Upgrades to the ion cyclotron emission diagnostic on the DIII-D tokamak.

The ion cyclotron emission diagnostic on the DIII-D tokamak comprises seven single-turn loops that measure high-frequency (1-100 MHz) magnetic field fluctuations that are often excited by energetic particles in the plasma. The raw voltage signals induced in the loops in response to these fluctuations travel through a series of cables, isolation transformer DC blocks, low-pass filters, and finally a digitizer before being analyzed in frequency space. The diagnostic has been recently upgraded, most notably to include four additional graphite tile loops and a new eight-channel digitizer. The previous three loops are all on the low-field side of the tokamak. The measurement capabilities of the system have been expanded by the addition of a new horizontally oriented loop on the low-field side, an additional toroidal loop on the low-field side, and two toroidal loops on the high-field side. These loops will be used to provide approximate mode polarization, improved toroidal mode number calculations, and information on modes in inward-shifted plasmas, respectively.

Perceptions of anthrax in livestock from Victorian dairy farmers in the Goulburn-Murray region of Victoria, Australia.

To inform future anthrax surveillance and response activities and to revitalise the communication strategy for producers and their communities, seven dairy farmers in the Goulburn-Murray region of Victoria participated in a Design Thinking process to create a better method to share information about the annual probability of anthrax in their region. Design Thinking is a structured, user-centric design process that begins with intentionally un-structured interviews. Following each interview, transcripts are disassembled into common themes identified by clustering similar statements from these interviews. This short contribution presents these themes re-framed into eight core statements. These statements provide a framework for the remainder of the Design Thinking process but in isolation provide a reference for stake-holding agencies seeking to maximise farmer participation in surveillance programs for early anthrax detection, to encourage active farmer participation during a response and to minimise any anthrax-associated stigma by affected farmers post-response.

AAV ancestral reconstruction library enables selection of broadly infectious viral variants.

Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV's evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes and, in general, ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not use sialic acids, galactose or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19- to 31-fold higher gene expression in the muscle compared with AAV1, a clinically used serotype for muscle delivery, highlighting their promise for gene therapy.

No evidence of Mycobacterium avium subsp. paratuberculosis in in vitro produced cryopreserved embryos derived from subclinically infected cows.

The aim of the project was to ascertain if Mycobacterium avium subsp. paratuberculosis (Map) could be cultured from frozen-thawed in vitro produced (IVP) embryos derived from cows with subclinical Johne's disease (JD). Straws of 109 IVP embryos were obtained from 267 cumulus-oocyte-complexes (COCs) collected from 12 clinically normal cows in which antibodies against Map were detected in blood by an enzyme-linked immunosorbent assay (ELISA). These embryos were processed, washed using the standard protocol as described by the International Embryo Transfer Society (IETS) and frozen in a commercial IVP embryo laboratory. Of the 12 donor cows, 11 had histopathological or bacteriological evidence of infection at post-mortem inspection. The frozen embryos were thawed and the contents of the straws were cultured using the radiometric mycobacterial culture method. No Map was detected in any of the 109 embryos or freezing media. This suggests that the use of in vitro produced and cryopreserved embryos derived from cows with subclinical JD poses very low, if any, risk of spreading infection to susceptible animals.

A grid-enabled lightweight computational steering client: a .NET PDA implementation.

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world. These grid resources comprise specialized distributed three-dimensional visualization environments through to massive computational systems. The scientist usually accesses these resources from reasonably high-end desktop computers. Even though most modern desktop computers are provided with reasonably powerful three-dimensional graphical hardware, not all scientific applications require high-end three-dimensional visualization because the data of interest is essentially numerical or two-dimensional graphical data. For these applications, a much simpler two-dimensional graphical displays can be used. Since large jobs can take many hours to complete the scientist needs access to a technology that will allow them to still monitor and control their job while away from their desks. This paper describes an effective method of monitoring and controlling a set of chained computer simulations by means of a lightweight steering client based on a small personal digital assistant (PDA). The concept of using a PDA to steer a series of computational jobs across a supercomputing resource may seem strange at first but when scientists realize they can use these devices to connect to their computation wherever there is a wireless network (or cellular phone network) the concept becomes very compelling. Apart from providing a much needed easy-to-use interface, the PDA-based steering client has the benefit of freeing the scientist from the desktop. It is during this monitoring stage that the hand-held PDA client is of particular value as it gives the application scientist greater freedom to leave his or her desk but still communicate with their simulation, with the proviso that they remain within the range of a wireless network.

