Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites

BACKGROUND: Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. RESULTS: Using the TFBS for the estrogen receptor (ER)α (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms whose binding to ERα has been experimentally confirmed or rejected. In silico analyses revealed significant sequence information flanking the standard binding consensus, discriminating ERE-like sequences that bind ERα from those that are nonbinders. We extended the ERE consensus by three bases, bearing a terminal G at the third position 3' and an initiator C at the third position 5', which were further validated using surface plasmon resonance spectroscopy. Our functional human ERE prediction algorithm (h-ERE) outperformed existing predictive algorithms and produced fewer than 5% false negatives upon experimental validation. CONCLUSION: Building upon a larger experimentally validated ERE set, the h-ERE algorithm is able to demarcate better the universe of ERE-like sequences that are potential ER binders. Only 14% of the predicted optimal binding sites were utilized under the experimental conditions employed, pointing to other selective criteria not related to EREs. Other factors, in addition to primary nucleotide sequence, will ultimately determine binding site selection

Natural Organochlorines as precursors of 3-monochloropropanediol esters in vegetable oils

During high-temperature refining of vegetable oils, 3-monochloropropanediol (3-MCPD) esters, possible carcinogens, are formed from acylglycerol in the presence of a chlorine source. To investigate organochlorine compounds in vegetable oils as possible precursors for 3-MCPD esters, we tested crude palm, soybean, rapeseed, sunflower, corn, coconut, and olive oils for the presence of organochlorine compounds. Having found them in all vegetable oils tested, we focused subsequent study on oil palm products. Analysis of the chlorine isotope mass pattern exhibited in high-resolution mass spectrometry enabled organochlorine compound identification in crude palm oils as constituents of wax esters, fatty acid, diacylglycerols, and sphingolipids, which are produced endogenously in oil palm mesocarp throughout ripening. Analysis of thermal decomposition and changes during refining suggested that these naturally present organochlorine compounds in palm oils and perhaps in other vegetable oils are precursors of 3-MCPD esters. Enrichment and dose-response showed a linear relationship to 3-MCPD ester formation and indicated that the sphingolipid-based organochlorine compounds are the most active precursors of 3-MCPD esters

Electrochemical detection study of DNA

In this thesis, we first carry out three studies of macro electrochemical detection for DNA analysis. Then, a portable microfluidic flow-through microdevice with an integrated electrochemical detection system for PCR products quantification is developed.DOCTOR OF PHILOSOPHY (MAE

Influence of Methacrylic-Acrylic Copolymer Composition on Plasticiser-free Optode Films for pH Sensors

In this work we have examined the use of plasticiser-free polymeric films incorporating a proton selective chromoionophore for optical pH sensor. Four types of methacrylic-acrylic copolymers containing different compositions of n-butyl acrylate (nBA) and methyl methacrylate (MMA) were synthesised for use as optical sensor films. The copolymers were mixed with appropriate amounts of chromoionophore (ETH5294) and a lipophilic salt before spin coated on glass slides to form films for the evaluation of pH response using spectrophotometry. Co-polymer films with high nBA content gave good response and the response time depended on the film thickness. A preliminary evaluation of the optical films of high nBA content with pHs from 2 - 14 showed distinguishable responses from pH 5 - 9. However, the adhesion of the pH sensitive film was good for copolymers with higher content of MMA but not for films with high nBA

Analysis of Popular Social Media Topics Regarding Plastic Pollution

Plastic pollution is one of the most significant environmental issues in the world. The rapid increase of the cumulative amount of plastic waste has caused alarm, and the public have called for actions to mitigate its impacts on the environment. Numerous governments and social activists from various non-profit organisations have set up policies and actively promoted awareness and have engaged the public in discussions on this issue. Nevertheless, social responsibility is the key to a sustainable environment, and individuals are accountable for performing their civic duty and commit to behavioural changes that can reduce the use of plastics. This paper explores a set of topic modelling techniques to assist policymakers and environment communities in understanding public opinions about the issues related to plastic pollution by analysing social media data. We report on an experiment in which a total of 274,404 tweets were collected from Twitter that are related to plastic pollution, and five topic modelling techniques, including (a) Latent Dirichlet Allocation (LDA), (b) Hierarchical Dirichlet Process (HDP), (c) Latent Semantic Indexing (LSI), (d) Non-Negative Matrix Factorisation (NMF), and (e) extension of LDA—Structural Topic Model (STM), were applied to the data to identify popular topics of online conversations, considering topic coherence, topic prevalence, and topic correlation. Our experimental results show that some of these topic modelling techniques are effective in detecting and identifying important topics surrounding plastic pollution, and potentially different techniques can be combined to develop an efficient system for mining important environment-related topics from social media data on a large scale

Fabrication and characterization of Clinacanthus nutans mediated reduced graphene oxide using green approach

