Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum

As part of a comparative mapping study between sugarcane and sorghum, a sugarcane cDNA clone with homology to the maize Rp1-D rust resistance gene was mapped in sorghum. The cDNA probe hybridised to multiple loci, including one on sorghum linkage group (LG) E in a region where a major rust resistance QTL had been previously mapped. Partial sorghum Rp1-D homologues were isolated from genomic DNA of rust-resistant and -susceptible progeny selected from a sorghum mapping population. Sequencing of the Rp1-D homologues revealed five discrete sequence classes: three from resistant progeny and two from susceptible progeny. PCR primers specific to each sequence class were used to amplify products from the progeny and confirmed that the five sequence classes mapped to the same locus on LG E. Cluster analysis of these sorghum sequences and available sugarcane, maize and sorghum Rp1-D homologue sequences showed that the maize Rp1-D sequence and the partial sugarcane Rp1-D homologue were clustered with one of the sorghum resistant progeny sequence classes, while previously published sorghum Rp1-D homologue sequences clustered with the susceptible progeny sequence classes. Full-length sequence information was obtained for one member of a resistant progeny sequence class (Rp1-SO) and compared with the maize Rp1-D sequence and a previously identified sorghum Rp1 homologue (Rph1-2). There was considerable similarity between the two sorghum sequences and less similarity between the sorghum and maize sequences. These results suggest a conservation of function and gene sequence homology at the Rp1 loci of maize and sorghum and provide a basis for convenient PCR-based screening tools for putative rust resistance alleles in sorghum.

Accelerating precursory activity within a class of earthquake analogue automata

A statistical fractal automaton model is described which displays two modes of dynamical behaviour. The first mode, termed recurrent criticality, is characterised by quasi-periodic, characteristic events that are preceded by accelerating precursory activity. The second mode is more reminiscent of SOC automata in which large events are not preceded by an acceleration in activity. Extending upon previous studies of statistical fractal automata, a redistribution law is introduced which incorporates two model parameters: a dissipation factor and a stress transfer ratio. Results from a parameter space investigation indicate that a straight line through parameter space marks a transition from recurrent criticality to unpredictable dynamics. Recurrent criticality only occurs for models within one corner of the parameter space. The location of the transition displays a simple dependence upon the fractal correlation dimension of the cell strength distribution. Analysis of stress field evolution indicates that recurrent criticality occurs in models with significant long-range stress correlations. A constant rate of activity is associated with a decorrelated stress field.

A new class of critical sets in Latin squares

Previously the process of finding critical sets in Latin squares has been inside cumbersome by the complexity and number of Latin trades that, must be constructed. In this paper we develop a theory of Latin trades that yields more transparent constructions. We use these Latin trades to find a new class of critical sets for Latin squares which are a product of the Latin square of order 2 with a. back circulant Latin square of odd order.

Receptor binding studies disclose a novel class of high-affinity inhibitors of the Escherichia coli FimH adhesin

Mannose-binding type 1 pili are important virulence factors for the establishment of Escherichia coli urinary tract infections (UTIs). These infections are initiated by adhesion of uropathogenic E. coli to uroplakin receptors in the uroepithelium via the FimH adhesin located at the tips of type 1 pili. Blocking of bacterial adhesion is able to prevent infection. Here, we provide for the first time binding data of the molecular events underlying type 1 fimbrial adherence, by crystallographic analyses of the FimH receptor binding domains from a uropathogenic and a K-12 strain, and affinity measurements with mannose, common mono- and disaccharides, and a series of alkyl and aryl mannosides. Our results illustrate that the lectin domain of the FimH adhesin is a stable and functional entity and that an exogenous butyl alpha- D-mannoside, bound in the crystal structures, exhibits a significantly better affinity for FimH (K-d = 0.15 muM) than mannose (K-d = 2.3 muM). Exploration of the binding affinities of alpha-D-mannosides with longer alkyl tails revealed affinities up to 5 nM. Aryl mannosides and fructose can also bind with high affinities to the FimH lectin domain, with a 100-fold improvement and 15-fold reduction in affinity, respectively, compared with mannose. Taken together, these relative FimH affinities correlate exceptionally well with the relative concentrations of the same glycans needed for the inhibition of adherence of type 1 piliated E. coli. We foresee that our findings will spark new ideas and initiatives for the development of UTI vaccines and anti-adhesive drugs to prevent anticipated and recurrent UTIs.

