Development of low-cost sensing and separation devices based on macro, micro and nano technology for health applications

The work presented in this thesis described the development of low-cost sensing and separation devices with electrochemical detections for health applications. This research employs macro, micro and nano technology. The first sensing device developed was a tonerbased micro-device. The initial development of microfluidic devices was based on glass or quartz devices that are often expensive to fabricate; however, the introduction of new types of materials, such as plastics, offered a new way for fast prototyping and the development of disposable devices. One such microfluidic device is based on the lamination of laser-printed polyester films using a computer, printer and laminator. The resulting toner-based microchips demonstrated a potential viability for chemical assays, coupled with several detection methods, particularly Chip-Electrophoresis-Chemiluminescence (CE-CL) detection which has never been reported in the literature. Following on from the toner-based microchip, a three-electrode micro-configuration was developed on acetate substrate. This is the first time that a micro-electrode configuration made from gold; silver and platinum have been fabricated onto acetate by means of patterning and deposition techniques using the central fabrication facilities in Tyndall National Institute. These electrodes have been designed to facilitate the integration of a 3- electrode configuration as part of the fabrication process. Since the electrodes are on acetate the dicing step can automatically be eliminated. The stability of these sensors has been investigated using electrochemical techniques with excellent outcomes. Following on from the generalised testing of the electrodes these sensors were then coupled with capillary electrophoresis. The final sensing devices were on a macro scale and involved the modifications of screenprinted electrodes. Screen-printed electrodes (SPE) are generally seen to be far less sensitive than the more expensive electrodes including the gold, boron-doped diamond and glassy carbon electrodes. To enhance the sensitivity of these electrodes they were treated with metal nano-particles, gold and palladium. Following on from this, another modification was introduced. The carbonaceous material carbon monolith was drop-cast onto the SPE and then the metal nano-particles were electrodeposited onto the monolith material

Development of block copolymer lithography for device structure fabrication

This thesis investigated well-ordered block copolymer (BCP) thin film characteristics and their use for nanoscale pattern formation using a series of polystyrene-block-polymethylmethacrylate (PS-b-PMMA), polystyrene-blockpolydimethylsiloxane (PS-b-PDMS) and polystyrene-block-poly(ethylene oxide) (PS-b-PEO) systems of various molecular weights. BCP thin films, which act as an ‘on-chip’ etch mask and material templates, are highly promising self-assembling process for future scalable nanolithography. Unlike conventional BCP processing methods, the work in this thesis demonstrates that well-ordered patterns can be achieved in a few seconds compared to several hours by use of a non-conventional microwave assisted technique. As a result, well-ordered BCP nanoscale structures can be developed in industry appropriate periods facilitating their incorporation into current technologies. An optimised and controlled plasma dry etch process was used for successful pattern transfer to the underlying silicon substrate. Long range ordered BCP templates were further modified by selective metal inclusion technique to form a hard mask template towards fabrication of high aspect ratio nanopillars and nanowires. The work described here is centred on how these templates might be used to generate function at substrate surfaces. Herein we describe a number of innovations which might allow their successful uptake in a number of applications.

Micro and nanostructured impedance sensors for biological and biomedical applications

