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1.  A Standardized and Reproducible Urine Preparation Protocol for Cancer Biomarkers Discovery 
Biomarkers in Cancer  2014;6:21-27.
A suitable and standardized protein purification technique is essential to maintain consistency and to allow data comparison between proteomic studies for urine biomarker discovery. Ultimately, efforts should be made to standardize urine preparation protocols. The aim of this study was to develop an optimal analytical protocol to achieve maximal protein yield and to ensure that this method was applicable to examine urine protein patterns that distinguish disease and disease-free states. In this pilot study, we compared seven different urine sample preparation methods to remove salts, and to precipitate and isolate urinary proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles showed that the sequential preparation of urinary proteins by combining acetone and trichloroacetic acid (TCA) alongside high speed centrifugation (HSC) provided the best separation, and retained the most urinary proteins. Therefore, this approach is the preferred method for all further urine protein analysis.
PMCID: PMC4219630  PMID: 25452700
breast cancer; proteomics; SDS-PAGE; LC-MS/MS; urine; biomarker
2.  Recommendations for Reporting and Flagging of Reference Limits on Pathology Reports 
The Clinical Biochemist Reviews  2014;35(4):199-202.
Surveys by the RCPA PITUS Project have shown significant variations in report rendering between Australasian Pathology Providers. The same project collected anecdotal evidence that this variation has led to the misunderstanding and misreading of results - a clinical safety issue. Recommendations are given for the rendering of reference limits on pathology reports, determination and rendering of result flags, and the documentation of sub-population partitions for reference intervals. These recommendations apply equally for paper or electronic reporting, but should not limit the use of novel techniques within electronic reports to convey additional meaning. PITUS Working Group 4 will publish draft recommendations for peer review and comment in relation to the above in the second half of 2014.
PMCID: PMC4310059
3.  Bias Assessment of General Chemistry Analytes using Commutable Samples 
The Clinical Biochemist Reviews  2014;35(4):203-211.
Harmonisation of reference intervals for routine general chemistry analytes has been a goal for many years. Analytical bias may prevent this harmonisation. To determine if analytical bias is present when comparing methods, the use of commutable samples, or samples that have the same properties as the clinical samples routinely analysed, should be used as reference samples to eliminate the possibility of matrix effect. The use of commutable samples has improved the identification of unacceptable analytical performance in the Netherlands and Spain. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has undertaken a pilot study using commutable samples in an attempt to determine not only country specific reference intervals but to make them comparable between countries. Australia and New Zealand, through the Australasian Association of Clinical Biochemists (AACB), have also undertaken an assessment of analytical bias using commutable samples and determined that of the 27 general chemistry analytes studied, 19 showed sufficiently small between method biases as to not prevent harmonisation of reference intervals. Application of evidence based approaches including the determination of analytical bias using commutable material is necessary when seeking to harmonise reference intervals.
PMCID: PMC4310060
4.  Harmonising Adult and Paediatric Reference Intervals in Australia and New Zealand: An Evidence-Based Approach for Establishing a First Panel of Chemistry Analytes 
The Clinical Biochemist Reviews  2014;35(4):213-235.
Scientific evidence supports the use of common reference intervals (RIs) for many general chemistry analytes, in particular those with sound calibration and traceability in place. Already the Nordic countries and United Kingdom have largely achieved harmonised RIs. Following a series of workshops organised by the Australasian Association of Clinical Biochemists (AACB) between 2012 and 2014 at which an evidence-based approach for determination of common intervals was developed, pathology organisations in Australia and New Zealand have reached a scientific consensus on what adult and paediatric intervals we should use across Australasia. The aim of this report is to describe the processes that the AACB and the Royal College of Pathologists of Australasia have taken towards recommending the implementation of a first panel of common RIs for use in Australasia.
PMCID: PMC4310061
5.  Colorectal cancer screening practices in Saskatchewan 
Canadian Family Physician  2013;59(12):e558-e563.
To evaluate current colorectal cancer (CRC) screening practices in Saskatchewan and identify barriers to screening with the goal of improving current practice.
Survey of family physicians.
A total of 773 family physicians were surveyed.
Main outcome measures
Demographic characteristics, individual screening practices, and perceived barriers to screening.
