A reanalysis of 409 European-Ancestry and African American schizophrenia pedigrees reveals significant linkage to 8p23.3 with evidence of locus heterogeneity

The detection and replication of schizophrenia risk loci can require substantial sample sizes, which has prompted various collaborative efforts for combining multiple samples. However, pooled samples may comprise sub-samples with substantial population genetic differences, including allele frequency differences. We investigated the impact of population differences via linkage reanalysis of Molecular Genetics of Schizophrenia 1 (MGS1) affected sibling-pair data, comprising two samples of distinct ancestral origin: European (EA: 263 pedigrees) and African-American (AA: 146 pedigrees). To exploit the linkage information contained within these distinct continental samples, we performed separate analyses of the individual samples, allowing for within-sample locus heterogeneity, and the pooled sample, allowing for both within-sample and between-sample heterogeneity. Significance levels, corrected for the multiple tests, were determined empirically. For all suggestive peaks, stronger linkage evidence was obtained in either the EA or AA sample than the combined sample, regardless of how heterogeneity was modeled for the latter. Notably, we report genomewide significant linkage of schizophrenia to 8p23.3 and evidence for a second, independent susceptibility locus, reaching suggestive linkage, 29 cM away on 8p21.3. We also detected suggestive linkage on chromosomes 5p13.3 and 7q36.2. Many regions showed pronounced differences in the extent of linkage between the EA and AA samples. This reanalysis highlights the potential impact of population differences upon linkage evidence in pooled data and demonstrates a useful approach for the analysis of samples drawn from distinct continental groups.

Susceptibility variants for male-pattern baldness on chromosome 20p11

We carried out a genome-wide association study in 296 individuals with male-pattern baldness (androgenetic alopecia) and 347 controls. We then investigated the 30 best SNPs in an independent replication sample and found highly significant association for five SNPs on chromosome 20p11 (rs2180439 combined P = 2.7 x 10(-15)). No interaction was detected with the X-chromosomal androgen receptor locus, suggesting that the 20p11 locus has a role in a yet-to-be-identified androgen-independent pathway.

Consistently replicating locus linked to migraine on 10q22-q23

Here, we present the results of two genome-wide scans in two diverse populations in which a consistent use of recently introduced migraine-phenotyping methods detects and replicates a locus on 10q22-q23, with an additional independent replication. No genetic variants have been convincingly established in migraine, and although several loci have been reported, none of them has been consistently replicated. We employed the three known migraine-phenotyping methods (clinical end diagnosis, latent-class analysis, and trait-component analysis) with robust multiple testing correction in a large sample set of 1675 individuals from 210 migraine families from Finland and Australia. Genome-wide multipoint linkage analysis that used the Kong and Cox exponential model in Finns detected a locus on 10q22-q23 with highly significant evidence of linkage (LOD 7.68 at 103 cM in female-specific analysis). The Australian sample showed a LOD score of 3.50 at the same locus (100 cM), as did the independent Finnish replication study (LOD score 2.41, at 102 cM). In addition, four previously reported loci on 8q21, 14q21, 18q12, and Xp21 were also replicated. A shared-segment analysis of 10q22-q23 linked Finnish families identified a 1.6-9.5 cM segment, centered on 101 cM, which shows in-family homology in 95% of affected Finns. This region was further studied with 1323 SNPs. Although no significant association was observed, four regions warranting follow-up studies were identified. These results support the use of symptomology-based phenotyping in migraine and suggest that the 10q22-q23 locus probably contains one or more migraine susceptibility variants.

Comparison of the reproductive ecology of two sympatric blacktip sharks (Carcharhinus limbatus and Carcharhinus tilstoni) off north-eastern Australia with species identification inferred from vertebral counts

Precaudal vertebral counts were used to distinguish between 237 morphologically similar Carcharhinus limbatus and Carcharhinus tilstoni and were congruent with differences in reproductive ecology between the species. In addition to differing lengths at maturity and adult body size, the two species had asynchronous parturition, were born at different sizes and the relative frequencies of neonates differed in two coastal nursery areas. Despite evidence that hybridization can occur, these differences suggest the species are largely reproductively isolated.

