http://espace.library.uq.edu.au/ The University of Queensland en Fez http://blogs.law.harvard.edu/tech/rss http://espace.library.uq.edu.au/view/UQ:183336 2009-09-03T00:00:00Z Kunin, V og He, S og Warnecke, F og Peterson, SB og Martin, HG og Haynes, M og Ivanova, N og Blackall, LL og Breitbart, M og Rohwer, F og McMahon, KD og Hugenholtz, P http://espace.library.uq.edu.au/view/UQ:187514 ATP-binding cassette (ABC) transporters form one of the largest and most ancient of protein families. ABC transporters couple hydrolysis of ATP to vectorial translocation of diverse substrates across cellular membranes. Many human ABC transporters are medically important in causing, for example, multidrug resistance to cytotoxic drugs. Seven complete prokaryotic structures and one eukaryotic structure have been solved for transporters from 2002 to date, and a wealth of research is being conducted on and around these structures to resolve the mechanistic conundrum of how these transporters couple ATP hydrolysis in cytosolic domains to substrate translocation through the transmembrane pore. Many questions remained unanswered about this mechanism, despite a plethora of data and a number of interesting and controversial models. 2009-11-23T00:00:00Z Jones, Peter M. og O'Mara, Megan L. og George, Anthony M. http://espace.library.uq.edu.au/view/UQ:115033 Glutamate-mediated toxicity has been implicated in the neurodegeneration observed in Alzheimer's disease. In particular, glutamate transport dysfunction may increase susceptibility to glutamate toxicity, thereby contributing to neuronal cell injury and death. In this study, we examined the cellular localization of the glial glutamate transporter excitatory amino acid transporter 1 (EAAT1) in the cerebral cortex of control, Alzheimer's disease, and non-Alzheimer dementia cases. We found that EAAT1 was strongly expressed in a subset of cortical pyramidal neurons in dementia cases showing Alzheimer-type pathology. In addition, tau (which is a marker of neurofibrillary pathology) colocalized to those same pyramidal cells that expressed EAAT1. These findings suggest that EAAT1 changes are related to tau expression (and hence neurofibrillary tangle formation) in dementia cases showing Alzheimer-type pathology. This study implicates aberrant glutamate transporter expression as a mechanism involved in neurodegeneration in Alzheimer's disease. 2007-10-17T00:00:00Z Scott, H. L. og Pow, D. V. og Tannenberg, A. E. G. og Dodd, P. R. http://espace.library.uq.edu.au/view/UQ:198828 2010-03-11T00:00:00Z Lim, Elgene og Vaillant, Francois og Wu, Di og Forrest, Natalie C. og Pal, Bhupinder og Hart, Adam H. og Asselin-Labat, Marie-Liesse og Gyorki, David E. og Ward, Teresa og Partanen, Audrey og Feleppa, Frank og Huschtscha, Lily I. og Thorne, Heather J. og kConFab og Fox, Stephen B. og Yan, Max og French, Juliet D. og Brown, Melissa A. og Smyth, Gordon K. og Visvader, Jane E. og Lindemann, G. J. http://espace.library.uq.edu.au/view/UQ:102346 2007-08-23T00:00:00Z Mackenzie, J. M. og Khromykh, A. og Parton, R. G. http://espace.library.uq.edu.au/view/UQ:242959 As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project. 2011-06-24T00:00:00Z Kunin, V og Copeland, A og Lapidus, A og Mavromatis, K og Hugenholtz, P http://espace.library.uq.edu.au/view/UQ:111703 Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. (C) 2004 Wiley Periodicals, Inc. 2007-09-19T00:00:00Z Oostenbrink, C. og Villa, A. og Mark, A. E. og Van Gunsteren, W. F. http://espace.library.uq.edu.au/view/UQ:244334 2011-07-19T00:00:00Z Huber, M. og Scaletta, C. og Benathan, M. og Frenk, E. og Greenhalgh, D. A. og Rothnagel, J. A. og Roop, D. R. og Hohl, D. http://espace.library.uq.edu.au/view/UQ:191229 Our ageing population has a high prevalence of neurodegenerative diseases, and infectious diseases of the nervous system are emerging in Asia. Extrapolation from animal research to humans has the disadvantage of species differences in anatomy, physiology, biochemistry, and genetics. The systematic collection and cryopreservation