The response rate to the survey was 44.5%. When asked what method they used for fecal occult blood testing, almost 40% of respondents were either unsure or did not answer the question. Of those who did respond, 35.8% employed hemoccult testing following digital rectal examination, a practice not recommended for CRC screening. Screening guidelines for average-risk patients were generally well adhered to, with 79.9% of respondents recommending screening beginning at age 50. For screening patients at increased risk of CRC owing to family history, only 64.2% of respondents began screening 10 years before the age of the index patient at diagnosis. Physicians who were more likely to follow guidelines were female, in practice fewer than 10 years, trained in Canada, and practising in urban areas. More than 90% of family physicians agreed that a standard provincewide screening program would be beneficial.
We have identified considerable knowledge gaps with regard to CRC screening. There is confusion about which fecal occult blood tests are recommended for screening. Also, screening guidelines for patients with a family history of CRC are poorly understood. These findings suggest that better physician education about CRC screening is required. Introduction of a provincewide screening program should improve overall screening success.
PMCID: PMC3860946  PMID: 24336561
6.  Combination Therapy with the Histone Deacetylase Inhibitor LBH589 and Radiation Is an Effective Regimen for Prostate Cancer Cells 
PLoS ONE  2013;8(8):e74253.
Radiation therapy (RT) continues to be one of the most popular treatment options for localized prostate cancer (CaP). The purpose of the study was to investigate the in vitro effect of LBH589 alone and in combination with RT on the growth and survival of CaP cell lines and the possible mechanisms of radiosensitization of this combination therapy. The effect of LBH589 alone or in combination with RT on two CaP cell lines (PC-3 and LNCaP) and a normal prostatic epithelial cell line (RWPE-1) was studied by MTT and clonogenic assays, cell cycle analysis, western blotting of apoptosis-related and cell check point proteins, and DNA double strand break (DSB) repair markers. The immunofluorescence staining was used to further confirm DSB expression in treated CaP cells. Our results indicate that LBH589 inhibited proliferation in both CaP and normal prostatic epithelial cells in a time-and-dose-dependent manner; low-dose of LBH589 (IC20) combined with RT greatly improved efficiency of cell killing in CaP cells; compared to RT alone, the combination treatment with LBH589 and RT induced more apoptosis and led to a steady increase of sub-G1 population and abolishment of RT-induced G2/M arrest, increased and persistent DSB, less activation of non-homologous end joining (NHEJ)/homologous recombination (HR) repair pathways and a panel of cell cycle related proteins. These results suggest that LBH589 is a potential agent to increase radiosensitivity of human CaP cells. LBH589 used either alone, or in combination with RT is an attractive strategy for treating human CaP.
PMCID: PMC3753304  PMID: 23991216
7.  In Vitro and In Vivo Prostate Cancer Metastasis and Chemoresistance Can Be Modulated by Expression of either CD44 or CD147 
PLoS ONE  2012;7(8):e40716.
CD44 and CD147 are associated with cancer metastasis and progression. Our purpose in the study was to investigate the effects of down-regulation of CD44 or CD147 on the metastatic ability of prostate cancer (CaP) cells, their docetaxel (DTX) responsiveness and potential mechanisms involved in vitro and in vivo. CD44 and CD147 were knocked down (KD) in PC-3M-luc CaP cells using short hairpin RNA (shRNA). Expression of CD44, CD147, MRP2 (multi-drug resistance protein-2) and MCT4 (monocarboxylate tranporter-4) was evaluated using immunofluorescence and Western blotting. The DTX dose-response and proliferation was measured by MTT and colony assays, respectively. The invasive potential was assessed using a matrigel chamber assay. Signal transduction proteins in PI3K/Akt and MAPK/Erk pathways were assessed by Western blotting. An in vivo subcutaneous (s.c.) xenograft model was established to assess CaP tumorigenecity, lymph node metastases and DTX response. Our results indicated that KD of CD44 or CD147 decreased MCT4 and MRP2 expression, reduced CaP proliferation and invasive potential and enhanced DTX sensitivity; and KD of CD44 or CD147 down-regulated p-Akt and p-Erk, the main signal modulators associated with cell growth and survival. In vivo, CD44 or CD147-KD PC-3M-luc xenografts displayed suppressed tumor growth with increased DTX responsiveness compared to control xenografts. Both CD44 and CD147 enhance metastatic capacity and chemoresistance of CaP cells, potentially mediated by activation of the PI3K and MAPK pathways. Selective targeting of CD44/CD147 alone or combined with DTX may limit CaP metastasis and increase chemosensitivity, with promise for future CaP treatment.
