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1.  Validation of eDNA Surveillance Sensitivity for Detection of Asian Carps in Controlled and Field Experiments 
PLoS ONE  2013;8(3):e58316.
In many North American rivers, populations of multiple species of non-native cyprinid fishes are present, including black carp (Mylpharyngodon piceus), grass carp (Ctenopharyngodon idella), bighead carp (Hypophthalmichthys nobilis), silver carp (Hypophthalmichthys molitrix), common carp (Cyprinus carpio), and goldfish (Carassius auratus). All six of these species are found in the Mississippi River basin and tracking their invasion has proven difficult, particularly where abundance is low. Knowledge of the location of the invasion front is valuable to natural resource managers because future ecological and economic damages can be most effectively prevented when populations are low. To test the accuracy of environmental DNA (eDNA) as an early indicator of species occurrence and relative abundance, we applied eDNA technology to the six non-native cyprinid species putatively present in a 2.6 river mile stretch of the Chicago (IL, USA) canal system that was subsequently treated with piscicide. The proportion of water samples yielding positive detections increased with relative abundance of the six species, as indicated by the number of carcasses recovered after poisoning. New markers for black carp, grass carp, and a common carp/goldfish are reported and details of the marker testing to ensure specificity are provided.
doi:10.1371/journal.pone.0058316
PMCID: PMC3589332  PMID: 23472178
2.  Rapid Microsatellite Marker Development Using Next Generation Pyrosequencing to Inform Invasive Burmese Python—Python molurus bivittatus—Management 
Invasive species represent an increasing threat to native ecosystems, harming indigenous taxa through predation, habitat modification, cross-species hybridization and alteration of ecosystem processes. Additionally, high economic costs are associated with environmental damage, restoration and control measures. The Burmese python, Python molurus bivittatus, is one of the most notable invasive species in the US, due to the threat it poses to imperiled species and the Greater Everglades ecosystem. To address population structure and relatedness, next generation sequencing was used to rapidly produce species-specific microsatellite loci. The Roche 454 GS-FLX Titanium platform provided 6616 di-, tri- and tetra-nucleotide repeats in 117,516 sequences. Using stringent criteria, 24 of 26 selected tri- and tetra-nucleotide loci were polymerase chain reaction (PCR) amplified and 18 were polymorphic. An additional six cross-species loci were amplified, and the resulting 24 loci were incorporated into eight PCR multiplexes. Multi-locus genotypes yielded an average of 61% (39%–77%) heterozygosity and 3.7 (2–6) alleles per locus. Population-level studies using the developed microsatellites will track the invasion front and monitor population-suppression dynamics. Additionally, cross-species amplification was detected in the invasive Ball, P. regius, and Northern African python, P. sebae. These markers can be used to address the hybridization potential of Burmese pythons and the larger, more aggressive P. sebae.
doi:10.3390/ijms14034793
PMCID: PMC3634432  PMID: 23449030
invasive species; exotic species; next generation sequencing; microsatellite marker; Everglades National Park; Roche 454; cross-species amplification
3.  Correction: Diabetes Care Provision in UK Primary Care Practices 
PLoS ONE  2012;7(8):10.1371/annotation/1957ad3b-e192-4faa-bf4c-5dce22c5560e.
doi:10.1371/annotation/1957ad3b-e192-4faa-bf4c-5dce22c5560e
PMCID: PMC3414526
4.  Diabetes Care Provision in UK Primary Care Practices 
PLoS ONE  2012;7(7):e41562.
Background
Although most people with Type 2 diabetes receive their diabetes care in primary care, only a limited amount is known about the quality of diabetes care in this setting. We investigated the provision and receipt of diabetes care delivered in UK primary care.
Methods
Postal surveys with all healthcare professionals and a random sample of 100 patients with Type 2 diabetes from 99 UK primary care practices.
Results
326/361 (90.3%) doctors, 163/186 (87.6%) nurses and 3591 patients (41.8%) returned a questionnaire. Clinicians reported giving advice about lifestyle behaviours (e.g. 88% would routinely advise about calorie restriction; 99.6% about increasing exercise) more often than patients reported having received it (43% and 42%) and correlations between clinician and patient report were low. Patients’ reported levels of confidence about managing their diabetes were moderately high; a median (range) of 21% (3% to 39%) of patients reporting being not confident about various areas of diabetes self-management.
Conclusions
Primary care practices have organisational structures in place and are, as judged by routine quality indicators, delivering high quality care. There remain evidence-practice gaps in the care provided and in the self confidence that patients have for key aspects of self management and further research is needed to address these issues. Future research should use robust designs and appropriately designed studies to investigate how best to improve this situation.
doi:10.1371/journal.pone.0041562
PMCID: PMC3408463  PMID: 22859997
5.  Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4 
Nucleic Acids Research  2011;40(1):360-370.
