Proteins control in biomineralization processes of the freshwater pearl mussel Hyriopsis cumingii

Pearls are an amazing example of calcium carbonate biomineralization. They show a classic brick and mortar internal structure in which the predominant inorganic part is composed by aragonite and vaterite tablets. The organic matrix is disposed in concentric layers tightly associated to the mineral structures. Freshwater cultivate pearls (FWCPs) and shells nacreous layers of the Chinese mussel Hyriopsis cumingii were demineralized using an ion exchange resin in order to isolate the organic matrix. From both starting materials a soluble fraction was obtained and further analyzed. The major component of the soluble extracts was represented by a similar glycoprotein having a molecular weight of about 48 kDa in pearls and 44 kDa in shells. Immunolocalization showed their wide distribution in the organic sheet surrounding calcium carbonate tablets of the nacre and in the interlamellar and intertabular matrix. These acidic glycoprotein also contained inside the aragonite platelets, are direct regulators during biomineralization processes, participating to calcium carbonate precipitation since the nucleation step. Selective calcium carbonate polymorph precipitation was performed using the two extracts. The polysaccharides moiety was demonstrate to be a crucial factor in polymorphs selection. In particular, the higher content in sugar groups found in pearls extract was responsible of stabilization of the high energetic vaterite during the in vitro precipitation assay; while irregular calcite was obtained using shells protein. Furthermore these polypeptides showed a carbonic anhydrase activity that, even if not directly involved in polymorphs determination, is an essential regulator in CaCO3 formation by means of carbonate anions production. The structural and functional characterization of the proteins included in biocomposites, gives important hints for understanding the complicated process of biomineralization. A better knowledge of this natural mechanism can offer new strategies for producing environmental friendly materials with controlled structures and enhanced chemical-physical features.

Determination of trace elemental species in periostracum of Cypraea shells

n this work, three Cypraea species (C. talpa, C. tigris and C. zebra) were exhaustively studied. The shells have been separated in the structural layers. The mineralogy, ultra- and micro-structure of each layer were analyzed by Confocal Laser Scanning Microscopy (CLSM), Scanning Electron Microscopy (SEM), X-Ray Diffractometry (XRD) and Raman Spectroscopy (RS). The presence of biologically relevant trace metals (Mn, Co, Fe, Zn, Cr, etc.) has been investigated using Instrumental Neutron Activation Analysis (INAA) and Inductively Coupled Plasma – Mass Spectrometry (ICP-MS) as detection tool. A new method has been developed and optimized to extract and analyze the soluble organic matrix (SOM) of the shell. Although the molecular nature of the SOM is not really known, it contains at least large protein fraction, if not only consists of proteins. The extracted matrices were compared between layers and species using Size Exclusion High Performance Liquid Chromatography coupled with Ultra Violet Spectrometry (SE-HPLC-UV), Gel electrophoresis (GE) and protein quantification tests. For the first time to our knowledge the association of trace elements to the protein in the SOM of the shell was studied using hyphenated on line as well as combined off line techniques and validated through inter-comparison tests between the different methods applied. Interesting correlations between the trace element concentration, the microstructure and the protein content were directly and indirectly detected. The metals Cu, Ni, Co and Zn have shown to bind to the SOM extracted from C. talpa, C. tigris and C. zebra shells. Within the conclusions of this work it was demonstrated that these protein-metal-complexes (or metal containing proteins) change from one layer to the other and are different between the three snails analyzed. In addition, the complexes are clearly related only to certain protein fractions of the SOM, and not to the whole SOM observed. These fractions and show not to be very metal-specific (i.e. some of these fractions bind two or three different metals).