Biochemical and structural properties of Potato virus A VPg

The potato virus A (PVA) genome linked protein (VPg) is a multifunctional protein that takes part in vital infection cycle events such as replication and movement of the virus from cell to cell. VPg is attached to the 5´ end of the genome and is carried in the tip structure of the filamentous virus particle. VPg is also the last protein to be cleaved from the polyprotein. VPg interacts with several viral and host proteins and is phosphorylated at several positions. These features indicate a central role in virus epidemiology and a requirement for an efficient but flexible mechanism for switching between different functions. -- This study examines some of the key VPg functions in more detail. Mutations in the positively charged region from Ala38 to Lys44 affected the NTP binding, uridylylation, and in vitro translation inhibition activities of VPg, whereas in vivo translation inhibition was not affected. Some of the data generated in this study implicated the structural flexibility of the protein in functional activities. VPg lacks a rigid structure, which could allow it to adapt conformationally to different functions as needed. A major finding of this study is that PVA VPg belongs to the class of ´intrinsically disordered proteins´ (IDPs). IDPs are a novel protein class that has helped to explain the observed lack of structure. The existence of IDPs clearly shows that proteins can be functional and adapt a native fold without a rigid structure. Evidence for the intrinsic disorder of VPg was provided by CD spectroscopy, NMR, fluorescence spectroscopy, bioinformatic analysis, and limited proteolytic digestion. The structure of VPg resembles that of a molten globule-type protein and has a hydrophobic core domain. Approximately 50% of the protein is disordered and an α-helical stabilization of these regions has been hypothesized. Surprisingly, VPg structure was stabilized in the presence of anionic lipid vesicles. The stabilization was accompanied by a change in VPg structure and major morphological modifications of the vesicles, including a pronounced increase in the size and appearance of pore or plaque like formations on the vesicle surface. The most likely scenario seems to be an α-helical stabilization of VPg which induces formation of a pore or channel-like structure on the vesicle surface. The size increase is probably due to fusion or swelling of the vesicles. The latter hypothesis is supported by the evident disruption of the vesicles after prolonged incubation with VPg. A model describing the results is presented and discussed in relation to other known properties of the protein.

In planta localization and interactions of impatiens necrotic spot tospovirus proteins

Impatiens necrotic spot tospovirus (INSV) is a significant pathogen of ornamentals. The tripartite negative- and ambi-sense RNA genome encodes six proteins that are involved in cytoplasmic replication, movement, assembly, insect transmission and defence. To gain insight into the associations of these viral proteins, we determined their intracellular localization and interactions in living plant cells. Nucleotide sequences encoding the nucleoprotein N, non-structural proteins NSs and NSm, and glycoproteins Gn and Gc of a Kentucky isolate of INSV were amplified by RTPCR, cloned, sequenced and transiently expressed as fusions with autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana. All proteins accumulated at the cell periphery and co-localized with an endoplasmic reticulum marker. The Gc protein fusion also localized to the nucleus. N and NSm protein self-interactions and an NSm-N interaction were observed by using bimolecular fluorescence complementation. A tospovirus NSm homotypic interaction had not been reported previously.

Electrotransformation of Haemophilus parasuis with in vitro modified DNA based on a novel shuttle vector

