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:235057 Cultured cells lose the ability of DNA synthesis, mitosis, and finally the ability of cell proliferation after they have undergone a finite number of population doublings in vitro, though the cells still maintain the basic metabolic process. This is termed replicative senescence. We review the prevalence of replicative senescence, summarize the features of senescent cells, and then focus on the links between systemic aging and replicative senescence. The present knowledge, albeit still incomplete, proposes that replicative senescence is a reflection of systemic aging at cell level, and it fully confirms replicative senescence as a good model for the research of systemic aging. 2011-03-11T00:00:00Z Zhao, Liang og Zhang, Zong Yo og Tong, Tan Jun http://espace.library.uq.edu.au/view/UQ:75556 The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport. Here, we show that both Osh6p and Osh7p interact with Vps4p, a member of the AAA ( ATPases associated with a variety of cellular activities) family. The coiled-coil domain of Osh7p was found to interact with Vps4p in a yeast two-hybrid screen and the interaction between Osh7p and Vps4p appears to be regulated by ergosterol. Deletion of VPS4 induced a dramatic increase in the membrane-associated pools of Osh6p and Osh7p and also caused a decrease in sterol esterification, which was suppressed by overexpression of OSH7. Lastly, overexpression of the coiled-coil domain of Osh7p (Osh7pCC) resulted in a multi-vesicular body sorting defect, suggesting a dominant negative role of Osh7pCC possibly through inhibiting Vps4p function. Our data suggest that a common mechanism may exist for AAA proteins to regulate the membrane association of yeast OSBP proteins and that these two protein families may function together to control subcellular lipid transport. 2007-08-15T00:00:00Z Wang, PH og Zhang, Y og Li, HZ og Chieu, HK og Munn, AL og Yang, HY http://espace.library.uq.edu.au/view/UQ:129044 Aard (alanine and arginine rich domain) is a gene of unknown function, previously reported to show sexually dimorphic expression in fetal mouse gonads. Here we describe the spatio-temporal expression profile of Aard during gonad development. The period of elevated mRNA expression coincides with early differentiation of the testis and is limited to Sertoli cells of the developing testis cords. Although low levels of Aard transcripts were detected in other tissues by quantitative RT-PCR assays, high levels of Aard expression is specific to the testis in both embryonic and adult mice. 2008-02-18T00:00:00Z Svingen, T og Beverdam, A og Verma, P og Wilhelm, D og Koopman, P http://espace.library.uq.edu.au/view/UQ:183387 Two isolates of a novel babuvirus causing "bunchy top" symptoms were characterised, one from abacá (Musa textilis) from the Philippines and one from banana (Musa sp.) from Sarawak (Malaysia). The name abacá bunchy top virus (ABTV) is proposed. Both isolates have a genome of six circular DNA components, each ca. 1.0-1.1 kb, analogous to those of isolates of Banana bunchy top virus (BBTV). However, unlike BBTV, both ABTV isolates lack an internal ORF in DNA-R, and the ORF in DNA-U3 found in some BBTV isolates is also absent. In all phylogenetic analyses of nanovirid isolates, ABTV and BBTV fall in the same clade, but on separate branches. However, ABTV and BBTV isolates shared only 79-81% amino acid sequence identity for the putative coat protein and 54-76% overall nucleotide sequence identity across all components. Stem-loop and major common regions were present in ABTV, but there was less than 60% identity with the major common region of BBTV. ABTV and BBTV were also shown to be serologically distinct, with only two out of ten BBTV-specific monoclonal antibodies reacting with ABTV. The two ABTV isolates may represent distinct strains of the species as they are less closely related to each other than are isolates of the two geographic subgroups (Asian and South Pacific) of BBTV. 2009-09-03T00:00:00Z Sharman, M. og Thomas, J.E. og Skabo, S. og Holton, T.A. http://espace.library.uq.edu.au/view/UQ:144620 We have developed a new 4-alkoxybenzyl-derived linker that anchors the C-terminal amino acid to the resin through the alpha-nitrogen atom. The linker allows BOC solid-phase peptide assembly and peptide cleavage using standard HF protocols. This linking strategy provides a versatile on-resin route to cyclic peptides and avoids the diketopiperazine formation that is prominent when using FMOC chemistry on backbone linkers. The linker was prepared by forming the aryl ether fi om 4-hydroxybenzaldehyde and bromovaleric acid. Subsequent reductive amination of the aldehyde with an allyl-protected amino acid eater and acylation of the resulting secondary amine provided the tertiary amide. After linking the amide to the resin, standard BOC SPPS, followed by allyl deprotection, cyclization, and HF cleavage gave cyclic peptides in high purity. To exemplify the strategy, the cytotoxic heptapeptide, stylostatin 1, was synthesized from two linear precursors. For comparison purposes, the yields of the on-resin and solution-phase cyclization were determined and found to be dependent upon the linear precursor. This linker technology provides new solid-phase avenues in accessing libraries of cyclic peptides. 