• A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

      Prendergast, James G D; Tong, Pin; Hay, David C; Farrington, Susan M; Semple, Colin A M (2012-05-19)
      AbstractBackgroundChromatin structure at a given site can differ between chromosome copies in a cell, and such imbalances in chromatin structure have been shown to be important in understanding the molecular mechanisms controlling several disease loci. Human genetic variation, DNA methylation, and disease have been intensely studied, uncovering many sites of allele-specific DNA methylation (ASM). However, little is known about the genome-wide occurrence of sites of allele-specific histone modification (ASHM) and their relationship to human disease. The aim of this study was to investigate the extent and characteristics of sites of ASHM in human embryonic stem cells (hESCs).ResultsUsing a statistically rigorous protocol, we investigated the genomic distribution of ASHM in hESCs, and their relationship to sites of allele-specific expression (ASE) and DNA methylation. We found that, although they were rare, sites of ASHM were substantially enriched at loci displaying ASE. Many were also found at known imprinted regions, hence sites of ASHM are likely to be better markers of imprinted regions than sites of ASM. We also found that sites of ASHM and ASE in hESCs colocalize at risk loci for developmental syndromes mediated by deletions, providing insights into the etiology of these disorders.ConclusionThese results demonstrate the potential importance of ASHM patterns in the interpretation of disease loci, and the protocol described provides a basis for similar studies of ASHM in other cell types to further our understanding of human disease susceptibility.
    • A hypoplastic patella fracture in nail patella syndrome: a case report

      Neill, Shane C O; Murphy, Colin G; McElwain, John P (2012-07-16)
      AbstractIntroductionNail patella syndrome is a rare autosomal dominant hereditary condition, with an incidence of 22 per million in the United Kingdom. The syndrome’s most common features include iliac horns, hypoplastic patella and nail dysplasia.Case presentationWe report the case of a 26-year-old Caucasian man with nail patella syndrome who sustained a fracture of his right hypoplastic patella after a fall. His right knee became swollen and he was unable to extend against gravity immediately post fall. Radiographs revealed a fracture of the lower pole of his right patella with associated complete disruption of the extensor mechanism of the knee. He underwent operative fixation and his post operative course was uneventful. He was further treated post operatively with a full knee cast and graded immobilization. At six months he had regained the full range of motion at the knee joint.ConclusionsTo the best of our knowledge, this is the only case report in the literature describing a patella fracture in an individual with nail patella syndrome. We hypothesize that given the extent of pre-existing knee joint impairment in these individuals, functional outcome may be inferior, suggesting the need for more frequent follow-up.
    • A longitudinal qualitative study examining the factors impacting on the ability of persons with T1DM to assimilate the Dose Adjustment For Normal Eating (DAFNE) principles into daily living and how these factors change over time

      Casey, Dympna; Murphy, Kathy; Lawton, Julia; Findlay-White, Florence; Dineen, Sean (2011-08-30)
      Abstract Background The literature reveals that structured education programmes, such as DAFNE, result in many positive outcomes for people with Type 1 diabetes including a decrease in HbA1c levels and reductions in hypoglycaemia. While there is evidence that some of these outcomes are maintained we do not know at present what factors are most important over time. The study aim was to identify the key factors impacting on persons with Type 1 diabetes ability to assimilate the Dose Adjustment For Normal Eating (DAFNE) DAFNE principles into their daily lives and how these factors change over time. Methods This is a longitudinal descriptive qualitative study. Interviews were undertaken with 40 participants who had attended DAFNE in one of 5 study sites across the Island of Ireland, at 6 weeks, 6 and 12 months after completion of the programme. The interviews lasted from 30 to 60 minutes and were transcribed verbatim. Data were analysed in three ways, a within time analysis, a cross sectional analysis for each participant and a thematic analysis which focused on examining changes over time Results Four themes that influenced participants' ability to assimilate DAFNE into their daily lives over time were identified. These were: embedded knowledge, continued responsive support, enduring motivation and being empowered. Support at the 6 month period was found to be crucial to continued motivation. Conclusions Understanding the factors that influence people's ability to assimilate DAFNE principles over time into their daily lives can help health professionals give focused responsive support that helps people with diabetes become more empowered. Understanding that continued support matters, particularly around 6 months, is important as health professionals can influence good management by providing appropriate support and enhancing motivation. Trial registration ISRCTN79759174
    • A method for improved clustering and classification of microscopy images using quantitative co-localization coefficients