Tool support for executable documentation of Java class hierarchies

While object-oriented programming offers great solutions for today's software developers, this success has created difficult problems in class documentation and testing. In Java, two tools provide assistance: Javadoc allows class interface documentation to be embedded as code comments and JUnit supports unit testing by providing assert constructs and a test framework. This paper describes JUnitDoc, an integration of Javadoc and JUnit, which provides better support for class documentation and testing. With JUnitDoc, test cases are embedded in Javadoc comments and used as both examples for documentation and test cases for quality assurance. JUnitDoc extracts the test cases for use in HTML files serving as class documentation and in JUnit drivers for class testing. To address the difficult problem of testing inheritance hierarchies, JUnitDoc provides a novel solution in the form of a parallel test hierarchy. A small controlled experiment compares the readability of JUnitDoc documentation to formal documentation written in Object-Z. Copyright (c) 2005 John Wiley & Sons, Ltd.

Subtypes of Illicit Drug Users: A Latent Class Analysis of Data From an Australian Twin Sample

This article applies methods of latent class analysis (LCA) to data on lifetime illicit drug use in order to determine whether qualitatively distinct classes of illicit drug users can be identified. Self-report data on lifetime illicit drug use (cannabis, stimulants, hallucinogens, sedatives, inhalants, cocaine, opioids and solvents) collected from a sample of 6265 Australian twins (average age 30 years) were analyzed using LCA. Rates of childhood sexual and physical abuse, lifetime alcohol and tobacco dependence, symptoms of illicit drug abuse/dependence and psychiatric comorbidity were compared across classes using multinomial logistic regression. LCA identified a 5-class model: Class 1 (68.5%) had low risks of the use of all drugs except cannabis; Class 2 (17.8%) had moderate risks of the use of all drugs; Class 3 (6.6%) had high rates of cocaine, other stimulant and hallucinogen use but lower risks for the use of sedatives or opioids. Conversely, Class 4 (3.0%) had relatively low risks of cocaine, other stimulant or hallucinogen use but high rates of sedative and opioid use. Finally, Class 5 (4.2%) had uniformly high probabilities for the use of all drugs. Rates of psychiatric comorbidity were highest in the polydrug class although the sedative/opioid class had elevated rates of depression/suicidal behaviors and exposure to childhood abuse. Aggregation of population-level data may obscure important subgroup differences in patterns of illicit drug use and psychiatric comorbidity. Further exploration of a 'self-medicating' subgroup is needed.

Zinc deposits and related mineralization of the Burketown mineral field, including the world-class Century Deposit, Northern Australia: Fluid inclusion and stable isotope evidence for basin fluid sources