2008-06-10T00:00:00Z Bourne, GT og Meutermans, WDF og Alewood, PF og McGeary, RP og Watson, AA og Smythe, ML http://espace.library.uq.edu.au/view/UQ:230870 Three new bastadins, bastadin 25 (1), 15-O-sulfonatobastadin 11 (2), and bastadin 26 (3), were isolated from a MeOH extract of the Australian marine sponge Ianthella flabelliformis. Their structures were determined by interpretation of 1D and 2D NMR spectra and mass spectrometry. Bastadin 26 (3) showed potent affinity for the guinea pig delta-opioid receptors with a K-i value of 100 nM. The other two bastadins had a 100-fold lower affinity. The three compounds were also tested for their affinity to guinea pig mu- and kappa-opioid receptors and shown to have either no affinity or only very weak affinity toward both of these apioid receptors. 2011-03-02T00:00:00Z Carroll, Anthony R. og Kaiser, Sonya M. og Davis, Rohan A. og Moni, Roger W. og Hooper, John N. A. og Quinn, Ronald J. http://espace.library.uq.edu.au/view/UQ:179280 Axon guidance by molecular gradients plays a crucial role in wiring up the nervous system. However, the mechanisms axons use to detect gradients are largely unknown. We first develop a Bayesian “ideal observer” analysis of gradient detection by axons, based on the hypothesis that a principal constraint on gradient detection is intrinsic receptor binding noise. Second, from this model, we derive an equation predicting how the degree of response of an axon to a gradient should vary with gradient steepness and absolute concentration. Third, we confirm this prediction quantitatively by performing the first systematic experimental analysis of how axonal response varies with both these quantities. These experiments demonstrate a degree of sensitivity much higher than previously reported for any chemotacting system. Together, these results reveal both the quantitative constraints that must be satisfied for effective axonal guidance and the computational principles that may be used by the underlying signal transduction pathways, and allow predictions for the degree of response of axons to gradients in a wide variety of in vivo and in vitro settings. 2009-07-14T00:00:00Z Mortimer, Duncan og Feldner, Julia og Vaughan, Timothy og Vetter, Irina og Pujic, Zac og Rosoff, William J. og Burrage, Kevin og Dayan, Peter og Richards, Linda J. og Goodhill, Geoffrey J. http://espace.library.uq.edu.au/view/UQ:208051 2010-07-18T00:00:00Z Boden, Mikael og Dellaire, Graham og Burrage, Kevin og Bailey, Timothy L. http://espace.library.uq.edu.au/view/UQ:253757 2011-09-30T00:00:00Z Subramaniam, G. og Ang, Kenny K. H. og Ng, Siewbee og Buss, Antony D. og Butler, Mark S. http://espace.library.uq.edu.au/view/UQ:112810 Mutations in the dysferlin (DYSF) and caveolin-3 (CAV3) genes are associated with muscle disease. Dysferlin is mislocalized, by an unknown mechanism, in muscle from patients with mutations in caveolin-3 (Cav-3). To examine the link between Cav-3 mutations and dysferlin mistargeting, we studied their localization at high resolution in muscle fibers, in a model muscle cell line, and upon heterologous expression of dysferlin in muscle cell lines and in wild-type or caveolin-null fibroblasts. Dysferlin shows only partial overlap with Cav-3 on the surface of isolated muscle fibers but co-localizes with Cav-3 in developing transverse (T)-tubules in muscle cell lines. Heterologously expressed dystrophy-associated mutant Cav3R26Q accumulates in the Golgi complex of muscle cell lines or fibroblasts. Cav3R26Q and other Golgi-associated mutants of both Cav-3 (Cav3P104L) and Cav-1 (Cav1P132L) caused a dramatic redistribution of dysferlin to the Golgi complex. Heterologously expressed epitope-tagged dysferlin associates with the plasma membrane in primary fibroblasts and muscle cells. Transport to the cell surface is impaired in the absence of Cav-1 or Cav-3 showing that caveolins are essential for dysferlin association with the PM. These results suggest a functional role for caveolins in a novel post-Golgi trafficking pathway followed by dysferlin. 