      Singan, Vasanth R; Handzic, Kenan; Curran, Kathleen M; Simpson, Jeremy C (2012-06-08)
      AbstractBackgroundThe localization of proteins to specific subcellular structures in eukaryotic cells provides important information with respect to their function. Fluorescence microscopy approaches to determine localization distribution have proved to be an essential tool in the characterization of unknown proteins, and are now particularly pertinent as a result of the wide availability of fluorescently-tagged constructs and antibodies. However, there are currently very few image analysis options able to effectively discriminate proteins with apparently similar distributions in cells, despite this information being important for protein characterization.FindingsWe have developed a novel method for combining two existing image analysis approaches, which results in highly efficient and accurate discrimination of proteins with seemingly similar distributions. We have combined image texture-based analysis with quantitative co-localization coefficients, a method that has traditionally only been used to study the spatial overlap between two populations of molecules. Here we describe and present a novel application for quantitative co-localization, as applied to the study of Rab family small GTP binding proteins localizing to the endomembrane system of cultured cells.ConclusionsWe show how quantitative co-localization can be used alongside texture feature analysis, resulting in improved clustering of microscopy images. The use of co-localization as an additional clustering parameter is non-biased and highly applicable to high-throughput image data sets.
    • A metric space approach to the information channel capacity of spike trains

      Houghton, Conor; Gillespie, James B. (2011-07-18)
    • A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags

      Tyson, Trevor; O'Mahony Zamora, Georgina; Wong, Simon; Skelton, Mairin; Daly, Brian; Jones, John T; Mulvihill, Eoin D; Elsworth, Benjamin; Phillips, Mark; Blaxter, Mark; et al. (2012-01-26)
      Abstract Background Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. Panagrolaimus superbus is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that P. superbus uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis. Results To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of P. superbus. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at http://www.nematodes.org/nembase4/species_info.php?species=PSC. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from P. superbus. Notable among those is a putative lineage expansion of the lea (late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific sxp/ral-2 family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from Phytophthora infestans. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This P. superbus sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants glutathione peroxidase, dj-1 and 1-Cys peroxiredoxin, an shsp sequence and an lea gene. Conclusions P. superbus appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of lea genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of P. superbus.
    • A multi-centre phase IIa clinical study of predictive testing for preeclampsia: improved pregnancy outcomes via early detection (IMPROvED)

      Navaratnam, Kate; Alfirevic, Zarko; Baker, Philip N; Gluud, Christian; Grüttner, Berthold; Kublickiene, Karolina; Zeeman, Gerda; Kenny, Louise C (2013-12-07)
      Abstract Background 5% of first time pregnancies are complicated by pre-eclampsia, the leading cause of maternal death in Europe. No clinically useful screening test exists; consequentially clinicians are unable to offer targeted surveillance or preventative strategies. IMPROvED Consortium members have pioneered a personalised medicine approach to identifying blood-borne biomarkers through recent technological advancements, involving mapping of the blood metabolome and proteome. The key objective is to develop a sensitive, specific, high-throughput and economically viable early pregnancy screening test for pre-eclampsia. Methods/Design We report the design of a multicentre, phase IIa clinical study aiming to recruit 5000 low risk primiparous women to assess and refine innovative prototype tests based on emerging metabolomic and proteomic technologies. Participation involves maternal phlebotomy at 15 and 20 weeks’ gestation, with optional testing and biobanking at 11 and 34 weeks. Blood samples will be analysed using two innovative, proprietary prototype platforms; one metabolomic based and one proteomic based, both of which outperform current biomarker based screening tests at comparable gestations. Analytical and clinical data will be collated and analysed via the Copenhagen Trials Unit. Discussion The IMPROvED study is expected to refine proteomic and metabolomic panels, combined with clinical parameters, and evaluate clinical applicability as an early pregnancy predictive test for pre-eclampsia. If ‘at risk’ patients can be identified, this will allow stratified care with personalised fetal and maternal surveillance, early diagnosis, timely intervention, and significant health economic savings. The IMPROvED biobank will be accessible to the European scientific community for high quality research into the cause and prevention of adverse pregnancy outcome. Trial registration Trial registration number NCT01891240 The IMPROvED project is funded by the seventh framework programme for Research and Technological development of the EU. http://www.fp7-improved.eu/
    • A novel assay of thrombotic risk

      Buskandar, Fahad; Alobaidly, M; Moran, N (2013-01-30)
    • A pilot study of the use of near-patient C-Reactive Protein testing in the treatment of adult respiratory tract infections in one Irish general practice.

