Quality and relevance of research and related activities at the Gorgas Memorial Laboratory.

"OTA-TM-H-18"--P. [4] of cover.

Bacteriological diagnosis and molecular strain typing of Mycobacterium bovis and Mycobacterium caprae

The primary isolation of a Mycobacterium sp. of the Mycobacterium tuberculosis complex from an infected animal provides a definitive diagnosis of tuberculosis. However, as Mycobacterium bovis and Mycobacterium caprae are difficult to isolate, particularly for animals in the early stages of disease, success is dependent on the optimal performance of all aspects of the bacteriological process, from the initial choice of tissue samples at post-mortem examination or clinical samples, to the type of media and conditions used to cultivate the microorganism. Each step has its own performance characteristics, which can contribute to sensitivity and specificity of the procedure, and may need to be optimized in order to achieve the gold standard diagnosis. Having isolated the slow-growing mycobacteria, species identification and fine resolution strain typing are keys to understanding the epidemiology of the disease and to devise strategies to limit transmission of infection. New technologies have emerged that can now even discriminate different isolates from the same animal. In this review we highlight the key factors that contribute to the accuracy of bacteriological diagnosis of M. bovis and M. caprae, and describe the development of advanced genotyping techniques that are increasingly used in diagnostic laboratories for the purpose of supporting detailed epidemiological investigations.

Small Bacteriological Laboratory

On verso: Physiology Laboratory

Living laboratories to support collaboration

Through a case study analysis, this paper discusses the essential elements of successful university-industry partnerships in the context of the integration of the scholarships of teaching, research and application. This scholarly integration is advocated as the modern paradigm of real-world laboratory activity termed the “living laboratory”. The paper further examines the application of the concepts of experimentation, engagement and regeneration as critical measures for evaluating successful university-industry partnerships. University-industry partnerships play an increasingly important role in the current climate of universities being held increasingly accountable for the benefits of their scholarship to be transferred to the wider community and to demonstrate measurable impacts.

Learning environments – Laboratories at the cross roads

Laboratories and technical hands on learning have always been a part of Engineering and Science based university courses. They provide the interface where theory meets practice and students may develop professional skills through interacting with real objects in an environment that models appropriate standards and systems. Laboratories in many countries are facing challenges to their sustainable operation and effectiveness. In some countries such as Australia, significantly reduced funding and staff reduction is eroding a once strong base of technical infrastructure. Other countries such as Thailand are seeking to develop their laboratory infrastructure and are in need of staff skill development, management and staff structure in technical areas. In this paper the authors will address the need for technical development with reference to work undertaken in Thailand and Australia. The authors identify the roads which their respective university sectors are on and point out problems and opportunities. It is hoped that the cross roads where we meet will result in better directions for both.

Trends in nurse-administered procedural sedation and analgesia across cardiac catheterisation laboratories in Australia and New Zealand : results of an electronic survey

Background Knowledge of current trends in nurse-administered procedural sedation and analgesia (PSA) in the cardiac catheterisation laboratory (CCL) may provide important insights into how to improve safety and effectiveness of this practice. Objective To characterise current practice as well as education and competency standards regarding nurse-administered PSA in Australian and New Zealand CCLs. Design A quantitative, cross-sectional, descriptive survey design was used. Methods Data were collected using a web-based questionnaire on practice, educational standards and protocols related to nurse-administered PSA. Descriptive statistics were used to analyse data. Results A sample of 62 nurses, each from a different CCL, completed a questionnaire that focused on PSA practice. Over half of the estimated total number of CCLs in Australia and New Zealand was represented. Nurse-administered PSA was used in 94% (n = 58) of respondents CCLs. All respondents indicated that benzodiazepines, opioids or a combination of both is used for PSA (n = 58). One respondent indicated that propofol was also used. 20% (n = 12) indicated that deep sedation is purposefully induced for defibrillation threshold testing and cardioversion without a second medical practitioner present. Sedation monitoring practices vary considerably between institutions. 31% (n = 18) indicated that comprehensive education about PSA is provided. 45% (n = 26) indicated that nurses who administer PSA should undergo competency assessment. Conclusion By characterising nurse-administered PSA in Australian and New Zealand CCLs, a baseline for future studies has been established. Areas of particular importance to improve include protocols for patient monitoring and comprehensive PSA education for CCL nurses in Australia and New Zealand.