This thesis work covered the fabrication and characterisation of impedance sensors for biological applications aiming in particular to the cytotoxicity monitoring of cultured cells exposed to different kind of chemical compounds and drugs and to the identification of different types of biological tissue (fat, muscles, nerves) using a sensor fabricated on the tip of a commercially available needle during peripheral nerve block procedures. Gold impedance electrodes have been successfully fabricated for impedance measurement on cells cultured on the electrode surface which was modified with the fabrication of gold nanopillars. These nanostructures have a height of 60nm or 100nm and they have highly ordered layout as they are fabricated through the e-beam technique. The fabrication of the threedimensional structures on the interdigitated electrodes was supposed to improve the sensitivity of the ECIS (electric cell-substrate impedance sensing) measurement while monitoring the cytotoxicity effects of two different drugs (Antrodia Camphorata extract and Nicotine) on three different cell lines (HeLa, A549 and BALBc 3T3) cultured on the impedance devices and change the morphology of the cells growing on the nanostructured electrodes. The fabrication of the nanostructures was achieved combining techniques like UV lithography, metal lift-off, evaporation and e-beam lithography techniques. The electrodes were packaged using a pressure sensitive, medical grade adhesive double-sided tape. The electrodes were then characterised with the aid of AFM and SEM imaging which confirmed the success of the fabrication processes showing the nanopillars fabricated with the right layout and dimensions figures. The introduction of nanopillars on the impedance electrodes, however, did not improve much the sensitivity of the assay with the exception of tests carried out with Nicotine. HeLa and A549 cells appeared to grow in a different way on the two surfaces, while no differences where noticed on the BALBc 3T3 cells. Impedance measurements obtained with the dead cells on the negative control electrodes or the test electrodes with the drugs can be compared to those done on the electrodes containing just media in the tested volume (as no cells are attached and cover the electrode surface). The impedance figures recorded using these electrodes were between 1.5kΩ and 2.5 kΩ, while the figures recorded on confluent cell layers range between 4kΩ and 5.5kΩ with peaks of almost 7 kΩ if there was more than one layer of cells growing on each other. There was then a very clear separation between the values of living cell compared to the dead ones which was almost 2.5 - 3kΩ. In this way it was very easy to determine whether the drugs affected the cells normal life cycle on not. However, little or no differences were noticed in the impedance analysis carried out on the two different kinds of electrodes using cultured cells. An increase of sensitivity was noticed only in a couple of experiments carried out on A549 cells growing on the nanostructured electrodes and exposed to different concentration of a solution containing Nicotine. More experiments to achieve a higher number of statistical evidences will be needed to prove these findings with an absolute confidence. The smart needle project aimed to reduce the limitations of the Electrical Nerve Stimulation (ENS) and the Ultra Sound Guided peripheral nerve block techniques giving the clinicians an additional tool for performing correctly the peripheral nerve block. Bioimpedance, as measured at the needle tip, provides additional information on needle tip location, thereby facilitating detection of intraneural needle placement. Using the needle as a precision instrument and guidance tool may provide additional information as to needle tip location and enhance safety in regional anaesthesia. In the time analysis, with the frequency fixed at 10kHz and the samples kept at 12°C, the approximate range for muscle bioimpedance was 203 – 616 Ω, the approximate bioimpedance range for fat was 5.02 - 17.8 kΩ and the approximate range for connective tissue was 790 Ω – 1.55 kΩ. While when the samples were heated at 37°C and measured again at 10kHz, the approximate bioimpedance range for muscle was 100-175Ω. The approximate bioimpedance range of fat was 627 Ω - 3.2 kΩ and the range for connective tissue was 221-540Ω. In the experiments done on the fresh slaughtered lamb carcass, replicating a scenario close to the real application, the impedance values recorded for fat were around 17 kΩ, for muscle and lean tissue around 1.3 kΩ while the nervous structures had an impedance value of 2.9 kΩ. With the data collected during this research, it was possible to conclude that measurements of bioimpedance at the needle tip location can give valuable information to the clinicians performing a peripheral nerve block procedure as the separation (in terms of impedance figures) was very marked between the different type of tissues. It is then feasible to use an impedance electrode fabricated on the needle tip to differentiate several tissues from the nerve tissue. Currently, several different methods are being studied to fabricate an impedance electrode on the surface of a commercially available needle used for the peripheral nerve block procedure.