      Kavanagh, Kim E; O' Shea, Eamonn; Halloran, Rita; Cantillon, Peter; Murphy, Andrew W (2011-08-31)
      Abstract Background New approaches are being sought to safely reduce community antibiotic prescribing. A recent study demonstrated that CRP testing resulted in decreased antibiotic prescribing for lower respiratory tract infection in primary care. There is little other published primary care data available evaluating CRP in the treatment of lower respiratory tract infections in routine clinical practice. This pilot study aims to describe the performance of near-patient CRP testing, in a mixed payments health system. Specific areas to be reviewed included the integrity of the study protocol, testing of data collection forma and acceptability of the intervention. Patients Patients over the age of 18 years, with acute cough and/or sore throat with a duration of one month or less, in routine clinical practice. Method Design: A pilot with a cross-sectional design. The first 60 recruited patients were treated with routine clinical management, and GP's had no access to a CRP test. For the subsequent 60 patients, access to CRP testing was available. Participants: 3 GP's in one Irish primary care practice recruited 120 patients, fulfilling the above criteria over five months, from January 1 to May 31, 2010. Main outcome measures: The primary outcome was antibiotic prescription at the index consultation. Secondary outcomes were the numbers of delayed prescriptions issued, patient satisfaction immediately after consultation and re-consultations and antibiotic prescriptions during 28 days follow-up. Results The protocol and data collection forms worked well and the intervention of CRP testing appeared acceptable. Thirty-five (58%) patients in the no-test group received antibiotic prescriptions compared to 27 (45%) in the test group. Both groups demonstrated similarly high level of patient satisfaction (85%). Fourteen (23%) patients in the CRP test group re-attended within 28 days compared to 9 (15%) in the no-CRP test group. Conclusion This pilot study confirms the potential feasibility of a full trial in Irish general practice. Further consideration of possible increased re-attendance rates in a mixed payments health system is appropriate. We intend to pursue a larger trial in a newly established regional primary care research network.
    • A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

      Proux-Wéra, Estelle; Armisén, David; Byrne, Kevin P; Wolfe, Kenneth H (2012-09-17)
      Abstract Background Yeasts are a model system for exploring eukaryotic genome evolution. Next-generation sequencing technologies are poised to vastly increase the number of yeast genome sequences, both from resequencing projects (population studies) and from de novo sequencing projects (new species). However, the annotation of genomes presents a major bottleneck for de novo projects, because it still relies on a process that is largely manual. Results Here we present the Yeast Genome Annotation Pipeline (YGAP), an automated system designed specifically for new yeast genome sequences lacking transcriptome data. YGAP does automatic de novo annotation, exploiting homology and synteny information from other yeast species stored in the Yeast Gene Order Browser (YGOB) database. The basic premises underlying YGAP's approach are that data from other species already tells us what genes we should expect to find in any particular genomic region and that we should also expect that orthologous genes are likely to have similar intron/exon structures. Additionally, it is able to detect probable frameshift sequencing errors and can propose corrections for them. YGAP searches intelligently for introns, and detects tRNA genes and Ty-like elements. Conclusions In tests on Saccharomyces cerevisiae and on the genomes of Naumovozyma castellii and Tetrapisispora blattae newly sequenced with Roche-454 technology, YGAP outperformed another popular annotation program (AUGUSTUS). For S. cerevisiae and N. castellii, 91-93% of YGAP's predicted gene structures were identical to those in previous manually curated gene sets. YGAP has been implemented as a webserver with a user-friendly interface at http://wolfe.gen.tcd.ie/annotation.
    • A prospective investigation of predictive and modifiable risk factors for breast cancer in unaffected BRCA1 and BRCA2 gene carriers