2007-09-19T00:00:00Z Hernandez-Deviez, D. J. og Martin, S. og Laval, S. H. og Lo, H. P. og Cooper, S. T. og North, K. N. og Bushby, K. og Parton, RG http://espace.library.uq.edu.au/view/UQ:283108 Classical cadherin adhesion receptors influence tissue integrity in health and disease. Their biological function is intimately linked to the actin cytoskeleton. To date, research has largely focused on identifying the molecular mechanisms that physically couple cadherin to cortical actin filaments. However, the junctional cytoskeleton is dynamic. Recent developments in understanding how filament dynamics and organization in the junctional cytoskeleton are controlled provide new insights into how the actin cytoskeleton regulates cadherin junctions in health and disease. 2012-10-11T00:00:00Z Ratheesh, Aparna og Yap, Alpha S. http://espace.library.uq.edu.au/view/UQ:75275 The effects of 31 plant extracts, which most are traditionally used to treat ciguatera fish poisoning in the Pacific area, were Studied on the cytotoxicity of mouse neuroblastoma cells produced by ouabain, veratridine and/or brevetoxin-3 or Pacific ciguatoxin-1. The cell viability was determined using a quantitative colorimetric method. A marked cytotoxicity of seven of the 31 plant extracts studied, was observed. Despite this, these plant extracts were suspected to contain active compound(s) against the cytotoxicity produced by brevetoxin (2 extracts), brevetoxin, ouabain and/or veratridine (3 extracts), or only against that of ouabain and/or veratridine (2 extracts). Among the 24 plant extracts that exhibited by themselves no cytotoxicity, 22 were active against the effect of brevetoxin or against that of both veratridine and brevetoxin. similar results were obtained when the seven most active plant extracts were reassayed using ciguatoxin instead of brevetoxin. In conclusion, the present work reports the first activity assessment of some plant extracts, achieved in vitro on a quite large scale. The fact that 27 plant extracts were found to exert, in vitro, a protective effect against the action of ciguatoxin and/or brevetoxin, paves the way for finding new active compounds to treat ciguatera fish poisoning, provided these compounds also reverse the effects of sodium channel activators. (c) 2005 Elsevier Ltd. All rights reserved. 2007-08-15T00:00:00Z Garrec, R. B. L. og Benoit, E. og Sauviat, M. P. og Lewis, R. J. og Molgo, J. og Laurent, D http://espace.library.uq.edu.au/view/UQ:248934 2011-09-09T00:00:00Z Brownlee, R. T. C. og Sadek, M. og Craik, D. J. http://espace.library.uq.edu.au/view/UQ:279312 2012-08-24T15:13:43Z Celik, Nermin og Webb. Chaukke T. og Leyton, Denusse L. og Holt, Kathryn E. og Heinz, Eva og Gorrell, Rebecca og Kwok, Terry og Naderer, Thomas og Strugnell, Richard A. og Speed, Terence P. og Teasdale, Rohan D. og Likic, Valdimir A. og Lithgow, Trevor http://espace.library.uq.edu.au/view/UQ:186556 The Rel/NF-kB family of eukaryotic transcription factors bind DNA with high specificity and affinity as homo- or heterodimers to mediate a diverse range of biological processes. By comparison, the nuclear factor of activated T-cells (NFAT) family has been recognised as Rel homologues due to structural similarities between the DNA-binding domains, yet they bind DNA as lower-affinity monomers. The structural and functional overlap between the NF-kB and NFAT families suggests that they may be evolutionarily divergent from a common, monomeric ancestor but have evolved different mechanisms to achieve high-affinity binding to their target DNA sequences. In order to understand the origin of these mechanistic differences, we constructed two chimeric proteins, based on molecular modelling, comprising the DNA-binding domain of NFAT and the dimerisation domain of NF-kB p50, differing only in the position of the splice site. Biophysical characterisation of the wild-type and chimeric proteins revealed that one of the chimeras bound DNA as a high-affinity, NF-kB-like cooperative dimer, whilst the other bound as a lower-affinity, NFAT-like monomer, demonstrating the importance of the interdomain linker in controlling the intrinsic ability of NFATc to form dimers. In addition, we have studied the rate of exchange of monomers between preformed NF-kB dimers and have determined, for the first time, the intrinsic homodimerisation constant for NF-kB p50. These data support a model in which NF-kB proteins bind DNA both in vitro and in vivo as high-affinity preformed homo- or heterodimers, which in an unbound form can still exchange monomer units on a physiologically relevant timescale in vivo. c 2004 Elsevier Ltd. All rights reserved. 