An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane

Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology.

Hidden credential retrieval from a reusable password

We revisit the venerable question of access credentials management, which concerns the techniques that we, humans with limited memory, must employ to safeguard our various access keys and tokens in a connected world. Although many existing solutions can be employed to protect a long secret using a short password, those solutions typically require certain assumptions on the distribution of the secret and/or the password, and are helpful against only a subset of the possible attackers. After briefly reviewing a variety of approaches, we propose a user-centric comprehensive model to capture the possible threats posed by online and offline attackers, from the outside and the inside, against the security of both the plaintext and the password. We then propose a few very simple protocols, adapted from the Ford-Kaliski server-assisted password generator and the Boldyreva unique blind signature in particular, that provide the best protection against all kinds of threats, for all distributions of secrets. We also quantify the concrete security of our approach in terms of online and offline password guesses made by outsiders and insiders, in the random-oracle model. The main contribution of this paper lies not in the technical novelty of the proposed solution, but in the identification of the problem and its model. Our results have an immediate and practical application for the real world: they show how to implement single-sign-on stateless roaming authentication for the internet, in a ad-hoc user-driven fashion that requires no change to protocols or infrastructure.

The Fukushima nuclear power plant disaster and percetions of health risk communication : a case study

This case study was conducted to explore the perceptions of health risk messages sent by the Japanese Government following the Fukushima nuclear power plant disaster. The content of health risk messages from the Japanese Government and the Japanese national broadcaster (NHK) were analysed and semi-structured interviews were conducted with a sample of Tokyo residents. Initially, participants trusted these messages but as the crisis unfolded they became sceptical about the messages. Participants felt the messages did not communicate health risk information effectively because the messages were; not supported by evidence, inconsistent, delayed and changed over time. Despite widespread access to the internet, social media and mobile telephones, most participants relied on television news for information about the health risks. The Japanese Government urgently needs to re-build trust by engaging the community in the planning and development phases of health risk communication strategies.

Remote sensing and core data needed to support planning and policy decision making

A variety of sustainable development research efforts and related activities are attempting to reconcile the issues of conserving our natural resources without limiting economic motivation while also improving our social equity and quality of life. Land use/land cover change, occurring on a global scale, is an aggregate of local land use decisions and profoundly impacts our environment. It is therefore the local decision making process that should be the eventual target of many of the ongoing data collection and research efforts which strive toward supporting a sustainable future. Satellite imagery data is a primary source of data upon which to build a core data set for use by researchers in analyzing this global change. A process is necessary to link global change research, utilizing satellite imagery, to the local land use decision making process. One example of this is the NASA-sponsored Regional Data Center (RDC) prototype. The RDC approach is an attempt to integrate science and technology at the community level. The anticipated result of this complex interaction between research and the decision making communities will be realized in the form of long-term benefits to the public.

Wetlands : a perspective for mapping, monitoring, and modeling

Experience gained from numerous projects conducted by the U.S. Environmental Protection Agency's (EPA) Environmental Monitoring Systems Laboratory in Las Vegas, Nevada has provided insight to functional issues of mapping, monitoring, and modeling of wetland habitats. Three case studies in poster form describe these issues pertinent to managing wetland resources as mandated under Federal laws. A multiphase project was initiated by the EPA Alaska operations office to provide detailed wetland mapping of arctic plant communities in an area under petroleum development pressure. Existing classification systems did not meet EPA needs. Therefore a Habitat Classification System (HCS) derived from aerial photography was compiled. In conjunction with this photointerpretive keys were developed. These products enable EPA personnel to map large inaccessible areas of the arctic coastal plain and evaluate the sensitivity of various wetland habitats relative to petroleum development needs.

Pilot plant studies of ion exchange for desalination of coal seam gas produced water

This paper reports a study of ion exchange (IX) as an alternative CSG water treatment to the widely used reverse osmosis (RO) desalination process. An IX pilot plant facility has been constructed and operated using both synthetic and real CSG water samples. Application of appropriate synthetic resin technology has proved the effectiveness of IX processes.

Design and construction of an in-plant activation cassette for transgene expression and recombinant protein production in plants

Virus-based transgene expression systems have become particularly valuable for recombinant protein production in plants. The dual-module in-plant activation (INPACT) expression platform consists of a uniquely designed split-gene cassette incorporating the cis replication elements of Tobacco yellow dwarf geminivirus (TYDV) and an ethanol-inducible activation cassette encoding the TYDV Rep and RepA replication-associated proteins. The INPACT system is essentially tailored for recombinant protein production in stably transformed plants and provides both inducible and high-level transient transgene expression with the potential to be adapted to diverse crop species. The construction of a novel split-gene cassette, the inducible nature of the system and the ability to amplify transgene expression via rolling-circle replication differentiates this system from other DNA- and RNA-based virus vector systems used for stable or transient recombinant protein production in plants. Here we provide a detailed protocol describing the design and construction of a split-gene INPACT cassette, and we highlight factors that may influence optimal activation and amplification of gene expression in transgenic plants. By using Nicotiana tabacum, the protocol takes 6-9 months to complete, and recombinant proteins expressed using INPACT can accumulate to up to 10% of the leaf total soluble protein.

