Design, synthesis and biological evaluation of potential antibacterial oligonucleotides

Purine and pyrimidine triplex-forming oligonucleotides (TFOs), as potential antibacterial agents, were designed to bind by Hoogsteen and reverse Hoogsteen hydrogen bonds in a sequence specific manner in the major groove of genomic DNA at specific polypurine sites within the gyrA gene of E. coli and S. pneumoniae. Sequences were prepared by automated synthesis, with purification and characterisation determined by high performance liquid chromatograpy, capillary electrophoresis and mass spectrometry. Triplex stability was assessed using melting curves where the binding of the third strand to the duplex target, was assessed over a temperature range of 0-80°C, and at pH 6.4 and 7.2. The most successful of the unmodified TFOs (6) showed a Tm value of 26 °C at both pH values with binding via reverse Hoogsteen bonds. Binding to genomic DNA was also demonstrated by spectrofluorimetry, using fluorescein-labelled TFOs, from which dissociation constants were determined. Modifications in the form of 5mC, 5' acridine attachment, phosphorothioation, 2'-0-methylation and phosphoramidation, were made in order to. increase Tm values. Phosphoramidate modification was the most with increased Tm values of 42°C. However, the final purity of these sequences was poor due to their difficult syntheses. FACS (fluorescent activated cell sorting) analysis was used to determine the potential uptake of a fluorescently labelled analogue of 6 via passive, coJd shock mediated, and anionic liposome aided, uptake. This was established at 20°C and 37°C. At both temperatures anionic lipid-mediated uptake produced unrivalled fluorescence, equivalent to 20 and 43% at 20 and 37°C respectively. Antibacterial activity of each oligonucleotide was assessed by viable count anaJysis relying on passive uptake, cold shocking techniques, chlorpromazine-mediated uptake, and, cationic and anionic lipid-aided uptake. All oligonucleotides were assessed for their ability to enhance uptake, which is a major barrier to the effectiveness of these agents. Compound 6 under cold shocking conditions produced the greatest consistent decline in colony forming units per ml. Results for this compound were sometimes variable indicating inconsistent uptake by this particular assay method.

Design, synthesis and development of PDE5 inhibitors

This research project is concerned with the design, synthesis and development of new phosphodiesterase 5 (PDE5) inhibitors with improved selectivities and lower toxicities. Two series of a 5 member and a 6 member ring fused heterocyclic compounds were designed, and synthesized. By alteration of starting materials and fragments, two virtual libraries, each is consisted of close to hundred compounds, were obtained successfully. The screening of sexual stimulation activity with rabbits demonstrated both groups of compounds were able to stimulate rabbit penile erection significantly. The following toxicity studies revealed 2-(substituted-sulfonylphenyl)-imidazo [1,5-a]-1,3,5-triazine-4-(3H)-one group possessed an unacceptable toxicity with oral LD50 about 200mg/kg; while 2-(substituted-sulfonylphenyl)-pyrrolo[2,3-d]pyrimidin-4-one group showed an acceptable toxicity with oral LD50 over 2000mg/kg. The continued bioactivity studies showed yonkenafil, the representative of 2-(substituted-sulfonylphenyl)-pyrrolo[2,3-d]pyrimidin-4-one group, has a better selectivity towards PDE5 and PDE6 than sildenafil and a better overall profile of sexual stimulation on animals than sildenafil. Chronic toxicity studies of yonkenafil further confirmed yonkenafil did not cause any serious side effect and damage on animal models and most actions were explainable. Based on evidences of the above studies, yonkenafil were recommended to enter clinical trials by the regulation authority of China, SFDA. Currently yonkenafil has been through the Phase I clinical trials and ready to progress into Phase II. Hopefully, yonkenafil will provide an alternative to the ED patients in the future.

Formation and characterization of ultra-sensitive surface plasmon resonance sensor based upon a nano-scale corrugated multi-layered coated D-shaped optical fiber

We present experimental results on the performance of a series of coated, D-shaped optical fiber sensors that display high spectral sensitivities to external refractive index. Sensitivity to the chosen index regime and coupling of the fiber core mode to the surface plasmon resonance (SPR) is enhanced by using specific materials as part of a multi-layered coating. We present strong evidence that this effect is enhanced by post ultraviolet radiation of the lamellar coating that results in the formation of a nano-scale surface relief corrugation structure, which generates an index perturbation within the fiber core that in turn enhances the coupling. We have found reasonable agreement when we modeling the fiber device. It was found that the SPR devices operate in air with high coupling efficiency in excess of 40 dB with spectral sensitivities that outperform a typical long period grating, with one device yielding a wavelength spectral sensitivity of 12000 nm/RIU in the important aqueous index regime. The devices generate SPRs over a very large wavelength range, (visible to 2 mu m) by alternating the polarization state of the illuminating light.