Nano- und mikrostrukturierte organische Erkennungsstrukturen in Lipidmembranen

Im Rahmen dieser Arbeit wurden zunächst die ausgewählten Lipide anhand ihrer p-ArnIsothermen charakterisiert. Dabei zeigte sich, dass die flüssiganaloge Phase umso ausgeprägter ist, je größer die hydrophile Kopfgruppe des jeweiligen Lipids ist, so dass diese schon bei sehr großen Flächen miteinander wechselwirken. Außerdem wurde das Mischungsverhalten und die Domänenbildung binärer und ternärer Mischungen untersucht.rnDabei konnte im Fall der binären Mischungen der polymerisierbaren Lipide 1 und 2 mit dem perfluorierten Lipid 3 eine Phasenseparation beobachtet werden. Hierbei zeigte sich, dass sowohl die Form als auch die Größe der Domänen durch zwei Faktoren kontrolliert werden konnte, nämlich zum einen durch den Lateraldruck und zum anderen durch die molare Zusammensetzung der binären Mischung. Bei niedrigen Lateraldrücken (10 mN/m) warenrnfluorierte und nichtfluorierte Lipide in der homogenen flüssiganalogen Phase vollständig mischbar. Bei sehr hohen Lateraldrücken (30 mN/m) lag eine nahezu vollständige Entmischung vor, da das Lipid 1 hier schon vollständig auskristallisiert war. Im Fall der binären Mischung 2/3 konnte ein solches Verhalten nicht beobachtet werden, was an dem Phasenverhalten des Lipids 2 liegt. Aber auch hier lies sich die Domänenbildung sowohl überrnden Lateraldruck als auch über die Komposition der binären Mischung kontrollieren. Des Weiteren konnte gezeigt werden, dass die Monoschichten dieser beiden binären Mischungen durch photochemische Polymerisation stabilisiert werden können.rnDer Einfluss des Fluorierungsgrades auf das Phasenseparationsverhalten wurde anhand der binären Mischungen 1/6 und 1/8 untersucht. Es zeigte sich hier, dass sich auch hier in beiden Fällen die Domänenbildung sowohl über den Lateraldruck als auch über die Komposiion der Mischung steuern lies. Ein Vergleich der gefundenen Strukturen belegte darüber hinaus klare Unterschiede zwischen dem fluorierten und teilfluorierten Lipid. Denn in der binären Mischung 1/8 (perfluoriertes Lipid) konnte die hexagonale Grundstruktur, die zuvor schon inrnder binären Mischung 1/3 gefunden wurde, beobachtet werden. Demgegenüber hatten die kristallinen Domänen, die in der binären Mischung 1/6 (teilfluoriertes Lipid) beobachtet wurden, die hexagonale Grundform verloren. Hier wurden rundliche unförmige Domänen gefunden, die zudem deutlich kleiner waren als die bei der Mischung mit dem perfluorierten Lipid gefundenen Domänen. In den ternären Mischungen zeigte sich, dass diese ternären Mischungen eine ähnliche Phasenseparation zeigten wie die binäre Mischung 1/3. Die hier auftretenden kristallanalogen Domänen bestanden aus Lipid 1, wobei die umgebendernflüssiganaloge Matrix die beiden fluorierten Lipide enthielt. Deswegen war es von besonderer Bedeutung wie sich die beiden fluorierten Verbindungen untereinander verhalten würden.rnDazu wurden die p-A Isothermen der binären Mischung 3/5 ausgewertet und dabei zeigte sich, dass sich das Vakzinlipid, sofern der Anteil nicht höher ist als der des fluorierten Matrixlipides, in idealer Weise mit diesem mischt. Eine Untersuchung der Antigen-Antikörper Erkennung der binären Mischungen 3/5 zeigte, dass die Reaktion mit dem Antikörper umso effektiver war, je größer der Anteil des Vakzinlipids 5 war. Allerdings konnte hier kein linearer Zusammenhang gefunden werden. Stattdessen handelte es sich umrneine Sättigungskurve, da bereits ein Anteil an Lipid 5 von 42,2 mol% eine nur geringfügig schwächere Antikörperanbindung zeigte, als das reine Vakzinlipid.