of human brains at autopsy in "brain banks" is a useful resource. Standardised protocols for brain retrieval, dissection, cryopreservation, and distribution have been established. Brain bank networks in the USA and Europe facilitate data and specimen exchange, and make high quality tissue available. The Sri Lankan population has distinctive demographic and ethnic features which may modulate the presentation of neurological disorders. Life expectancy of 74.1 years is the highest in the region. The over-60 population (currently 9.6%) is expected to increase rapidly to reach 13% in 2010 and 21% in 2025. To develop effective management strategies, it is essential to have baseline scientific data on nervous system disorders. Due to its cultural and religious practices, Sri Lanka is in a unique position to obtain brain tissue for research 2010-01-04T00:00:00Z Da Silva, K.R.D og Shankar, S,K. og Mahadevan, A. og Dodd, P. R. http://espace.library.uq.edu.au/view/UQ:182545 2009-09-03T00:00:00Z Alvarez, Alejandra Castillo og Brunck, Mario E. G. og Boyd, Victoria og Lai, Richard og Virtue, Elena og Chen, Wenbin og Bletchly, Cheryl og Heine, Hans G. og Barnard, Ross http://espace.library.uq.edu.au/view/UQ:231674 Male-specific volatile components released by the banana weevil, Cosmopolites sordidus Germar, from Australia have been identified as (1S,3R,5R,7S)-1-ethyl-3,5,7-trimethyl-2,8-dioxabicyclo [3.2.1]octane and the 7R-epimer (as a minor component) by synthesis and enantioselective gas chromatography. 2011-03-07T00:00:00Z Fletcher, Mary T. og Moore, CHristopher J. og Kitching, William http://espace.library.uq.edu.au/view/UQ:237699 Absolute entropies was calculated using the molecular dynamics (MD) simulation trajectories. The heuristic formula for the calculation of entropies from the covariance matrix of atom-positional fluctuations was tested. The approximation formula for entropy was obtained by comparing the results with analytical expressions for an ensemble of harmonic oscillators, for the ideal gas, and to the numerical results obtained from the equation of state for the Lennard-Jones fluid. 2011-03-21T00:00:00Z Schafer, Heiko og Mark, Alan E. og van Gunsteren, Wilfred F. http://espace.library.uq.edu.au/view/UQ:181329 2009-09-03T00:00:00Z Yong, Ken W., L. og Garson, Mary J. og Bernhardt, Paul V. http://espace.library.uq.edu.au/view/UQ:128421 2008-02-18T00:00:00Z Yee, Benjamin og Lafi, Feras F. og Oakley, Brian og Staley, James T. og Fuerst, John A. http://espace.library.uq.edu.au/view/UQ:148043 2008-06-06T00:00:00Z Stok, J. og Cryle, M. J. og De Voss, J. J. http://espace.library.uq.edu.au/view/UQ:238261 2011-03-23T00:00:00Z Ward, L.C. og Battersby, K. J. og Kilbreath S. L. http://espace.library.uq.edu.au/view/UQ:60925 Recent studies have indicated a role for caveolin in regulating cholesterol-dependent signaling events. In the present study we have analyzed the role of caveolins in intracellular cholesterol cycling using a dominant negative caveolin mutant. The mutant caveolin protein, cav-3(DGV) specifically associates with the membrane surrounding large lipid droplets. These structures contain neutral lipids, and are accessed by caveolin 1-3 upon overexpression. Fluorescence, electron, and video microscopy observations are consistent with formation of the membrane-enclosed lipid rich structures by maturation of subdomains of the ER. The caveolin mutant causes the intracellular accumulation of free cholesterol (FC) in late endosomes, a decrease in surface cholesterol and a decrease in cholesterol efflux and synthesis. The amphiphile U18666A acts synergistically with cav(DGV) to increase intracellular accumulation of FC. Incubation of cells with oleic acid induces a significant accumulation of full-length caveolins in the enlarged lipid droplets. We conclude that caveolin can associate with the membrane surrounding lipid droplets and is a key component involved in intracellular cholesterol balance and lipid transport in fibroblasts. 