Performance measures for Australian laboratories reporting cervical cytology : a decade of data 1998–2008

Aim Performance measures for Australian laboratories reporting cervical cytology are a set of quantifiable measures relating to the profile and accuracy of reporting. This study reviews aggregate data collected over the ten years in which participation in the performance measures has been mandatory. Methods Laboratories submit annual data on performance measures relating to the profile of reporting, including reporting rates for technically unsatisfactory specimens, high grade or possible high grade abnormalities and abnormal reports. Cytology-histology correlation data and review findings of negative smears reported from women with histological high grade disease are also collected. Suggested acceptable standards are set for each measure. This study reviews the aggregate data submitted by all laboratories for the years 1998-2008 and examines trends in reporting and the performance of laboratories against the suggested standards. Results The performance of Australian laboratories has shown continued improvement over the study period. There has been a fall in the proportion of laboratories with data outside the acceptable standard range in all performance measures. Laboratories are reporting a greater proportion of specimens as definite or possible high grade abnormality. This is partly attributable to an increase in the proportion of abnormal results classified as high grade or possible high grade abnormality. Despite this, the positive predictive value for high grade and possible high grade abnormalities has continued to rise. Conclusion Performance measures for cervical cytology have provided a valuable addition to external quality assurance procedures in Australia. They have documented continued improvements in the aggregate performance, as well as providing benchmarking data and goals for acceptable performance for individual laboratories.

Rice molecular breeding laboratories in the genomics era: Current status and future considerations

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.

Laboratories transformation

BACKGROUND OR CONTEXT Laboratories provide the physical spaces for engineering students to connect with theory and have a personal hands-on learning experience. Learning space design and development is well established in many universities however laboratories are often not part of that movement. While active, collaborative and group learning pedagogies are all key words in relation to these new spaces the concepts have always been central to laboratory based learning. The opportunity to build on and strengthen good practice in laboratories is immense. In the 2001 review “Universities in Crisis” many references are made to the decline of laboratories. One such comment in the review was made by Professor Ian Chubb (AVCC), who in 2013, as Chief Scientist for Australia, identifies the national concern about STEM education and presents a strategic plan to address the challenges ahead. What has been achieved and changed in engineering teaching and research laboratories in this time? PURPOSE OR GOAL A large number of universities in Australia and New Zealand own laboratory and other infrastructure designed well for the era they were built but now showing signs of their age, unable to meet the needs of today’s students, limiting the effectiveness of learning outcomes and presenting very low utilisation rates. This paper will present a model for new learning space design that improves student experience and engagement, supporting academic aims and significantly raising the space utilisation rate. APPROACH A new approach in laboratory teaching and research including new management has been adopted by the engineering disciplines at QUT. Flexibility is an underpinning principle along with the modularisation of fixed teaching and learning equipment, high utilisation of spaces and dynamic pedagogical approaches. The revitalised laboratories and workshop facilities are used primarily for the engineering disciplines and increasingly for integrated use across many disciplines in the STEM context. The new approach was built upon a base of an integrated faculty structure from 2005 and realised in 2010 as an associated development with the new Science and Engineering Centre (SEC). Evaluation through student feedback surveys for practical activities, utilisation rate statistics and uptake by academic and technical staff indicate a very positive outcome. DISCUSSION Resulting from this implementation has been increased satisfaction by students, creation of social learning and connecting space and an environment that meets the needs and challenges of active, collaborative and group learning pedagogies. Academic staff are supported, technical operations are efficient and laboratories are effectively utilised. RECOMMENDATIONS/IMPLICATIONS/CONCLUSION Future opportunities for continuous improvement are evident in using the student feedback to rectify faults and improve equipment, environment and process. The model is easily articulated and visible to other interested parties to contribute to sector wide development of learning spaces.

Report on the physical, bacteriological and biochemical analyses of seawater samples collected off existing sewage outfalls in the Sierra Leone River Estuary

The studies reported were undertaken as part of a wide environmental feasibility study for the establishment of a modern sewage system in Freetown. The aim of this part of the study was to determine whether the hydrological regime of the Sierra Leone River Estuary would permit the large-scale introduction of sewage into the estuary without damaging the environment. The important factors were whether: 1) there would be sufficient dilution of the sewage; 2) fleatable particles or other substances would create significant adverse effects in the estuarine ecosystem. The outfall sites are described together with the sampling stations, methods and analyses. Results include: 1) T/S profiles; 2) chemical analysis of the water. A review of literature on the Sierra Leone River Estuary is included which provides information on the plankton, benthos and fisheries. Results suggest that at certain points where local circulations occur it would be inadvisable to locate untreated sewage outfalls. Such points are frequently observed in small embayments. These studies have been of short duration but the data can serve as baseline for more extended investigations which would give a more complete picture of the seasonal patterns in the estuary.