Sensemaking tools for understanding research literatures:design, implementation and user evaluation

This paper describes the work undertaken in the Scholarly Ontologies Project. The aim of the project has been to develop a computational approach to support scholarly sensemaking, through interpretation and argumentation, enabling researchers to make claims: to describe and debate their view of a document's key contributions and relationships to the literature. The project has investigated the technicalities and practicalities of capturing conceptual relations, within and between conventional documents in terms of abstract ontological structures. In this way, we have developed a new kind of index to distributed digital library systems. This paper reports a case study undertaken to test the sensemaking tools developed by the Scholarly Ontologies project. The tools used were ClaiMapper, which allows the user to sketch argument maps of individual papers and their connections, ClaiMaker, a server on which such models can be stored and saved, which provides interpretative services to assist the querying of argument maps across multiple papers and ClaimFinder, a novice interface to the search services in ClaiMaker.

The formation and properties of some cyclic compounds of silicon an dtin

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Design, synthesis and evaluation of dipeptides as probes for studies of gastrointestinal tract dipeptide transport system

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Design, synthesis and evaluation of dipeptides as probes for studies of gastro-intestinal tract dipeptide transport

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Investigations into the formation and cleavage of siloxanes

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Flt1 acts as a negative regulator of tip cell formation and branching morphogenesis in the zebrafish embryo

Endothelial tip cells guide angiogenic sprouts by exploring the local environment for guidance cues such as vascular endothelial growth factor (VegfA). Here we present Flt1 (Vegf receptor 1) loss- and gain-of-function data in zebrafish showing that Flt1 regulates tip cell formation and arterial branching morphogenesis. Zebrafish embryos expressed soluble Flt1 (sFlt1) and membrane-bound Flt1 (mFlt1). In Tg(flt1(BAC):yfp) × Tg(kdrl:ras-cherry)(s916) embryos, flt1:yfp was expressed in tip, stalk and base cells of segmental artery sprouts and overlapped with kdrl:cherry expression in these domains. flt1 morphants showed increased tip cell numbers, enhanced angiogenic behavior and hyperbranching of segmental artery sprouts. The additional arterial branches developed into functional vessels carrying blood flow. In support of a functional role for the extracellular VEGF-binding domain of Flt1, overexpression of sflt1 or mflt1 rescued aberrant branching in flt1 morphants, and overexpression of sflt1 or mflt1 in controls resulted in short arterial sprouts with reduced numbers of filopodia. flt1 morphants showed reduced expression of Notch receptors and of the Notch downstream target efnb2a, and ectopic expression of flt4 in arteries, consistent with loss of Notch signaling. Conditional overexpression of the notch1a intracellular cleaved domain in flt1 morphants restored segmental artery patterning. The developing nervous system of the trunk contributed to the distribution of Flt1, and the loss of flt1 affected neurons. Thus, Flt1 acts in a Notch-dependent manner as a negative regulator of tip cell differentiation and branching. Flt1 distribution may be fine-tuned, involving interactions with the developing nervous system.

Design, synthesis and RAFT polymerisation of a quinoline-based monomer for use in metal-binding composite microfibres

Metal-binding polymer fibres have attracted major attention for diverse applications in membranes for metal sequestration from waste waters, non-woven wound dressings, matrices for photocatalysis, and many more. This paper reports the design and synthesis of an 8-hydroxyquinoline-based zinc-binding styrenic monomer, QuiBoc. Its subsequent polymerisation by reversible addition–fragmentation chain transfer (RAFT) yielded well-defined polymers, PQuiBoc, of controllable molar masses (6 and 12 kg mol−1) with low dispersities (Đ, Mw/Mn < 1.3). Protected (PQuiBoc) and deprotected (PQuiOH) derivatives of the polymer exhibited a high zinc-binding capacity, as determined by semi-quantitative SEM/EDXA analyses, allowing the electrospinning of microfibres from a PQuiBoc/polystyrene (PS) blend without the need for removal of the protecting group. Simple “dip-coating” of the fibrous mats into ZnO suspensions showed that PQuiBoc/PS microfibres with only 20% PQuiBoc content had almost three-fold higher loadings of ZnO (29%) in comparison to neat PS microfibres (11%).