2009-11-17T00:00:00Z de Lumley, Marie og Hart, Darren J. og Cooper, Matthew A. og Symeonides, Stefan og Blackburn, Jonathon M. http://espace.library.uq.edu.au/view/UQ:241537 2011-05-30T00:00:00Z Ross, Ian http://espace.library.uq.edu.au/view/UQ:173914 2009-04-06T00:00:00Z De Jong-Curtain, Tanya A. og Parslow, Adam C. og Trotter, Andrew J. og Hall , Nathan E. og Verkade, Heather og Tabone, Tania og Christie, Elizabeth L. og Crowhurst, Meredith O. og Layton, Judith E. og Shepherd, Iain T. og Nixon, Susan J. og Parton, Robert G. og Zon. Leonard I. og Stainier, Didier Y.R. og Lieschke, Graham J. og Heath, Joan K. http://espace.library.uq.edu.au/view/UQ:270863 2012-03-21T00:00:00Z Nagaraj, Shivashankar H. og Reverter, Antonio http://espace.library.uq.edu.au/view/UQ:209167 2010-07-19T00:00:00Z Burrage, K og Burrage, PM og Belward, JA http://espace.library.uq.edu.au/view/UQ:179886 2009-08-18T00:00:00Z Malintan, Nancy og Nguyen, Tam H og Han, Liping og Latham, Catherine F. og Osborne, Shona L. og Wen, Peter og Lim, Siew, Joo, Tiffany og Sugita, Shuzo og Collins, Brett M. og Meunier, Frederic A. http://espace.library.uq.edu.au/view/UQ:275219 2012-06-04T12:29:51Z Ghosh, Shibaji K. og Somanadhan, Brinda og Tan, Kevin S.-W. og Butler, Mark S. og Lear, Martin J. http://espace.library.uq.edu.au/view/UQ:185070 Degradative studies have permitted an absolute stereochemistry to be assigned to the marine natural product puupehenone (1). On biosynthetic grounds 10 related co-metabolites were assigned to the same antipodal series. 2009-10-20T00:00:00Z Urban, Sylvia og Capon, Robert J. http://espace.library.uq.edu.au/view/UQ:209179 2010-07-19T00:00:00Z Pun, K. K. og Chan, W. L. og Lau, P. og Ho, P. W. M. og Wang, C. http://espace.library.uq.edu.au/view/UQ:286624 2012-12-02T00:00:00Z Muttenthaler, Markus og Dutertre, Sebastien og Wingerd, Joshua S. og Aini, John W. og Walton, Hugh og Alewood, Paul F. og Lewis, Richard J. http://espace.library.uq.edu.au/view/UQ:292213 2013-02-24T01:02:42Z Wang, Qian og Song, Fuhang og Xiao, Xue og Huang, Pei og Li, Li og Monte, Aaron og Abdel-Mageed, Wael M. og Wang, Jian og Guo, Hui og He, Wenni og Xie, Feng og Dai, Huanqin og Liu, Miaomiao og Chen, Caixia og Xu, Hao og Liu, Mei og Piggott, Andrew M. og Liu, Xueting og Capon, Robert J. og Zhang, Lixin http://espace.library.uq.edu.au/view/UQ:238523 2011-03-24T00:00:00Z Ivanova, Natalia og Tringe, Susannah G. og Liolios, Konstantinos og Liu, Wen-Tso og Morrison, Norman og Hugenholtz, Philip og Kyrpides, Nikos C. http://espace.library.uq.edu.au/view/UQ:63001 The 101 residue protein early pregnancy factor (EPF), also known as human chaperonin 10, was synthesized from four functionalized, but unprotected, peptide segments by a sequential thioether ligation strategy. The approach exploits the differential reactivity of a peptide-NHCH2CH2SH thiolate with XCH2CO-peptides, where X = Cl or I/Br. Initial model studies with short functionalized (but unprotected) peptides showed a significantly faster reaction of a peptide-NHCH2CH2SH thiolate with a BrCH2CO-peptide than with a CICH2CO-peptide, where thiolate displacement of the halide leads to chemoselective formation of a thioether surrogate for the Gly-Gly peptide bond. This rate difference was used as the basis of a novel sequential ligation approach to the synthesis of large polypeptide chains. Thus, ligation of a model bifunctional N-alpha-chloroacetyl, C-terminal thiolated peptide with a second N-alpha-bromoacetyl peptide demonstrated chemoselective bromide displacement by the thiol group. Further investigations showed that the relatively unreactive N-alpha-chloroacetyl peptides could be activated by halide exchange using saturated KI solutions to yield the highly reactive No-iodoacetyl peptides. These findings were used to formulate a sequential thioether ligation strategy for the synthesis of EPF, a 101 amino acid protein containing three Gly-Gly sites approximately equidistantly spaced within the peptide chain. Four peptide segments or cassettes comprising the EPF protein sequence (BrAc-[EPF 78-101] 12, ClAc-[EPF 58-75]-[NHCH2CH2SH] 13, ClAc-[EPF 30-55]-[NHCH2CH2SH] 14, and Ac-[EPF 1-27]-[NHCH2CH2SH] 15) of EPF were synthesized in high yield and purity using Boc SPPS chemistry. In the stepwise sequential ligation strategy, reaction of peptides 12 and 13 was followed by conversion of the N-terminal chloroacetyl functional group to an iodoacetyl, thus activating the product peptide for further ligation with peptide 14. The process of ligation followed by iodoacetyl activation was repeated to yield an analogue of EPF (EPF psi(CH2S)(28-29,56-57,76-77)) 19 in 19% overall yield. 