PMCID: PMC3411712  PMID: 22870202
8.  A blinded randomised controlled trial to determine the effect of enteric coating on enzyme treatment for canine exocrine pancreatic efficiency 
Enzyme treatment is the mainstay for management of exocrine pancreatic insufficiency (EPI) in dogs. ‘Enteric-coated’ preparations have been developed to protect the enzyme from degradation in the stomach, but their efficacy has not been critically evaluated. The hypothesis of the current study was that enteric coating would have no effect on the efficacy of pancreatic enzyme treatment for dogs with EPI.
Thirty-eight client-owned dogs with naturally occurring EPI were included in this multicentre, blinded, randomised controlled trial. Dogs received either an enteric-coated enzyme preparation (test treatment) or an identical preparation without the enteric coating (control treatment) over a period of 56 days.
There were no significant differences in either signalment or cobalamin status (where cobalamin deficient or not) between the dogs on the test and control treatments. Body weight and body condition score increased in both groups during the trial (P<0.001) but the magnitude of increase was greater for the test treatment compared with the control treatment (P<0.001). By day 56, mean body weight increase was 17% (95% confidence interval 11-23%) in the test treatment group and 9% (95% confidence interval 4-15%) in the control treatment group. The dose of enzyme required increased over time (P<0.001) but there was no significant difference between treatments at any time point (P=0.225). Clinical disease severity score decreased over time for both groups (P=0.011) and no difference was noted between groups (P=0.869). No significant adverse effects were reported, for either treatment, for the duration of the trial.
Enteric coating a pancreatic enzyme treatment improves response in canine EPI.
PMCID: PMC3412697  PMID: 22839732
Dog; Pancreas; Malabsorption; Diarrhoea; Lipase; Trypsin
9.  Prefrontal Cortical Inputs to the Basal Amygdala Undergo Pruning During Late Adolescence in the Rat 
The Journal of Comparative Neurology  2010;518(14):2693-2709.
Transformations in affective and social behaviors, many of which involve amygdalar circuits, are hallmarks of adolescence in many mammalian species. In this study, using the rat as a model, we provide the first evidence that afferents of the basal amygdala (BA) undergo significant structural remodeling during adolescence. We used quantitative tract-tracing and gene expression profiling methods to characterize changes in the medial prefrontal cortical (mPFC) inputs to the BA across ages analogous to the late juvenile period [postnatal day (P) 25], late adolescence (P45), and adulthood (P90) in the rat. As assessed after deposition of Fluorogold into the BA, the number of BA-projecting neurons in the mPFC remained stable between P25 and P45 but decreased by about 50% between P45 and P90. Anterograde tract tracing with biotin dextran amine deposits centered in the ventral prelimbic cortex revealed that, during this period, the density of mPFC-derived axon terminals in the BA also decrease significantly, an effect particularly evident in the dorsal basolateral nucleus. Within the BA, there were also highly significant changes in gene expression indicative of neurite or synaptic plasticity, most notably in the Ras/GTPase superfamily, and in pathways that regulate cytoskeletal dynamics and steroid synthesis/lipid metabolism. These data provide convergent evidence that mPFC inputs to the BA are pruned during late adolescence or early adulthood. Moreover, the structural remodeling within these afferents may be accompanied by significant changes in neurite plasticity within the BA.
PMCID: PMC3377974  PMID: 20506471
amygdala; prefrontal cortex; axonal retraction; adolescence; Ras GTPase; gene expression profiling; anterograde; retrograde
10.  Low levels of ATM in breast cancer patients with clinical radiosensitivity 
Genome Integrity  2010;1:9.
