bluuebunny/crossref_metadata_2025 huggingface dataset:
Delinquency Control and Juvenile Justice in China
Authors: Wong Dennis S.W.
Published: January 2011

This paper provides an overview of the recent developments in juvenile justice in China. With the improvement in the overall economy, there has been a genuine rise in delinquency. This paper describes the trend of youth crimes, and how informal grassroots networks and formal correctional institutions play their roles in delinquency control. The author argues that the inseparable relationship between the Communist Party and control systems, the frequent turnover of volunteers, and insufficient professional manpower hinder the development of a fair and independent juvenile justice system. Finally, the paper highlights what should be preliminary direction for the further development of the systems of delinquency control and juvenile justice.
A Reply to the NSW Royal Commission Inquiry into Paedophilia: Victim Report Studies and Child Sex Offender Profiles — A Bad Match?
Authors: Cossins Anne
Published: January 2011

This article questions the validity of the fixated/regressed classification scheme of child sex offenders used by the Royal Commission into the New South Wales Police Service. Since the scheme is based on incar-cerated offender profiles, it does not accord with empirical data derived from victim report studies, and is contradicted by a number of other studies on the sexual behaviour of child sex offenders. The article discusses how the classification scheme appears to have been influential in the Royal Commission's decision to focus its inquiry into paedophilia on the activities of homosexual, fixated offenders. As a result of this focus, the Royal Commission engaged in very little analysis of the extent of child sexual abuse within the family and abuse concerning female children in general. The article concludes by questioning some of the Royal Commission's recommendations for the future policing of child sexual abuse within New South Wales.
The Criminal Use of Firearms in New Zealand
Authors: Newbold Greg
Published: January 2011

Early In 1997 a survey was conducted on 51 New Zealand prison inmates who had been convicted of illegal possession of a firearm, aggravated robbery with a firearm and murder with a firearm. Respondents were asked questions relating to their acquisition and usage of illegal firearms in order to obtain information about patterns of firearms owner-ship within the criminal community. Many of the results were similar to an American study which took place in the mid-1980s but the New Zealanders differed from the Americans in being armed less frequently and in being more restricted in their access to handguns. Among the New Zealanders the most common, popular, cheap and easily acquired weapon was the shotgun. Shotguns were used in more than half the crimes for which the respondents had been imprisoned and in seventy percent of cases the weapon had a sawn off butt or barrel. The next most common weapons used were pistols and rifles. Usage of military semi-automatics was rare. This research confirms that there is a large pool of illegally-held firearms in New Zealand and that firearms of almost any type can be obtained relatively easily from within the criminal community.
Prisons are the Problem: A Re-Examination of Aboriginal and Non-Aboriginal Deaths in Custody
Authors: Harding Richard W.
Published: January 2011

The background to the establishment in 1987 of the Royal Commission into Aboriginal Deaths in Custody was a belief that the defining risk characteristic of persons dying in custody was their Aboriginality. Australia's long history of violence and injustice towards its Indigenous population underpinned the expectation that continuing racism in custodial situations was the principal driver of high Aboriginal mortality rates. On that basis, analysis and proposed solutions would focus upon the specifics of Aboriginal custodial experience as well as broader issues of criminal justice system administration.

This paper suggests that, in the context of prison custody, equal or greater emphasis should have been placed on the nature of prison regimes and prisoner management generally, as they impact upon all prisoners. Rates of prison deaths have remained unacceptably high since the RCIADIC, in contrast to police custodial death rates which have improved markedly. A great deal was generally known about the epidemiology of prison custodial deaths before the work of the RCIADIC. Across-the-board implementation of this prior and subsequently acquired knowledge would arguably have made more effective impact upon Aboriginal as well as non-Aboriginal deaths. The defining risk characteristic of prison mortality was, and still is, the nature of prison custodial regimes.
“This is How We Did It”: One Canadian First Nation Community's Efforts to Achieve Aboriginal Justice
Authors: Barry Warhaft E. , Palys Ted , Boyce Wilma
Published: January 2011