The objective of the present study was to establish a valid transformation method of Haemophilus parasuis, the causative agent of Glasser's disease in pigs, using a novel H. parasuis-Escherichia coli shuttle vector. A 4.2 kb endogenous plasmid pYC93 was extracted from an H. parasuis field isolate and completely sequenced. Analysis of pYC93 revealed a region approximately 800 bp showing high homology with the defined replication origin oriV of pLS88, a native plasmid identified in Haemophilus ducreyi. Based on the origin region of pYC93, E. coli cloning vector pBluescript SK(+) and the Tn903 derived kanamycin cassette, a shuttle vector pSHK4 was constructed by overlapping PCR strategy. When electroporation of the 15 H. parasuis serovar reference strains and one clinical isolate SH0165 with pSHK4 was performed, only one of these strains yielded transformants with an efficiency of 8.5 x 10(2) CFUhlg of DNA. Transformation efficiency was notably increased (1.3 x 10(5) CFU/mu g of DNA) with vector DNA reisolated from the homologous transformants. This demonstrated that restriction-modification systems were involved in the barrier to transformation of H. parasuis. By utilizing an in vitro DNA modification method with cell-free extracts of the host H. parasuis strains, 15 out of 16 strains were transformable. The novel shuttle vector pSHK4 and the established electrotransformation method constitute useful tools for the genetic manipulation of H. parasuis to gain a better understanding of the pathogen. (C) 2011 Elsevier B.V. All rights reserved.

Spatial and temporal effects of grazing management and rainfall on the vertebrate fauna of a tropical savanna

Grazing by domestic livestock is one of the most widespread uses of the rangelands of Australia. There is limited information on the effects of grazing by domestic livestock on the vertebrate fauna of Australia and the establishment of a long-term grazing experiment in north-eastern Queensland at Wambiana provided an opportunity to attempt an examination of the changes in vertebrate fauna as a consequence of the manipulation of stocking rates. The aim was to identify what the relative effects of vegetation type, stocking rate and other landscape-scale environmental factors were on the patterns recorded. Sixteen 1-ha sites were established within three replicated treatments (moderate, heavy and variable stocking rates). The sites were sampled in the wet and dry seasons in 1999-2000 (T-0) and again in 2003-04 (T-1). All paddocks of the treatments were burnt in 1999. Average annual rainfall declined markedly between the two sampling periods, which made interpretation of the data difficult. A total of 127 species of vertebrate fauna comprising five amphibian, 83 bird, 27 reptile and 12 mammal species were recorded. There was strong separation in faunal composition from T-0 to T-1 although changes in mean compositional dissimilarity between the grazing stocking rate treatments were less well defined. There was a relative change in abundance of 24 bird, four mammal and five reptile species from T-0 to T-1. The generalised linear modelling identified that, in the T-1 data, there was significant variation in the abundance of 16 species explained by the grazing and vegetation factors. This study demonstrated that vertebrate fauna assemblage did change and that these changes were attributable to the interplay between the stocking rates, the vegetation types on the sites surveyed, the burning of the experimental paddocks and the decrease in rainfall over the course of the two surveys. It is recommended that the experiment is sampled again but that the focus should be on a rapid survey of abundant taxa (i.e. birds and reptiles) to allow an increase in the frequency of sampling and replication of the data. This would help to articulate more clearly the trajectory of vertebrate change due to the relative effects of stocking rates compared with wider landscape environmental changes. Given the increasing focus on pastoral development in northern Australia, any opportunity to incorporate the collection of data on biodiversity into grazing manipulation experiments should be taken for the assessment of the effects of land management on faunal species.

Lost in Translation : Translation Mechanisms in Production of Cocksfoot Mottle Virus Proteins

