Mass spectrometry-based metabolomics towards understanding of gene functions with a diversity of biological contexts

Currently, mass spectrometry-based metabolomics studies extend beyond conventional chemical categorization and metabolic phenotype analysis to understanding gene function in various biological contexts (e.g., mammalian, plant, and microbial). These novel utilities have led to many innovative discoveries in the following areas: disease pathogenesis, therapeutic pathway or target identification, the biochemistry of animal and plant physiological and pathological activities in response to diverse stimuli, and molecular signatures of host-pathogen interactions during microbial infection. In this review, we critically evaluate the representative applications of mass spectrometry-based metabolomics to better understand gene function in diverse biological contexts, with special emphasis on working principles, study protocols, and possible future development of this technique. Collectively, this review raises awareness within the biomedical community of the scientific value and applicability of mass spectrometry-based metabolomics strategies to better understand gene function, thus advancing this application's utility in a broad range of biological fields

A family of Alltop functions that are EA-inequivalent to the cubic function

Sequences with optimal correlation properties are much sought after for applications in communication systems. In 1980, Alltop (\emph{IEEE Trans. Inf. Theory} 26(3):350-354, 1980) described a set of sequences based on a cubic function and showed that these sequences were optimal with respect to the known bounds on auto and crosscorrelation. Subsequently these sequences were used to construct mutually unbiased bases (MUBs), a structure of importance in quantum information theory. The key feature of this cubic function is that its difference function is a planar function. Functions with planar difference functions have been called \emph{Alltop functions}. This paper provides a new family of Alltop functions and establishes the use of Alltop functions for construction of sequence sets and MUBs.

A framework for security analysis of key derivation functions

This paper presents a comprehensive formal security framework for key derivation functions (KDF). The major security goal for a KDF is to produce cryptographic keys from a private seed value where the derived cryptographic keys are indistinguishable from random binary strings. We form a framework of five security models for KDFs. This consists of four security models that we propose: Known Public Inputs Attack (KPM, KPS), Adaptive Chosen Context Information Attack (CCM) and Adaptive Chosen Public Inputs Attack(CPM); and another security model, previously defined by Krawczyk [6], which we refer to as Adaptive Chosen Context Information Attack(CCS). These security models are simulated using an indistinguisibility game. In addition we prove the relationships between these five security models and analyse KDFs using the framework (in the random oracle model).

Effect of coffee combining green coffee bean constituents with typical roasting products on the Nrf2/ARE pathway in vitro and in vivo

This study investigated Nrf2-activating properties of a coffee blend combining raw coffee bean constituents with 5-O-caffeoylquinic acid (CGA) as a lead component with typical roasting products such as N-methylpyridinium (NMP). In cell culture (HT29) the respective coffee extract (CN-CE) increased nuclear Nrf2 translocation and enhanced the transcription of ARE-dependent genes as exemplified for NAD(P)H:quinone oxidoreductase and glutathione-S-transferase (GST)A1, reflected in the protein level by an increase in GST enzyme activity. In a pilot human intervention study (29 healthy volunteers), daily consumption of 750 mL of CN-coffee for 4 weeks increased Nrf2 transcription in peripheral blood lymphocytes on average. However, the transcriptional response pattern of Nrf2/ARE-dependent genes showed substantial interindividual variations. The presence of SNPs in the Nrf2-promoter, reported recently, as well as the detection of GSTT1*0 (null) genotypes in the study collective strengthens the hypothesis that coffee acts as a modulator of Nrf2-dependent gene response in humans, but genetic polymorphisms play an important role in the individual response pattern.

