29 research outputs found
Enterovirus Database
No full textEnterovirus reference sequence databases (EV_3kb and EV_7kb). Used for analysis of Enterovirus sequences, as described in Rames, E and Macdonald, J (2018) "Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping", Submitted to Virus Research
Rapid assessment of viral water quality using a novel recombinase polymerase amplification test for human adenovirus
No full textSensitive and rapid methods for determining viral contamination of water are critical, since illness can be caused by low numbers of viruses and bacterial indicators do not adequately predict viral loads. We developed novel rapid assays for detecting the viral water quality indicator human adenovirus (HAdV). A simple 15-min recombinase polymerase amplification step followed by a 5-min lateral flow detection is used. Species-specific assays were developed to discriminate HAdV A, B, C and F, and combined into a multiplex test (Ad-FAC). Species-specific assays enabled detection of 10–50 copies of the HAdV plasmid. Sample testing using methods optimised for wastewater analysis indicated the Ad-FAC assay showed 100% sensitivity and 100% specificity when compared with HAdV qPCR, with a detection limit as low as 50 gene copies. This is the first study to demonstrate the use of RPA for detecting enteric viruses in water samples, to assess virological water quality. The ability to rapidly detect enteric virus contamination of water could assist in more effective management of water safety and better protection of public health.No Full Tex
Microbial indicators related to yield and disease and changes in soil microbial community structure with ginger farm management practices
No full textTRFLP (terminal restriction fragment length polymorphism) was used to assess whether management practices that improved disease suppression and/or yield in a 4-year ginger field trial were related to changes in soil microbial community structure. Bacterial and fungal community profiles were defined by presence and abundance of terminal restriction fragments (TRFs), where each TRF represents one or more species. Results indicated inclusion of an organic amendment and minimum tillage increased the relative diversity of dominant fungal populations in a system dependant way. Inclusion of an organic amendment increased bacterial species richness in the pasture treatment. Redundancy analysis showed shifts in microbial community structure associated with different management practices and treatments grouped according to TRF abundance in relation to yield and disease incidence. ANOVA also indicated the abundance of certain TRFs was significantly affected by farming system management practices, and a number of these TRFs were also correlated with yield or disease suppression. Further analyses are required to determine whether identified TRFs can be used as general or soil-type specific bio-indicators of productivity (increased and decreased) and Pythium myriotylum suppressiveness.E. K. Rames, M. K. Smith, S. D. Hamill, J. De Faver
A Classification Model for Reusable Software Components
No full textTIris paper presents work which has been carried out in the ESF-ROSE project (referred to as ROSE in the remainder of this paper). Funded under the Eureka programme (Eureka is the famous interjection used by Archimedes in his bath and not an acronym), the ESF project (Eureka Software Factory) aims at providing a highly effective software manufacturing environment The use of the wordfactory in the software context has very little connection to traditional assemblyline factories. Instead, a Software Factory is a factory in the modem sense providing Computer Integrated Software Manufacturing with emphasis on integration. A software factory covers the total software production process, including all technical and managerial tasks, with a high degree of automation and resource utilization. The ROSE project is a collaborative effon involving MATRA Espace, the software house Serna Group (France), and the University of Dortmund (Federal Republic of Gennany). Pan of the work on classification is the Ph.D. research of author Eric Rames. The main goals of the ROSE project (Reuse Of SoftwarE) are: • to analyze and to define in a comprehensive way the concept of software reuse; • to develop an environment for the reuse of software components within a factory. A precondition for reuse in software development is the existence of libraries of reusable software components. In order to suppon reuse, the collection must contain not only the components themselves, but also be accessible by a system that provides descriptions of the components and retrieval mechanisms so that users may match their specific requirements against these descriptions. Indexing reusable software components according to a classification scheme allows reusers to have a better understanding and more efficient access to the libraries' contents. Therefore a classification scheme is built so that it represents selection criteria the reuser might have. These indexes would be searchable and keyed to retrievable software descriptions. Based on retrievals, users may then access the actual software. Building such a collection is a domain analysis process [PRI90] that includes activities such as: • Identification of software components that should be reusable and description in terms of reusable software components. • Definition of a classification scheme appropriate for indexing and retrieving the reusable software components. TIris paper focuses on the latter topic and how it is performed in the ROSE project. A case study carried out from the aerospace domain is then presented. A discussion of ongoing and future work will conclude this paper
