosphorus pesticides respectively. The quality check/quality assurance tests were performed by the analysis of field and laboratory blanks, standard reference materials, spiked control and sample matrices, surrogate standards, sampling and analysis replicates. It is observed that, sample matrix lowers average percent recoveries from 89% to 76%. The uncertainties of measurements were calculated to determine major factors affecting the analysis results. It was observed that uncertainty arising from extraction procedure was generally the highest. The most commonly observed pesticide was endosulfan (70%) and chlorpyriphos (53%) for organophosphorus and organochlorine pesticides. The highest average concentration was observed for heptachlor (26 ng/L) and fenamiphos (184 ng/L). Generally pesticides were detected more often in surface waters, where the concentrations were also higher. The concentrations of organophosphorus pesticides in spring, and organochlorine pesticides in fall season were higher. The high occurrences and detection of degradation products of chlorinated pesticides clearly indicate their intense use before 1980s. It is shown that, in Kumluca environment, degradation of these pesticides mostly occurs in surface waters. It is observed that agricultural activities affect water quality in the region. The total concentration limit (500ng/L) was exceeded for 27% of surface and 14% of ground water samples, at least once in both seasons. The legal limit for a single pesticide (100ng/L) was exceeded by 32 % of surface, 24 % of ground water samples.

Aldehydes in lung cancer cell culture have been investigated using gas chromatography/mass spectrometry and solid-phase microextraction with on-fiber derivatization. In this study, the poly(dimethylsiloxane/divinylbenzene (PDMS/DVB) fiber was used and o-2,3,4,5,6-(pentafluorobenzyl) hydroxylamine hydrochloride (PFBHA) was first loaded on the fiber. Aldehydes in the headspace of lung cancer cell culture were extracted by solid-phase microextraction (SPME) fiber and subsequently derivatized by PFBHA on the fiber. Finally, the aldehyde oximes formed on the fiber were analyzed by gas chromatography/mass spectrometry (GC/MS). Using this method, acetaldehyde decrease was found in both non-small lung cancer cell cultures studied compared to the medium control study. The results of spiking the cell culture with acetaldehyde solution showed that 5 million SK-MES-1 cell lines could consume up to 4.5 uM acetaldehyde in 15-ml medium, and 5 million NCI-H522 cell lines could consume 5.9 uM acetaldehyde in 15-ml medium. The decrease of acetaldehyde may contribute to the metabolism of lung cancer cells. It was proved that GC/MS and SPME with on-fiber derivatization is a simple, rapid, sensitive and solvent-free method for the detection of aldehydes in lung cancer cell culture.

<p>The development of improved sequencing technologies hasenabled the field of genomics to evolve. Handling andsequencing of large numbers of samples require an increasedlevel of automation in order to obtain high throughput andconsistent quality. Improved performance has lead to thesequencing of numerous microbial genomes and a few genomes fromhigher eukaryotes and the benefits of comparing sequences bothwithin and between species are now becoming apparent. Thisthesis describes both the development of automated purificationmethods for DNA, mainly sequencing products, and a comparativesequencing project.</p><p>The initially developed purification technique is dedicatedto single stranded DNA containing vector specific sequences,exemplified by sequencing products. Specific capture probescoupled to paramagnetic beads together with stabilizing modularprobes hybridize to the single stranded target. After washing,the purified DNA can be released using water. When sequencingproducts are purified they can be directly loaded onto acapillary sequencer after elution. Since this approach isspecific it can be applied to multiplex sequencing products.Different probe sets are used for each sequencing product andthe purifications are performed iteratively.</p><p>The second purification approach, which can be applied to anumber of different targets, involves biotinylated PCR productsor sequencing products that are captured using streptavidinbeads. This has been described previously, buthere theinteraction between streptavidin and biotin can be disruptedwithout denaturing the streptavidin, enabling the re-use of thebeads. The relatively mild elution conditions also enable therelease of sensitive biotinylated molecules.</p><p>Another project described in this thesis is the comparativesequencing of the 40 kb<i>cag</i>pathogenicity island (PAI) in four<i>Helicobacter pylori</i>strains. The results included thediscovery of a novel gene, present in approximately half of theSwedish strains tested. In addition, one of the strainscontained a major rearrangement dividing the<i>cag</i>PAI into two parts. Further, information about thevariability of different genes could be obtained.</p><p><b>Keywords:</b>DNA sequencing, DNA purification, automation,solid-phase, streptavidin, biotin, modular probes,<i>Helicobacter pylori</i>,<i>cag</i>PAI.</p>

No description available.

Thesis (Ph.D.)--University of Western Sydney, 2008. / A thesis presented to the University of Western Sydney, College of Health and Science, School of Biomedical and Health Sciences, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographies.

Source: Masters Abstracts International, Volume: 47-06, page: 3475. Advisers: Elaine Symanski; Thomas H. Stock. Includes bibliographical references