The current proliferation of community-based Aboriginal restorative justice programmes in Canada cannot be understood solely as the direct expression of Aboriginal Peoples asserting their right to self-determination, or the result of the Canadian government's appropriation, compartmentalization and administration of restorative justice. To explain the ambiguous state of Aboriginal justice in Canada, and to illuminate government and community responses to these Aboriginal justice initiatives, we offer a case study of one such initiative in Canim Lake, British Columbia. Through interviews, the Canim Lake Band and their supporters tell of the development and implementation of a Family Violence Programme, which we (re)present as a process-oriented story of community ownership, community development and community/government relationship building. Their example suggests that justice on Aboriginal terms can be realized provided that the solutions to crime and justice issues are community-generated and that political will is not limited by narrow interpretations of government policy.
Aboriginal Criminology and the Postmodern Condition: From Anomie to Anomaly
Authors: Tyler William
Published: January 2011

The very high rates of Aboriginal over-representation in the criminal justice systems of the white ‘settler’ societies are conventionally explained in terms of pervasive effects of cultural dispossession and social and economic disadvantage and dislocation. These approaches have been recently elaborated to account for the wide regional variations in patterns of offending in countries such as Canada and Australia. However, these approaches are more attuned to the pathologies of the transition into modernity rather than the current environment of postmodernity which is marked by unstable identity, indeterminate social and cultural processes and a global rather than a national positioning of the Aboriginal subject. A model based on anomaly rather than anomie as the generative dynamic of the Aboriginal condition is developed, based on the insights of theorists within the Durkheimian tradition.
The Australian and New Zealand Journal of Criminology Thirty Years On
Authors: Pratt John
Published: January 2011

This paper, in celebration of the Australian and New Zealand Journal's thirty years of existence provides a reflective, self-critical analysis of its contents over this period and, for comparative purposes, the content of the British Journal of Criminology. While the findings of such an exercise must be treated with caution, they provide interesting glimpses of the way in which the discipline of criminology has been shaped and developed in the journal.
Reward, Law and Power: Toward a Jurisprudence of the Carrot
Authors: Freiberg Arie
Published: January 2011

Positive sanctions play an important but underestimated role in societal regulation. This article examines reward in political and legal theory and explores the conceptual and practical dimensions of reward in the civil and criminal law. It argues that the mechanisms and ideology of reward have facilitated state intervention into private and corporate activity, delayed or denied due process and maintained social inequality. Possible changes in the nature of social control, from punishments to institutionalized rewards through the welfare state, are observed and the implications of such a change for sanction theory are discussed.
Man, Bound and Free
Authors: Cupitt Don
Published: January 2011

This essay is part of a lecture recently given at Lampeter and at Cambridge, and continues a series of which three have already appeared in Theology. In the deleted first section I illustrated the persistence of the old paradoxes of bondage and freedom in the new sciences of man. In what follows note two distinctions: that between soul and spirit; and that between the abstract and theoretical self-transcendence which makes the sciences of man possible, and the concrete ethical self-transcendence which is the business of religion.
Science, Faith and the Vision of a New Society
Authors: Pritchard Colin
Published: January 2011

This paper owes much to the ideas, insights and inspiration of a group of people brought together in Mexico City in August 1975 at the behest of the World Council of Churches for a consultation on the Christian Faith and the Changing Face of Science and Technology. I have drawn freely on their written papers and their report (published in Anticipation No. 22) believing that this important work needs to be interpreted and made much more widely known. I have also drawn on the fertile ideas of a number of British scientists and philosophers, notably Sir Bernard Lovell the astronomer, and Professor Derek Bryce-Smith the chemist, who have given us, from their studies of the incomprehensibly vast universe and the infinitesimally small atom, a picture of a universe with a truly remarkable property: the ability to produce life.
Myth Understood
Authors: Cupitt Don
Published: January 2011

This short statement was written to introduce a lay audience to a current controversy.
Exit, voice, and family policy in Japan: limited changes despite broad recognition of the declining fertility problem
Authors: Schoppa Leonard
Published: January 2011

Japanese policymakers have been troubled by the ‘declining fertility problem’ for two decades, ever since a sharp drop in births raised public awareness of the issue in 1990. This article explores why it took a full decade before government officials diagnosed the problem and called for a shift toward gender-egalitarian labour market policies in order to reverse the fertility decline. It also asks why the prescribed changes have yet to be adopted, despite continued hand-wringing over fertility rates. Both delays, it argues, stem from the ability of Japanese women — who began entering the workforce in an era when they had already gained full control of their fertility — to ‘exit’ from the work—family reconciliation challenge by postponing or opting out of motherhood. This deprived the reform movement of the ‘voice’ needed to transform male breadwinner structures that are rooted not only in public policies, but also in private sector practices.
The reframing of family policies in France: processes and actors
Authors: Martin Claude
Published: January 2011