      Guinan, Emer M; Hussey, Juliette; McGarrigle, Sarah A; Healy, Laura A; O’Sullivan, Jacintha N; Bennett, Kathleen; Connolly, Elizabeth M (2013-03-21)
      Abstract Background Breast cancer is the most common female cancer worldwide. The lifetime risk of a woman being diagnosed with breast cancer is approximately 12.5%. For women who carry the deleterious mutation in either of the BRCA genes, BRCA1 or BRCA2, the risk of developing breast or ovarian cancer is significantly increased. In recent years there has been increased penetrance of BRCA1 and BRCA2 associated breast cancer, prompting investigation into the role of modifiable risk factors in this group. Previous investigations into this topic have relied on participants recalling lifetime weight changes and subjective methods of recording physical activity. The influence of obesity-related biomarkers, which may explain the link between obesity, physical activity and breast cancer risk, has not been investigated prospectively in this group. This paper describes the design of a prospective cohort study investigating the role of predictive and modifiable risk factors for breast cancer in unaffected BRCA1 and BRCA2 gene mutation carriers. Methods/design Participants will be recruited from breast cancer family risk clinics and genetics clinics. Lifestyle risk factors that will be investigated will include body composition, metabolic syndrome and its components, physical activity and dietary intake. PBMC telomere length will be measured as a potential predictor of breast cancer occurrence. Measurements will be completed on entry to the study and repeated at two years and five years. Participants will also be followed annually by questionnaire to track changes in risk factor status and to record cancer occurrence. Data will be analysed using multiple regression models. The study has an accrual target of 352 participants. Discussion The results from this study will provide valuable information regarding the role of modifiable lifestyle risk factors for breast cancer in women with a deleterious mutation in the BRCA gene. Additionally, the study will attempt to identify potential blood biomarkers which may be predictive of breast cancer occurrence.
    • A proteomic analysis of the functional effects of fatty acids in NIH 3T3 fibroblasts

      Magdalon, Juliana; Hatanaka, Elaine; Romanatto, Talita; Rodrigues, Hosana G; Kuwabara, Wilson MT; Scaife, Caitriona; Newsholme, Philip; Curi, Rui (2011-11-24)
      Abstract Previous studies have demonstrated that long chain fatty acids influence fibroblast function at sub-lethal concentrations. This study is the first to assess the effects of oleic, linoleic or palmitic acids on protein expression of fibroblasts, as determined by standard proteomic techniques. The fatty acids were not cytotoxic at the concentration used in this work as assessed by membrane integrity, DNA fragmentation and the MTT assay but significantly increased cell proliferation. Subsequently, a proteomic analysis was performed using two dimensional difference gel electrophoresis (2D-DIGE) and MS based identification. Cells treated with 50 μM oleic, linoleic or palmitic acid for 24 h were associated with 24, 22, 16 spots differentially expressed, respectively. Among the identified proteins, α-enolase and far upstream element binding protein 1 (FBP-1) are of importance due to their function in fibroblast-associated diseases. However, modulation of α-enolase and FBP-1 expression by fatty acids was not validated by the Western blot technique.
    • A proteomic study of cMyc improvement of CHO culture

      Kuystermans, Darrin; Dunn, Michael J; Al-Rubeai, Mohamed (2010-03-22)
      Abstract Background The biopharmaceutical industry requires cell lines to have an optimal proliferation rate and a high integral viable cell number resulting in a maximum volumetric recombinant protein product titre. Nutrient feeding has been shown to boost cell number and productivity in fed-batch culture, but cell line engineering is another route one may take to increase these parameters in the bioreactor. The use of CHO-K1 cells with a c-myc plasmid allowing for over-expressing c-Myc (designated cMycCHO) gives a higher integral viable cell number. In this study the differential protein expression in cMycCHO is investigated using two-dimensional gel electrophoresis (2-DE) followed by image analysis to determine the extent of the effect c-Myc has on the cell and the proteins involved to give the new phenotype. Results Over 100 proteins that were differentially expressed in cMycCHO cells were detected with high statistical confidence, of which 41 were subsequently identified by tandem mass spectrometry (LC-MS/MS). Further analysis revealed proteins involved in a variety of pathways. Some examples of changes in protein expression include: an increase in nucleolin, involved in proliferation and known to aid in stabilising anti-apoptotic protein mRNA levels, the cytoskeleton and mitochondrial morphology (vimentin), protein biosysnthesis (eIF6) and energy metabolism (ATP synthetase), and a decreased regulation of all proteins, indentified, involved in matrix and cell to cell adhesion. Conclusion These results indicate several proteins involved in proliferation and adhesion that could be useful for future approaches to improve proliferation and decrease adhesion of CHO cell lines which are difficult to adapt to suspension culture.
    • A psychometric appraisal of the DREEM

