RNA silencing platforms in plants

Since the discovery of RNAi, its mechanism in plants and animals has been intensively studied, widely exploited as a research tool, and used for a number of potential commercial applications. In this article, we discuss the platforms for delivering RNAi in plants. We provide a brief background to these platforms and concentrate on discussing the more recent advances, comparing the RNAi technologies used in plants with those used in animals, and trying to predict the ways in which RNAi technologies may further develop. © 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Interestingness Measures for Multi-Level Association Rules

Association rule mining is one technique that is widely used when querying databases, especially those that are transactional, in order to obtain useful associations or correlations among sets of items. Much work has been done focusing on efficiency, effectiveness and redundancy. There has also been a focusing on the quality of rules from single level datasets with many interestingness measures proposed. However, with multi-level datasets now being common there is a lack of interestingness measures developed for multi-level and cross-level rules. Single level measures do not take into account the hierarchy found in a multi-level dataset. This leaves the Support-Confidence approach, which does not consider the hierarchy anyway and has other drawbacks, as one of the few measures available. In this chapter we propose two approaches which measure multi-level association rules to help evaluate their interestingness by considering the database’s underlying taxonomy. These measures of diversity and peculiarity can be used to help identify those rules from multi-level datasets that are potentially useful.

Provisional matrix deposition in hemostasis and venous insufficiency: Tissue preconditioning for nonhealing venous ulcers

Significance: Chronic wounds represent a major burden on global healthcare systems and reduce the quality of life of those affected. Significant advances have been made in our understanding of the biochemistry of wound healing progression. However, knowledge regarding the specific molecular processes influencing chronic wound formation and persistence remains limited. Recent Advances: Generally, healing of acute wounds begins with hemostasis and the deposition of a plasma-derived provisional matrix into the wound. The deposition of plasma matrix proteins is known to occur around the microvasculature of the lower limb as a result of venous insufficiency. This appears to alter limb cutaneous tissue physiology and consequently drives the tissue into a ‘preconditioned’ state that negatively influences the response to wounding. Critical Issues: Processes, such as oxygen and nutrient suppression, edema, inflammatory cell trapping/extravasation, diffuse inflammation, and tissue necrosis are thought to contribute to the advent of a chronic wound. Healing of the wound then becomes difficult in the context of an internally injured limb. Thus, interventions and therapies for promoting healing of the limb is a growing area of interest. For venous ulcers, treatment using compression bandaging encourages venous return and improves healing processes within the limb, critically however, once treatment concludes ulcers often reoccur. Future Directions: Improved understanding of the composition and role of pericapillary matrix deposits in facilitating internal limb injury and subsequent development of chronic wounds will be critical for informing and enhancing current best practice therapies and preventative action in the wound care field.

Genome stability pathways in head and neck cancers

Genomic instability underlies the transformation of host cells toward malignancy, promotes development of invasion and metastasis and shapes the response of established cancer to treatment. In this review, we discuss recent advances in our understanding of genomic stability in squamous cell carcinoma of the head and neck (HNSCC), with an emphasis on DNA repair pathways. HNSCC is characterized by distinct profiles in genome stability between similarly staged cancers that are reflected in risk, treatment response and outcomes. Defective DNA repair generates chromosomal derangement that can cause subsequent alterations in gene expression, and is a hallmark of progression toward carcinoma. Variable functionality of an increasing spectrum of repair gene polymorphisms is associated with increased cancer risk, while aetiological factors such as human papillomavirus, tobacco and alcohol induce significantly different behaviour in induced malignancy, underpinned by differences in genomic stability. Targeted inhibition of signalling receptors has proven to be a clinically-validated therapy, and protein expression of other DNA repair and signalling molecules associated with cancer behaviour could potentially provide a more refined clinical model for prognosis and treatment prediction. Development and expansion of current genomic stability models is furthering our understanding of HNSCC pathophysiology and uncovering new, promising treatment strategies. © 2013 Glenn Jenkins et al.