French family policy is generally considered as one of the oldest, most explicit and extensive in Europe. To understand the changes in this public policy sector during the past decades, we first discuss the roots and scope of family policy and then propose a ‘process tracing’ to identify sequences, based on two sets of opposing principles that have shaped French family policy history: universality versus selectivity and French ‘familialisme’ versus individualism. In the last two sections, a detailed analysis of the dynamics of change is presented before focusing on the role of the different protagonists of this change: political actors, high-ranking civil servants, family associations and experts. We underline the importance of a small group of high-ranking civil servants, called the ‘welfare elite’, in this specific sector, whose contribution explains the permanent French specificity and path dependency.
Changes in the regulation of responsibilities towards childcare needs in Italy and the Netherlands: different timing, increasingly different approaches
Authors: Knijn Trudie , Saraceno Chiara
Published: January 2011

This article comparatively analyses how the responsibilities towards childcare needs have been framed and addressed in Italy and the Netherlands following the increase in women’s labour market participation. According to the authors, the differing developments in these two countries partly disconfirm the thesis according to which facilitating family/work conciliation is at the heart of the new social policy paradigms in all Bismarckian welfare states. This concern has indeed been an explicit driver of social policy changes in the Netherlands, but not in Italy. The authors argue instead that these two countries offer evidence for the thesis that timing matters. Italy has been an ‘early bird’ in changing family law and in putting in place childcare policies, but has not been able to innovate these policies when the economic and social context has changed and, in particular, has not reframed them fully as work-family conciliating policies. The Netherlands, on the other hand, was comparatively late in changing family law and developing parental leaves and childcare policies, the latter being framed largely as work-family conciliation strategies. Following the liberal cultural and political developments of the 1990s, which favoured individualisation and freedom of choice, the changes in the Netherlands systematically introduced an increasing mix of individual, family and market responsibility via both commodification supported by tax expenditure and the underpinning of the one-and-a-half breadwinner model offered by the regulation of protected part-time labour contracts.
Germany outpaces Austria in childcare policy: the historical contingencies of ‘conservative’ childcare policy
Authors: Leitner Sigrid
Published: January 2011

The article compares the development of childcare policies in Germany and Austria. Although both countries are characterized by a conservative welfare regime, they developed very different childcare policies. Historically speaking, Austria pioneered in the introductory period whereas Germany outpaced Austria with the latest reforms. The article argues that ideological party differences account for policy change. The gender and family models promoted by the governing parties shaped the development of childcare policies decisively. But party positions changed over time due to general emancipation processes, intra-party conflicts and constraints by coalition partners. Thus, the ‘parties matter’ thesis explains policy development only partly. The historical context of policy making has to be taken into consideration as well.
On Becoming a Bilingual Teacher: A Transformative Process for Preservice and Novice Teachers
Authors: Osterling Jorge P. , Webb Whitney
Published: January 2011

This study explores the personal transformation process experienced by future bilingual educators enrolled in a graduate school of education that is committed to rigorous, collaborative, innovative, and transformational research. The majority of these preservice (PST) and novice teachers (NT), largely White, monolingual women, has little direct knowledge about or experience with teaching culturally, linguistically and ability diverse students. Educational researchers have long emphasized the importance of providing PST and NT graduate students with opportunities to analyze and reflect on their personal theoretical beliefs concerning teaching standards and methods of student learning. Additionally, it has been determined that teacher educators must communicate the necessary theoretical foundations to provide their students with a starting point for analyzing their emerging teaching philosophies, the goal being the development of their new visions of reform-minded practices and innovative techniques of teaching. Data indicated that all the PSTs entered the program with images of teaching that were related to their earlier classroom experiences as students, and that, during their 2-year tenure in the graduate school of education, teaching internship, and master’s-level coursework, most experienced professional and personal epiphanies.
What You See Depends Upon How You Look: A Photographic Journey of Transformative Learning
Authors: Lipson Lawrence Randee , Cranton Patricia
Published: January 2011

In this article, the authors explore the camera lens as a metaphor for seeing the world in different ways. Their own stories and backgrounds with photography illustrate how they have come to make these connections. The authors present six increasingly abstract approaches to photography, as a way of demonstrating ‘‘what you see depends upon how you look.’’ They relate this to a holistic approach to transformative learning.
Characterization of a core fragment of the rhesus monkey TRIM5α protein
Authors: Kar Alak K , Mao Youdong , Bird Gregory , Walensky Loren , Sodroski Joseph
Published: January 2011

Background

Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown.

