Repeated sequences as genetic markers in pooled tissue samples

We show, using the PDR1 element of pea, that dispersed repeated sequences of moderate copy number can be used simply and efficiently to generate markers linked to a trait of interest. Inspection of hybridization patterns of repeated sequences to DNA mixtures of pooled genotypes is a sensitive way of detecting such markers. The large number of bands in tracks of digests of these mixtures allows the simultaneous sampling of loci at many places in the genome, and the many unlinked loci serve as internal controls. It is also shown that intensity ratios calculated from these band differences can be used to give a rough estimate of linkage distance.

Task-relationship-self : a framework for understanding service encounter behaviors

Research conducted over past decades has investigated selected service encounter behaviors from either a customer or service provider perspective. However, a comprehensive, dual-perspective framework is lacking. Such a framework is needed to organize knowledge of these behaviors, and thereby provide structure, clarity, and parsimony to the field. This paper describes a three-tier framework of service encounter behavior that was developed by applying grounded theory principles to interviews with customers, service employees, and other stakeholders. These informants described many ways in which they behave when executing service exchanges, dealing with service difficulties, and managing themselves in the process. Using an iterative inductive approach, a conceptual framework was developed in which specific (Tier 1) behaviors were placed within broader (Tier 2) categories, and these lower classification levels were, in turn, interpreted within a conceptual space defined by the (Tier 3) dimensions of task, relationship, and self. This framework was then elaborated and refined by reference to the psychology and marketing literature, a set of 157 audio-recorded service interactions, and an expert panel study. The paper includes comparisons between the framework and those previously proposed, propositions regarding service encounter processes and outcomes, and implications for future research and practice.

Quantitative stem-loop RT-PCR for detection of microRNAs

Plant microRNAs (miRNAs) are a class of endogenous small RNAs that are essential for plant development and survival. They arise from larger precursor RNAs with a characteristic hairpin structure and regulate gene activity by targeting mRNA transcripts for cleavage or translational repression. Efficient and reliable detection and quantification of miRNA expression has become an essential step in understanding their specific roles. The expression levels of miRNAs can vary dramatically between samples and they often escape detection by conventional technologies such as cloning, northern hybridization and microarray analysis. The stem-loop RT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate and reliable manner. First, a miRNA-specific stem-loop RT primer is hybridized to the miRNA and then reverse transcribed. Next, the RT product is amplified and monitored in real time using a miRNA-specific forward primer and the universal reverse primer. This method enables miRNA expression profiling from as little as 10 pg of total RNA and is suitable for high-throughput miRNA expression analysis.

Promoting physical activity to older adults : a preliminary evaluation of three general practice-based strategies

The aim of this study was to explore the feasibility of an exercise scientist (ES) working in general practice to promote physical activity (PA) to 55 to 70 year old adults. Participants were randomised into one of three groups: either brief verbal and written advice from a general practitioner (GP) (G1, N=9); or individualised counselling and follow-up telephone calls from an ES, either with (G3, N=8) or without a pedometer (G2, N=11). PA levels were assessed at week 1, after the 12-wk intervention and again at 24 weeks. After the 12-wk intervention, the average increase in PA was 116 (SD=237) min/wk; N=28, p < 0.001. Although there were no statistically significant between-group differences, the average increases in PA among G2 and G3 participants were 195 (SD=207) and 138 (SD=315) min/wk respectively, compared with no change (0.36, SD=157) in G1. After 24 weeks, average PA levels remained 56 (SD=129) min/wk higher than in week 1. The small numbers of participants in this feasibility study limit the power to detect significant differences between groups, but it would appear that individualised counselling and follow-up contact from an ES, with or without a pedometer, can result in substantial changes in PA levels. A larger study is now planned to confirm these findings.