Solo and Chamber Music of Pulitzer Prize-Winning Composers

The Pulitzer Prize in Music, established in 1943, is one of America's most prestigious awards. It has been awarded to fifty-three composers for a "distinguished musical composition of significant dimension by an American that has had its first performance in the United States during the year." Composers who have won the Pulitzer Prize are considered to be at the pinnacle of their creativity and have provided the musical world with classical music compositions worthy of future notice. By tracing the history of Pulitzer Prize-winning composers and their compositions, researchers and musicians enhance their understanding of the historical evolution of American music, and its impact on American culture. Although the clarinet music of some of these composers is rarely performed today, their names will be forever linked to the Pulitzer, and because of that, their compositions will enjoy a certain sense of immortality. Of the fifty-four composers who have won the award, forty-seven have written for the clarinet in a solo or chamber music setting (five or less instruments). Just as each Pulitzer Prize-winning composition is a snapshot of the state of American music at that time, these works trace the history of American clarinet musical development, and therefore, they are valuable additions to the clarinet repertoire and worthy of performance. This dissertation project consists of two recitals featuring the solo and chamber clarinet music of sixteen Pulitzer Prize-winning composers, extended program notes containing information on each composer's life, their music, the Pulitzer Prize-winning composition and the recital selection, and a complete list of all Pulitzer Prize-winning composers and their solo and chamber clarinet music. Featured Composers Dominick Argento, To Be Sung Upon the Water Leslie Bassett, Soliloquies William Bolcom, Little Suite of Four Dances Aaron Copland, As it Fell Upon a Day John Corigliano, Soliloquy Norman Dello Joio, Concertante Morton Gould, Benny's Gig Charles Ives, Largo Douglas Moore, Quintet for Clarinet and Strings George Perle, Three Sonatas Quincy Porter, Quintet for Clarinet and Strings Mel Powell, Clarinade Shulamit Ran, Private Game Joseph Schwantner, Entropy Leo Sowerby, Sonata Ernst Toch, Adagio elegiaco

Spatial vision in the purple sea urchin Strongylocentrotus purpuratus (Echinoidea).

Recent evidence that echinoids of the genus Echinometra have moderate visual acuity that appears to be mediated by their spines screening off-axis light suggests that the urchin Strongylocentrotus purpuratus, with its higher spine density, may have even more acute spatial vision. We analyzed the movements of 39 specimens of S. purpuratus after they were placed in the center of a featureless tank containing a round, black target that had an angular diameter of 6.5 deg. or 10 deg. (solid angles of 0.01 sr and 0.024 sr, respectively). An average orientation vector for each urchin was determined by testing the animal four times, with the target placed successively at bearings of 0 deg., 90 deg., 180 deg. and 270 deg. (relative to magnetic east). The urchins showed no significant unimodal or axial orientation relative to any non-target feature of the environment or relative to the changing position of the 6.5 deg. target. However, the urchins were strongly axially oriented relative to the changing position of the 10 deg. target (mean axis from -1 to 179 deg.; 95% confidence interval +/- 12 deg.; P<0.001, Moore's non-parametric Hotelling's test), with 10 of the 20 urchins tested against that target choosing an average bearing within 10 deg. of either the target center or its opposite direction (two would be expected by chance). In addition, the average length of the 20 target-normalized bearings for the 10 deg. target (each the vector sum of the bearings for the four trials) were far higher than would be expected by chance (P<10(-10); Monte Carlo simulation), showing that each urchin, whether it moved towards or away from the target, did so with high consistency. These results strongly suggest that S. purpuratus detected the 10 deg. target, responding either by approaching it or fleeing it. Given that the urchins did not appear to respond to the 6.5 deg. target, it is likely that the 10 deg. target was close to the minimum detectable size for this species. Interestingly, measurements of the spine density of the regions of the test that faced horizontally predicted a similar visual resolution (8.3+/-0.5 deg. for the interambulacrum and 11+/-0.54 deg. for the ambulacrum). The function of this relatively low, but functional, acuity - on par with that of the chambered Nautilus and the horseshoe crab - is unclear but, given the bimodal response, is likely to be related to both shelter seeking and predator avoidance.