Results

Here, we express and characterize a protease-resistant 29-kD core fragment containing the B-box 2, coiled coil and adjacent linker (L2) region of TRIM5α. This BCCL2 protein formed dimers and higher-order oligomers in solution. Approximately 40% of the BCCL2 secondary structure consisted of alpha helices. Partial loss of alpha-helical content and dissociation of dimers occurred at 42°C, with the residual alpha helices remaining stable up to 80°C.

Conclusions

These results indicate that the B-box 2, coiled-coil and linker 2 regions of TRIM5α form a core dimerization motif that exhibits a high level of alpha-helical content.
Island species radiation and karyotypic stasis in Pachycladonallopolyploids
Authors: Mandáková Terezie , Heenan Peter B , Lysak Martin A
Published: January 2011

Background

Pachycladon(Brassicaceae, tribe Camelineae) is a monophyletic genus of ten morphologically and ecogeographically differentiated, and presumably allopolyploid species occurring in the South Island of New Zealand and in Tasmania. AllPachycladonspecies possess ten chromosome pairs (2n = 20). The feasibility of comparative chromosome painting (CCP) in crucifer species allows the origin and genome evolution in this genus to be elucidated. We focus on the origin and genome evolution ofPachycladonas well as on its genomic relationship to other crucifer species, particularly to the allopolyploid Australian Camelineae taxa. As species radiation on islands is usually characterized by chromosomal stasis, i.e. uniformity of chromosome numbers/ploidy levels, the role of major karyotypic reshuffling during the island adaptive and species radiation inPachycladonis investigated through whole-genome CCP analysis.

Results

The four analyzedPachycladonspecies possess an identical karyotype structure. The consensual ancestral karyotype is most likely common to allPachycladonspecies and corroborates the monophyletic origin of the genus evidenced by previous phylogenetic analyses. The ancestralPachycladonkaryotype (n = 10) originated through an allopolyploidization event between two genomes structurally resembling the Ancestral Crucifer Karyotype (ACK, n = 8). The primary allopolyploid (apparently with n = 16) has undergone genome reshuffling by descending dysploidy toward n = 10. Chromosome "fusions" were mediated by inversions, translocations and centromere inactivation/loss.Pachycladonchromosome 3 (PC3) resulted from insertional fusion, described in grasses. The allopolyploid ancestor originated in Australia, from the same or closely related ACK-like parental species as the Australian Camelineae allopolyploids. However, the two whole-genome duplication (WGD) events were independent, with thePachycladonWGD being significantly younger. The long-distance dispersal of the diploidizedPachycladonancestor to New Zealand was followed by the Pleistocene species radiation in alpine habitats and characterized by karyotypic stasis.

Conclusions

Karyotypic stasis inPachycladonsuggests that the insular species radiation in this genus proceeded through homoploid divergence rather than through species-specific gross chromosomal repatterning. The ancestralPachycladongenome originated in Australia through an allopolyploidization event involving two closely related parental genomes, and spread to New Zealand by a long-distance dispersal. We argue that the chromosome number decrease mediated by inter-genomic reshuffling (diploidization) could provide thePachycladonallopolyploid founder with an adaptive advantage to colonize montane/alpine habitats. The ancestralPachycladonkaryotype remained stable during the Pleistocene adaptive radiation into ten different species.
Unusual conservation of mitochondrial gene order in Crassostreaoysters: evidence for recent speciation in Asia
Authors: Ren Jianfeng , Liu Xiao , Jiang Feng , Guo Ximing , Liu Bin
Published: January 2011

Background

Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis.

Results

The six Asian Crassostrea mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the rrnL gene and duplication of trnM, trnK and trnQ genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from S. mordax in protein-coding genes. Phylogenetic analysis indicates that the six Asian Crassostrea species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago.