Disparate companions : tissue engineering meets cancer research

Recreating an environment that supports and promotes fundamental homeostatic mechanisms is a significant challenge in tissue engineering. Optimizing cell survival, proliferation, differentiation, apoptosis and angiogenesis, and providing suitable stromal support and signalling cues are keys to successfully generating clinically useful tissues. Interestingly, those components are often subverted in the cancer setting, where aberrant angiogenesis, cellular proliferation, cell signalling and resistance to apoptosis drive malignant growth. In contrast to tissue engineering, identifying and inhibiting those pathways is a major challenge in cancer research. The recent discovery of adult tissue-specific stem cells has had a major impact on both tissue engineering and cancer research. The unique properties of these cells and their role in tissue and organ repair and regeneration hold great potential for engineering tissue-specific constructs. The emerging body of evidence implicating stem cells and progenitor cells as the source of oncogenic transformation prompts caution when using these cells for tissue-engineering purposes. While tissue engineering and cancer research may be considered as opposed fields of research with regard to their proclaimed goals, the compelling overlap in fundamental pathways underlying these processes suggests that cross-disciplinary research will benefit both fields. In this review article, tissue engineering and cancer research are brought together and explored with regard to discoveries that may be of mutual benefit.

CFTR expression is regulated during both the cycle of the seminiferous epithelium and the oestrous cycle of rodents

Severely reduced fertility is a common finding in cystic fibrosis (CF). We used in situ hybridization to examine the cell-specific expression of CFTR in the reproductive organs of rodents. In males CFTR mRNA is found in the round spermatids (spermatogenic stages V-X) and in the principal cells that line the initial segment of the epididymis. In both the testis and the epididymis, CFTR expression is developmentally regulated suggesting that the defect in the genital tract of male CF patients is of developmental origin. CFTR expression in the luminal and glandular epithelium of the uterus is regulated during the oestrous cycle and is maximal at pro-oestrus. Our results provide a biological rationale for the reduced fertility of CF patients, and suggest a possible cause for the comparatively poorer prognosis for women with CF.

Targeting cancer with a lupus autoantibody

Systemic lupus erythematosus (SLE) is distinct among autoimmune diseases because of its association with circulating autoantibodies reactive against host DNA. The precise role that anti-DNA antibodies play in SLE pathophysiology remains to be elucidated, and potential applications of lupus autoantibodies in cancer therapy have not previously been explored. We report the unexpected finding that a cell-penetrating lupus autoantibody, 3E10, has potential as a targeted therapy for DNA repair–deficient malignancies. We find that 3E10 preferentially binds DNA single-strand tails, inhibits key steps in DNA single-strand and double-strand break repair, and sensitizes cultured tumor cells and human tumor xenografts to DNA-damaging therapy, including doxorubicin and radiation. Moreover, we demonstrate that 3E10 alone is synthetically lethal to BRCA2-deficient human cancer cells and selectively sensitizes such cells to low-dose doxorubicin. Our results establish an approach to cancer therapy that we expect will be particularly applicable to BRCA2-related malignancies such as breast, ovarian, and prostate cancers. In addition, our findings raise the possibility that lupus autoantibodies may be partly responsible for the intrinsic deficiencies in DNA repair and the unexpectedly low rates of breast, ovarian, and prostate cancers observed in SLE patients. In summary, this study provides the basis for the potential use of a lupus anti-DNA antibody in cancer therapy and identifies lupus autoantibodies as a potentially rich source of therapeutic agents.

An attack-localizing watermarking scheme for natural language documents

We present a text watermarking scheme that embeds a bitstream watermark Wi in a text document P preserving the meaning, context, and flow of the document. The document is viewed as a set of paragraphs, each paragraph being a set of sentences. The sequence of paragraphs and sentences used to embed watermark bits is permuted using a secret key. Then, English language sentence transformations are used to modify sentence lengths, thus embedding watermarking bits in the Least Significant Bits (LSB) of the sentences’ cardinalities. The embedding and extracting algorithms are public, while the secrecy and security of the watermark depends on a secret key K. The probability of False Positives is extremely small, hence avoiding incidental occurrences of our watermark in random text documents. Majority voting provides security against text addition, deletion, and swapping attacks, further reducing the probability of False Positives. The scheme is secure against the general attacks on text watermarks such as reproduction (photocopying, FAX), reformatting, synonym substitution, text addition, text deletion, text swapping, paragraph shuffling and collusion attacks.