The present study focuses on the translational strategies of Cocksfoot mottle virus (CfMV, genus Sobemovirus), which infects monocotyledonous plants. CfMV RNA lacks the 5'cap and the 3'poly(A) tail that ensure efficient translation of cellular messenger RNAs (mRNAs). Instead, CfMV RNA is covalently linked to a viral protein VPg (viral protein, genome-linked). This indicates that the viral untranslated regions (UTRs) must functionally compensate for the lack of the cap and poly(A) tail. We examined the efficacy of translation initiation in CfMV by comparing it to well-studied viral translational enhancers. Although insertion of the CfMV 5'UTR (CfMVe) into plant expression vectors improved gene expression in barley more than the other translational enhancers examined, studies at the RNA level showed that CfMVe alone or in combination with the CfMV 3'UTR did not provide the RNAs translational advantage. Mutation analysis revealed that translation initiation from CfMVe involved scanning. Interestingly, CfMVe also promoted translation initiation from an intercistronic position of dicistronic mRNAs in vitro. Furthermore, internal initiation occurred with similar efficacy in translation lysates that had reduced concentrations of eukaryotic initiation factor (eIF) 4E, suggesting that initiation was independent of the eIF4E. In contrast, reduced translation in the eIF4G-depleted lysates indicated that translation from internally positioned CfMVe was eIF4G-dependent. After successful translation initiation, leaky scanning brings the ribosomes to the second open reading frame (ORF). The CfMV polyprotein is produced from this and the following overlapping ORF via programmed -1 ribosomal frameshift (-1 PRF). Two signals in the mRNA at the beginning of the overlap program approximately every fifth ribosome to slip one nucleotide backwards and continue translation in the new -1 frame. This leads to the production of C-terminally extended polyprotein, which encodes the viral RNA-dependent RNA polymerase (RdRp). The -1 PRF event in CfMV was very efficient, even though it was programmed by a simple stem-loop structure instead of a pseudoknot, which is usually required for high -1 PRF frequencies. Interestingly, regions surrounding the -1 PRF signals improved the -1 PRF frequencies. Viral protein P27 inhibited the -1 PRF event in vivo, putatively by binding to the -1 PRF site. This suggested that P27 could regulate the occurrence of -1 PRF. Initiation of viral replication requires that viral proteins are released from the polyprotein. This is catalyzed by viral serine protease, which is also encoded from the polyprotein. N-terminal amino acid sequencing of CfMV VPg revealed that the junction of the protease and VPg was cleaved between glutamate (E) and asparagine (N) residues. This suggested that the processing sites used in CfMV differ from the glutamate and serine (S) or threonine (T) sites utilized in other sobemoviruses. However, further analysis revealed that the E/S and E/T sites may be used to cleave out some of the CfMV proteins.

Formal description, compression and transformation of digital pictures II. Picture algebra and geometry

In an earlier paper (Part I) we described the construction of Hermite code for multiple grey-level pictures using the concepts of vector spaces over Galois Fields. In this paper a new algebra is worked out for Hermite codes to devise algorithms for various transformations such as translation, reflection, rotation, expansion and replication of the original picture. Also other operations such as concatenation, complementation, superposition, Jordan-sum and selective segmentation are considered. It is shown that the Hermite code of a picture is very powerful and serves as a mathematical signature of the picture. The Hermite code will have extensive applications in picture processing, pattern recognition and artificial intelligence.

Formal description, compression and transformation of digital pictures

This paper describes the application of vector spaces over Galois fields, for obtaining a formal description of a picture in the form of a very compact, non-redundant, unique syntactic code. Two different methods of encoding are described. Both these methods consist in identifying the given picture as a matrix (called picture matrix) over a finite field. In the first method, the eigenvalues and eigenvectors of this matrix are obtained. The eigenvector expansion theorem is then used to reconstruct the original matrix. If several of the eigenvalues happen to be zero this scheme results in a considerable compression. In the second method, the picture matrix is reduced to a primitive diagonal form (Hermite canonical form) by elementary row and column transformations. These sequences of elementary transformations constitute a unique and unambiguous syntactic code-called Hermite code—for reconstructing the picture from the primitive diagonal matrix. A good compression of the picture results, if the rank of the matrix is considerably lower than its order. An important aspect of this code is that it preserves the neighbourhood relations in the picture and the primitive remains invariant under translation, rotation, reflection, enlargement and replication. It is also possible to derive the codes for these transformed pictures from the Hermite code of the original picture by simple algebraic manipulation. This code will find extensive applications in picture compression, storage, retrieval, transmission and in designing pattern recognition and artificial intelligence systems.