2007-08-14T00:00:00Z Pol, Albert og Luetterforst, Robert og Lindsay, Margaret og Heino, Sanna og Ikonen, Elina og Parton, Robert G. http://espace.library.uq.edu.au/view/UQ:193687 2010-01-24T00:00:00Z Oliver, Peter L. og Goodstadt, Leo og Bayes, Joshua J. og Birtle, Zoe og Roach, Kevin C. og Phadnis, Nitin og Beatson, Scott A. og Lunter, Gerton og Malik, Harmit S. og Ponting, Chris P. http://espace.library.uq.edu.au/view/UQ:75277 The RAFT-CLD-T methodology is demonstrated to be not only applicable to 1-substituted monomers such as styrene and acrylates, but also to 1,1-disubstituted monomers such as MMA. The chain length of the terminating macromolecules is controlled by CPDB in MMA bulk free radical polymerization at 80 degrees C. The evolution of the chain length dependent termination rate coefficient, k(t)(i,i), was constructed in a step-wise fashion, since the MMA/CPDB system displays hybrid behavior (between conventional and living free radical polymerization) resulting in initial high molecular weight polymers formed at low RAFT agent concentrations. The obtained CLD of k(t) in MMA polymerizations is compatible with the composite model for chain length dependent termination. For the initial chain-length regime, up to a degree of polymerization of 100, k(t) decreases with alpha (in the expression k(t)(i,i) = k(t)(0) . i(-alpha)) being close to 0.65 at 80 degrees C. At chain lengths exceeding 100, the decrease is less pronounced (affording an alpha of 0.15 at 80 degrees C). However, the data are best represented by a continuously decreasing nonlinear functionality implying a chain length dependent alpha. 2007-08-15T00:00:00Z Johnston-Hall, Geoffrey og Theis, Alexander og Monteiro, Michael J. og Davis, Thomas P. og Stenzel, Martina H. og Barner-Kowollik, Christopher http://espace.library.uq.edu.au/view/UQ:139242 Carcinoma of the breast is thought to evolve through a sequential progression from normal to proliferative epithelium and eventually into carcinoma. Here lumpectomy specimens from five patients were studied, selected for the presence of ductal hyperplasia without atypia, atypical ductal hyperplasia. ductal carcinoma in situ, and invasive ductal carcinoma. Laser microdissection of tissue allowed precise sampling and direct correlation of phenotypic and genotypic changes. Analyses of the samples revealed an increasing mean number of chromosomal changes occurring with increasing histologic severity, and for the first time chromosomal abnormalities were demonstrated in ductal hyperplasia without atypia. Chromosomal changes found in each of the four histologic entities included gains on 10q, 12q, 16p, and 20q and loss on 13q. In ductal hyperplasia without atypia, gain on 20q as well as loss on 13q was detected with high frequency (four of five samples). Alterations identified in more than 50% of atypical ductal hyperplasia samples included gains on 3p, 8q, 15q, and 22q and loss on 16q. In ductal carcinoma in situ, gain of DNA on Iq and 17q and loss on 4q were additionally found, and in invasive ductal carcinoma, further gains on 6p, 10q, 11q13, and 17p were identified. The chromosomal alterations occurring in the different histopathologic lesions strongly suggest that these regions harbor tumor suppressor genes or oncogenes significant for the development of ductal carcinoma of the breast. 2008-06-10T00:00:00Z Aubele, M. M. og Cummings, M. C. og Mattis, A. E. og Zitzelsberger, H. F. og Walch, A. K. og Kremer, M. og Hofler, H. og Werner, M http://espace.library.uq.edu.au/view/UQ:59616 As a facultative aerobe with a high iron requirement and a highly active aerobic respiratory chain, Neisseria gonorrhoeae requires defence systems to respond to toxic oxygen species such as superoxide. It has been shown that supplementation of media with 100 muM Mn(II) considerably enhanced the resistance of this bacterium to oxidative killing by superoxide. This protection was not associated with the superoxide dismutase enzymes of N. gonorrhoeae. In contrast to previous studies, which suggested that some strains of N. gonorrhoeae might not contain a superoxide