      Hammond, Sean M; O'Rourke, Margaret; Kelly, Martina; Bennett, Deirdre; O'Flynn, Siun (2012-01-12)
      Abstract Background The quality of the Educational environment is a key determinant of a student centred curriculum. Evaluation of the educational environment is an important component of programme appraisal. In order to conduct such evaluation use of a comprehensive, valid and reliable instrument is essential. One of most widely used contemporary tools for evaluation of the learning environment is the Dundee Ready Education Environment Measure (DREEM). Apart from the initial psychometric evaluation of the DREEM, few published studies report its psychometric properties in detail. The aim of this study was to examine the psychometric quality of the DREEM measure in the context of medical education in Ireland and to explore the construct validity of the device. Methods 239 final year medical students were asked to complete the DREEM inventory. Anonymised responses were entered into a database. Data analysis was performed using PASW 18 and confirmatory factor analysis performed. Results Whilst the total DREEM score had an acceptable level of internal consistency (alpha 0.89), subscale analysis shows that two subscales had sub-optimal internal consistency. Multiple group confirmatory factor analysis (using Fleming's indices) shows an overall fit of 0.76, representing a weak but acceptable level of fit. 17 of the 50 items manifest fit indices less than 0.70. We sought the best fitting oblique solution to the 5-subscale structure, which showed large correlations, suggesting that the independence of the separate scales is open to question. Conclusions There has perhaps been an inadequate focus on establishing and maintaining the psychometric credentials of the DREEM. The present study highlights two concerns. Firstly, the internal consistency of the 5 scales is quite variable and, in our sample, appears rather low. Secondly, the construct validity is not well supported. We suggest that users of the DREEM will provide basic psychometric appraisal of the device in future published reports.
    • A qualitative study of psychological, social and behavioral barriers to appropriate food portion size control

      Spence, Michelle; Livingstone, M BE; Hollywood, Lynsey E; Gibney, Eileen R; O’Brien, Sinéad A; Pourshahidi, L K; Dean, Moira (2013-08-01)
      Abstract Background Given the worldwide prevalence of overweight and obesity, there is a clear need for meaningful practical healthy eating advice - not only in relation to food choice, but also on appropriate food portion sizes. As the majority of portion size research to date has been overwhelmingly quantitative in design, there is a clear need to qualitatively explore consumers’ views in order to fully understand how food portion size decisions are made. Using qualitative methodology this present study aimed to explore consumers’ views about factors influencing their portion size selection and consumption and to identify barriers to appropriate portion size control. Methods Ten focus groups with four to nine participants in each were formed with a total of 66 persons (aged 19–64 years) living on the island of Ireland. The semi-structured discussions elicited participants’ perceptions of suggested serving size guidance and explored the influence of personal, social and environmental factors on their food portion size consumption. Audiotapes of the discussions were professionally transcribed verbatim, loaded into NVivo 9, and analysed using an inductive thematic analysis procedure. Results The rich descriptive data derived from participants highlight that unhealthy portion size behaviors emanate from various psychological, social and behavioral factors. These bypass reflective and deliberative control, and converge to constitute significant barriers to healthy portion size control. Seven significant barriers to healthy portion size control were apparent: (1) lack of clarity and irrelevance of suggested serving size guidance; (2) guiltless eating; (3) lack of self-control over food cues; (4) distracted eating; (5) social pressures; (6) emotional eating rewards; and (7) quantification habits ingrained from childhood. Conclusions Portion size control strategies should empower consumers to overcome these effects so that the consumption of appropriate food portion sizes becomes automatic and habitual.
    • A randomised control trial of low glycaemic index carbohydrate diet versus no dietary intervention in the prevention of recurrence of fetal macrosomia.