Contemplating an evolutionary approach to entrepreneurship

This paper explores that application of evolutionary approaches to the study of entrepreneurship. It is argued an evolutionary theory of entrepreneurship must give as much concern to the foundations of evolutionary thought as it does the nature entrepreneurship. The central point being that we must move beyond a debate or preference of the natural selection and adaptationist viewpoints. Only then can the interrelationships between individuals, firms, populations and the environments within which they interact be better appreciated.

Complete genome sequence and intracellular protein localization of Datura yellow vein nucleorhabdovirus

A limited number of plant rhabdovirus genomes have been fully sequenced, making taxonomic classification, evolutionary analysis and molecular characterization of this virus group difficult. We have for the first time determined the complete genome sequence of 13,188 nucleotides of Datura yellow vein nucleorhabdovirus (DYVV). DYVV genome organization resembles that of its closest relative, Sonchus yellow net virus (SYNV), with six ORFs in antigenomic orientation, separated by highly conserved intergenic regions and flanked by complementary 3′ leader and 5′ trailer sequences. As is typical for nucleorhabdoviruses, all viral proteins, except the glycoprotein, which is targeted to the endoplasmic reticulum, are localized to the nucleus. Nucleocapsid (N) protein, matrix (M) protein and polymerase, as components of nuclear viroplasms during replication, have predicted strong canonical nuclear localization signals, and N and M proteins exclusively localize to the nucleus when transiently expressed as GFP fusions. As in all nucleorhabdoviruses studied so far, N and phosphoprotein P interact when co-expressed, significantly increasing P nuclear localization in the presence of N protein. This research adds to the list of complete genomes of plant-infecting rhabdoviruses, provides molecular tools for further characterization and supports classification of DYVV as a nucleorhabdovirus closely related to but with some distinct differences from SYNV.

Efficient Content-based Routing, Mobility-aware Topologies, and Temporal Subspace Matching

Event-based systems are seen as good candidates for supporting distributed applications in dynamic and ubiquitous environments because they support decoupled and asynchronous many-to-many information dissemination. Event systems are widely used, because asynchronous messaging provides a flexible alternative to RPC (Remote Procedure Call). They are typically implemented using an overlay network of routers. A content-based router forwards event messages based on filters that are installed by subscribers and other routers. The filters are organized into a routing table in order to forward incoming events to proper subscribers and neighbouring routers. This thesis addresses the optimization of content-based routing tables organized using the covering relation and presents novel data structures and configurations for improving local and distributed operation. Data structures are needed for organizing filters into a routing table that supports efficient matching and runtime operation. We present novel results on dynamic filter merging and the integration of filter merging with content-based routing tables. In addition, the thesis examines the cost of client mobility using different protocols and routing topologies. We also present a new matching technique called temporal subspace matching. The technique combines two new features. The first feature, temporal operation, supports notifications, or content profiles, that persist in time. The second feature, subspace matching, allows more expressive semantics, because notifications may contain intervals and be defined as subspaces of the content space. We also present an application of temporal subspace matching pertaining to metadata-based continuous collection and object tracking.

Performance of Ajax Applications on Mobile Devices

The Ajax approach has outgrown its origin as shorthand for "Asynchronous JavaScript + XML". Three years after its naming, Ajax has become widely adopted by web applications. Therefore, there exists a growing interest in using those applications with mobile devices. This thesis evaluates the presentational capability and measures the performance of five mobile browsers on the Apple iPhone and Nokia models N95 and N800. Performance is benchmarked through user-experienced response times as measured with a stopwatch. 12 Ajax toolkit examples and 8 production-quality applications are targeted, all except one in their real environments. In total, over 1750 observations are analyzed and included in the appendix. Communication delays are not considered; the network connection type is WLAN. Results indicate that the initial loading time of an Ajax application can often exceed 20 seconds. Content reordering may be used to partially overcome this limitation. Proper testing is the key for success: the selected browsers are capable of presenting Ajax applications if their differing implementations are overcome, perhaps using a suitable toolkit.