Direct lipid profiling of single cells from inkjet printed microarrays

The on-demand printing of living cells using inkjet technologies has recently been demonstrated and allows for the controlled deposition of cells in microarrays. Here, we show that such arrays can be interrogated directly by robot-controlled liquid microextraction coupled with chip-based nanoelectospray mass spectrometry. Such automated analyses generate a profile of abundant membrane lipids that are characteristic of cell type. Significantly, the spatial control in both deposition and extraction steps combined with the sensitivity of the mass spectrometric detection allows for robust molecular profiling of individual cells. © 2012 American Chemical Society.

Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

Gene expression profiling using microarrays and xenograft transplants of human cancer cell lines are both popular tools to investigate human cancer. However, the undefined degree of cross hybridization between the mouse and human genomes hinders the use of microarrays to characterize gene expression of both the host and the cancer cell within the xenograft. Since an increasingly recognized aspect of cancer is the host response (or cancer-stroma interaction), we describe here a bioinformatic manipulation of the Affymetrix profiling that allows interrogation of the gene expression of both the mouse host and the human tumour. Evidence of microenvironmental regulation of epithelial mesenchymal transition of the tumour component in vivo is resolved against a background of mesenchymal gene expression. This tool could allow deeper insight to the mechanism of action of anti-cancer drugs, as typically novel drug efficacy is being tested in xenograft systems.

Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry

The global demand for food, feed, energy and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.

Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics

Early full-term pregnancy is one of the most effective natural protections against breast cancer. To investigate this effect, we have characterized the global gene expression and epigenetic profiles of multiple cell types from normal breast tissue of nulliparous and parous women and carriers of BRCA1 or BRCA2 mutations. We found significant differences in CD44+ progenitor cells, where the levels of many stem cell-related genes and pathways, including the cell-cycle regulator p27, are lower in parous women without BRCA1/BRCA2 mutations. We also noted a significant reduction in the frequency of CD44+p27+ cells in parous women and showed, using explant cultures, that parity-related signaling pathways play a role in regulating the number of p27+ cells and their proliferation. Our results suggest that pathways controlling p27+ mammary epithelial cells and the numbers of these cells relate to breast cancer risk and can be explored for cancer risk assessment and prevention.

Profiling human resource management practices in innovative firms

It has been argued that different bundles or configurations of human resource practices can improve innovation performance, but there is little empirically-based research that provides details of the practices utilised by different types of innovative firms. This study aimed to identify how different types of firms vary their HR practices to build organisation-specific innovation capabilities. The paper presents findings from a qualitative study of 26 innovative Danish firms categorised as technology-based, knowledge-intensive, or hybrid in their industry orientation. The findings highlight that knowledge-intensive firms have notably different profiles of HRM practices to technology-based firms, suggesting that firms utilise different practices to build innovation capacity depending on the core capabilities required for success in their respective industries. This paper contributes by demonstrating how HR practices differ across types of firms rather than relying on a universal perspective or one best way to design and implement HR practices.

Profiling the prosumer in the workplace : an exploration of traits, self-efficacy and motivators

This research has built on the growing interest in the prosumer in the workplace – prosumers are those users with high technological skills who both produce and consume their own technology solutions. Prosumers are leaders in their industrial or professional fields and who expect to obtain significant benefit from innovating. The literature reveals that commercially attractive products tend to be developed by prosumers who are at the leading edge of important marketplace trends and therefore this group is increasingly important. This study surveyed prosumers across a variety of occupations and workplaces and explored the motivators and personality traits of the prosumer.

Profiling contextual factors which influence safety in heavy vehicle industries

A significant proportion of worker fatalities within Australia result from truck-related incidents. Truck drivers face a number of health and safety concerns. Safety culture, viewed here as the beliefs, attitudes and values shared by an organisation’s workers, which interact with their surrounding context to influence behaviour, may provide a valuable lens for exploring safety-related behaviours in heavy vehicle operations. To date no major research has examined safety culture within heavy vehicle industries. As safety culture provides a means to interpret experiences and generate behaviour, safety culture research should be conducted with an awareness of the context surrounding safety. The current research sought to examine previous health and safety research regarding heavy vehicle operations to profile contextual factors which influence health and safety. A review of 104 peer-reviewed papers was conducted. Findings of these papers were then thematically analysed. A number of behaviours and scenarios linked with crashes and non-crash injuries were identified, along with a selection of health outcomes. Contextual factors which were found to influence these outcomes were explored. These factors were found to originate from government departments, transport organisations, customers and the road and work environment. The identified factors may provide points of interaction, whereby culture may influence health and safety outcomes.

Profiling emergency nurse practitioner service

The aim of this study was to investigate the practice profile of emergency nurse practitioners across Australia. Nurse practitioners have been providing health service in the emergency setting internationally for more than 30 years, and evidence supports the value of this role in terms of patient satisfaction, effectiveness in improving service indicators, and acceptability of the role. The introduction of this service model has been instrumental in reducing waiting times for low-acuity patients and impacting positively on emergency department service delivery. Recent rapid uptake of this role internationally has outpaced development of the service model to inform education and ongoing service development. This was a national study that used interpretive research methods to identify the practice profile of emergency nurse practitioners. Data were collected from December 2012 to February 2013 through in-depth interviews. An inductive approach was used in data analysis to identify conceptual themes and develop an analysis framework. The study participants worked in a range of service models and managed patient presentations across all levels of acuity and complexity. The findings show that although there is no single definable model of the emergency nurse practitioner role in Australia, there are practice features that are common across all service models; these have been conceptualized as "modes of practice." This study has produced new knowledge about the practice profile of emergency nurse practitioners. The findings will inform development of practice standards for education and continuing professional development for emergency nurse practitioners and facilitate standardized operational definitions for ongoing research into this growing service model.