Effective detection and treatment of tumor malignancies depends upon identifying targets – molecular markers that differentiate cancer cells from healthy cells. Current cancer therapies involve targeting overexpressed specific gene products. An alternative approach is proposed here: to specifically target combinations of cell-surface receptors using heteromultivalent ligands (htMVLs). There are about 2500 genes encoding for cellsurface proteins in the human genome that can potentially be targeted. Taken as sets, there can be ~ 10⁶ two-receptor combinations and ~ 10⁹ three-receptor combinations available. Our group envisions that using cell-surface protein combinations that are expressed on a cancer cell but not on a normal cell, multivalent constructs displaying complementary ligands of weak affinities can be assembled. These multivalent ligands should bind with high avidity to cancer populations in vivo, and provide a degree of specificity not seen with current approaches. As a proof-of-concept, a series of multivalent ligands were designed and synthesized for a model system consisting of the human Melanocortin subtype 4 receptor (hMC4R) and the Cholecystokinin subtype 2 receptor (CCK-2R). Modeling studies on GPCR dimers predicted that a minimum linker span of 20 - 50 Å would be required to non-covalently crosslink these two receptors. The multivalent ligands were assembled using a modular parallel synthesis approach and using solidphase chemistries. A variety of linkers were explored ranging from highly rigid to highly flexible, and using natural and/or synthetic building blocks. Ligand binding affinities were evaluated using a lanthanide based competitive binding assay in cells that expressed both receptors (bivalent binding) vs those that expressed only one of the receptors (monovalent binding), and were demonstrated to have enhanced binding affinities of up to nearly two orders of magnitude. The promising ligands were further explored by synthesizing fluorescently labeled and/or lanthanide chelate labeled monovalent and heterobivalent ligands designed for in vitro and in vivo studies. More explorative work using these labeled constructs is in progress. To the best of our knowledge, the author believes this is the first such demonstration of a 'synthetic htMVL' directed recruitment and crosslinking of two heterologous cell-surface receptors. This receptor combination approach opens up new possibilities for single cell imaging, cancer detection and therapeutic intervention, and can provide a revolutionary new platform technology with which to direct therapeutics to defined cell populations.

Protein biomarkers circulating in blood hold the promise of improved diagnosis, prognosis and follow-up of treatment of disease via minimally invasive procedures. For the discovery and validation of such biomarkers, methods are needed that can facilitate parallel, highly specific and in-depth analysis of the blood proteome. The work presented in this thesis intends to develop and apply such assays, building on the concept of the proximity ligation assay (PLA). In paper I, I present an easy and non-expensive alternative for the conjugation of oligonucleotides to antibodies via biotin-streptavidin-biotin interaction. This approach can be used when large sets of antibodies and/or oligos need to be validated for their performance as probes in PLA reactions. In paper II, a solid-phase variant of PLA (SP-PLA) for the detection and quantification of proteins in blood is presented. SP-PLA exhibited an improved limit of detection compared to commercial ELISA assays by two orders of magnitude. In addition SP-PLA exhibited a broader dynamic range by at least one order of magnitude and required only 5 μl of sample, rendering the method very well suited for analyses of precious bio-banked material. Last but not least, SP-PLA was used to validate the diagnostic potential of GDF-15 as a biomarker for cardiovascular disease in a set of cardiovascular disease patients and healthy controls. Paper III discusses the development of a multiplex SP-PLA (MultiPLAy) for the simultaneous detection of 36 proteins in just 5 μl of sample. MultiPLAy exhibited an improved LOD when compared to state-of-the-art bead-based sandwich assays. Most importantly, we observed only a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that much higher levels of multiplexing will be possible. The assay was used to identify putative biomarkers in sample cohorts of colorectal cancer (CRC) and cardiovascular disease (CVD). Subsequent multivariate analysis revealed previously known diagnostic biomarkers. Furthermore, we successfully applied next-generation sequencing as a readout for the protein assays, allowing for the first time digital recording of protein profiles in blood. In paper IV, we investigated the suitability of prostasomes as blood biomarkers in patients with prostate cancer using a newly developed PLA assay (4PLA) that utilizes five binders for the detection of complex target molecules. The assay successfully detected significantly elevated levels of prostasomes in blood samples from prostate cancer patients prior to radical prostatectomy, compared to controls and men with benign biopsy results.

Ultra-stable cystine knotted microproteins, in which two disulfides and their connecting backbones form a circle that is penetrated by the third disulfide bonds, have attracted high interest due to their resistance to degradation in vitro and potential for the development of peptide drugs. This thesis gives new insights into engineering of that framework of microproteins, including approaches to their chemical synthesis, backbone engineering, structural and biological evaluations. Synthetic and oxidative folding approaches for bracelet cyclotides, a family of cyclic cystine knotted microproteins, was developed using a model peptide, cycloviolacin O2. Following assembly of the peptide chain, protected peptide was generated by mild cleavage that was subsequently thioesterified and cyclized in solution. The cyclic peptide was oxidatively folded under optimized conditions containing co-solvent and non-ionic detergent affording native cycloviolacin O2 as a major product. To gain further insights into the heterogeneity, efficiency and kinetics of cyclotides’ oxidative folding, the intermediates that accumulate in oxidative refolding pathways of all cyclotide subfamilies: Möbius, bracelet and the hybrid cyclotides were quantitatively determined under four different folding conditions. The results were used for defining major folding pathways, which indicated that Möbius cyclotides might accumulate heterogeneous folding intermediates with one-, two- and three-disulfides, whereas bracelet tend to accumulate a homogenous intermediate with three-disulfides, depending on the buffer systems used. Furthermore, to probe the internal factors contributing to inefficiency of oxidative folding, as well as undesired bioactivities of bracelet cyclotides (e.g., cytotoxic activity), polymer-hybridized cyclotides were designed by replacing non-conserved residues with small isosteric polymers. The designed hybrid analogs in which hybridization involved replacement of loop 3 with isosteric polymers showed improved synthetic and oxidative folding properties. The cytoxicity of a model hybrid designed with replacement of loop 3 and 5 exhibited no cytotoxic activity at concentration of 128-fold relative to that of native peptide. Furthermore, 1D and 2D 1H NMR analysis of this hybrid showed that it had well structured fold.