The stratiform Century Zn-Pb deposit and the discordant Zn-Pb lode deposits of the Burketown mineral field, northern Australia, host ore and gangue minerals with primary fluid inclusions that have not been affected by the Isan orogeny, thus providing a unique opportunity to investigate the nature of the ore-forming brines. All of the deposits are hosted in shales and siltstones belonging to the Isa superbasin and comprise sphalerite, pyrite, carbonate, quartz, galena, minor chalcopyrite, and minor illite. According to Pb model ages, the main ore stage of mineralization at Century formed at I575 Ma, some 20 m.y. after deposition of the host shale sequence. Microthermometry on undeformed, primary fluid inclusions hosted in porous sphalerite shows that the Zn at Century was transported to the deposit by a homogeneous, Ca2+- and Na+-bearing brine with a salinity of 21.6 wt percent NaCl equiv. delta D-fluid of the fluid inclusion water ranges from -89 to -83 per mil, consistent with a basinal brine that evolved from meteoric water. Fluid inclusion homogenization temperatures range between 74 degrees and 125 degrees C, which are lower than the 120 degrees to 160 degrees C range calculated from vitrinite reflectance and illite crystallinity data from the deposit. This discrepancy indicates that mineralization likely formed at 50 to 85 Mpa, corresponding to a depth of 1,900 to 3,100 m. Transgressive galena-sphalerite veins that cut stratiform mineralization at Century and breccia-filled quartz-dolomite-sphalerite-galena veins in the discordant Zn-Pb lodes have Pb model ages between 1575 and 1485 Ma. Raman spectroscopy and microthermometry reveal that the primary fluid inclusions in these veins contain Ca2+, Na+. but they have lower salinities between 23 and 10 wt percent NaCl equiv and higher delta D-fluid values ranging from -89 to -61 per mil than fluid inclusions in porous sphalerite from Century. Fluid inclusion water from sphalerite in one of the lode deposits has delta O-18(fluid) values of 1.6 and 2.4 per mil, indistinguishable from delta O-18(fluid) values between -0.3 to +7.4 per mil calculated from the isotopic composition of coexisting quartz, dolomite, and illite. The trend toward lower salinities and higher delta D-fluid values relative to the earlier mineralizing fluids is attributed to mixing between the fluid that formed Century and a seawater-derived fluid from a different source. Based on seismic data from the Lawn Hill platform and paragenetic and geochemical results from the Leichhardt River fault trough to the south, diagenetic aquifers in the Underlying Calvert superbasin appear to have been the most likely sources for the fluids that formed Century and the discordant lode deposits. Paragenetically late sphalerite and calcite cut sphalerite, quartz, and dolomite in the lode deposits and contain Na+-dominated fluid inclusions with much lower salinities than their older counterparts. The isotopic composition of calcite also indicates delta O-18(fluid) from 3.3 to 10.7 per mil, which is larger than the range obtained from synmineralization minerals, supporting the idea that a unique fluid source was involved. The absolute timing of this event is unclear, but a plethora of Pb model, K-Ar, and Ar-40/Ar-39 ages between 1440 and 1300 Ma indicate that a significant volume of fluid was mobilized at this time. The deposition of the Roper superbasin from ca. 1492 +/- 4 Ma suggests that these late veins formed from fluids that may have been derived from aquifers in overlying sediments of the Roper superbasin. Clear, buck, and drusy quartz in veins unrelated to any form of Pb-Zn mineralization record the last major fluid event in the Burketown mineral field and form distinct outcrops and ridges in the district. Fluid inclusions in these veins indicate formation from a low-salinity, 300 degrees +/- 80 degrees C fluid. Temperatures approaching 300 degrees C recorded in organic matter adjacent to faults and at sequence boundaries correspond to K-Ar ages spanning 1300 to 1100 Ma, which coincides with regional hydrothermal activity in the northern Lawn Hill platform and the emplacement of the Lakeview Dolerite at the time of assemblage of the Rodinia supercontinent.

MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors

T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.

Edges and bars: where do people see features in 1-D images?

There have been two main approaches to feature detection in human and computer vision - based either on the luminance distribution and its spatial derivatives, or on the spatial distribution of local contrast energy. Thus, bars and edges might arise from peaks of luminance and luminance gradient respectively, or bars and edges might be found at peaks of local energy, where local phases are aligned across spatial frequency. This basic issue of definition is important because it guides more detailed models and interpretations of early vision. Which approach better describes the perceived positions of features in images? We used the class of 1-D images defined by Morrone and Burr in which the amplitude spectrum is that of a (partially blurred) square-wave and all Fourier components have a common phase. Observers used a cursor to mark where bars and edges were seen for different test phases (Experiment 1) or judged the spatial alignment of contours that had different phases (e.g. 0 degrees and 45 degrees ; Experiment 2). The feature positions defined by both tasks shifted systematically to the left or right according to the sign of the phase offset, increasing with the degree of blur. These shifts were well predicted by the location of luminance peaks (bars) and gradient peaks (edges), but not by energy peaks which (by design) predicted no shift at all. These results encourage models based on a Gaussian-derivative framework, but do not support the idea that human vision uses points of phase alignment to find local, first-order features. Nevertheless, we argue that both approaches are presently incomplete and a better understanding of early vision may combine insights from both. (C)2004 Elsevier Ltd. All rights reserved.