Laboratory measurement of hydraulic conductivity functions of two unsaturated sandy soils during drying and wetting processes

The importance of applying unsaturated soil mechanics to geotechnical engineering design has been well understood. However, the consumption of time and the necessity for a specific laboratory testing apparatus when measuring unsaturated soil properties have limited the application of unsaturated soil mechanics theories in practice. Although methods for predicting unsaturated soil properties have been developed, the verification of these methods for a wide range of soil types is required in order to increase the confidence of practicing engineers in using these methods. In this study, a new permeameter was developed to measure the hydraulic conductivity of unsaturated soils using the steady-state method and directly measured suction (negative pore-water pressure) values. The apparatus is instrumented with two tensiometers for the direct measurement of suction during the tests. The apparatus can be used to obtain the hydraulic conductivity function of sandy soil over a low suction range (0-10 kPa). Firstly, the repeatability of the unsaturated hydraulic conductivity measurement, using the new permeameter, was verified by conducting tests on two identical sandy soil specimens and obtaining similar results. The hydraulic conductivity functions of the two sandy soils were then measured during the drying and wetting processes of the soils. A significant hysteresis was observed when the hydraulic conductivity was plotted against the suction. However, the hysteresis effects were not apparent when the conductivity was plotted against the volumetric water content. Furthermore, the measured unsaturated hydraulic conductivity functions were compared with predictions using three different predictive methods that are widely incorporated into numerical software. The results suggest that these predictive methods are capable of capturing the measured behavior with reasonable agreement.

Polymorphisms of the VDR gene are associated with presence of solar keratoses on the skin

Background Vitamin D has a range of biological effects including antiproliferative functions that are mediated through its receptors, encoded by the VDR gene. Objectives We investigated polymorphisms within the VDR gene for association with solar keratosis (SK), a biomarker for skin cancer, and examined interactions with skin phenotype. Methods Among participants of the community-based Nambour Skin Cancer Study, we genotyped 190 people with SKs and 190 without for ApaI, TaqI and FokI polymorphisms. Results We found a significant difference in genotype frequencies of the TaqI polymorphism between affected and unaffected populations (P = 0Æ008). The TT ⁄tt genotype group was associated with a twofold increase in odds of being affected by one or more SK. Individuals with fair skin and the TT ⁄tt genotype had about a sevenfold increase, whereas fair-skinned people with the Tt genotype had a fourfold increase in odds of being affected by SK. Individuals with the TT ⁄tt genotype who were prone to burn and not tan on acute sun exposure had about a sixfold increase in odds of SK. Fair-skinned people with VDR-Apa AA ⁄aa genotypes had about an eightfold increase in odds of being affected by SK compared with a fivefold increase in individuals with the Aa genotype and fair skin. Conclusions The trend for homozygote genotypes to increase the odds of SK suggests that intermediate VDR activity is important in protection or that the heterodimer formed by a heterozygous genotype may have an altered binding potential. Overall, these analyses indicate that VDR may be important in SK development.

What it means to be green : an examination of early stage environmental and sustainability focused firms

This paper examines ‘green’ entrepreneurial nascent and young firms in Australia. Findings of interest in this paper include: • Green entrepreneurs are more likely to be highly educated and have an extended depth of experience within their industry and are more likely to have started a business prior to their current venture. • Green entrepreneurs exhibit increased levels of innovation, with an increased focus on new & high technology, R&D and the development of proprietary technology. • Green entrepreneurs are most likely to be based upon a product rather than a service and have a higher emphasis upon growth when compared with non-green entrepreneurs. • Green entrepreneurial firms tend to have a longer venture creation process and draw financial resources from a larger number of sources and rely more upon equity as a means of financing their venture.

On effective accounting information systems in a dynamic business environment : the role of complementing capabilities

The global business environment is witnessing tough times, and this situation has significant implications on how organizations manage their processes and resources. Accounting information system (AIS) plays a critical role in this situation to ensure appropriate processing of financial transactions and availability to relevant information for decision-making. We suggest the need for a dynamic AIS environment for today’s turbulent business environment. This environment is possible with a dynamic AIS, complementary business intelligence systems, and technical human capability. Data collected through a field survey suggests that the dynamic AIS environment contributes to an organization’s accounting functions of processing transactions, providing information for decision making, and ensuring an appropriate control environment. These accounting processes contribute to the firm-level performance of the organization. From these outcomes, one can infer that a dynamic AIS environment contributes to organizational performance in today’s challenging business environment.