The reduction of graphene oxide (rGO) utilizing green methods such as plants has attracted much attention due to its productivity, eco—friendly features, and cost effectiveness. In the present study, the reflux method was employed to synthesize Clinacanthus nutans (C. nutans) leaf extract mediated rGO using a simple approach. The synthesized rGO was characterized using various spectroscopic and microscopic techniques. The UV-Vis spectrum demonstrated the absorption peak of rGO (270 nm) at distinct locations, while the FTIR analysis demonstrated that the amount of oxygen group in rGO was reduced. The Raman analysis confirms the reduction of GO by a slight increase in the D—band to G—band intensity ratio. The XRD spectra demonstrated that rGO was successfully produced based on the illustrated 2Ɵ angles at a peak of 22.12° with d-spacing of 0.40 nm. FESEM clearly reveals the morphology of rGO that shows crumpled thin sheets, a rougher surface, and a wave—shaped corrugated structure. The reduction of GO was analyzed in the removal of the hydroxyl group and amorphotization of sp2 carbon structures. The C/O ratio in rGO was higher than GO which indicates the small amount of oxygen-containing functional groups were still presented in the reduced graphene oxide. Furthermore, the cyclic voltammetry behavior of a modified screen—printed carbon electrode (SPCE) was measured. The redox reactivity of rGO—SPCE has been affirmed and compared with GO—SPCE and bare—SPCE. The toxicity using A. salina cysts demonstrated that rGO is less toxic compared to GO. The analysis adequately supports the synthesis of rGO and the effective removal of oxygen-containing functional groups from GO. The findings herein illustrate that C. nutans mediates the synthesis of rGO and is a promising eco-friendly substitute to conventional carbon-based fabrication

Fabrication and Characterization of Clinacanthus nutans Mediated Reduced Graphene Oxide Using a Green Approach

The reduction of graphene oxide (rGO) utilizing green methods such as plants has attracted much attention due to its productivity, eco—friendly features, and cost effectiveness. In the present study, the reflux method was employed to synthesize Clinacanthus nutans (C. nutans) leaf extract mediated rGO using a simple approach. The synthesized rGO was characterized using various spectroscopic and microscopic techniques. The UV-Vis spectrum demonstrated the absorption peak of rGO (270 nm) at distinct locations, while the FTIR analysis demonstrated that the amount of oxygen group in rGO was reduced. The Raman analysis confirms the reduction of GO by a slight increase in the D—band to G—band intensity ratio. The XRD spectra demonstrated that rGO was successfully produced based on the illustrated 2Ɵ angles at a peak of 22.12° with d-spacing of 0.40 nm. FESEM clearly reveals the morphology of rGO that shows crumpled thin sheets, a rougher surface, and a wave—shaped corrugated structure. The reduction of GO was analyzed in the removal of the hydroxyl group and amorphotization of sp2 carbon structures. The C/O ratio in rGO was higher than GO which indicates the small amount of oxygen-containing functional groups were still presented in the reduced graphene oxide. Furthermore, the cyclic voltammetry behavior of a modified screen—printed carbon electrode (SPCE) was measured. The redox reactivity of rGO—SPCE has been affirmed and compared with GO—SPCE and bare—SPCE. The toxicity using A. salina cysts demonstrated that rGO is less toxic compared to GO. The analysis adequately supports the synthesis of rGO and the effective removal of oxygen-containing functional groups from GO. The findings herein illustrate that C. nutans mediates the synthesis of rGO and is a promising eco-friendly substitute to conventional carbon-based fabrication

Roles and principles of sterilisation process in palm oil mills

Sterilisation in palm oil mills is considered a pre-treatment process as it affects stripping efficiency and oil quality. Although sterilisation technology has been well-established in the palm oil milling industry, the roles and principles of sterilisation, particularly related to the chemical changes in fruits and stalks occurring during the process, have been rarely reported. The review begins with the background literature on the biochemical properties of the FFBs, such as the compositions of binding carbohydrates and the phenomena of natural fruit detachment. Followed by the harvesting practice to understand the type of FFBs supplied to the industry. In addition, a comparison of the well-established conventional and alternative sterilisation technologies and sterilisation functions is critically reviewed and assessed. Establishing the current sterilisation process initiatives to address the natural fruit’s separation more efficiently in palm oil mills is important. Particularly visualise sterilisation as a breakup of specific binding carbohydrates that leads to strippability. It will provide a further understanding of the sterilisation mechanism, which would benefit the palm oil miller in optimising the processing of fresh fruit bunches. The information provided in this review is necessary to mitigate the percentage of unstripped bunches and reduce the oil losses and ultimately enhance the oil extraction rate

Amino Acid and Secondary Metabolite Production in Embryogenic and Non-Embryogenic Callus of Fingerroot Ginger (Boesenbergia rotunda).

Interest in the medicinal properties of secondary metabolites of Boesenbergia rotunda (fingerroot ginger) has led to investigations into tissue culture of this plant. In this study, we profiled its primary and secondary metabolites, as well as hormones of embryogenic and non-embryogenic (dry and watery) callus and shoot base, Ultra Performance Liquid Chromatography-Mass Spectrometry together with histological characterization. Metabolite profiling showed relatively higher levels of glutamine, arginine and lysine in embryogenic callus than in dry and watery calli, while shoot base tissue showed an intermediate level of primary metabolites. For the five secondary metabolites analyzed (ie. panduratin, pinocembrin, pinostrobin, cardamonin and alpinetin), shoot base had the highest concentrations, followed by watery, dry and embryogenic calli. Furthermore, intracellular auxin levels were found to decrease from dry to watery calli, followed by shoot base and finally embryogenic calli. Our morphological observations showed the presence of fibrils on the cell surface of embryogenic callus while diphenylboric acid 2-aminoethylester staining indicated the presence of flavonoids in both dry and embryogenic calli. Periodic acid-Schiff staining showed that shoot base and dry and embryogenic calli contained starch reserves while none were found in watery callus. This study identified several primary metabolites that could be used as markers of embryogenic cells in B. rotunda, while secondary metabolite analysis indicated that biosynthesis pathways of these important metabolites may not be active in callus and embryogenic tissue