Infection rates in reactors to an absorbed ELISA used in a test and cull program for bovine Johne's disease.

OBJECTIVE: To determine the proportion of cattle, whose sera gave positive reactions in a commercial enzyme linked immunosorbent assay (ELISA) for bovine Johne's disease, that were confirmed infected with Mycobacterium avium subsp paratuberculosis by histology and culture of tissues. PROCEDURE: Dairy cattle (n = 493) from the Echuca district of Victoria, whose sera were positive in the ELISA, were slaughtered at an abattoir where standard specimens were collected for histology and culture. Only if samples were histologically negative were further samples submitted for culture. RESULTS: The proportion of cattle in which infection was confirmed increased from 70.4% in 1996 to 89.4% in 2001 giving an overall confirmation rate of 79.9%. This was mainly because more reactors were confirmed by culture each year, the proportion increasing from 0% in 1997 to 27.5% in 2000 but decreasing to 16.7% in 2001. If all unconfirmed reactors were presumed to be uninfected, the minimum specificity of the ELISA was 99.62%. There were no significant differences between the age groups in the proportion confirmed infected. CONCLUSION: Confirmation rates and specificity of the ELISA were high when used in a typical JD-infected Victorian dairy cattle population. Imperfect sensitivity of histology and culture and the selection of reactors which favoured more false positives, means the estimates were probably conservative. Confirmation rates were not affected by age of ELISA reactor.

A "Long Indel" model for evolutionary sequence alignment.

We present a new probabilistic model of sequence evolution, allowing indels of arbitrary length, and give sequence alignment algorithms for our model. Previously implemented evolutionary models have allowed (at most) single-residue indels or have introduced artifacts such as the existence of indivisible "fragments." We compare our algorithm to these previous methods by applying it to the structural homology dataset HOMSTRAD, evaluating the accuracy of (1) alignments and (2) evolutionary time estimates. With our method, it is possible (for the first time) to integrate probabilistic sequence alignment, with reliability indicators and arbitrary gap penalties, in the same framework as phylogenetic reconstruction. Our alignment algorithm requires that we evaluate the likelihood of any specific path of mutation events in a continuous-time Markov model, with the event times integrated out. To this effect, we introduce a "trajectory likelihood" algorithm (Appendix A). We anticipate that this algorithm will be useful in more general contexts, such as Markov Chain Monte Carlo simulations.

Using guide trees to construct multiple-sequence evolutionary HMMs.

MOTIVATION: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree. METHODS: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM. RESULTS: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.

Pairwise RNA structure comparison with stochastic context-free grammars.

Pairwise stochastic context-free grammars ("Pair SCFGs") are powerful tools for finding conserved RNA structures, but unconstrained alignment to Pair SCFGs is prohibitively expensive. We develop versions of the Pair SCFG dynamic programming algorithms that can be conditioned on precomputed structures, significantly reducing the time complexity of alignment. We have implemented these algorithms for general Pair SCFGs in software that is freely available under the GNU Public License.

An expectation maximization algorithm for training hidden substitution models.

We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the Pfam database. Measuring the accuracy of multiple alignment algorithms with reference to BAliBASE (a database of structural reference alignments) our substitution matrices consistently outperform the PAM series, with the improvement steadily increasing as up to four hidden site classes are added. We discuss several applications of this algorithm in bioinformatics.

Evolutionary HMMs: a Bayesian approach to multiple alignment.