Design of an integrated platform for V2X wireless communications and positioning supporting C-ITS safety applications

In this paper, an integrated inter-vehicles wireless communications and positioning system supporting alternate positioning techniques is proposed to meet the requirements of safety applications of Cooperative Intelligent Transportation Systems (C-ITS). Recent advances have repeatedly demonstrated that road safety problems can be to a large extent addressed via a range of technologies including wireless communications and positioning in vehicular environments. The novel communication stack utilizing a dedicated frequency spectrum (e.g. at 5.9 GHz band), known as Dedicated Short-Range Communications (DSRC), has been particularly designed for Wireless Access in Vehicular Environments (WAVE) to support safety applications in highly dynamic environments. Global Navigation Satellite Systems (GNSS) is another essential enabler to support safety on rail and roads. Although current vehicle navigation systems such as single frequency Global Positioning System (GPS) receivers can provide route guidance with 5-10 meters (road-level) position accuracy, positioning systems utilized in C-ITS must provide position solutions with lane-level and even in-lane-level accuracies based on the requirements of safety applications. This article reviews the issues and technical approaches that are involved in designing a vehicular safety communications and positioning architecture; it also provides technological solutions to further improve vehicular safety by integrating the DSRC and GNSS-based positioning technologies.

Silicate-based bioceramics for periodontal regeneration

Periodontal disease is characterized by the destruction of the tissues that attach the tooth to the alveolar bone. Various methods for regenerative periodontal therapy including the use of barrier membranes, bone replacement grafts, and growth factor delivery have been investigated; however, true regeneration of periodontal tissue is still a significant challenge to scientists and clinicians. The focus on periodontal tissue engineering has shifted from attempting to recreate tissue replacements/constructs to the development of biomaterials that incorporate and release regulatory signals to achieve in situ periodontal regeneration. The release of ions and molecular cues from biomaterials may help to unlock latent regenerative potential in the body by regulating cell proliferation and differentiation towards different lineages (e.g. osteoblasts and cementoblasts). Silicate-based bioactive materials, including bioactive silicate glasses and ceramics, have become the materials of choice for periodontal regeneration, due to their favourable osteoconductivity and bioactivity. This article will focus on the most recent advances in the in vitro and in vivo biological application of silicate-based ceramics, specifically as it relates to periodontal tissue engineering.

Bone regeneration based on tissue engineering conceptions – a 21st century perspective

The role of Bone Tissue Engineering in the field of Regenerative Medicine has been the topic of substantial research over the past two decades. Technological advances have improved orthopaedic implants and surgical techniques for bone reconstruction. However, improvements in surgical techniques to reconstruct bone have been limited by the paucity of autologous materials available and donor site morbidity. Recent advances in the development of biomaterials have provided attractive alternatives to bone grafting expanding the surgical options for restoring the form and function of injured bone. Specifically, novel bioactive (second generation) biomaterials have been developed that are characterised by controlled action and reaction to the host tissue environment, whilst exhibiting controlled chemical breakdown and resorption with an ultimate replacement by regenerating tissue. Future generations of biomaterials (third generation) are designed to be not only osteo- conductive but also osteoinductive, i.e. to stimulate regeneration of host tissues by combining tissue engineer- ing and in situ tissue regeneration methods with a focus on novel applications. These techniques will lead to novel possibilities for tissue regeneration and repair. At present, tissue engineered constructs that may find future use as bone grafts for complex skeletal defects, whether from post-traumatic, degenerative, neoplastic or congenital/developmental “origin” require osseous reconstruction to ensure structural and functional integrity. Engineering functional bone using combinations of cells, scaffolds and bioactive factors is a promising strategy and a particular feature for future development in the area of hybrid materials which are able to exhibit suitable biomimetic and mechanical properties. This review will discuss the state of the art in this field and what we can expect from future generations of bone regeneration concepts.