Human uterine leiomyoma-derived fibroblasts stimulate uterine leiomyoma cell proliferation and collagen type I production, and activate RTKs and TGF beta receptor signaling in coculture.

BACKGROUND: Uterine leiomyomas (fibroids) are benign smooth muscle tumors that often contain an excessive extracellular matrix (ECM). In the present study, we investigated the interactions between human uterine leiomyoma (UtLM) cells and uterine leiomyoma-derived fibroblasts (FB), and their importance in cell growth and ECM protein production using a coculture system. RESULTS: We found enhanced cell proliferation, and elevated levels of ECM collagen type I and insulin-like growth factor-binding protein-3 after coculturing. There was also increased secretion of vascular endothelial growth factor, epidermal growth factor, fibroblast growth factor-2, and platelet derived growth factor A and B in the media of UtLM cells cocultured with FB. Protein arrays revealed increased phosphorylated receptor tyrosine kinases (RTKs) of the above growth factor ligands, and immunoblots showed elevated levels of the RTK downstream effector, phospho-mitogen activated protein kinase 44/42 in cocultured UtLM cells. There was also increased secretion of transforming growth factor-beta 1 and 3, and immunoprecipitated transforming growth factor-beta receptor I from cocultured UtLM cells showed elevated phosphoserine expression. The downstream effectors phospho-small mothers against decapentaplegic -2 and -3 protein (SMAD) levels were also increased in cocultured UtLM cells. However, none of the above effects were seen in normal myometrial cells cocultured with FB. The soluble factors released by tumor-derived fibroblasts and/or UtLM cells, and activation of the growth factor receptors and their pathways stimulated the proliferation of UtLM cells and enhanced the production of ECM proteins. CONCLUSIONS: These data support the importance of interactions between fibroid tumor cells and ECM fibroblasts in vivo, and the role of growth factors, and ECM proteins in the pathogenesis of uterine fibroids.

Nuclear import of Cdk/cyclin complexes: identification of distinct mechanisms for import of Cdk2/cyclin E and Cdc2/cyclin B1.

Reversible phosphorylation of nuclear proteins is required for both DNA replication and entry into mitosis. Consequently, most cyclin-dependent kinase (Cdk)/cyclin complexes are localized to the nucleus when active. Although our understanding of nuclear transport processes has been greatly enhanced by the recent identification of nuclear targeting sequences and soluble nuclear import factors with which they interact, the mechanisms used to target Cdk/cyclin complexes to the nucleus remain obscure; this is in part because these proteins lack obvious nuclear localization sequences. To elucidate the molecular mechanisms responsible for Cdk/cyclin transport, we examined nuclear import of fluorescent Cdk2/cyclin E and Cdc2/cyclin B1 complexes in digitonin-permeabilized mammalian cells and also examined potential physical interactions between these Cdks, cyclins, and soluble import factors. We found that the nuclear import machinery recognizes these Cdk/cyclin complexes through direct interactions with the cyclin component. Surprisingly, cyclins E and B1 are imported into nuclei via distinct mechanisms. Cyclin E behaves like a classical basic nuclear localization sequence-containing protein, binding to the alpha adaptor subunit of the importin-alpha/beta heterodimer. In contrast, cyclin B1 is imported via a direct interaction with a site in the NH2 terminus of importin-beta that is distinct from that used to bind importin-alpha.

Inhibition of the anaphase-promoting complex by the Xnf7 ubiquitin ligase.