Estrogen and the endometrium: lessons learned from gene expression profiling in rodents and human

To date, research into the biological processes and molecular mechanisms associated with endometrial receptivity and embryo implantation has been a focus of attention, whereas the complex events that occur in the human endometrium during the menstrual and proliferative phase under the influence of estrogen have received little attention. The objective of this review is to provide an update of our current understanding of the actions of estrogen on both human and rodent endometrium, with special emphasis on the regulation of uterine growth and cell proliferation, and the value of global gene expression analysis, in increasing understanding of these processes.

Profiling of immunoglobulins in resting and mechanically stimulated saliva

Background: Dysregulation of salivary immunoglobulins has been implicated in illnesses ranging from periodontal disease to HIV aids and malignant cancers. Despite these advances there is a lack of agreement among studies with regard to the salivary immunoglobulin levels in healthy controls. Methodology: Resting and mechanically stimulated saliva samples and matching serum samples were collected from healthy individuals (n = 33; 40-55 years of age; gender: 23 female, 10 male). A matrix-matched AlphaLISA((R)) assay was developed to determine the concentrations of IgG1 and IgG4 in serum and saliva samples. Conclusion: Clear relationships were observed in the flow rate and concentration of each immunoglobulin in the two types of saliva. This study affirms the need to establish and standardize collection methods before salivary IgGs are used for diagnostic purposes.

Profiling : an application assignment approach for green data centers

In the past few years, there has been a steady increase in the attention, importance and focus of green initiatives related to data centers. While various energy aware measures have been developed for data centers, the requirement of improving the performance efficiency of application assignment at the same time has yet to be fulfilled. For instance, many energy aware measures applied to data centers maintain a trade-off between energy consumption and Quality of Service (QoS). To address this problem, this paper presents a novel concept of profiling to facilitate offline optimization for a deterministic application assignment to virtual machines. Then, a profile-based model is established for obtaining near-optimal allocations of applications to virtual machines with consideration of three major objectives: energy cost, CPU utilization efficiency and application completion time. From this model, a profile-based and scalable matching algorithm is developed to solve the profile-based model. The assignment efficiency of our algorithm is then compared with that of the Hungarian algorithm, which does not scale well though giving the optimal solution.

Performance profiling for predictive train schedules

In this article an alternate sensitivity analysis is proposed for train schedules. It characterises the schedules robustness or lack thereof and provides unique profiles of performance for different sources of delay and for different values of delay. An approach like this is necessary because train schedules are only a prediction of what will actually happen. They can perform poorly with respect to a variety of performance metrics, when deviations and other delays occur, if for instance they can even be implemented, and as originally intended. The information provided by this analytical approach is beneficial because it can be used as part of a proactive scheduling approach to alter a schedule in advance or to identify suitable courses of action for specific “bad behaviour”. Furthermore this information may be used to quantify the cost of delay. The effect of sectional running time (SRT) deviations and additional dwell time in particular were quantified for three railway schedule performance measures. The key features of this approach were demonstrated in a case study.

Computational epigenetic profiling of CpG islets in MTHFR

Computational epigenetics is a new area of research focused on exploring how DNA methylation patterns affect transcription factor binding that affect gene expression patterns. The aim of this study was to produce a new protocol for the detection of DNA methylation patterns using computational analysis which can be further confirmed by bisulfite PCR with serial pyrosequencing. The upstream regulatory element and pre-initiation complex relative to CpG islets within the methylenetetrahydrofolate reductase gene were determined via computational analysis and online databases. The 1,104 bp long CpG island located near to or at the alternative promoter site of methylenetetrahydrofolate reductase gene was identified. The CpG plot indicated that CpG islets A and B, within the island, contained 62 and 75 % GC content CpG ratios of 0.70 and 0.80–0.95, respectively. Further exploration of the CpG islets A and B indicates that the transcription start sites were GGC which were absent from the TATA boxes. In addition, although six PROSITE motifs were identified in CpG B, no motifs were detected in CpG A. A number of cis-regulatory elements were found in different regions within the CpGs A and B. Transcription factors were predicted to bind to CpGs A and B with varying affinities depending on the DNA methylation status. In addition, transcription factor binding may influence the expression patterns of the methylenetetrahydrofolate reductase gene by recruiting chromatin condensation inducing factors. These results have significant implications for the understanding of the architecture of transcription factor binding at CpG islets as well as DNA methylation patterns that affect chromatin structure.

Molecular profiling of exudate from chronic ulcerated wounds

Non-healing wounds represent a significant burden to healthcare systems and societies worldwide. Current best practice treatments of chronic wounds can require patients to undergo extensive periods of therapy without any positive outcome. This consumes substantial healthcare resources and severely impacts patient quality of life. At present, there are no measures to predict a patient's response to best practice care. The hypothesis of this thesis was that biochemical markers could be found within the wound fluid of chronic ulcers and these markers could predict the healing outcome of an ulcer undergoing best practice care. Discovery phase proteomic and mass spectrometry techniques were utilised to determine novel proteins that correlated with the healing outcome of ulcers. These candidate biomarkers could be developed into simple dip-stick tools for use in clinical practice. This would aid clinicians in the choice of effective wound management strategies to address hard-to-heal wounds.