An effective indexing method for banana tissue culture provides long-term freedom from bacterial contamination
No full textThe global banana industry relies on tissue culture for uniform plants for better farm management, improved production and for prevention of pests and diseases otherwise transferred in soil or plant material. Banana tissue culture is also required by quarantine authorities to import/export banana plants and used in banana cultivar collections to safely maintain plantlets free of disease in the long term and protected against impacts of weather events or disease incursion. Production needs to be efficient to minimise costs and to deliver large quantities of plants on schedule. Both commercial tissue culture production and research applications involving long-term storage of banana tissue culture and cryopreservation are negatively impacted by bacterial contamination. Endophytic bacteria in tissue cultured plantlets that build up over time and adapt to culture conditions are a problem in banana tissue culture. While fungal contamination is relatively easy to identify and remove from the system, bacteria in tissue culture plants is not always apparent and can rapidly spread during plant micropropagation. Commonly bacteria may only become obvious after an extended culture time such as towards the end of a mass production cycle or in long term storage in a cultivar collection. The widespread bacteria contamination towards the end of a production cycle causes significant loss of plants and unreliable supply. Use of antibiotics rarely eliminates bacteria and can disadvantage plant growth and does not provide a contamination solution. This paper describes an effective assay allowing identification of explants used in banana tissue culture that contain culturable bacteria. Banana cultures initiated via meristem culture were indexed using a combination of four methods using modified nutrient agar that includes: streaking explant, plating macerated tissue taken adjacent explant into agar and broth, and observation of initiated cultures. Cultures initiated and indexed using this multi-culture assay have remained completely free from culturable bacteria for more than 12 years. This paper describes the bacterial screening assay and demonstrates its effectiveness by producing long-term bacterial free banana tissue cultures within the Australian banana germplasm collection
Bacterially-induced growth promotion of micropropagated ginger
No full textThis study evaluated a range of bacteria for their potential to promote growth and improve resistance to Foz in micropropagated ginger plants. Trials were established under greenhouse conditions using minimal levels of synthetic fertilisers. B. subtilis DAR26659 significantly improved growth of ginger tissue culture plants, where rhizome fresh weight, shoot dry weight, and root dry weight were increased by 60.4%, 53.6%, and 49.1% respectively compared to control treatments. Inconsistent infection of plants by Foz (under low levels of inoculum tested) limited evaluation of biocontrol activity of bacteria. This report demonstrates the potential of beneficial bacteria to improve the growth of micropropagated ginger using reduced fertiliser inputs with the aim to improve farm productivity
Natural antimicrobials for a post-COVID era
No full textNatural products have long served as a resource for novel pharmaceutical drugs supporting human health. Climate change and habitat destruction threatens drug discovery as natural habitats are compromised and botanical species become endangered. The original objective of this dissertation addressed the need for preserving plant metabolites and streamlining drug discovery, however this dissertation was impacted, and inspired by, the COVID-19 pandemic. Due to this, the work discussed here is transdisciplinary and has evolved over the years accumulating it, beginning with its original premise of drug discovery, and concluding with the foundations of a potential antimcirobial product.
To promote the preservation of endangered biodiversity due to climate change and habitat destruction, Chapter 2 details the development of Rapid Metabolome Extraction and Storage (RAMES) technology, and how this method translates into Screens-to-Nature (STN) assays. RAMES extracts 2 grams of plant tissue in 70% ethanol and dries it onto glass fiber discs. These discs are later stored in a -20ºC freezer and can be transported in an envelope to anywhere around the world. These discs are compatible with STN assays, highly portable assays that efficiently determine the active properties of botanicals, such as antimicorbial or antioxidant activity. This method was validated and put into action in chapter three.
Chapter three investigated metabolomic differences in native plants compared to their invaded areas. We hypothesized that if a species were displaced and invaded a foreign environment, its metabolomic profile would differ from its native counterpart, while still retaining its original, species-specific, metabolomic signature. Botanical species were collected, via RAMES technology, in their native populations in the USA and their invaded areas in South Africa. Extracts were later characterized via ultra-performance liquid chromatography - mass spectrometry (UPLC/MS). Our findings supported the above hypothesis and we concluded that metabolomic analysis can differentiate species from one another, as well as among global populations.