      Walsh, Jennifer; Mahony, Rhona; Foley, Michael; Mc Auliffe, Fionnuala M (2010-04-23)
      Abstract Background Maternal weight and maternal weight gain during pregnancy exert a significant influence on infant birth weight and the incidence of macrosomia. Fetal macrosomia is associated with an increase in both adverse obstetric and neonatal outcome, and also confers a future risk of childhood obesity. Studies have shown that a low glycaemic diet is associated with lower birth weights, however these studies have been small and not randomised 1 2 . Fetal macrosomia recurs in a second pregnancy in one third of women, and maternal weight influences this recurrence risk 3 . Methods/Design We propose a randomised control trial of low glycaemic index carbohydrate diet vs. no dietary intervention in the prevention of recurrence of fetal macrosomia. Secundigravid women whose first baby was macrosomic, defined as a birth weight greater than 4000 g will be recruited at their first antenatal visit. Patients will be randomised into two arms, a control arm which will receive no dietary intervention and a diet arm which will be commenced on a low glycaemic index diet. The primary outcome measure will be the mean birth weight centiles and ponderal indices in each group. Discussion Altering the source of maternal dietary carbohydrate may prove to be valuable in the management of pregnancies where there has been a history of fetal macrosomia. Fetal macrosomia recurs in a second pregnancy in one third of women. This randomised control trial will investigate whether or not a low glycaemic index diet can affect this recurrence risk. Current Controlled Trials Registration Number ISRCTN54392969
    • A review of the differences and similarities between generic drugs and their originator counterparts, including economic benefits associated with usage of generic medicines, using Ireland as a case study

      Dunne, Suzanne; Shannon, Bill; Dunne, Colum; Cullen, Walter (2013-01-05)
      Abstract Generic medicines are those where patent protection has expired, and which may be produced by manufacturers other than the innovator company. Use of generic medicines has been increasing in recent years, primarily as a cost saving measure in healthcare provision. Generic medicines are typically 20 to 90% cheaper than originator equivalents. Our objective is to provide a high-level description of what generic medicines are and how they differ, at a regulatory and legislative level, from originator medicines. We describe the current and historical regulation of medicines in the world’s two main pharmaceutical markets, in addition to the similarities, as well as the differences, between generics and their originator equivalents including the reasons for the cost differences seen between originator and generic medicines. Ireland is currently poised to introduce generic substitution and reference pricing. This article refers to this situation as an exemplar of a national system on the cusp of significant health policy change, and specifically details Ireland’s history with usage of generic medicines and how the proposed changes could affect healthcare provision.
    • A simplified and cost-effective enrichment protocol for the isolation of Campylobacter spp. from retail broiler meat without microaerobic incubation

      Zhou, Ping; Hussain, Syeda K.; Liles, Mark R.; Arias, Covadonga R.; Backert, Steffen; Kieninger, Jessica; Oyarzabal, Omar A. (2011-08-03)
      Abstract Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat.
    • A systematic review of the effectiveness of alternative cadres in community based rehabilitation

      Mannan, Hasheem; Boostrom, Camille; MacLachlan, Malcolm; McAuliffe, Eilish; Khasnabis, Chapal; Gupta, Neeru (2012-08-13)
      Abstract Background The Millennium Development Goals (MDGs) aim to improve population health and the quality and dignity of people’s lives, but their achievement is constrained by the crisis in human resources for health. An important potential contribution towards achieving the MDGs for persons with disabilities will be the newly developed Guidelines for Community Based Rehabilitation (CBR), launched in 2010. Given the global shortage of medical and nursing personnel and highly skilled rehabilitation practitioners, effective implementation of the CBR guidelines will require additional health workers, with improved distribution and a new skill set, allowing them to work across the health, education, livelihoods, social, and development sectors. Methods We conducted a systematic review to evaluate existing evidence regarding the effectiveness of alternative cadres working in CBR in low and middle income countries. We searched the following databases: PUBMED, LILACS, SCIE, ISMEAR, WHOLIS, AFRICAN MED IND. We also searched the online archive of the Asia Pacific Disability Rehabilitation Journal (available from 2002 to 2010), which was not covered by any of the other databases. There was no limit set on inclusion with regard to how recent a publication was in the general search. Results The search yielded 235 abstracts, only 6 of which addressed CBR through some type of evaluative component. Three of the studies explored the effects of CBR interventions, mainly related to physical disabilities, while three explored issues concerned with the work performance of rehabilitation workers. Altogether the studies covered four different countries. Conclusion All six studies related to specific service delivery in local contexts, using outcome measures that were not comparable across studies. We do not, therefore, feel that the current results provide adequate methodology or evidence for reliably generalizing their results. Due to the dearth of evidence regarding the effectiveness of alternative cadres in CBR, systematic research is needed on the training, performance and impacts of rehabilitation workers, including their capability of working across sectors and engaging with and making use of health systems research.