Sensemaking and sustainable practicing: Functional affordances of information systems in green transformations

This paper explores how a world-wide operating software solutions provider implemented environmentally sustainable business practices in response to emerging environmental concerns. Through an interpretive case study, we develop a theoretical framework that identifies four important functional affordances originating in information systems, which are required in environmental sustainability transformations as they create an actionable context in which (1) organizations can engage in a sensemaking process related to understanding emerging environmental requirements, and (2) individuals can implement environmentally sustainable work practices. Through our work, we provide several contributions, including a better understanding of IS-enabled organizational change and the types of functional affordances of information systems that are required in sustainability transformations. We describe implications relating to (1) how information systems can contribute to the creation of environmentally sustainable organizations, (2) the design of information systems to create required functional affordances, (3) the management of sustainability transformations, and (4) the further development of the concept of functional affordances in IS research.

A Sustainable Community for Older People : Case Studies of Green Retirement Villages in Australia

In Australia, the proportion of the population aged 65 years and over reached 13.5% in 2010 and is expected to increase steadily to around 20% by the year 2056 [Australia Bureau of Statistics (ABS), 2010], creating what has been regarded as a looming crisis in how to house and care for older people. As a viable accommodation option, the retirement village is widely accepted as a means of promoting and enhancing independence, choice and quality of life for older people. Recent research by Barker (2010) indicates that the current and potential residents of retirement villages are generally very conscious of resource consumption and would like their residences and community to be more sustainable. The aim of this study was to understand the perception of older people toward sustainability ideas and identify the sustainable practices involved in retirement villages to improve the wellbeing of residents. Multiple research methods, including content analysis, questionnaire survey, interviews and case studies were conducted for the research purpose. The results indicate that most retirement village residents understand and recognize the importance of sustainability in their lifestyle. However, their sustainability requirements need to be supported and enhanced by the provision of affordable sustainability features. Additionally, many retirement village developers and operators realize the importance of providing a sustainable retirement community for their residents, and that a sustainable retirement village (that is environmental-friendly, affordable, and improves social engagement) can be achieved through the consideration of project planning, design, construction, and operations throughout the project life cycle. The clear shift from healthcare to lifestyle-focused services in the recent development of retirement villages together with the increasing number of aged people moving into retirement villages (Simpson and Cheney, 2007) has raised awareness of the need for the retirement village industry to provide a sustainable community for older people to improve their life quality after retirement. This is the first critical study of sustainable development in the retirement village industry and its potential in addressing the housing needs of older people, providing a contribution towards improving the life quality of older people and with direct and immediate significance to the community as a whole.

Green skills for the construction industry

The skill shortage issues have long existed in the construction industry in countries like Australia. Couple this with the lead and lag time between market demand and resultant supply has traditionally seen cyclical fluctuation of skills demand within the construction industry. Skills demand and shortages are generally well documented and can even have a level of predictability in Australia given the tendency to have a delayed reaction to global economic downturns. Sustainability issues in the construction industry have attracted growing public awareness. Traditionally driven by ever increasing, if only gradual, mandated minimum requirements, drive towards sustainable developments is now increasingly being created by the client. As this demand increases, accordingly a demand for people with the skills to provide these services should be felt. This research examines the green skill shortage issues within the context of construction industry. Stakeholders from across relevant sectors of the built environment were engaged to ascertain the industry’s utilisation and demand for ‘green skilled’ personnel. These findings will assist stakeholders within the construction industry in negating the effects of a skills shortage in the event of accelerated demand for sustainable construction.

Creeping insulation - Hong Kong green wall

Hong Kong is a densely populated city suffering badly from the urban heat island effect. Green wall offers a means of ameliorating the situation but there are doubts over its suitability in Hong Kong’s unique environment. In this paper, we look at the potential for green walls in Hong Kong first by summarising some of the Chinese green walling systems and associated vegetation in use, then by an introduction to three existing green walls in Hong Kong, and finally through a small experiment aimed at identifying the likely main effects of green walled housing. The results indicate that green walling in Hong Kong is likely to provide enhanced internal house environment in terms of warm weather temperature reduction, stabilisation and damping, with direct energy savings in air-conditioning and indirect district benefits of reduced heat island effect and carbon emissions. The green walling insulation properties also suggest the possibility of warmer homes in winter and/or energy savings in mechanical heating provision.