Chapter four was inspired by the COVID-19 pandemic and addresses the need for new antimicrobial products. We hypothesized that combinations of ethanolic plant extracts, containing anti-microbial compounds with differing modes of action, will display synergistic effects against bacteria. Qualitative screening was done using STN assays and nine botanicals were chosen for quantitative analysis using Clinical and Laboratory Standards Institute (CLSI) broth microdillution methods. Four botanicals moved onto synergy testing via checkerboard assays and calculation of fractional inhibitory concentration (FIC) index values. A final total of five synergistic pairs were identified. Our hypothesis was supported as all botanical synergies were compromised of differing bioactives. The impact of this research will be more sustainable, naturally based, antibiotic alternatives to overused single compound antibiotic drugs.Ph.D.Includes bibliographical reference
Minimal suture associated with fibrin adhesive in microvascular arterial anastomosis: comparative experimental study with the conventional suture technique
No full textO domínio da técnica de microanastomose vascular é um pré-requisito essencial para a realização de procedimentos microcirúrgicos reconstrutivos, como reimplantes e transferência livre de tecidos. Até hoje, a técnica de sutura convencional é a mais aceita na prática clínica, por sua segurança e versatilidade. Apesar disso, ela apresenta alguns problemas por ser tecnicamente difícil, consumir tempo considerável e causar traumatismo adicional à parede do vaso. O objetivo deste estudo, foi testar um método alternativo de microanastomose arterial, reduzindo o número de pontos de sutura com aplicação do adesivo de fibrina. Sessenta ratos da raça Wistar foram submetidos a microanastomose vascular nas artérias femorais ou carótidas. Os animais foram divididos em quatro subgrupos de acordo com a artéria operada e a técnica de sutura empregada: FSC (femoral - sutura convencional), FAF (femoral - sutura mínima com adesivo de fibrina), CSC (carótida - sutura convencional) e CAF (carótida - sutura mínima com adesivo de fibrina). As duas técnicas de anastomose foram comparadas através de análise estatística dos parâmetros clínicos e histopatológicos. A média de pontos de sutura por anastomose nos subgrupos FSC e CSC foi de 7,7 e 9,5, respectivamente. No subgrupo FAF, as anastomoses foram realizadas com apenas quatro pontos de sutura e no subgrupo CAF, com apenas seis. O tempo de anastomose foi, em média: 15,81 minutos no subgrupo FSC, 13,62 minutos no subgrupo FAF, 18,87 minutos no subgrupo CSC e 17,33 minutos no subgrupo CAF. A aplicação do adesivo de fibrina reduziu, significativamente, o número de pontos e o tempo necessário para realização das anastomoses, nos subgrupos FAF e CAF. A intensidade do sangramento anastomótico também foi reduzida de maneira significativa nestes subgrupos. A freqüência da permeabilidade imediata e tardia foi de 100% em todos os subgrupos, exceto no subgrupo FAF, onde a permeabilidade tardia foi de 93,33%. Não foram observadas diferenças significativas entre as duas técnicas, em relação aos parâmetros histopatológicos avaliados (processo inflamatório, fibrose da camada média e hiperplasia subintimal). O autor concluiu que a técnica de sutura mínima com aplicação do adesivo de fibrina foi mais fácil e rápida que a técnica de sutura convencional, sem aumento da trombogenicidade das anastomoses, no modelo experimental utilizado.Mastering of the microvascular anastomosis technique is an essencial requirement to perform reconstructive microsurgical procedures, such as replantation surgery and free tissue transfers. Until now, the conventional suture technique is the most widely accepted in the clinical setting, for its safety and versatility. However, this technique presents some problems for being technically difficult, time consuming and causes additional trauma to the vessel wall. The aim of this study was to test an alternative method of microvascular arterial anastomosis, by reducing the number of sutures with application of fibrin adhesive. Sixty Wistar rats underwent to microvascular anastomosis at the femoral or carotid arteries. The animals were divided into four subgroups, according to the operated artery and the employed suture technique: FCS (femoral - conventional suture), FFA (femoral - minimal suture with fibrin adhesive), CCS (carotid - conventional suture) and CFA (carotid - minimal suture with fibrin adhesive). Both anastomosis techniques were compared by means of statistical analisys of the clinical and histopathological parameters. The mean number of sutures required to complete the anastomosis was 7,7 in subgroup FCS and 9,5 in subgroup CCS. In subgroup FFA, the anastomosis was performed with only four sutures and in subgroup CFA, with only six. The mean anastomotic time was 15,81 minutes in subgroup FCS, 13,62 minutes in subgroup FFA, 18,87 minutes in subgroup CCS and 17,33 minutes in subgroup CCS. The application of fibrin adhesive, significantly reduced the number of sutures and the time taken to perform the anastomosis, in subgroups FFA and CFA. The amount of anastomotic bleeding was also significantly reduced in these subgroups. The immediate and late patency rates were 100% in all subgroups, except in subgroup FFA where it was 93,33%. No significant differences were observed among the two techniques, concerning the evaluated histopathological parameters (inflammatory process, medial fibrosis and subintimal hyperplasia). The author concluded that, the fibrin adhesive application with minimal suture technique was faster and easier than the conventional suture technique, without increasing the trombogenicity of the anastomosis, in this experimental model