Thiostrepton, a macrocyclic thiopeptide antibiotic, inhibits prokaryotic translation by interfering with the function of elongation factor G (EF-G). Here, we have used 70S ribosome binding and GTP hydrolysis assays to study the effects of thiostrepton on EF-G and a newly described translation factor, elongation factor 4 (EF4). In the presence of thiostrepton, ribosome-dependent GTP hydrolysis is inhibited for both EF-G and EF4, with IC(50) values equivalent to the 70S ribosome concentration (0.15 µM). Further studies indicate the mode of thiostrepton inhibition is to abrogate the stable binding of EF-G and EF4 to the 70S ribosome. In support of this model, an EF-G truncation variant that does not possess domains IV and V was shown to possess ribosome-dependent GTP hydrolysis activity that was not affected by the presence of thiostrepton (>100 µM). Lastly, chemical footprinting was employed to examine the nature of ribosome interaction and tRNA movements associated with EF4. In the presence of non-hydrolyzable GTP, EF4 showed chemical protections similar to EF-G and stabilized a ratcheted state of the 70S ribosome. These data support the model that thiostrepton inhibits stable GTPase binding to 70S ribosomal complexes, and a model for the first step of EF4-catalyzed reverse-translocation is presented.
doi:10.1093/nar/gkr623
PMCID: PMC3245911  PMID: 21908407
6.  Instrument development, data collection, and characteristics of practices, staff, and measures in the Improving Quality of Care in Diabetes (iQuaD) Study 
Background
Type 2 diabetes is an increasingly prevalent chronic illness and an important cause of avoidable mortality. Patients are managed by the integrated activities of clinical and non-clinical members of primary care teams. This study aimed to: investigate theoretically-based organisational, team, and individual factors determining the multiple behaviours needed to manage diabetes; and identify multilevel determinants of different diabetes management behaviours and potential interventions to improve them. This paper describes the instrument development, study recruitment, characteristics of the study participating practices and their constituent healthcare professionals and administrative staff and reports descriptive analyses of the data collected.
Methods
The study was a predictive study over a 12-month period. Practices (N = 99) were recruited from within the UK Medical Research Council General Practice Research Framework. We identified six behaviours chosen to cover a range of clinical activities (prescribing, non-prescribing), reflect decisions that were not necessarily straightforward (controlling blood pressure that was above target despite other drug treatment), and reflect recommended best practice as described by national guidelines. Practice attributes and a wide range of individually reported measures were assessed at baseline; measures of clinical outcome were collected over the ensuing 12 months, and a number of proxy measures of behaviour were collected at baseline and at 12 months. Data were collected by telephone interview, postal questionnaire (organisational and clinical) to practice staff, postal questionnaire to patients, and by computer data extraction query.
Results
All 99 practices completed a telephone interview and responded to baseline questionnaires. The organisational questionnaire was completed by 931/1236 (75.3%) administrative staff, 423/529 (80.0%) primary care doctors, and 255/314 (81.2%) nurses. Clinical questionnaires were completed by 326/361 (90.3%) primary care doctors and 163/186 (87.6%) nurses. At a practice level, we achieved response rates of 100% from clinicians in 40 practices and > 80% from clinicians in 67 practices. All measures had satisfactory internal consistency (alpha coefficient range from 0.61 to 0.97; Pearson correlation coefficient (two item measures) 0.32 to 0.81); scores were generally consistent with good practice. Measures of behaviour showed relatively high rates of performance of the six behaviours, but with considerable variability within and across the behaviours and measures.
Discussion
We have assembled an unparalleled data set from clinicians reporting on their cognitions in relation to the performance of six clinical behaviours involved in the management of people with one chronic disease (diabetes mellitus), using a range of organisational and individual level measures as well as information on the structure of the practice teams and across a large number of UK primary care practices. We would welcome approaches from other researchers to collaborate on the analysis of this data.
doi:10.1186/1748-5908-6-61
PMCID: PMC3130687  PMID: 21658211
7.  Improving the delivery of care for patients with diabetes through understanding optimised team work and organisation in primary care 
Background
Type 2 diabetes is an increasingly prevalent chronic illness and is an important cause of avoidable mortality. Patients are managed by the integrated activities of clinical and non-clinical members of the primary care team. Studies of the quality of care for patients with diabetes suggest less than optimum care in a number of areas.
Aim
The aim of this study is to improve the quality of care for patients with diabetes cared for in primary care in the UK by identifying individual, team, and organisational factors that predict the implementation of best practice.
Design
Participants will be clinical and non-clinical staff within 100 general practices sampled from practices who are members of the MRC General Practice Research Framework. Self-completion questionnaires will be developed to measure the attributes of individual health care professionals, primary care teams (including both clinical and non-clinical staff), and their organisation in primary care. Questionnaires will be administered using postal survey methods. A range of validated theories will be used as a framework for the questionnaire instruments. Data relating to a range of dimensions of the organisational structure of primary care will be collected via a telephone interview at each practice using a structured interview schedule. We will also collect data relating to the processes of care, markers of biochemical control, and relevant indicator scores from the quality and outcomes framework (QOF). Process data (as a proxy indicator of clinical behaviours) will be collected from practice databases and via a postal questionnaire survey of a random selection of patients from each practice. Levels of biochemical control will be extracted from practice databases. A series of analyses will be conducted to relate the individual, team, and organisational data to the process, control, and QOF data to identify configurations associated with high quality care.
Study registration
UKCRN ref:DRN120 (ICPD)
doi:10.1186/1748-5908-4-22
PMCID: PMC2680803  PMID: 19397796

Results 1-8 (8)