2007-08-14T00:00:00Z Englebretsen, D. R. og Garnham, B. og Alewood, P. F. http://espace.library.uq.edu.au/view/UQ:286155 2012-11-23T18:56:59Z Vetter, Irina og Lewis, Richard J. http://espace.library.uq.edu.au/view/UQ:144612 The chemical synthesis of peptides and small proteins is a powerful complementary strategy to recombinant protein overexpression and is widely used in structural biology, immunology, protein engineering, and biomedical research. Despite considerable improvements in the fidelity of peptide chain assembly, side-chain protection, and postsynthesis analysis, a limiting factor in accessing polypeptides containing greater than 50 residues remains the time taken for chain assembly. The ultimate goal of this work is to establish highly efficient chemical procedures that achieve chain-assembly rates of approximately 10-15 residues per hour, thus underpinning the rapid chemical synthesis of long polypeptides and proteins, including cytokines, growth factors, protein domains, and small enzymes, Here we report Boc chemistry that employs O-(7-azabenzo-triazol-1-yl)-N,N,N',N'-tetramethyluronium hexafluorophosphate (HATU)/dimethyl sulfoxide in situ neutralization as the coupling agent and incorporates a protected amino acid residue every 5 min to produce peptides of good quality. This rapid coupling chemistry was successfully demonstrated by synthesizing several small to medium peptides, including the difficult C-terminal sequence of HIV-1 proteinase (residues 81-99); fragment 65-74 of the acyl carrier protein; conotoxin PnIA(A10L), a potent neuronal nicotinic receptor antagonist; and the proinflammatory chemotactic protein CP10, an 88-residue protein, by means of native chemical ligation, The benefits of this approach include enhanced ability to identify and characterize difficult couplings, rapid access to peptides for biological and structure-activity studies, and accelerated synthesis of tailored large peptide segments (<50 residues) for use in chemoselective ligation methods. 2008-06-10T00:00:00Z Miranda, LP og Alewood, PF http://espace.library.uq.edu.au/view/UQ:103653 Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods. 2007-08-23T00:00:00Z Burrage, Kevin og Mac, Shev og Tian, Tianhai http://espace.library.uq.edu.au/view/UQ:75719 Many growing networks possess accelerating statistics where the number of links added with each new node is an increasing function of network size so the total number of links increases faster than linearly with network size. In particular, biological networks can display a quadratic growth in regulator number with genome size even while remaining sparsely connected. These features are mutually incompatible in standard treatments of network theory which typically require that every new network node possesses at least one connection. To model sparsely connected networks, we generalize existing approaches and add each new node with a probabilistic number of links to generate either accelerating, hyperaccelerating, or even decelerating network statistics in different regimes. Under preferential attachment for example, slowly accelerating networks display stationary scale-free statistics relatively independent of network size while more rapidly accelerating networks display a transition from scale-free to exponential statistics with network growth. Such transitions explain, for instance, the evolutionary record of single-celled organisms which display strict size and complexity limits. 2007-08-15T00:00:00Z Gagen, M. J. og Mattick, J. S. http://espace.library.uq.edu.au/view/UQ:76337 2007-08-15T00:00:00Z Mattick, JS og Gagen, MJ http://espace.library.uq.edu.au/view/UQ:279265 2012-08-23T09:46:47Z Davies, Jamie A. og Little, Melissa H. og Aronow, Bruce og Armstrong, Jane og Brennan, Jane og Lloyd-MacGilp, Sue og Armit, Chris og Harding, Simon og Piu, Xinjun og Roochun, Yogmatee og Haggarty, Bernard og Houghton, Derek og Davidson, Duncan og Baldock, Richard http://espace.library.uq.edu.au/view/UQ:162350 The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to span the decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site crafted for a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide, the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein that results in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial termination complex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stop codon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix alpha5. The anticodon loop also makes contact with the base following the stop codon that is known to strongly influence termination efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. The mRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflect structural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiased SELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in its different binding conformations within the active centre of the ribosome. 