Prospects for the development of sugarcane biorefineries

Sugarcane biorefineries co-producing fuels, green chemicals and bio-products offer great potential for improving the profitability and sustainability of sugarcane industries around the world. Sugarcane bagasse is widely regarded as one of the best biomass feedstocks for early adoption and commercialisation of biorefining technologies because of the large scale of the resource and its availability at sugar factories. Biomass biorefineries aim to convert bagasse through biochemical and thermochemical processes to produce low cost fermentable sugars which are a platform for value-adding. Through subsequent fermentation technologies or chemical synthesis, the sugars can be converted to fuels including ethanol and butanol, oils, organic acids such as succinic and levulinic and polymer precursors. Other biorefinery products can include food and animal feeds, plastics, fibre products and resins. Recent advances in biorefinery production technologies are being demonstrated in a unique research facility at the Queensland University of Technology’s Mackay Renewable Biocommodities Pilot Plant in Mackay, Australia. This pilot scale production facility located at Mackay Sugar Ltd’s Racecourse Mill is demonstrating the production of a range of fuels and other products from sugarcane bagasse. This paper will address the opportunities available for sugarcane biorefineries to contribute to future profitability and sustainability of the sugarcane industry.

Ozonolysis of phospholipid double bonds during electrospray ionization : A new tool for structure determination

Phospholipids are the key structural component of cell membranes, and recent advances in electrospray ionization mass spectrometry provide for the fast and efficient analysis of these compounds in biological extracts.1-3 The application of electrospray ionization tandem mass spectrometry (ESI-MS/MS) to phospholipid analysis has demonstrated several key advantages over the more traditional chromatographic methods, including speed and greater structural information.4 For example, the ESI-MS/MS spectrum of a typical phospholipidsparticularly in negative ion modesreadily identifies the carbon chain length and the degree of unsaturation of each of the fatty acids esterified to the parent molecule.5 A critical limitation of conventional ESI-MS/MS analysis, however, is the inability to uniquely identify the position of double bonds within the fatty acid chains. This is especially problematic given the importance of double bond position in determining the biological function of lipid classes.6 Previous attempts to identify double bond position in intact phospholipids using mass spectrometry employ either MS3 or offline chemical derivatization.7-11 The former method requires specialized instrumentation and is rarely applied, while the latter methods suffer from complications inherent in sample handling prior to analysis. In this communication we outline a novel on-line approach for the identification of double bond position in intact phospholipids. In our method, the double bond(s) present in unsaturated phospholipids are cleaved by ozonolysis within the ion source of a conventional ESI mass spectrometer to give two chemically induced fragment ions that may be used to unambiguously assign the position of the double bond. This is achieved by using oxygen as the electrospray nebulizing gas in combination with high electrospray voltages to initiate the formation of an ozoneproducing.

Random projections on manifolds of symmetric positive definite matrices for image classification

Recent advances suggest that encoding images through Symmetric Positive Definite (SPD) matrices and then interpreting such matrices as points on Riemannian manifolds can lead to increased classification performance. Taking into account manifold geometry is typically done via (1) embedding the manifolds in tangent spaces, or (2) embedding into Reproducing Kernel Hilbert Spaces (RKHS). While embedding into tangent spaces allows the use of existing Euclidean-based learning algorithms, manifold shape is only approximated which can cause loss of discriminatory information. The RKHS approach retains more of the manifold structure, but may require non-trivial effort to kernelise Euclidean-based learning algorithms. In contrast to the above approaches, in this paper we offer a novel solution that allows SPD matrices to be used with unmodified Euclidean-based learning algorithms, with the true manifold shape well-preserved. Specifically, we propose to project SPD matrices using a set of random projection hyperplanes over RKHS into a random projection space, which leads to representing each matrix as a vector of projection coefficients. Experiments on face recognition, person re-identification and texture classification show that the proposed approach outperforms several recent methods, such as Tensor Sparse Coding, Histogram Plus Epitome, Riemannian Locality Preserving Projection and Relational Divergence Classification.

Dictionary learning and sparse coding on Grassmann manifolds : an extrinsic solution

Recent advances in computer vision and machine learning suggest that a wide range of problems can be addressed more appropriately by considering non-Euclidean geometry. In this paper we explore sparse dictionary learning over the space of linear subspaces, which form Riemannian structures known as Grassmann manifolds. To this end, we propose to embed Grassmann manifolds into the space of symmetric matrices by an isometric mapping, which enables us to devise a closed-form solution for updating a Grassmann dictionary, atom by atom. Furthermore, to handle non-linearity in data, we propose a kernelised version of the dictionary learning algorithm. Experiments on several classification tasks (face recognition, action recognition, dynamic texture classification) show that the proposed approach achieves considerable improvements in discrimination accuracy, in comparison to state-of-the-art methods such as kernelised Affine Hull Method and graph-embedding Grassmann discriminant analysis.