Higher order universal one-way hash functions from the subset sum assumption

Universal One-Way Hash Functions (UOWHFs) may be used in place of collision-resistant functions in many public-key cryptographic applications. At Asiacrypt 2004, Hong, Preneel and Lee introduced the stronger security notion of higher order UOWHFs to allow construction of long-input UOWHFs using the Merkle-Damgård domain extender. However, they did not provide any provably secure constructions for higher order UOWHFs. We show that the subset sum hash function is a kth order Universal One-Way Hash Function (hashing n bits to m < n bits) under the Subset Sum assumption for k = O(log m). Therefore we strengthen a previous result of Impagliazzo and Naor, who showed that the subset sum hash function is a UOWHF under the Subset Sum assumption. We believe our result is of theoretical interest; as far as we are aware, it is the first example of a natural and computationally efficient UOWHF which is also a provably secure higher order UOWHF under the same well-known cryptographic assumption, whereas this assumption does not seem sufficient to prove its collision-resistance. A consequence of our result is that one can apply the Merkle-Damgård extender to the subset sum compression function with ‘extension factor’ k+1, while losing (at most) about k bits of UOWHF security relative to the UOWHF security of the compression function. The method also leads to a saving of up to m log(k+1) bits in key length relative to the Shoup XOR-Mask domain extender applied to the subset sum compression function.

Development of reverse phase protein microarrays for clinical applications and patient-tailored therapy

While genomics provide important information about the somatic genetic changes, and RNA transcript profiling can reveal important expression changes that correlate with outcome and response to therapy, it is the proteins that do the work in the cell. At a functional level, derangements within the proteome, driven by post-translational and epigenetic modifications, such as phosphorylation, is the cause of a vast majority of human diseases. Cancer, for instance, is a manifestation of deranged cellular protein molecular networks and cell signaling pathways that are based on genetic changes at the DNA level. Importantly, the protein pathways contain the drug targets in signaling networks that govern overall cellular survival, proliferation, invasion and cell death. Consequently, the promise of proteomics resides in the ability to extend analysis beyond correlation to causality. A critical gap in the information knowledge base of molecular profiling is an understanding of the ongoing activity of protein signaling in human tissue: what is activated and “in use” within the human body at any given point in time. To address this gap, we have invented a new technology, called reverse phase protein microarrays, that can generate a functional read-out of cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This “wiring diagram” can serve as the basis for both, selection of a therapy and patient stratification.

Transforming the future of treatment for ovarian cancer

As for many other cancers, metastasis is the leading cause of death of patients with ovarian cancer. Vigorous basic and clinical research is being performed to initiate more efficacious treatment strategies to improve the poor outcome of women with this cancer. Current treatment for ovarian cancer includes advanced cyto-reductive surgery and traditional platinum and taxane combined chemotherapy. Clinical trials using novel cytotoxic reagents and tyrosine kinase inhibitors have also been progressing. In parallel, the application of robust unbiased high throughput research platforms using transcriptomic and proteomic approaches has identified that not only individual cell signalling pathways, but a network of molecular pathways, play an important role in the biology of ovarian cancer. Furthermore, intensive genomic and epigenetic analyses have also revealed single nucleotide polymorphisms associated with risk and/or aetiology of this cancer including patient response to treatment. Taken together, these approaches, that are advancing our understanding, will have an impact on the generation of new therapeutic approaches and strategies for improving the outcome and quality of life of patients with ovarian cancer in the near future.