dismutase, we identified a sodB gene by genome analysis and confirmed its presence in all strains examined by Southern blotting, but found no evidence for sodA or sodC. A sodB mutant showed very similar susceptibility to superoxide killing to that of wild-type cells, indicating that the Fe-dependent SOD B did not have a major role in resistance to oxidative killing under the conditions tested. The absence of a sodA gene indicated that the Mn-dependent protection against oxidative killing was independent of Mn-dependent SOD A. As a sodB mutant also showed Mn-dependent resistance to oxidative killing, then it is concluded that this resistance is independent of superoxide dismutase enzymes. Resistance to oxidative killing was correlated with accumulation of Mn(II) by the bacterium. We hypothesize that this bacterium uses Mn(II) as a chemical quenching agent in a similar way to the already established process in Lactobacillus plantarum. A search for putative Mn(II) uptake systems identified an ABC cassette-type system (MntABC) with a periplasmic-binding protein (MntC). An mntC mutant was shown to have lowered accumulation of Mn(II) and was also highly susceptible to oxidative killing, even in the presence of added Mn(II). Taken together, these data show that N. gonorrhoeae possesses a Mn(II) uptake system that is critical for resistance to oxidative stress. 2007-08-14T00:00:00Z Tseng, Hsing-Ju og Srikhanta, Yogitha og McEwan, Alastair G. og Jennings, Michael P. http://espace.library.uq.edu.au/view/UQ:262356 2011-11-28T00:00:00Z McHardy, Alice Carolyn og Martin, Hector Garcia og Tsirigos, Aristotelis og Hugenholtz, Philip og Rigoutsos, Isidore http://espace.library.uq.edu.au/view/UQ:142915 The envelope of hepatitis B virus (HBV) consists of three related proteins known as the large (L), middle (M) and small (S) hepatitis B surface antigens (HBsAg), L-HBsAg has a 108-119 amino acid extension at the N terminus compared with M-HBsAg and contains the preS1 sequence of the HBV envelope. Previous research has identified this region as the likely virus attachment protein which is thought to interact with the cellular receptor for the virus. However, as the receptor has still not been identified unequivocally, we used the preS1 region of L-HBsAg to screen a human liver cDNA library by the yeast two-hybrid system. Several positive clones were isolated which encoded cellular proteins that interacted with the HBV preS1 protein. The specificity was examined in an independent manner in experiments in which baculovirus-derived glutathione S-transferase (GST)-preS1 was incubated with S-35-labelled protein expressed by in vitro translation from the positive clones. The intensity of the interactions using this alternative approach mirrored those observed in the yeast two-hybrid system and two proteins (an unidentified protein and a mitochondrial protein) were selected for further study. The specificity of the binding reaction between the preS1 protein and these two proteins was further confirmed in a competition assay; HBV purified from serum, but not purified HBsAg, was able to compete with preS1 and thus block GST-preS1 binding to the unidentified protein but not to the mitochondrial protein. The unidentified protein was then expressed as a fusion protein with GST and this was able to bind HBV virions in a direct manner. 2008-06-10T00:00:00Z Harvey, T. J. og Macnaughton, T. B. og Park, D. S. og Gowans, E. J. http://espace.library.uq.edu.au/view/UQ:140764 Acetohydroxyacid synthase (EC 4.1.3.18) catalyses the first reaction in the pathway for synthesis of the branched-chain amino acids. The enzyme is inhibited by several commercial herbicides and has been subjected to detailed study over the last 20 to 30 years. Here we review the progress that has been made in understanding its structure, regulation, mechanism, and inhibition. 2008-06-10T00:00:00Z Duggleby, R. G. og Pang, S. S. http://espace.library.uq.edu.au/view/UQ:79496 The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years. 