Creeping insulation - Hong Kong green wall

Hong Kong is a densely populated city suffering badly from the urban heat island effect. Green wall offers a means of ameliorating the situation but there are doubts over its suitability in Hong Kong’s unique environment. In this paper, we look at the potential for green walls in Hong Kong first by summarizing some of the Chinese green walling systems and associated vegetation in use, then by an introduction to three existing green walls in Hong Kong, and finally through a small experiment aimed at identifying the likely main effects of green walled housing. The results indicate that green walling in Hong Kong is likely to provide enhanced internal house environment in terms of warm weather temperature reduction, stabilization and damping, with direct energy savings in air-conditioning and indirect district benefits of reduced heat island effect and carbon emissions. The green walling insulation properties also suggest the possibility of warmer homes in winter and/or energy savings in mechanical heating provision.

Gemcitabine reactivates epigenetically silenced genes and functions as a DNA methyltransferase inhibitor

Gemcitabine is indicated in combination with cisplatin as first-line therapy for solid tumours including non-small cell lung cancer (NSCLC), bladder cancer and mesothelioma. Gemcitabine is an analogue of pyrimidine cytosine and functions as an anti-metabolite. Structurally, however, gemcitabine has similarities to 5-aza-2-deoxycytidine (decitabine/Dacogen®), a DNA methyltransferase inhibitor (DNMTi). NSCLC, mesothelioma and prostate cancer cell lines were treated with decitabine and gemcitabine. Reactivation of epigenetically silenced genes was examined by RT-PCR/qPCR. DNA methyltransferase activity in nuclear extracts and recombinant proteins was measured using a DNA methyltransferase assay, and alterations in DNA methylation status were examined using methylation-specific PCR (MS-PCR) and pyrosequencing. We observe a reactivation of several epigenetically silenced genes including GSTP1, IGFBP3 and RASSF1A. Gemcitabine functionally inhibited DNA methyltransferase activity in both nuclear extracts and recombinant proteins. Gemcitabine dramatically destabilised DNMT1 protein. However, DNA CpG methylation was for the most part unaffected by gemcitabine. In conclusion, gemcitabine both inhibits and destabilises DNA methyltransferases and reactivates epigenetically silenced genes having activity equivalent to decitabine at concentrations significantly lower than those achieved in the treatment of patients with solid tumours. This property may contribute to the anticancer activity of gemcitabine.

Construct design for efficient, effective and high-throughput gene silencing in plants

Post-transcriptional silencing of plant genes using anti-sense or co-suppression constructs usually results in only a modest proportion of silenced individuals. Recent work has demonstrated the potential for constructs encoding self-complementary 'hairpin' RNA (hpRNA) to efficiently silence genes. In this study we examine design rules for efficient gene silencing, in terms of both the proportion of independent transgenic plants showing silencing, and the degree of silencing. Using hpRNA constructs containing sense/anti-sense arms ranging from 98 to 853 nt gave efficient silencing in a wide range of plant species, and inclusion of an intron in these constructs had a consistently enhancing effect. Intron-containing constructs (ihpRNA) generally gave 90-100% of independent transgenic plants showing silencing. The degree of silencing with these constructs was much greater than that obtained using either co-suppression or anti-sense constructs. We have made a generic vector, pHANNIBAL, that allows a simple, single PCR product from a gene of interest to be easily converted into a highly effective ihpRNA silencing construct. We have also created a high-throughput vector, pHELLSGATE, that should facilitate the cloning of gene libraries or large numbers of defined genes, such as those in EST collections, using an in vitro recombinase system. This system may facilitate the large-scale determination and discovery of plant gene functions in the same way as RNAi is being used to examine gene function in Caenorhabditis elegans.