Degradation of specific protein substrates by the anaphase-promoting complex/cyclosome (APC) is critical for mitotic exit. We have identified the protein Xenopus nuclear factor 7 (Xnf7) as a novel APC inhibitor able to regulate the timing of exit from mitosis. Immunodepletion of Xnf7 from Xenopus laevis egg extracts accelerated the degradation of APC substrates cyclin B1, cyclin B2, and securin upon release from cytostatic factor arrest, whereas excess Xnf7 inhibited APC activity. Interestingly, Xnf7 exhibited intrinsic ubiquitin ligase activity, and this activity was required for APC inhibition. Unlike other reported APC inhibitors, Xnf7 did not associate with Cdc20, but rather bound directly to core subunits of the APC. Furthermore, Xnf7 was required for spindle assembly checkpoint function in egg extracts. These data suggest that Xnf7 is an APC inhibitor able to link spindle status to the APC through direct association with APC core components.

Control of cyclin B1 localization through regulated binding of the nuclear export factor CRM1.

Activation of the Cyclin B/Cdc2 kinase complex triggers entry into mitosis in all eukaryotic cells. Cyclin B1 localization changes dramatically during the cell cycle, precipitously transiting from the cytoplasm to the nucleus at the beginning of mitosis. Presumably, this relocalization promotes the phosphorylation of nuclear targets critical for chromatin condensation and nuclear envelope breakdown. We show here that the previously characterized cytoplasmic retention sequence of Cyclin B1, responsible for its interphase cytoplasmic localization, is actually an autonomous nuclear export sequence, capable of directing nuclear export of a heterologous protein, and able to bind specifically to the recently identified export mediator, CRM1. We propose that the observed cytoplasmic localization of Cyclin B1 during interphase reflects the equilibrium between ongoing nuclear import and rapid CRM1-mediated export. In support of this hypothesis, we found that treatment of cells with leptomycin B, which disrupted Cyclin B1-CRM1 interactions, led to a marked nuclear accumulation of Cyclin B1. In mitosis, Cyclin B1 undergoes phosphorylation at several sites, a subset of which have been proposed to play a role in Cyclin B1 accumulation in the nucleus. Both CRM1 binding and the ability to direct nuclear export were affected by mutation of these phosphorylation sites; thus, we propose that Cyclin B1 phosphorylation at the G2/M transition prevents its interaction with CRM1, thereby reducing nuclear export and facilitating nuclear accumulation.

BLAZE: Bettering the lives of animals in zoo environments

Gemstone Team BLAZE

FROM THE AETHIOPICA TO THE RENAISSANCE: RECOVERING A STAGE TRADITION OF POSITIVE REPRESENTATION OF AFRICANS IN EARLY MODERN ENGLAND

This dissertation looks at the connection between Heliodorus's fifth-century prose romance, An Aethiopian History, certain Renaissance texts, and how these texts helped influence an alternate representation of Africans in the early modern world. Through their portrayals of Africans, early modern English playwrights frequently give the impression that Africans, especially black Africans, were people without accomplishments, without culture. Previously, however, this was not the case. Africans were depicted with dignity, as a tradition existed for this kind of representation--and Renaissance Europe had long been acquainted with the achievements of Africans, dating back to antiquity. As the source of several lost plays, the Aethiopica is instrumental in dramatizing Africans favorably, especially on the early modern stage, and helped shape a stage tradition that runs alongside the stereotyping of Africans. This Heliodoran tradition can be seen in works of Greene, Heywood, Jonson, Shakespeare, and others in the motifs of crosscultural and transracial romance, male and female chastity, racial metamorphosis, lost or abandoned babies, wandering heroes, and bold heroines. In Jonson's Masque of Blackness and Masque of Beauty, I establish a connection between these two masques and Heliodorus's Aethiopica and argue for a Heliodoran stage tradition implicit in both masques through the conceit of blanching. In The English Moore, I explore how Richard Brome uses the Heliodoran and Jonsonian materials to create a negative quality of blackness that participates in the dramatic tradition of the degenerate African on the English Renaissance stage. With Othello, I contend that it is a drama that can be seen in the Heliodoran tradition by stressing certain motifs found in the play that derives from the Aethiopica. Reading Othello this way provides us with a more layered and historicized interpretation of Shakespeare's protagonists. Othello's nationality and faith make his exalted position in Venice and the Venetian army credible and logical. His nobility and heroic status become more sharply defined, giving us a fuller understanding of the emphasis he places on chastity--both for himself and for Desdemona. Instead of a traditional, compliant, and submissive Desdemona, a courageous, resourceful, witty, and pure heroine emerges--one who lives by the dictates of her conscience than by the constraints of societal norms. Recovering the tradition of positive portrayal of Africans that originated from the Aethiopica necessitated an examination of eleven plays that I contend helped to frame the dramatic tradition under investigation. Six of these plays are continental dramas, and five are English. Although three of the English plays are lost and the other two are seventeenth-century dramas, their titles and names of their protagonists, like those of the six extant continental plays, share the names of Heliodorus's hero and heroine, making an exploration of the continental plays imperative to facilitate their use as paradigms in reconstructing the three lost English plays. These continental dramas show that plays whose titles derive from the Aethiopica itself or reflect the names of its major characters follow Heliodorus's text closely, enabling an investigation of the Heliodoran tradition on the early modern English stage. Recovering the Heliodoran tradition adds to the exploration of racial politics and the understanding of the dramatic tradition that constrained and enabled Renaissance playwrights' representation of race and gender.