2009-01-30T00:00:00Z Poole, Elizabeth S. og Young, David J. og Askarian-Amiri, Marjan E . og Scarlett, Debbie-Jane G. og Tate, Warren P. http://espace.library.uq.edu.au/view/UQ:183633 We devise explicit partitioned numerical methods for second–order-in-time scalar stochastic differential equations, using one Gaussian random variable per timestep. The construction proceeds by analysis of the stationary density in the case of constant-coefficient linear equations, imposing exact stationary statistics in the position variable and absence of correlation between position and velocity; the remaining error is in the velocity variable. A new two-stage “reverse leapfrog” method has good properties in the position variable and is symplectic in the limit of zero damping. Explicit new “Runge–Kutta leapfrog” methods are constructed, sharing the property that $q_{n+1}=q_n+\frac{1}{2}(p_n+p_{n+1})\Delta t$, whose mean-square velocity order increases with the number of stages. ©2009 Society for Industrial and Applied Mathematics 2009-09-04T00:00:00Z Burrage, Kevin og Lythe, Grant http://espace.library.uq.edu.au/view/UQ:183562 Human patients with Frasier syndrome express reduced levels of the +KTS isoforms of the developmental regulator WT1 and exhibit complete XY gonadal dysgenesis and male-to-female sex reversal. Mice with a targeted mutation that blocks production of these isoforms show a reduction in Sry mRNA in the gonad, but the molecular and cellular basis of this reduction has not been established. Using immunofluorescence analysis, we found a significantly lower level of SRY protein per cell in XY Wt1(+KTS)-null mouse gonads. We also found a reduced number of SRY-expressing cells, correlating with a decrease in cell proliferation at and near the coelomic epithelium at 11.5 dpc. No reduction in somatic cell numbers was seen in XX Wt1(+KTS)-null gonads, indicating that the effect of WT1 on cell proliferation is mediated by Sry. Sertoli cell differentiation was blocked in XY Wt1(+KTS)-null mouse gonads, as indicated by the loss of SOX9 and Fgf9 expression, but the addition of recombinant FGF9 to ex vivo gonad cultures rescued the mutant phenotype, as indicated by the induction of the Sertoli-cell specific marker anti-Müllerian hormone. Our data suggest that WT1(+KTS) is involved in the cell-autonomous regulation of Sry expression, which in turn influences cell proliferation and Sertoli cell differentiation via FGF9. Thus, sex reversal in Wt1(+KTS)-null mice and Frasier syndrome patients results from a failure of Sertoli cells both to fully differentiate and to reach sufficient numbers to direct testis development. 2009-09-04T00:00:00Z Bradford, Stephen T. og Wilhelm, Dagmar og Bandiera, Roberto og Vidal, Valerie og Schedl, Andreas og Koopman, Peter http://espace.library.uq.edu.au/view/UQ:129879 Neuronal nAChRs are a diverse family of pentameric ion channels with wide distribution throughout cells of the nervous and immune systems. However, the role of specific subtypes in normal and pathological states remains poorly understood due to the lack of selective probes. Here, we used a binding assay based on acetylcholine-binding protein (AChBP), a homolog of the nicotinic acetylcholine ligand- binding domain, to discover a novel alpha-conotoxin (alpha-TxIA) in the venom of Conus textile. alpha-TxIA bound with high affinity to AChBPs from different species and selectively targeted the alpha(3)beta(2) nAChR subtype. A co-crystal structure of Ac- AChBP with the enhanced potency analog TxIA(A10L), revealed a 201 backbone tilt compared to other AChBP - conotoxin complexes. This reorientation was coordinated by a key salt bridge formed between Arg5 (TxIA) and Asp195 (Ac-AChBP). Mutagenesis studies, biochemical assays and electrophysiological recordings directly correlated the interactions observed in the co-crystal structure to binding affinity at AChBP and different nAChR subtypes. Together, these results establish a new pharmacophore for the design of novel subtype-selective ligands with therapeutic potential in nAChR-related diseases. 2008-02-18T00:00:00Z Dutertre, S. og Ulens, C og Buttner, R og Fish, A og van Elk, R og Kendel, Y og Hopping, G. og Alewood, P. F. og Schroeder, C. og Nicke, A og Smit, AB og Sixma, TK og Lewis, R. J. http://espace.library.uq.edu.au/view/UQ:240073 2011-04-07T00:00:00Z Spillman, Natalie J. og Allen, Richard J. W. og Kirk, Kiaran http://espace.library.uq.edu.au/view/UQ:240081 2011-04-07T00:00:00Z Saliba, Kevin J. og Allen, Richard J. W. og Zissis, Stephanie og Bray, Patrick G. og Ward, Stephen A. og Kirk, Kiaran http://espace.library.uq.edu.au/view/UQ:34610 The acid-mediated transformation of syn and anti methylene interrupted cis,cis and cis,trans bisepoxides to tetrahydrofurans is high yielding, and demonstrates both regioselectivity and stereoselectivity. Trans,trans methylene interrupted bisepoxides do not yield tetrahydrofurans under the same conditions. 