2007-08-15T00:00:00Z McCourt, J. A. og Duggleby, R. G. http://espace.library.uq.edu.au/view/UQ:35108 Acetylcholinesterase is the target of organophosphate and carbamate pesticides. Organophosphate resistance is widespread in the cattle tick, Boophilus microplus, in Australia. We have isolated a cDNA of acetylcholinesterase from B. microplus and show that it would encode a protein 62 kDa in size. The predicted amino acid sequence contains all the residues characteristic of an acetylcholinesterase. Alternative splicing of the transcript was detected at both the 5' and 3' ends. Alternative splicing at the 5' end would result in two proteins differing by six amino acids. This is the first report of alternative splicing of the N-terminal coding region in a cholinesterase. No point mutations were detected in the acetylcholinesterase gene from organophosphate resistant strains of B. microplus. Alternative explanations for resistance to organophosphates in B. microplus are discussed. (C) 1998 Elsevier Science Ltd. All rights reserved. 2007-08-13T00:00:00Z Baxter, GD og Barker, SC http://espace.library.uq.edu.au/view/UQ:181453 2009-09-03T00:00:00Z Richardson, Des R. og Kalinowski, Danuta S. og Richardson, Vera og Sharpe, Philip C. og Lovejoy, David B. og Islam, Mohammad og Bernhardt, Paul V. http://espace.library.uq.edu.au/view/UQ:242961 2011-06-24T00:00:00Z Hugenholtz, P og Kyrpides, NC http://espace.library.uq.edu.au/view/UQ:232665 2011-03-07T00:00:00Z Whyte, Andrew R. og Gilbert, Robert G. http://espace.library.uq.edu.au/view/UQ:212930 2010-08-22T00:00:00Z Stacey, Katryn J. og Sagulenko, Vitaliya http://espace.library.uq.edu.au/view/UQ:280974 The tandem chain extension-aldol (TCA) reaction of β-keto esters provides an α-substituted γ-keto ester with an average syn:anti selectivity of 10:1. It is proposed that the reaction proceeds via a carbon-zinc bound organometallic intermediate potentially bearing mechanistic similarity to the Reformatsky reaction. Evidence, derived from control Reformatsky reactions and a study of the structure of the TCA intermediate utilizing DFT methods and NMR spectroscopy, suggests the γ-keto group of the TCA intermediate plays a significant role in diastereoselectivity observed in this reaction. Such coordination effects have design implications for future zinc mediated reactions. 2012-09-02T00:11:40Z Aiken, Karelle S. og Eger, Wilhelm A. og Williams, Craig M. og Spencer, Carley M. og Zercher, Charles K. http://espace.library.uq.edu.au/view/UQ:237315 We describe a new method for producing homogeneous eukaryotic N-glycoproteins. The method involves the engineering and functional transfer of the Campylobacter jejuni glycosylation machinery in Escherichia coli to express glycosylated proteins with the key GlcNAc-Asn linkage. The bacterial glycans were then trimmed and remodeled in vitro by enzymatic transglycosylation to fulfill a eukaryotic N-glycosylation. It provides a potentially general platform for producing eukaryotic N-glycoproteins. © 2010 Nature America, Inc. All rights reserved. 2011-03-18T00:00:00Z Schwarz, Flavio og Huang, Wei og Li, Cishan og Schulz, Benjamin L. og Lizak, Christian og Palumbo, Alessandro og Numao, Shin og Neri, Dario og Aebi, Markus og Wang, Lai-Xi http://espace.library.uq.edu.au/view/UQ:219452 2010-10-31T00:00:00Z Crossman, LC og Chaudhuri, RR og Beatson, SA og Wells, TJ og Desvaux, M og Cunningham, AF og Petty, NK og Mahon, V og Brinkley, C og Hobman, JL og Savarino, SJ og Turner, SM og Pallen, MJ og Penn, CW og Parkhill, J og Turner, AK og Johnson, TJ og Thomson, NR og Smith, SGJ og Henderson, IR http://espace.library.uq.edu.au/view/UQ:103752 2007-08-23T00:00:00Z Rudiyansyah, .. og Garson, M J http://espace.library.uq.edu.au/view/UQ:98126 2007-08-24T00:00:00Z Seib, K. L. og Tseng, Hsing-Ju og McEwan, A. G. og Jennings, M. P. http://espace.library.uq.edu.au/view/UQ:58946 A comparative study of the high energy radiation resistance to formation of radicals in two pairs of polymers is reported. In one pair of polymers the phenyl groups containing the imide rings are