MOTIVATION: We review proposed syntheses of probabilistic sequence alignment, profiling and phylogeny. We develop a multiple alignment algorithm for Bayesian inference in the links model proposed by Thorne et al. (1991, J. Mol. Evol., 33, 114-124). The algorithm, described in detail in Section 3, samples from and/or maximizes the posterior distribution over multiple alignments for any number of DNA or protein sequences, conditioned on a phylogenetic tree. The individual sampling and maximization steps of the algorithm require no more computational resources than pairwise alignment. METHODS: We present a software implementation (Handel) of our algorithm and report test results on (i) simulated data sets and (ii) the structurally informed protein alignments of BAliBASE (Thompson et al., 1999, Nucleic Acids Res., 27, 2682-2690). RESULTS: We find that the mean sum-of-pairs score (a measure of residue-pair correspondence) for the BAliBASE alignments is only 13% lower for Handelthan for CLUSTALW(Thompson et al., 1994, Nucleic Acids Res., 22, 4673-4680), despite the relative simplicity of the links model (CLUSTALW uses affine gap scores and increased penalties for indels in hydrophobic regions). With reference to these benchmarks, we discuss potential improvements to the links model and implications for Bayesian multiple alignment and phylogenetic profiling. AVAILABILITY: The source code to Handelis freely distributed on the Internet at http://www.biowiki.org/Handel under the terms of the GNU Public License (GPL, 2000, http://www.fsf.org./copyleft/gpl.html).

Non-lytic extraction and characterisation of receptors for multiple strains of rotavirus.

To characterise the cellular receptors for rotavirus, we used the detergent octyl-beta-D-glucopyranoside (octyl-glucoside/OG) to extract the receptors for bovine, simian, porcine and human rotaviruses from MA104 and HT29 cells. An octyl-glucoside concentration of 0.2% dramatically reduced the susceptibility of treated cells to infection, while leaving them metabolically active, and as a result the depleted receptors were able to regenerate. Periodate treatment of the MA104 and HT29 octyl-glucoside extracts significantly decreased the ability of these extracts to neutralise rotavirus infectivity, revealing carbohydrate as component of the extracted receptors for Wa and NCDV. Treatment of MA104 cells with the metabolic inhibitors tunicamycin, deoxymannojirimycin and BenzylGalNAc suggested N-linked carbohydrate may be more important than O-linked in infection by some strains of rotavirus. Furthermore, by including cycloheximide during the regeneration of depleted receptors we found evidence that porcine rotavirus CRW8 may use a glycolipid-based receptor, while NCDV and Wa use a glycoprotein. The regenerating properties of the rotavirus receptors allowed repeated harvesting of cell surface molecules using octyl-glucoside on consecutive days, and these extracts were used to visualise virus binding in a virus overlay protein blot assay (VOPBA). Using VOPBAs, we observed both Wa and NCDV appear to recognise proteins of approximately the same molecular weight present on MA104 and HT29 cells.

Selection of rotavirus VP4 cell receptor binding domains for MA104 cells using a phage display library.

Rotavirus infection of host cells, like other viruses, is a complex process that has not been fully elucidated, and much attention has been focused on the regions of the viral attachment protein, VP4, that are involved in binding to the cellular receptor. In this study, phage display technology was employed to generate a g3p VP4 gene-targeted phage display peptide library using the porcine rotavirus strain CRW8, and a method was optimised for panning this library on adherent MA104 cells to identify receptor binding domains. Recombinant phage that displayed expressed peptides from both the rotavirus VP4 trypsin cleavage products VP8* and VP5* were selected, and while some of the phage clones contained insert sequences from regions of VP4 implicated previously in cell binding and infection, new domains were also identified. In all, four regions within VP8* and six regions of VP5* were selected by panning. To our knowledge, this paper is the first description of using a gene-targeted phage display library to identify receptor binding domains on viral proteins.

Synthesis and biological evaluation of sialylmimetics as rotavirus inhibitors.