Conclusions

The complete conservation of gene order in the six Asian Crassostrea species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six Crassostrea species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood.
Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus
Authors: Marx Patrick , Nuhn Michael , Kovács Martá , Hakenbeck Regine , Brückner Reinhold
Published: January 2011

Background

Post-transcriptional regulation by small RNAs (sRNAs) in bacteria is now recognized as a wide-spread regulatory mechanism modulating a variety of physiological responses including virulence. InStreptococcus pneumoniae, an important human pathogen, the first sRNAs to be described were found in the regulon of the CiaRH two-component regulatory system. Five of these sRNAs were detected and designated csRNAs for cia-dependent small RNAs. CiaRH pleiotropically affects β-lactam resistance, autolysis, virulence, and competence development by yet to be defined molecular mechanisms. Since CiaRH is highly conserved among streptococci, it is of interest to determine if csRNAs are also included in the CiaRH regulon in this group of organisms consisting of commensal as well as pathogenic species. Knowledge on the participation of csRNAs in CiaRH-dependent regulatory events will be the key to define the physiological role of this important control system.

Results

Genes for csRNAs were predicted in streptococcal genomes and data base entries other thanS. pneumoniaeby searching for CiaR-activated promoters located in intergenic regions that are followed by a transcriptional terminator. 61 different candidate genes were obtained specifying csRNAs ranging in size from 51 to 202 nt. Comparing these genes among each other revealed 40 different csRNA types. All streptococcal genomes harbored csRNA genes, their numbers varying between two and six. To validate these predictions,S. mitis,S. oralis, andS. sanguiniswere subjected to csRNA-specific northern blot analysis. In addition, a csRNA gene fromS. thermophilusplasmid pST0 introduced intoS. pneumoniaewas also tested. Each of the csRNAs was detected on these blots and showed the anticipated sizes. Thus, the method applied here is able to predict csRNAs with high precision.

Conclusions

The results of this study strongly suggest that genes for small non-coding RNAs, csRNAs, are part of the regulon of the two-component regulatory system CiaRH in all streptococci.
Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements
Authors: Devonshire Alison S , Elaswarapu Ramnath , Foy Carole A
Published: January 2011

Background

Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mRNA expression makes the evaluation and standardization of transcriptomic data problematic due to differences in protocols, data processing and analysis methods. Thus, universal RNA standards, such as those developed by the External RNA Controls Consortium (ERCC), are proposed to aid validation of research findings from diverse platforms such as microarrays and RT-qPCR, and play a role in quality control (QC) processes as transcriptomic profiling becomes more commonplace in the clinical setting.

Results

Panels of ERCC RNA standards were constructed in order to test the utility of these reference materials (RMs) for performance characterization of two selected gene expression platforms, and for discrimination of biomarker profiles between groups. The linear range, limits of detection and reproducibility of microarray and RT-qPCR measurements were evaluated using panels of RNA standards. Transcripts of low abundance (≤ 10 copies/ng total RNA) showed more than double the technical variability compared to higher copy number transcripts on both platforms. Microarray profiling of two simulated 'normal' and 'disease' panels, each consisting of eight different RNA standards, yielded robust discrimination between the panels and between standards with varying fold change ratios, showing no systematic effects due to different labelling and hybridization runs. Also, comparison of microarray and RT-qPCR data for fold changes showed agreement for the two platforms.

Conclusions

ERCC RNA standards provide a generic means of evaluating different aspects of platform performance, and can provide information on the technical variation associated with quantification of biomarkers expressed at different levels of physiological abundance. Distinct panels of standards serve as an ideal quality control tool kit for determining the accuracy of fold change cut-off threshold and the impact of experimentally-derived noise on the discrimination of normal and disease profiles.
A new implementation of high-throughput five-dimensional clone pooling strategy for BAC library screening
Authors: You Frank M , Luo Ming-Cheng , Xu Kenong , Deal Karin R , Anderson Olin D , Dvorak Jan
Published: January 2011

Background

A five-dimensional (5-D) clone pooling strategy for screening of bacterial artificial chromosome (BAC) clones with molecular markers utilizing highly-parallel Illumina GoldenGate assays and PCR facilitates high-throughput BAC clone and BAC contig anchoring on a genetic map. However, this strategy occasionally needs manual PCR to deconvolute pools and identify truly positive clones.