2007-08-13T00:00:00Z Capon, RJ og Barrow, RA http://espace.library.uq.edu.au/view/UQ:183423 2009-09-03T00:00:00Z Frith, Martin C. og Valen, Eivind og Krogh, Anders og Hayashizaki, Yoshihide og Carninci, Piero og Sandelin, Albin http://espace.library.uq.edu.au/view/UQ:248985 2011-09-09T00:00:00Z Huang, Yen-Hua og Colgrave, Michelle L. og Kotze, Andrew C. og Craik, David J. http://espace.library.uq.edu.au/view/UQ:270729 A combined theoretical and experimental study of the vibrational absorption (VA)/IR, vibrational circular dichroism (VCD), Raman and Raman optical activity (ROA) spectra of l-histidine in aqueous solution has been undertaken to answer the questions (i) what are the species present and (ii) which conformers of the species are present under various experimental conditions. The VA spectra of l-histidine have been measured in aqueous solution and the spectral bands which can be used to identify both species (cation, zwitterion, anion) and conformer of the species have been identified and subsequently used to identify the species (zwitterion) and conformer (gauche minus minus, gauche minus plus for the side chain dihedral angles) present in solution at pH 7.6. The VCD spectral intensities have been used subsequently in combination with further theoretical studies to confirm the conclusions that have been arrived at by only analyzing the VA/IR spectra. Finally a comparison of measured Raman and ROA spectra of l-histidine with Raman and ROA spectral simulations for the conformers and species derived from the combined VA/IR and VCD experimental and theoretical work is presented as a validation of the conclusions arrived at from VA/IR and VCD spectroscopy. The combination of VA/IR and VCD with Raman and ROA is clearly superior and both sets of experiments should be performed. 2012-03-20T00:00:00Z Deplazes, E. og van Bronswijk, W. og Zhu, F. og Barron, L.D. og Ma, S. og Nafie, L.A. og Jalkanen, K.J. http://espace.library.uq.edu.au/view/UQ:255744 Obesity is a serious international health problem that increases the risk of several common diseases. The genetic factors predisposing to obesity are poorly understood. A genome-wide search for type 2 diabetes–susceptibility genes identified a common variant in the FTO (fat mass and obesity associated) gene that predisposes to diabetes through an effect on body mass index (BMI). An additive association of the variant with BMI was replicated in 13 cohorts with 38,759 participants. The 16% of adults who are homozygous for the risk allele weighed about 3 kilograms more and had 1.67-fold increased odds of obesity when compared with those not inheriting a risk allele. This association was observed from age 7 years upward and reflects a specific increase in fat mass. 2011-10-13T00:00:00Z Frayling, Timothy M. og Timpson, Nicholas J. og Weedon, Michael N. og Zeggini, Eleftheria og Freathy, Rachel M. og Lindgren, Cecilia M. og Perry, John R. B. og Elliott, Katherine S. og Lango, Hana og Rayner, Nigel W. og Shields, Beverley og Harries, Lorna W. og Barrett, Jeffrey C. og Ellard, Sian og Groves, Christopher J. og Knight, Bridget og Patch, Ann-Marie og Ness, Andrew R. og Ebrahim, Shah og Lawlor, Debbie A. og Ring, Susan M. og Ben-Shlomo, Yoav og Jarvelin, Marjo-Riitta og Sovio, Ulla og Bennett, Amanda J. og Melzer, David og Ferrucci, Luigi og Loos, Ruth J. F. og Barroso, Inês og Wareham, Nicholas J. og Karpe, Fredrik og Owen, Katharine R. og Cardon, Lon R. og Walker, Mark og Hitman, Graham A. og Palmer, Colin N. A. og Doney, Alex S. F.Graham A. og Morris, Andrew D. og Smith, George Davey og Hattersley, Andrew T. og McCarthy, Mark I. og Wellcome Trust Case Control http://espace.library.uq.edu.au/view/UQ:282238 2012-09-21T14:35:47Z Halai, Reena og Croker, Daniel E. og Suen, Jacky Y. og Fairlie, David P. og Cooper, Matthew A. http://espace.library.uq.edu.au/view/UQ:97813 2007-08-24T00:00:00Z Iqbal, M. J. og Maguire, T. L. og Meksem, K. og Yegaeshi, S. og Triwitayakorn, K. og Schulz, J. og Grimmond, S. M. og Gresshoff, P.M. og Lightfoot, D. http://espace.library.uq.edu.au/view/UQ:160196 This study evaluated GSK's combined DTPa-IPV vaccine (Infanrix™-IPV) given as a fifth consecutive acellular pertussis booster dose in conjunction with the second dose of MMR vaccine (Priorix™) in children aged 4–6 years. The immunogenicity and reactogenicity of this