Simulation of plant cell shrinkage during drying : A SPH–DEM approach

Plant based dried food products are popular commodities in global market where much research is focused to improve the products and processing techniques. In this regard, numerical modelling is highly applicable and in this work, a coupled meshfree particle-based two-dimensional (2-D) model was developed to simulate micro-scale deformations of plant cells during drying. Smoothed Particle Hydrodynamics (SPH) was used to model the viscous cell protoplasm (cell fluid) by approximating it to an incompressible Newtonian fluid. The visco-elastic characteristic of the cell wall was approximated to a Neo-Hookean solid material augmented with a viscous term and modelled with a Discrete Element Method (DEM). Compared to a previous work [H. C. P. Karunasena, W. Senadeera, Y. T. Gu and R. J. Brown, Appl. Math. Model., 2014], this study proposes three model improvements: linearly decreasing positive cell turgor pressure during drying, cell wall contraction forces and cell wall drying. The improvements made the model more comparable with experimental findings on dried cell morphology and geometric properties such as cell area, diameter, perimeter, roundness, elongation and compactness. This single cell model could be used as a building block for advanced tissue models which are highly applicable for product and process optimizations in Food Engineering.

Calibration functions for estimating soil moisture from GPR dielectric constant measurements

Ground-penetrating radar (GPR) is widely used for assessment of soil moisture variability in field soils. Because GPR does not measure soil water content directly, it is common practice to use calibration functions that describe its relationship with the soil dielectric properties and textural parameters. However, the large variety of models complicates the selection of the appropriate function. In this article an overview is presented of the different functions available, including volumetric models, empirical functions, effective medium theories, and frequency-specific functions. Using detailed information presented in summary tables, the choice for which calibration function to use can be guided by the soil variables available to the user, the frequency of the GPR equipment, and the desired level of detail of the output. This article can thus serve as a guide for GPR practitioners to obtain soil moisture values and to estimate soil dielectric properties.

pGreen : a versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation

Binary Ti vectors are the plasmid vectors of choice in Agrobacterium-mediated plant transformation protocols. The pGreen series of binary Ti vectors are configured for ease-of-use and to meet the demands of a wide range of transformation procedures for many plant species. This plasmid system allows any arrangement of selectable marker and reporter gene at the right and left T-DNA borders without compromising the choice of restriction sites for cloning, since the pGreen cloning sites are based on the well-known pBluescript general vector plasmids. Its size and copy number in Escherichia coli offers increased efficiencies in routine in vitro recombination procedures. pGreen can replicate in Agrobacterium only if another plasmid, pSoup, is co-resident in the same strain. pSoup provides replication functions in trans for pGreen. The removal of RepA and Mob functions has enabled the size of pGreen to be kept to a minimum. Versions of pGreen have been used to transform several plant species with the same efficiencies as other binary Ti vectors. Information on the pGreen plasmid system is supplemented by an Internet site (http://www.pgreen.ac.uk) through which comprehensive information, protocols, order forms and lists of different pGreen marker gene permutations can be found.

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.

Mini-scale method for nuclear run-on transcription assay in plants

We present a mini-scale method for nuclear run-on transcription assay. In our method, all the centrifuge steps can be carried out by using micro-tubes for short time (5 min each) throughout the process, including isolation of transcriptionally active nuclei and purification of labeled RNA after synthesis of RNA in isolated nuclei. The assay can be performed using a small amount of plant tissue, which enables analysis of developmental changes in transcriptional status of given genes in a single individual plant. Successful results were obtained using the tissues of flower and leaf of petunia and embryo of pea, suggesting that the method is potentially applicable to a variety of plant tissues.

A meshfree model for plant tissue deformations during drying

Plant tissue has a complex cellular structure which is an aggregate of individual cells bonded by middle lamella. During drying processes, plant tissue undergoes extreme deformations which are mainly driven by moisture removal and turgor loss. Numerical modelling of this problem becomes challenging when conventional grid-based modelling techniques such as Finite Element Methods (FEM) and Finite Difference Methods (FDM) have grid-based limitations. This work presents a meshfree approach to model and simulate the deformations of plant tissues during drying. This method demonstrates the fundamental capabilities of meshfree methods in handling extreme deformations of multiphase systems. A simplified 2D tissue model is developed by aggregating individual cells while accounting for the stiffness of the middle lamella. Each individual cell is simply treated as consisting of two main components: cell fluid and cell wall. The cell fluid is modelled using Smoothed Particle Hydrodynamics (SPH) and the cell wall is modelled using a Discrete Element Method (DEM). During drying, moisture removal is accounted for by reduction of cell fluid and wall mass, which causes local shrinkage of cells eventually leading to tissue scale shrinkage. The cellular deformations are quantified using several cellular geometrical parameters and a favourably good agreement is observed when compared to experiments on apple tissue. The model is also capable of visually replicating dry tissue structures. The proposed model can be used as a step in developing complex tissue models to simulate extreme deformations during drying.

An introduction to radiation protection in medicine

"Combining facets of health physics with medicine, An Introduction to Radiation Protection in Medicine covers the background of the subject and the medical situations where radiation is the tool to diagnose or treat human disease. Encouraging newcomers to the field to properly and efficiently function in a versatile and evolving work setting, it familiarizes them with the particular problems faced during the application of ionizing radiation in medicine. The text builds a fundamental knowledge base before providing practical descriptions of radiation safety in medicine. It covers basic issues related to radiation protection, including the physical science behind radiation protection and the radiobiological basis of radiation protection. The text also presents operational and managerial tools for organizing radiation safety in a medical workplace. Subsequent chapters form the core of the book, focusing on the practice of radiation protection in different medical disciplines. They explore a range of individual uses of ionizing radiation in various branches of medicine, including radiology, nuclear medicine, external beam radiotherapy, and brachytherapy. With contributions from experienced practicing physicists, this book provides essential information about dealing with radiation safety in the rapidly shifting and diverse environment of medicine."--publisher website