Rotaviruses cause severe gastroenteritis in infants and are estimated to be responsible for over 600 000 deaths annually, primarily in developing countries. The development of potential inhibitors of this virus is therefore of great interest, particularly since the safety and efficacy of rotaviral vaccines has recently been questioned. This study describes the synthesis of a variety of compounds that can be considered as mimetics of N-acetylneuraminic acid thioglycosides and the subsequent in vitro biological evaluation of these sialylmimetics as inhibitors of rotaviral infection. Our results show that readily accessible carbohydrate-based compounds have the potential to act as inhibitors of rotaviral replication in vitro, presumably through inhibition of the rotaviral adhesion process.

Are changes in left ventricular volume as measured with the biplane Simpson's method predominantly related to changes in its area or long axis in the prognostic evaluation of remodelling following a myocardial infarction?

AIMS: Two-dimensional (2D) echocardiography has been widely applied to measure left ventricular volumes with the biplane Simpson's method in the assessment of left ventricular remodelling following an acute myocardial infarction. This volume formula is based upon tracings of endocardium and measurement of long axis on left ventricular images. In the present follow-up study of post-myocardial infarction patients we evaluated the prognostic impact of changes in left ventricular areas and geometry versus long axis to determine if only long-axis measurements may be used for prognostic purposes. METHODS AND RESULTS: Two-dimensional echocardiographic video recordings of the apical four-chamber and long-axis views were obtained in 756 patients 2--7 days and 3 months following an acute myocardial infarction. All videotapes were sent to a core laboratory and left ventricular volumes were measured with the biplane Simpson's method in end-diastole and end-systole. During the first 3 months 44 patients had suffered one of the following end-points and were excluded: cardiac death, recurrent myocardial infarction, heart failure or chronic arrhythmia. Over a period of 3--24 months 58 such end-points occurred. With the Cox proportional hazards model the increase in left ventricular systolic volume was the strongest predictor for such events (Chi-square 18.5, P<0.0001), followed by an increase in end-systolic area (Chi-square 17.0, P<0.0001) and end-systolic spherity index (Chi-square 8.74,P =0.003). The increase in end-systolic long axis had only a borderline predictive value (Chi-square 4.3, P=0.04). The change in long-axis shortening from end-diastole to end-systole had no significant predictive value at all. CONCLUSION: In the studied population changes in left ventricular area and geometry, but not in the long axis, were mainly related to cardiac morbidity. The proper assessment of changes in left ventricular dimensions should therefore be based upon tracings of the area and not on long axis measurements only.

Rotavirus infection of MA104 cells is inhibited by Ricinus lectin and separately expressed single binding domains.

Various lectins were tested for blocking rotavirus infection of MA104 cells and it was observed that galactose-specific lectins were the most inhibitory. Of these Ricinus agglutinin was able to inhibit infection (by human and animal strains) at concentrations as low as 10(-9) M. In addition, in a virus overlay protein blot assay Ricinus agglutinin competed with simian rotavirus SA11 for binding to solubilized MA104 proteins. Amino acid sequence comparisons revealed similarity between the ricin toxin B subunit (which contains two separate carbohydrate-binding motifs: single binding domains (SBD) 1 and 2) and rotavirus spike protein VP4. A filamentous phage display system was used to independently express the two binding domains and while SBD1 inhibited infection of MA104 cells by CRW8, NCDV, and to a lesser extent Wa, SBD2 blocked only CRW8 and NCDV infection. Furthermore inhibition of CRW8 infection was a direct result of phage inhibiting virus attachment to cells. When amino acid 248 within SBD2 was mutated from the ricin toxin to the Ricinus agglutinin sequence this phage clone showed reduced binding to galactose and was no longer able to inhibit virus infection. Thus, rotavirus recognizes galactose as an important component of the receptor on MA104 cells.

Finding regulatory elements using joint likelihoods for sequence and expression profile data.

A recent, popular method of finding promoter sequences is to look for conserved motifs upstream of genes clustered on the basis of expression data. This method presupposes that the clustering is correct. Theoretically, one should be better able to find promoter sequences and create more relevant gene clusters by taking a unified approach to these two problems. We present a likelihood function for a "sequence-expression" model giving a joint likelihood for a promoter sequence and its corresponding expression levels. An algorithm to estimate sequence-expression model parameters using Gibbs sampling and Expectation/Maximization is described. A program, called kimono, that implements this algorithm has been developed: the source code is freely available on the Internet.