vaccine regimen was compared with separate injections of DTPa and IPV when given concomitantly with MMR. A cohort of 362 children previously primed with four doses of DTPa and OPV, and a single dose of MMR were randomized to receive either DTPa-IPV + MMR (N = 181) or DTPa + IPV + MMR (N = 181). Antibody concentrations were measured prior to and 1 month after the booster dose. After immunisation all subjects from both groups had seroprotective antibody levels against diphtheria, tetanus and the three poliovirus serotypes, ≥96% showed vaccine response to PT, FHA and PRN, all were seropositive to mumps and rubella, and all but one subject were seropositive to measles. Immunogenicity results for each component antigen were similar for DTPa-IPV and separately co-administered DTPa and IPV. Local reactions were common with 24.0% and 31.1% of children experiencing swelling >50 mm at the DTPa-IPV and DTPa injection sites, respectively. The DTPa-IPV combination did not increase the incidence or intensity of adverse events compared with separately administered DTPa + IPV. The response to the concomitantly administered MMR vaccine was similar in the two groups and similar to previously reported responses for a second dose of MMR. This combined DTPa-IPV vaccine has a similar reactogenicity profile to DTPa, is immunogenic when given as a booster dose at 4–6 years of age, and has no impact on the immunogenicity of a co-administered second dose of MMR vaccine. 2009-01-08T15:58:53Z Marshall, H. og Nolan, T. og Roberton, D. og Richmond, P. og Lambert, S. W. og Jacquet, J. M. og Schuerman, L. http://espace.library.uq.edu.au/view/UQ:39997 The recently discovered cyclotides kalata B1 and kalata B2 are miniproteins containing a head-to-tail cyclized backbone and a cystine knot motif, in which disulfide bonds and the connecting backbone segments form a ring that is penetrated by the third disulfide bond. This arrangement renders the cyclotides extremely stable against thermal and enzymatic decay, making them a possible template onto which functionalities can be grafted.We have compared the hydrodynamic properties of two prototypic cyclotides, kalata B1 and kalata B2, using analytical ultracentrifugation techniques. Direct evidence for oligomerization of kalata B2 was shown by sedimentation velocity experiments in which a method for determining size distribution of polydisperse molecules in solution was employed. The shape of the oligomers appears to be spherical. Both sedimentation velocity and equilibrium experiments indicate that in phosphate buffer kalata B1 exists mainly as a monomer, even at millimolar concentrations. In contrast, at 1.6 mM, kalata B2 exists as an equilibrium mixture of monomer (30%), tetramer (42%), octamer (25%), and possibly a small proportion of higher oligomers. The results from the sedimentation equilibrium experiments show that this self-association is concentration dependent and reversible. We link our findings to the three-dimensional structures of both cyclotides, and propose two putative interaction interfaces on opposite sides of the kalata B2 molecule, one involving a hydrophobic interaction with the Phe(6), and the second involving a charge-charge interaction with the Asp(25) residue. An understanding of the factors affecting solution aggregation is of vital importance for future pharmaceutical application of these molecules. 2007-08-13T00:00:00Z Nourse, A. og Trabi, M. og Daly, N. L. og Craik, D. J. http://espace.library.uq.edu.au/view/UQ:234022 2011-03-09T00:00:00Z Holmes, Rebecca og Williamson, Christine og Peters, Jo og Denny, Paul og Wells, Christine http://espace.library.uq.edu.au/view/UQ:38120 Protein kinases exhibit various degrees of substrate specificity. The large number of different protein kinases in the eukaryotic proteomes makes it impractical to determine the specificity of each enzyme experimentally. To test if it were possible to discriminate potential substrates from non-substrates by simple computational techniques, we analysed the binding enthalpies of modelled enzyme-substrate complexes and attempted to correlate it with experimental enzyme kinetics measurements. The crystal structures of phosphorylase kinase and cAMP-dependent protein kinase were used to generate models of the enzyme with a series of known peptide substrates and non-substrates, and the approximate enthalpy of binding assessed following energy minimization. We show that the computed enthalpies do not correlate closely with kinetic measurements, but the method can distinguish good substrates from weak substrates and non-substrates. Copyright (C) 2002 John Wiley Sons, Ltd. 2007-08-13T00:00:00Z Brinkworth, R. I. og Horne, J. og Kobe, B.