Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods

Previous studies have indicated that the conventional tests used for the identification of mycobacteria may (i) frequently result in erroneous identification and (ii) underestimate the diversity within the genus Mycobacterium. To address this issue in a more systematic fashion, a study comparing phenotypic and molecular methods for the identification of mycobacteria was initiated. Focus was given to isolates which were difficult to identify to species level and which yielded inconclusive results by conventional tests performed under day-to-day routine laboratory conditions. Traditional methods included growth rate, colonial morphology, pigmentation, biochemical profiles, and gas-liquid chromatography of short-chain fatty acids. Molecular identification was done by PCR-mediated partial sequence analysis of the gene encoding the 16S rRNA. A total of 34 isolates was included in this study; 13 of the isolates corresponded to established species, and 21 isolates corresponded to previously uncharacterized taxa. For five isolates, phenotypic and molecular analyses gave identical results. For five isolates, minor discrepancies were present; four isolates remained unidentified after biochemical testing. For 20 isolates, major discrepancies between traditional and molecular typing methods were observed. Retrospective analysis of the data revealed that the discrepant results were without exception due to erroneous biochemical test results or interpretations. In particular, phenotypic identification schemes were compromised with regard to the recognition of previously undescribed taxa. We conclude that molecular typing by 16S rRNA sequence determination is not only more rapid (12 to 36 h versus 4 to 8 weeks) but also more accurate than traditional typing.     

Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family

Bovine acyl-coenzyme A binding protein is a four-helix bundle protein belonging to a group of homologous eukaryote proteins that binds medium and long-chain acyl-coenzyme A esters with a very high affinity. The three-dimensional structure of both the free and the ligated protein together with the folding kinetics have been described in detail for the bovine protein and with four new sequences reported here, a total of 16 closely related sequences ranging from yeasts and plants to human are known. The kinetics of folding and unfolding in different concentrations of guanidine hydrochloride together with equilibrium unfolding have been measured for bovine, rat and yeast acyl-coenzyme A binding protein. The bovine and rat sequences are closely related whereas the yeast is more distantly related to these. In addition to the three natural variants, kinetics of a bovine mutant protein, Tyr31 --> Asn, have been studied. Both the folding and unfolding rates in water of the yeast protein are 15 times faster than those of bovine. The folding rates in water of the two mammalian forms, rat and bovine, are similar, though still significantly different. A faster unfolding rate both for rat and the bovine mutant protein results from a lower stability of the native states of these. These hydrophobic regions, mini cores, have been identified in the three-dimensional structure of the bovine protein and found to be formed primarily by residues that have been conserved throughout the entire eukaryote evolution from yeasts to both plants and mammals as seen in the sample of 16 sequences. The conserved residues are found to stabilize helix-helix interactions and serve specific functional purposes for ligand binding. The fast one-step folding mechanism of ACBP has been shown to be a feature that seems to be maintained throughout evolution despite numerous differences in sequence and even dramatic differences in folding kinetics and protein stability. The protein study raises the question to what extent does the conserved hydrophobic residues provide a scaffold for an efficient one-step folding mechanism.     

An ET-Based Two-Phase Method for the Calibration and Application of Distributed Hydrological Models

Water Resources Management - Parameter calibration is a core process for the application of distributed hydrological models, which depends strongly on river runoff records. However, the sparse...     

Demonstration of Sustainable Development of Groundwater through Aquifer Storage and Recovery (ASR)

Water Resources Management - Sustained pumping of groundwater can lead to declining water levels in wellfields and concerns regarding the sustainability of groundwater resources. Aquifer Storage...     

Scheduling Optimization Modelling: A Case Study of a Woven Label Manufacturing Company

Production scheduling involves all activities of building production schedules, including coordinating and assigning activities to each person, group of people, or machine and arranging work orders in each workplace. Production scheduling must solve all problems such as minimizing customer wait time, storage costs, and production time; and effectively using the enterprise’s human resources. This paper studies the application of flexible job shop modelling on scheduling a woven labelling process. The labelling process includes several steps which are handled in different work-stations. Each workstation is also comprised of several identical parallel machines. In this study, job splitting is allowed so that the power of work stations can be utilized better. The final objective is to minimize the total completion time of all jobs. The results show a significant improvement since the new planning may save more than 60% of lead time compared to the current schedule. The contribution of this research is to propose a flexible job shop model for scheduling a woven labelling process. The proposed approach can also be applied to support complex production scheduling processes under fuzzy environments in different industries. A practical case study demonstrates the effectiveness of the proposed model.     

Mining sequential rules with itemset constraints

Applied Intelligence - Mining sequential rules from a sequence database usually returns a set of rules with great cardinality. However, in real world applications, the end-users are often...     

An evaluation of web-based voting usability and accessibility

Several countries are considering web-based voting as an alternative to, or a replacement of, traditional voting methods. It is argued that electronic voting could increase voter participation and help strengthen democracy, as e-voting would increase accessibility for large sections of the population, particularly with regard to groups that previously have experienced difficulties with the traditional voting setup. With a focus on usability and accessibility, this paper reports on a study evaluating several electronic voting prototypes in Norway, involving technical aspects as well as expert evaluation and user testing in the field, with users from a wide range of disabled user groups participating in the study. Technical testing regarding accessibility standard compliance, testing with the personas method and user testing revealed that many rather basic universal design principles were either not fully understood or not prioritized for implementation by the solution providers. However, despite various accessibility difficulties, the participants generally showed a positive attitude towards web-based elections. Through the findings of this study, the authors highlight factors that are important to consider in the development and testing of web-based voting systems.