Rotavirus VP7 epitope mapping using fragments of VP7 displayed on phages.

cDNA copies of the complete porcine rotavirus CRW-8 VP7 gene were randomly digested to fragments of about 30-60 or 30-500 base pairs by DNase1 in the presence of Mn(2+). The fragments were cloned and expressed in a filamentous phage fd-tet-derived vector to create specific-gene-related peptide libraries. Polyclonal antibodies were then used to pan the SGRP libraries for antibody-binding phages. Analysis of the phage isolates revealed that the majority (86%) of them only had a single insert. However, phages displaying composite inserts containing the VP7 antigenic regions A, B, and C, originally defined by neutralising monoclonal antibody escape mutants, were also isolated. Inserts containing A or C region peptide were found to contain extra sequences from the C region, while the B region epitope was linear and had additional sequence from either upstream or downstream. In addition a dominant and possibly non-neutralising VP7 epitope was identified around amino acids 263-270. One of the recreated antigenic epitopes has also been fused to the outer membrane protein A (OmpA) of Escherichia coli and shown to maintain its antigenicity. The results in this study may have significant implication for recreation of conformational epitopes and vaccine development.

Haloalkane dehalogenases: structure of a Rhodococcus enzyme.

The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic agents. Two general classes of dehalogenases have been reported from Xanthobacter and Rhodococcus. While these enzymes share 30% amino acid sequence identity, they have significantly different substrate specificities and halide-binding properties. We report the 1.5 A resolution crystal structure of the Rhodococcus dehalogenase at pH 5.5, pH 7.0, and pH 5.5 in the presence of NaI. The Rhodococcus and Xanthobacter enzymes have significant structural homology in the alpha/beta hydrolase core, but differ considerably in the cap domain. Consistent with its broad specificity for primary, secondary, and cyclic haloalkanes, the Rhodococcus enzyme has a substantially larger active site cavity. Significantly, the Rhodococcus dehalogenase has a different catalytic triad topology than the Xanthobacter enzyme. In the Xanthobacter dehalogenase, the third carboxylate functionality in the triad is provided by D260, which is positioned on the loop between beta7 and the penultimate helix. The carboxylate functionality in the Rhodococcus catalytic triad is donated from E141. A model of the enzyme cocrystallized with sodium iodide shows two iodide binding sites; one that defines the normal substrate and product-binding site and a second within the active site region. In the substrate and product complexes, the halogen binds to the Xanthobacter enzyme via hydrogen bonds with the N(eta)H of both W125 and W175. The Rhodococcusenzyme does not have a tryptophan analogous to W175. Instead, bound halide is stabilized with hydrogen bonds to the N(eta)H of W118 and to N(delta)H of N52. It appears that when cocrystallized with NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of C187.

Bacterial expression of the major antigenic regions of porcine rotavirus VP7 induces a neutralizing immune response in mice.

The outer capsid protein of rotavirus, VP7, is a major neutralization antigen. A chimeric protein comprising Escherichia coli (E. coli) outer membrane protein A (OmpA) and part of porcine rotavirus VP7 containing all three antigenic regions (217 amino acids) was expressed in Salmonella and E. coli as an outer-membrane associated protein. Mice immunized intraperitoneally or orally, respectively, with live E. coli or Salmonella cells expressing this chimeric protein produced antibodies against native VP7 as determined by enzyme-linked immunosorbent assays and neutralization tests. This indicates that the VP7 fragment from a porcine rotavirus which is antigenically similar to human rotavirus serotype 3, when expressed in bacteria as a chimeric protein, can form a structure resembling its native form at least in some of the major neutralization domains. These results indicate that the use of a live bacterial vector expressing rotavirus VP7 may represent a strategy for the development of vaccines against rotavirus-induced diarrhoea in infants.