Background and Purpose
Adjuvant radiotherapy for cancer can result in severe adverse side effects for normal tissues. In this respect, individuals with anomalies of the ATM (ataxia telangiectasia) protein/gene are of particular interest as they may be at risk of both breast cancer and clinical radiosensitivity. The association of specific ATM gene mutations with these pathologies has been well documented, however, there is uncertainty regarding pathological thresholds for the ATM protein.
Semi-quantitative immuno-blotting provided a reliable and reproducible method to compare levels of the ATM protein for a rare cohort of 20 cancer patients selected on the basis of their severe adverse normal tissue reactions to radiotherapy. We found that 4/12 (33%) of the breast cancer patients with severe adverse normal tissue reactions following radiotherapy had ATM protein levels < 55% compared to the mean for non-reactor controls.
ATM mutations are generally considered low risk alleles for breast cancer and clinical radiosensitivity. From results reported here we propose a tentative ATM protein threshold of ~55% for high-risk of clinical radiosensitivity for breast cancer patients.
PMCID: PMC2914013  PMID: 20678261
11.  The Beck inventory. 
PMCID: PMC1314577  PMID: 12879835
12.  Competitive Ability and Efficiency in Nodule Formation of Strains of Bradyrhizobium japonicum† 
Applied and Environmental Microbiology  1990;56(10):3035-3039.
In the American Midwest, superior N2-fixing inoculant strains of Bradyrhizobium japonicum consistently fail to produce the majority of nodules on the roots of field-grown soybean. Poor nodulation by inoculant strains is partly due to their inability to stay abreast of the expanding soybean root system in numbers sufficient for them to be competitive with indigenous bradyrhizobia. However, certain strains are noncompetitive even when numerical dominance is not a factor. In this study, we tested the hypothesis that the nodule occupancy achieved by strains is related to their nodule-forming efficiency. The nodulation characteristics and competitiveness of nine strains of B. japonicum were compared at both 20 and 30°C. The root tip marking technique was used, with the nodule-forming efficiency of each strain estimated from the average position of the uppermost nodule and the number of nodules formed above the root tip mark. The competitiveness of the nine strains relative to B. japonicum USDA 110 was determined by using immunofluorescence to identify nodule occupants. The strains differed significantly in competitiveness with USDA 110 and in nodulation characteristics, strains that were poor competitors usually proving to be inferior in both the average position of the uppermost root nodule and the number of nodules formed above the root tip mark. Thus, competitiveness was correlated with both the average position of the uppermost nodule (r = 0.5; P = 0.036) and the number of nodules formed above the root tip mark (r = 0.64; P = 0.005), while the position of the uppermost nodule was also correlated to the percentage of plants nodulated above the root tip mark (r = 0.81; P < 0.001) and the percentage of plants nodulated on the taproot (r = 0.67; P = 0.002).
PMCID: PMC184895  PMID: 16348311
13.  Bradyrhizobium japonicum Inoculant Mobility, Nodule Occupancy, and Acetylene Reduction in the Soybean Root System 
Applied and Environmental Microbiology  1989;55(10):2493-2498.
In the American Midwest, superior inoculant rhizobia applied to soybeans usually occupy only 5 to 20% of nodules, and response to inoculation is the exception rather than the rule. Attempts to overcome this problem have met with limited success. We evaluated the ability of Bradyrhizobium japonicum, supplied as a seed coat inoculant, to stay abreast of the infectible region of the developing soybean root system. The rhizoplane population of the inoculant strain declined with distance from site of placement, the decrease being more pronounced on lateral than on taproots. This decline was paralleled by a decrease in inoculant-strain nodule occupancy. Inoculant bradyrhizobia contributed little to nodulation of lateral roots, which at pod-fill accounted for more than 50% of nodule number and mass, and were major contributors to acetylene reduction activity. From these data, it appears that inoculant bradyrhizobia are competitive with indigenous soil strains at the point of placement in the soil but have limited mobility and so are incapable of sustaining high populations throughout the developing root system. The result is low nodule occupancy by the inoculant strain in the tapand lateral roots. Future studies should address aspects of inoculant placement and establishment.
PMCID: PMC203110  PMID: 16348026
14.  Testing overseas doctors 
BMJ : British Medical Journal  1988;297(6645):420-421.
PMCID: PMC1834301

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