Dynamic matrix control on wind-induced vibration of spatial latticed structures [Chinese title = 空间网壳结构风振抑制的动态矩阵预测控制分析]

Ameliorated strategies were put forward to improve the model predictive control in reducing the wind induced vibration of spatial latticed structures. The dynamic matrix control (DMC) predictive method was used and the reference trajectory which is called the decaying functions was suggested for the analysis of spatial latticed structure (SLS) under wind loads. The wind-induced vibration control model of SLS with improved DMC model predictive control was illustrated, then the different feedback strategies were investigated and a typical SLS was taken as example to investigate the reduction of wind-induced vibration. In addition, the robustness and reliability of DMC strategy were discussed by varying the model configurations.

Decision Matrix Compared with Partnering Principles

The ideas for this CRC research project are based directly on Sidwell, Kennedy and Chan (2002). That research examined a number of case studies to identify the characteristics of successful projects. The findings were used to construct a matrix of best practice project delivery strategies. The purpose of this literature review is to test the decision matrix against established theory and best practice in the subject of construction project management.

Report on the Development and Validation of the Best Practice Decision Matrix

The Co-operative Research Centre for Construction Innovation (CRC-CI) is funding a project known as Value Alignment Process for Project Delivery. The project consists of a study of best practice project delivery and the development of a suite of products, resources and services to guide project teams towards the best procurement approach for a specific project or group of projects. These resources will be focused on promoting the principles that underlie best practice project delivery rather than simply identifying an off-the-shelf procurement system. This project builds on earlier work by Sidwell, Kennedy and Chan (2002), on re-engineering the construction delivery process, which developed a procurement framework in the form of a Decision Matrix

Towards a rule-based matrix for evaluating distress mechanisms in bridges

The effective management of bridge stock involves making decisions as to when to repair, remedy, or do nothing, taking into account the financial and service life implications. Such decisions require a reliable diagnosis as to the cause of distress and an understanding of the likely future degradation. Such diagnoses are based on a combination of visual inspections, laboratory tests on samples and expert opinions. In addition, the choice of appropriate laboratory tests requires an understanding of the degradation mechanisms involved. Under these circumstances, the use of expert systems or evaluation tools developed from “realtime” case studies provides a promising solution in the absence of expert knowledge. This paper addresses the issues in bridge infrastructure management in Queensland, Australia. Bridges affected by alkali silica reaction and chloride induced corrosion have been investigated and the results presented using a mind mapping tool. The analysis highights that several levels of rules are required to assess the mechanism causing distress. The systematic development of a rule based approach is presented. An example of this application to a case study bridge has been used to demonstrate that preliminary results are satisfactory.

Towards a Rule-based matrix for evaluating distress mechanisms in bridges

One of the key issues facing public asset owners is the decision of refurbishing aged built assets. This decision requires an assessment of the “remaining service life” of the key components in a building. The remaining service life is significantly dependent upon the existing condition of the asset and future degradation patterns considering durability and functional obsolescence. Recently developed methods on Residual Service Life modelling, require sophisticated data that are not readily available. Most of the data available are in the form of reports prior to undertaking major repairs or in the form of sessional audit reports. Valuable information from these available sources can serve as bench marks for estimating the reference service life. The authors have acquired similar informations from a public asset building in Melbourne. Using these informations, the residual service life of a case study building façade has been estimated in this paper based on state-of-the-art approaches. These estimations have been evaluated against expert opinion. Though the results are encouraging it is clear that the state-of-the-art methodologies can only provide meaningful estimates provided the level and quality of data are available. This investigation resulted in the development of a new framework for maintenance that integrates the condition assessment procedures and factors influencing residual service life

Inducing shades of meaning by matrix methods : a first step towards thematic analysis of opinion

This article explores two matrix methods to induce the ``shades of meaning" (SoM) of a word. A matrix representation of a word is computed from a corpus of traces based on the given word. Non-negative Matrix Factorisation (NMF) and Singular Value Decomposition (SVD) compute a set of vectors corresponding to a potential shade of meaning. The two methods were evaluated based on loss of conditional entropy with respect to two sets of manually tagged data. One set reflects concepts generally appearing in text, and the second set comprises words used for investigations into word sense disambiguation. Results show that for NMF consistently outperforms SVD for inducing both SoM of general concepts as well as word senses. The problem of inducing the shades of meaning of a word is more subtle than that of word sense induction and hence relevant to thematic analysis of opinion where nuances of opinion can arise.

Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Botanical matrix

Botanical matrix is a graphic map produced via a process involving an initial site installation (350 m contour transect), a botanical survey and photographic documentation of species. The site is a housing subdivision at Point Henry, on the SE coast of Western Australia which is a landscape which is host the most botanically diverse vegetation found worldwide - known locally as 'kwongan'. Notoriously difficult vegetation to measure and map, kwongan is a visual 'engima', for paradoxically it appears to the lay person as visually bland and highly homogenous. There is thus is a critical need for the development of new forms of representation which overcome the barriers between the perception and reality of this botanical condition. Botanical Matrix is one result of the author's research which seeks to address this important problem.

The osteogenic differentiation of adipose tissue-derived precursor cells in A 3D scaffold/matrix environment

Abstract: This paper details an in-vitro study using human adipose tissue-derived precursor/stem cells (ADSCs) in three-dimensional (3D) tissue culture systems. ADSCs from 3 donors were seeded onto NaOH-treated medical grade polycaprolactone-tricalcium phosphate (mPCL-TCP) scaffolds with two different matrix components; fibrin glue and lyophilized collagen. ADSCs within these scaffolds were then induced to differentiate along the osteogenic lineage for a 28-day period and various assays and imaging techniques were performed at Day 1, 7, 14, 21 and 28 to assess and compare the ADSC’s adhesion, viability, proliferation, metabolism and differentiation along the osteogenic lineage when cultured in the different scaffold/matrix systems. The ADSC cells were proliferative in both collagen and fibrin mPCL-TCP scaffold systems with a consistently higher cell number (by comparing DNA amounts) in the induced group over the non-induced groups for both scaffold systems. In response to osteogenic induction, these ADSCs expressed elevated osteocalcin, alkaline phosphatase and osteonectin levels. Cells were able to proliferate within the pores of the scaffolds and form dense cellular networks after 28 days of culture and induction. The successful cultivation of osteogenic by FDM process manufactured ADSCs within a 3D matrix comprising fibrin glue or collagen, immobilized within a robust synthetic scaffold is a promising technique which should enhance their potential usage in the regenerative medicine arena, such as bone tissue engineering.

A hydrogen tethered inhibitor of matrix metalloproteinases

During wound repair, the balance between matrix metalloproteinases (MMPs) and their natural inhibitors (the TIMPs) is crucial for the normal extra cellular matrix turnover. However, the over expression of several MMPs including MMP-1, 2, 3, 8, 9 and MMP-10, combined with abnormally high levels of activation or low expression of TIMPs, may contribute to excessive degradation of connective tissue and formation of chronic ulcers. There are many groups exploring strategies for promoting wound healing involving delivery of growth factors, cells, ECM components and small molecules. Our approach for improving the balance of MMPs is not to add anything more to the wound, but instead to neutralise the over-expressed MMPs using inhibitors tethered to a bandage-like hydrogel. Our in vitro experiments using designed synthetic pseudo peptide inhibitors have been demonstrated to inhibit MMP activity in standard solutions. These inhibitors have also been tethered to polyethylene glycol hydrogels using a facile reaction between the linker unit on the inhibitor and the gel. After tethering the inhibition of MMPs diminishes to some extent and we postulate that this arises due to poor diffusion of the MMPs into the gels. When the tethered inhibitors were tested against chronic wound fluid obtained against patients we observed over 40% inhibition in proteolytic activity suggesting our approach may prove useful in rebalancing MMPs within chronic wounds.