separated by an ether linkage and in the other pair they are separated by an hexafluoroisopropylidine group. Two of the polymers contained aromatic amine units linked through an ether linkage and the other two polymers contained a trifluoromethyl biphenyl diamine. The polymers were shown to retain a high level of transparency in the visible region following radiolysis to doses as high as 8 Gy. ESR studies of the resistance to radical formation on radiolysis. at 77 K revealed that the polymers containing ether linkages were more stable than their fluorinated analogues, but all were less stable than Kapton (R). (C) 2001 Elsevier Science Ltd. All rights reserved. 2007-08-14T00:00:00Z Devasahayam, S. og Hill, D. J. T. og Connell, J. W. http://espace.library.uq.edu.au/view/UQ:110429 Melioidosis is caused by the Gram-negative bacillus Burkholderia pseudomallei. Most clinical reports of disease are from south-east Asia and northern Australia. The organism is intrinsically resistant to most commonly available antibiotics. Standard therapy includes ceftazidime either alone or in combination with co-trimoxazole. The clinical advantage in adding co-trimoxazole has never been determined; nor has the activity of newer, fourth-generation cephalosporins, such as cefepime, been studied in the treatment of this condition. BALB/c mice have been shown to represent an animal model of melioidosis. This animal model was used in this study to compare the efficacy of ceftazidime and cefepime alone or with co-trimoxazole, in the therapy of melioidosis. Antibiotic levels in the mice were determined by HPLC, and dosing was modified to keep plasma antibiotic levels at or above the MIC for the organism-antibiotic combination for a significant part of a 12 h period. Bacterial load, as determined by splenic counts, showed that ceftazidime in combination with co-trimoxazole was the most effective therapeutic option. The animal model described in this study can be used as a preliminary evaluation of therapeutic options for melioidosis. 2007-09-19T00:00:00Z Ulett, Glen C. og Hirst, Robert og Bowden, Bruce og Powell, Kellie og Norton, Robert http://espace.library.uq.edu.au/view/UQ:110057 Melioidosis is caused by the Gram-negative soil saprophyte, Burkholderia pseudomallei and is endemic in tropical and subtropical regions of southeast Asia and northern Australia. Cotrimoxazole has been traditionally used for the therapy of melioidosis despite results indicating resistance often produced in the disc diffusion test against B. pseudomallei. This inconsistency was addressed by comparing this method with the agar dilution, Microscan and E-test methods. The results demonstrated that by disc diffusion, 41.3% of 80 B. pseudomallei clinical isolates tested were susceptible to cotrimoxazole, whereas the Microscan, agar dilution and the, E-test demonstrated 92.5, 90 and 97.5% of the isolates to be susceptible, respectively. These results indicate that an MIC based method is required to test the susceptibility of B. pseudomallei against cotrimoxazole. (C) 2002 Published by Elsevier Science B.V. and International Society of Chemotherapy. 2007-09-19T00:00:00Z Peter Piliouras og Ulett, Glen C. og Ashhurst-Smith, Christopher og Hirst, Robert G. og Norton, Robert E. http://espace.library.uq.edu.au/view/UQ:218732 2010-10-19T00:00:00Z Czerniec, S.A. og Ward, L.C. og Meerkin, J. og Refshauge, K. og Kilbreath, S. http://espace.library.uq.edu.au/view/UQ:243264 2011-07-05T00:00:00Z Lin, S.K. og Lambert, J.R. og Schembri, M. og Nicholson, L. og Finlay, M. og Wong, C. og Coulepis, A. http://espace.library.uq.edu.au/view/UQ:35166 Elevated concentrations of plasma proinflammatory cytokines have been detected in patients with alcoholic hepatitis (AH) and in a model of lipopolysaccharide-induced hepatitis in ethanol-fed Wistar rats. These cytokines have been implicated in the pathogenesis of the liver damage. Considering the likely involvement of the immune system in AH, and the frequent use of Lewis rats in autoimmune disease models, Lewis rats were examined