Multi-frequency segmental bio-impedance device:design, development and applications

Bio-impedance analysis (BIA) provides a rapid, non-invasive technique for body composition estimation. BIA offers a convenient alternative to standard techniques such as MRI, CT scan or DEXA scan for selected types of body composition analysis. The accuracy of BIA is limited because it is an indirect method of composition analysis. It relies on linear relationships between measured impedance and morphological parameters such as height and weight to derive estimates. To overcome these underlying limitations of BIA, a multi-frequency segmental bio-impedance device was constructed through a series of iterative enhancements and improvements of existing BIA instrumentation. Key features of the design included an easy to construct current-source and compact PCB design. The final device was trialled with 22 human volunteers and measured impedance was compared against body composition estimates obtained by DEXA scan. This enabled the development of newer techniques to make BIA predictions. To add a ‘visual aspect’ to BIA, volunteers were scanned in 3D using an inexpensive scattered light gadget (Xbox Kinect controller) and 3D volumes of their limbs were compared with BIA measurements to further improve BIA predictions. A three-stage digital filtering scheme was also implemented to enable extraction of heart-rate data from recorded bio-electrical signals. Additionally modifications have been introduced to measure change in bio-impedance with motion, this could be adapted to further improve accuracy and veracity for limb composition analysis. The findings in this thesis aim to give new direction to the prediction of body composition using BIA. The design development and refinement applied to BIA in this research programme suggest new opportunities to enhance the accuracy and clinical utility of BIA for the prediction of body composition analysis. In particular, the use of bio-impedance to predict limb volumes which would provide an additional metric for body composition measurement and help distinguish between fat and muscle content.

Practically oriented design projects in mechatronics engineering:a case study of design experiences and outcomes

This paper discusses and presents a case study of a practically oriented design project together with a few examples of implemented design projects recently incorporated into an undergraduate system course at the mechatronics engineering department in Ah-Balqa’ Applied University. These projects have had a positive impact on both the department and its graduates. The focus of these projects is the design and implementation of processor-based system. This helps graduate students cross the border between hardware design and software design. Our case study discusses the research methodology adopted for the physical development of the project, the technology used in the project, and the design experiences and outcomes.

Design, synthesis and thermal behaviour of a series of well-defined clickable and triggerable sulfonate polymers

In the printing industry, the exploitation of triggerable materials that can have their surface properties altered on application of a post-deposition external stimulus has been crucial for the production of robust layers and patterns. To this end, herein, a series of clickable poly(R-alkyl p-styrene sulfonate) homopolymers, with systematically varied thermally-labile protecting groups, has been synthesised via reversible addition-fragmentation chain transfer (RAFT) polymerisation. The polymer range has been designed to offer varied post-deposition thermal treatment to switch them from hydrophobic to hydrophilic. Suitable RAFT conditions have been identified to produce well-defined homopolymers (Đ, Mw/Mn < 1.11 in all cases) at high monomer conversions (>80% for all but one monomer) with controllable molar mass. Poly(p-styrene sulfonate) with an isobutyl protecting group has been shown to be the most readily thermolysed polymer that remains stable at room temperature, and was thus investigated further by incorporation into a diblock copolymer, P3HT-b-PiBSS, by click chemistry. The strategy for preparation of thermal modifiable block copolymers exploiting R-protected p-styrene sulfonates and azide-alkyne click chemistry presented herein allows the design of new, roll-to-roll processable materials for potential application in the printing industry, particularly organic electronics.

Green manufacturing supply chain design and operations decision support

This special issue of International Journal of Production Research provides a platform for sharing the knowledge base, recent research outputs and a review of recent developments highlighting the critical aspects of green manufacturing supply chain design and operations decision support. The special issue includes 15 contributions presenting new and significant research in the relevant area. Contributions mainly present either a novel green/sustainable manufacturing supply chain design and operations decision support approach applied to a problem, or a state-of-the-art method on green/sustainable factors in supply chain design and operations. The article delineates an overview of the contributions and their significance, and an introspection on the ‘green’ factors involved.