WormSizer: high-throughput analysis of nematode size and shape.

The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.

CD45+ Cells Present Within Mesenchymal Stem Cell Populations Affect Network Formation of Blood-Derived Endothelial Outgrowth Cells.

Mesenchymal stem cells (MSCs) and endothelial progenitor cells (EPCs) represent promising cell sources for angiogenic therapies. There are, however, conflicting reports regarding the ability of MSCs to support network formation of endothelial cells. The goal of this study was to assess the ability of human bone marrow-derived MSCs to support network formation of endothelial outgrowth cells (EOCs) derived from umbilical cord blood EPCs. We hypothesized that upon in vitro coculture, MSCs and EOCs promote a microenvironment conducive for EOC network formation without the addition of angiogenic growth supplements. EOC networks formed by coculture with MSCs underwent regression and cell loss by day 10 with a near 4-fold and 2-fold reduction in branch points and mean segment length, respectively, in comparison with networks formed by coculture vascular smooth muscle cell (SMC) cocultures. EOC network regression in MSC cocultures was not caused by lack of vascular endothelial growth factor (VEGF)-A or changes in TGF-β1 or Ang-2 supernatant concentrations in comparison with SMC cocultures. Removal of CD45+ cells from MSCs improved EOC network formation through a 2-fold increase in total segment length and number of branch points in comparison to unsorted MSCs by day 6. These improvements, however, were not sustained by day 10. CD45 expression in MSC cocultures correlated with EOC network regression with a 5-fold increase between day 6 and day 10 of culture. The addition of supplemental growth factors VEGF, fibroblastic growth factor-2, EGF, hydrocortisone, insulin growth factor-1, ascorbic acid, and heparin to MSC cocultures promoted stable EOC network formation over 2 weeks in vitro, without affecting CD45 expression, as evidenced by a lack of significant differences in total segment length (p=0.96). These findings demonstrate the ability of MSCs to support EOC network formation correlates with removal of CD45+ cells and improves upon the addition of soluble growth factors.

Enhancing the Hodgkin-Huxley Equations: Simulations Based on the First Publication in the Biophysical Journal.

The experiments in the Cole and Moore article in the first issue of the Biophysical Journal provided the first independent experimental confirmation of the Hodgkin-Huxley (HH) equations. A log-log plot of the K current versus time showed that raising the HH variable n to the sixth power provided the best fit to the data. Subsequent simulations using n(6) and setting the resting potential at the in vivo value simplifies the HH equations by eliminating the leakage term. Our article also reported that the K current in response to a depolarizing step to ENa was delayed if the step was preceded by a hyperpolarization. While the interpretation of this phenomenon in the article was flawed, subsequent simulations show that the effect completely arises from the original HH equations.