Minimal suture associated with fibrin adhesive in microvascular arterial anastomosis: comparative experimental study with the conventional suture technique
No full textO domínio da técnica de microanastomose vascular é um pré-requisito essencial para a realização de procedimentos microcirúrgicos reconstrutivos, como reimplantes e transferência livre de tecidos. Até hoje, a técnica de sutura convencional é a mais aceita na prática clínica, por sua segurança e versatilidade. Apesar disso, ela apresenta alguns problemas por ser tecnicamente difícil, consumir tempo considerável e causar traumatismo adicional à parede do vaso. O objetivo deste estudo, foi testar um método alternativo de microanastomose arterial, reduzindo o número de pontos de sutura com aplicação do adesivo de fibrina. Sessenta ratos da raça Wistar foram submetidos a microanastomose vascular nas artérias femorais ou carótidas. Os animais foram divididos em quatro subgrupos de acordo com a artéria operada e a técnica de sutura empregada: FSC (femoral - sutura convencional), FAF (femoral - sutura mínima com adesivo de fibrina), CSC (carótida - sutura convencional) e CAF (carótida - sutura mínima com adesivo de fibrina). As duas técnicas de anastomose foram comparadas através de análise estatística dos parâmetros clínicos e histopatológicos. A média de pontos de sutura por anastomose nos subgrupos FSC e CSC foi de 7,7 e 9,5, respectivamente. No subgrupo FAF, as anastomoses foram realizadas com apenas quatro pontos de sutura e no subgrupo CAF, com apenas seis. O tempo de anastomose foi, em média: 15,81 minutos no subgrupo FSC, 13,62 minutos no subgrupo FAF, 18,87 minutos no subgrupo CSC e 17,33 minutos no subgrupo CAF. A aplicação do adesivo de fibrina reduziu, significativamente, o número de pontos e o tempo necessário para realização das anastomoses, nos subgrupos FAF e CAF. A intensidade do sangramento anastomótico também foi reduzida de maneira significativa nestes subgrupos. A freqüência da permeabilidade imediata e tardia foi de 100% em todos os subgrupos, exceto no subgrupo FAF, onde a permeabilidade tardia foi de 93,33%. Não foram observadas diferenças significativas entre as duas técnicas, em relação aos parâmetros histopatológicos avaliados (processo inflamatório, fibrose da camada média e hiperplasia subintimal). O autor concluiu que a técnica de sutura mínima com aplicação do adesivo de fibrina foi mais fácil e rápida que a técnica de sutura convencional, sem aumento da trombogenicidade das anastomoses, no modelo experimental utilizado.Mastering of the microvascular anastomosis technique is an essencial requirement to perform reconstructive microsurgical procedures, such as replantation surgery and free tissue transfers. Until now, the conventional suture technique is the most widely accepted in the clinical setting, for its safety and versatility. However, this technique presents some problems for being technically difficult, time consuming and causes additional trauma to the vessel wall. The aim of this study was to test an alternative method of microvascular arterial anastomosis, by reducing the number of sutures with application of fibrin adhesive. Sixty Wistar rats underwent to microvascular anastomosis at the femoral or carotid arteries. The animals were divided into four subgroups, according to the operated artery and the employed suture technique: FCS (femoral - conventional suture), FFA (femoral - minimal suture with fibrin adhesive), CCS (carotid - conventional suture) and CFA (carotid - minimal suture with fibrin adhesive). Both anastomosis techniques were compared by means of statistical analisys of the clinical and histopathological parameters. The mean number of sutures required to complete the anastomosis was 7,7 in subgroup FCS and 9,5 in subgroup CCS. In subgroup FFA, the anastomosis was performed with only four sutures and in subgroup CFA, with only six. The mean anastomotic time was 15,81 minutes in subgroup FCS, 13,62 minutes in subgroup FFA, 18,87 minutes in subgroup CCS and 17,33 minutes in subgroup CCS. The application of fibrin adhesive, significantly reduced the number of sutures and the time taken to perform the anastomosis, in subgroups FFA and CFA. The amount of anastomotic bleeding was also significantly reduced in these subgroups. The immediate and late patency rates were 100% in all subgroups, except in subgroup FFA where it was 93,33%. No significant differences were observed among the two techniques, concerning the evaluated histopathological parameters (inflammatory process, medial fibrosis and subintimal hyperplasia). The author concluded that, the fibrin adhesive application with minimal suture technique was faster and easier than the conventional suture technique, without increasing the trombogenicity of the anastomosis, in this experimental model