BDNF SNPs are implicated in comorbid alcohol dependence in schizophrenia but not in alcohol-dependent patients without schizophrenia

Aims The functional BDNF single nucleotide polymorphism (SNP) rs6265 has been associated with many disorders including schizophrenia and alcohol dependence. However, studies have been inconsistent, reporting both positive and negative associations. Comorbid alcohol dependence has a high prevalence in schizophrenia so we investigated the role of rs6265 in alcohol dependence in Australian populations of schizophrenia and alcohol dependent patients. Methods Two BDNF SNPs rs6265 and a nearby SNP rs7103411 were genotyped in a total of 848 individuals. These included a schizophrenia group (n = 157) and a second schizophrenia replication group (n = 235), an alcohol dependent group (n = 231) that had no schizophrenia diagnosis and a group of healthy controls (n = 225). Results Allelic association between rs7103411 and comorbid alcohol dependence was identified (P = 0.044) in the primary schizophrenia sample. In the replication study, we were able to detect allelic associations between both BDNF SNPs and comorbid alcohol dependence (rs6265, P = 0.006; rs7103411, P = 0.014). Moreover, we detected association between both SNPs and risk-taking behaviour after drinking (rs6265, P = 0.005; rs7103411, P = 0.009) and we detected strong association between both SNPs and alcohol dependence in males (rs6265, P = 0.009; rs7103411, P = 0.013) while females showed association with multiple behavioural measures reflecting repetitive alcohol consumption. Haplotype analysis revealed the rs6265-rs7103411 A/C haplotype is associated with comorbid alcohol dependence (P = 0.002). When these SNPs were tested in the non-schizophrenia alcohol dependent group we were unable to detect association. Conclusion We conclude that these BDNF SNPs play a role in development of comorbid alcohol dependence in schizophrenia while our data does not indicate that they play a role in alcohol dependent patients who do not have schizophrenia.

Slaving and release in co-infection control

Background Animal and human infection with multiple parasite species is the norm rather than the exception, and empirical studies and animal models have provided evidence for a diverse range of interactions among parasites. We demonstrate how an optimal control strategy should be tailored to the pathogen community and tempered by species-level knowledge of drug sensitivity with use of a simple epidemiological model of gastro-intestinal nematodes. Methods We construct a fully mechanistic model of macroparasite co-infection and use it to explore a range of control scenarios involving chemotherapy as well as improvements to sanitation. Results Scenarios are presented whereby control not only releases a more resistant parasite from antagonistic interactions, but risks increasing co-infection rates, exacerbating the burden of disease. In contrast, synergisms between species result in their becoming epidemiologically slaved within hosts, presenting a novel opportunity for controlling drug resistant parasites by targeting co-circulating species. Conclusions Understanding the effects on control of multi-parasite species interactions, and vice versa, is of increasing urgency in the advent of integrated mass intervention programmes.

A study of the effects metal residues in poly(9,9-dioctylfluorene) have on field-effect transistor device characteristics

The amount of metal residues from organometallic reagents used in preparation of poly(9,9-dioctylfluorene) by palladium catalysed Suzuki and nickel-induced Yamamoto polycondensations have been determined, and their effect upon the behaviour of the polymer in field-effect transistors (FETs) has been measured. The metal levels from material polymerised by Suzuki method were found to be much higher than from that made by the Yamamoto procedure. Simple treatment of the polymers with suitable metal trapping reagents lowered the metal levels significantly, with EDTA giving best results for nickel and triphenylphosphine for palladium. Comparison of the behaviour of FETs using polyfluorenes with varying levels of metal contamination, showed that the metal residues have little effect upon the mobility values, but often affect the degree of hysteresis, possibly acting as charge traps. Satisfactory device performances were obtained from polymer with palladium levels of 2000 μg/g suggesting that complete removal of metal residues may not be necessary for satisfactory device performance.

Drinking games participation among female students at a regional Australian university

Participation in drinking games (DGs) by university students is often associated with heavy drinking and negative social and health impacts. Although research in Australia indicates that university students tend to drink at risky levels, there is paucity of literature on DGs among students, especially those residing at regional universities. This research examined drinking among female college students of white background. Eighteen female students participated in face-to-face in-depth interviews to describe their DG experiences. Most women played DGs for social and monetary reasons, with many drinking high volumes of alcohol during the game. Excessive drinking was linked with the type of beverage consumed. Despite knowing the health risks associated with DGs, there was a strong social imperative for these young women to play these games. Research and public health initiatives to better understand and address problematic drinking activities in rural and regional Australia have tended to ignore women and the dominant white populations whose heavy drinking has been largely restricted to private spheres.