in the model to determine whether they would more closely mimic the immune status of a chronic alcoholic and be a preferable strain for use in future experiments. Lipopolysaccharide-induced hepatic tumor necrosis factor-cu, interleukin-1 alpha, interleukin-1 beta, and interleukin-6 mRNA expression was examined in both rat strains. The overall pattern of histological (panlobular piecemeal necrosis) and biochemical liver damage (plasma ALT levels), and cytokine expression was similar in both strains. Thus, it would appear that, despite the known susceptibility of Lewis rats to autoimmune phenomena, they do not respond to the experimental regime significantly better than Wistar rats. This study confirms that unknown mediators are contributing to the liver damage seen in this model and possibly in AH. 2007-08-13T00:00:00Z Pennington, HL og Wilce, PA og Worrall, S http://espace.library.uq.edu.au/view/UQ:110203 Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The importance of the accuracy of the simulation versus the amount of sampling of phase space has also been assessed by comparing different length simulations performed with different time step schemes. A nine-residue peptide from the protein HPr of index. E. Coli was used as a test system. The work shows that, in this case, single conformations or a limited ensemble of configurations are insufficient to properly describe the behavior of the peptide and that different approaches to incorporate molecular motions lead to significant differences in the cross-relaxation rates calculated. The correlation between the cross-relaxation rates calculated from simulations performed with different time step schemes was high and increased with increasing simulation length indicating that the extent of sampling is more important than the details of the atomic motion. 2007-09-19T00:00:00Z Feenstra, K. A. og Peter, C. og Scheek, R. M. og van Gunsteren, W. F. og Mark, A. E. http://espace.library.uq.edu.au/view/UQ:74110 Various marker systems exist for genetic analysis of horticultural species. Isozymes were first applied to the woody perennial nut crop, macadamia, in the early 1990s. The advent of DNA markers saw the development, for macadamia, of STMS (sequence-tagged microsatellite site), RAPD (randomly amplified polymorphic DNA), and RAF (randomly amplified DNA fingerprinting). The RAF technique typically generates dominant markers, but within the dominant marker profiles, certain primers also amplify multi-allelic co-dominant markers that are suspected to be microsatellites. In this paper, we confirm this for one such marker, and describe how RAF primers can be chosen that amplify one or more putative microsatellites. This approach of genotyping anonymous microsatellite markers via RAF is designated RAMiFi (randomly amplified microsatellite fingerprinting). Several marker systems were compared for the type, amount, and cost-efficiency of the information generated, using data from published studies on macadamia. The markers were also compared for the way they clustered a common set of accessions. The RAMiFi approach was identified as the most efficient and economical. The availability of such a versatile tool offers many advantages for the genetic characterisation of horticultural species. 2007-08-15T00:00:00Z Peace, C. P. og Vithanage, V. og Neal, J. og Turnbull, C. G. N. og Carroll, B. J. http://espace.library.uq.edu.au/view/UQ:34740 The common approach of bioelectrical impedance analysis to estimate body water uses a wrist-to-ankle methodology which, although not indicated by theory, has the advantage of ease of application particularly for clinical studies involving patients with debilitating diseases. A number of authors have suggested the use of a segmental protocol in which the impedances of the trunk and limbs are measured separately to provide a methodology more in keeping with basic theory. The segmental protocol hits not, however, been generally adopted, partly because of the increased complexity involved in its application, and partly