Time to face the fats : What can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

Guided ionization waves : theory and experiments

This review focuses on one of the fundamental phenomena that occur upon application of sufficiently strong electric fields to gases, namely the formation and propagation of ionization waves-streamers. The dynamics of streamers is controlled by strongly nonlinear coupling, in localized streamer tip regions, between enhanced (due to charge separation) electric field and ionization and transport of charged species in the enhanced field. Streamers appear in nature (as initial stages of sparks and lightning, as huge structures-sprites above thunderclouds), and are also found in numerous technological applications of electrical discharges. Here we discuss the fundamental physics of the guided streamer-like structures-plasma bullets which are produced in cold atmospheric-pressure plasma jets. Plasma bullets are guided ionization waves moving in a thin column of a jet of plasma forming gases (e.g.,He or Ar) expanding into ambient air. In contrast to streamers in a free (unbounded) space that propagate in a stochastic manner and often branch, guided ionization waves are repetitive and highly-reproducible and propagate along the same path-the jet axis. This property of guided streamers, in comparison with streamers in a free space, enables many advanced time-resolved experimental studies of ionization waves with nanosecond precision. In particular, experimental studies on manipulation of streamers by external electric fields and streamer interactions are critically examined. This review also introduces the basic theories and recent advances on the experimental and computational studies of guided streamers, in particular related to the propagation dynamics of ionization waves and the various parameters of relevance to plasma streamers. This knowledge is very useful to optimize the efficacy of applications of plasma streamer discharges in various fields ranging from health care and medicine to materials science and nanotechnology.

Plasma nanoscience : setting directions, tackling grand challenges

This review paper presents historical perspectives, recent advances and future directions in the multidisciplinary research field of plasma nanoscience. The current status and future challenges are presented using a three-dimensional framework. The first and the largest dimension covers the most important classes of nanoscale objects (nanostructures, nanofeatures and nanoassemblies/nanoarchitectures) and materials systems, namely carbon nanotubes, nanofibres, graphene, graphene nanoribbons, graphene nanoflakes, nanodiamond and related carbon-based nanostructures; metal, silicon and other inorganic nanoparticles and nanostructures; soft organic nanomaterials; nano-biomaterials; biological objects and nanoscale plasma etching. In the second dimension, we discuss the most common types of plasmas and plasma reactors used in nanoscale plasma synthesis and processing. These include low-temperature non-equilibrium plasmas at low and high pressures, thermal plasmas, high-pressure microplasmas, plasmas in liquids and plasma–liquid interactions, high-energy-density plasmas, and ionized physical vapour deposition as well as some other plasma-enhanced nanofabrication techniques. In the third dimension, we outline some of the 'Grand Science Challenges' and 'Grand Socio-economic Challenges' to which significant contributions from plasma nanoscience-related research can be expected in the near future. The urgent need for a stronger focus on practical, outcome-oriented research to tackle the grand challenges is emphasized and concisely formulated as from controlled complexity to practical simplicity in solving grand challenges.

Pituitary tumours : all silent on the epigenetics front

Investigation of the epigenome of sporadic pituitary tumours is providing a more detailed understanding of aberrations that characterise this tumour type. Early studies, in this and other tumour types adopted candidate-gene approaches to characterise CpG island methylation as a mechanism responsible for or associated with gene silencing. However, more recently, investigators have adopted approaches that do not require a priori knowledge of the gene and transcript, as example differential display techniques, and also genome-wide, array-based approaches, to 'uncover' or 'unmask' silenced genes. Furthermore, through use of chromatin immunoprecipitation as a selective enrichment technique; we are now beginning to identify modifications that target the underlying histones themselves and that have roles in gene-silencing events. Collectively, these studies provided convincing evidence that change to the tumour epigenome are not simply epiphenomena but have functional consequences in the context of pituitary tumour evolution. Our ability to perform these types of studies has been and is increasingly reliant upon technological advances in the genomics and epigenomics arena. In this context, other more recent advances and developing technologies, and, in particular, next generation or flow cell re-sequencing techniques offer exciting opportunities for our future studies of this tumour type.