because studies comparing the two methodologies have not clearly demonstrated a significant improvement from the segmental methodology. We have conducted a small pilot study involving ten subjects to investigate the efficacy of the two methodologies in a group of normal subjects. The study did not require the independent measure of body water, by for example isotope dilution, as the subjects were maintained in a state of constant hydration with only the distribution between limbs and trunk changing as a result of change in posture. The results demonstrate a significant difference between the two methodologies in predicting the expected constancy of body water in this study, with the segmental methodology indicating a mean percentage change in extracellular water of -2.2%; which was not significantly different from the expected null result, whereas the wrist-to-ankle methodology indicated a mean percentage change in extracellular water of -6.6%. This is significantly different from the null result, and from the value obtained from the segmental methodology (p = 0.006). Similar results were obtained using estimates of total body water from the two methodologies. (C) 1998 Elsevier Science Ltd. All rights reserved. 2007-08-13T00:00:00Z Thomas, BJ og Cornish, BH og Ward, LC og Patterson, MA http://espace.library.uq.edu.au/view/UQ:292453 2013-03-01T10:44:21Z Moore, Evan G. og Grilj, Jakob og Vauthey, Eric og Ceroni, Paola http://espace.library.uq.edu.au/view/UQ:132542 Specimens of the Indo-Pacific sponge Acanthella cavernosa Dendy collected from locations along the Eastern coastline of Australia have been shown to contain a range of sesquiterpenes including isothiocyanate 1, isocyanide 10, and the isocyanates 15 and 22. These metabolite studies have provided a basis for chemical comparisons between sponge populations from different geographic locations and between individual specimens collected from a single location. 2008-03-18T00:00:00Z Jumaryatno, Pinus og Stapleton, Bronwin L. og Hooper, John N. A. og Brecknell, Douglas J. og Blanchfield, Joanne T. og Garson, Mary J. http://espace.library.uq.edu.au/view/UQ:97094 2007-08-24T00:00:00Z Thomas, B.J. og Cornish, B. H. og Pattemore, M.J. og Jacobs, M. og Ward, L. C. http://espace.library.uq.edu.au/view/UQ:65794 Theory supports the use of a segmental methodology (SM) for bioimpedance analysis (BIA) of body water (BW). However, previous studies have generally failed to show a significant improvement when the SM is used in place of a whole-body methodology. A pilot study was conducted to compare the two methodologies in control and overweight subjects. BW of each subject was measured by D2O dilution and also estimated from BIA measurements. Bland and Altman analysis was used to compare the two values of BW. The SM resulted in a small but not significantly improved limits of agreement of measured and BIA estimated BW (psimilar to0.3). This and the results of previous studies suggest that improvements in prediction of BW obtained from application of the SM may be intrinsically small and may not justify the additional effort in application. 2007-08-15T00:00:00Z Thomas, B. J. og Cornish, B. H. og Pattemore, M. J. og Jacobs, M. og Ward, L. C. http://espace.library.uq.edu.au/view/UQ:34741 2007-08-13T00:00:00Z Stroud, DB og Cornish, BH og Thomas, BJ og Ward, LC http://espace.library.uq.edu.au/view/UQ:137127 Cercariae capricornia I–VI, six new cercariae putatively identified as belonging to the Acanthocolpidae, are described and named from prosobranch gastropods of the family Nassariidae collected from the intertidal zone in the Capricornia region, Central Queensland, Australia. Four species are reported from Nassarius olivaceus and two from N. dorsatus. The cercariae have a unique and complex three-dimensional body shape, including a keel, which differentiates them from previously described acanthocolpid cercariae. These are the first cercariae to be described from these gastropods. 2008-05-01T00:00:00Z Barnett, Leonie J. og Smales, Leslie R. og Cribb, Thomas H.