Results

A new implementation is reported here for our previously reported clone pooling strategy. Row and column pools of BAC clones are divided into sub-pools with 1~2× genome coverage. All BAC pools are screened with Illumina's GoldenGate assay and the BAC pools are deconvoluted to identify individual positive clones. Putative positive BAC clones are then further analyzed to find positive clones on the basis of them being neighbours in a contig. An exhaustive search or brute force algorithm was designed for this deconvolution and integrated into a newly developed software tool, FPCBrowser, for analyzing clone pooling data. This algorithm was used with empirical data for 55 Illumina GoldenGate SNP assays detecting SNP markers mapped on Aegilops tauschii chromosome 2D and Ae. tauschii contig maps. Clones in single contigs were successfully assigned to 48 (87%) specific SNP markers on the map with 91% precision.

Conclusion

A new implementation of 5-D BAC clone pooling strategy employing both GoldenGate assay screening and assembled BAC contigs is shown here to be a high-throughput, low cost, rapid, and feasible approach to screening BAC libraries and anchoring BAC clones and contigs on genetic maps. The software FPCBrowser with the integrated clone deconvolution algorithm has been developed and is downloadable at http://avena.pw.usda.gov/wheatD/fpcbrowser.shtml.
Human transcriptional interactome of chromatin contribute to gene co-expression
Authors: Dong Xiao , Li Chao , Chen Yunqin , Ding Guohui , Li Yixue
Published: January 2011

Background

Transcriptional interactome of chromatin is one of the important mechanisms in gene transcription regulation. By chromatin conformation capture and 3D FISH experiments, several chromatin interactions cases among sequence-distant genes or even inter-chromatin genes were reported. However, on genomics level, there is still little evidence to support these mechanisms. Recently based on Hi-C experiment, a genome-wide picture of chromatin interactions in human cells was presented. It provides a useful material for analysing whether the mechanism of transcriptional interactome is common.

Results

The main work here is to demonstrate whether the effects of transcriptional interactome on gene co-expression exist on genomic level. While controlling the effects of transcription factors control similarities (TCS), we tested the correlation between Hi-C interaction and the mutual ranks of gene co-expression rates (provided by COXPRESdb) of intra-chromatin gene pairs. We used 6,084 genes with both TF annotation and co-expression information, and matched them into 273,458 pairs with similar Hi-C interaction ranks in different cell types. The results illustrate that co-expression is strongly associated with chromatin interaction. Further analysis using GO annotation reveals potential correlation between gene function similarity, Hi-C interaction and their co-expression.

Conclusions

According to the results in this research, the intra-chromatin interactome may have relation to gene function and associate with co-expression. This study provides evidence for illustrating the effect of transcriptional interactome on transcription regulation.
Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)
Authors: Chao Shiaoman , Dubcovsky Jorge , Dvorak Jan , Luo Ming-Cheng , Baenziger Stephen P , Matnyazov Rustam , Clark Dale R , Talbert Luther E , Anderson James A , Dreisigacker Susanne , Glover Karl , Chen Jianli , Campbell Kim , Bruckner Phil L , Rudd Jackie C , Haley Scott , Carver Brett F , Perry Sid , Sorrells Mark E , Akhunov Eduard D
Published: January 2011

Background

Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.

Results

Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FSTwere detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM).

Conclusions

Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.
Genic SNP markers and legume synteny reveal candidate genes underlying QTL for Macrophomina phaseolina resistance and maturity in cowpea [Vigna unguiculata (L) Walp.]
Authors: Muchero Wellington , Ehlers Jeffrey D , Close Timothy J , Roberts Philip A
Published: January 2011

Background

Macrophomina phaseolinais an emerging and devastating fungal pathogen that causes significant losses in crop production under high temperatures and drought stress. An increasing number of disease incidence reports highlight the wide prevalence of the pathogen around the world and its contribution toward crop yield suppression. In cowpea [Vigna unguiculata(L) Walp.], limited sources of low-level host resistance have been identified, the genetic basis of which is unknown. In this study we report on the identification of strong sources of host resistance toM. phaseolinaand the genetic mapping of putative resistance loci on a cowpea genetic map comprised of gene-derived single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs).

Results

Nine quantitative trait loci (QTLs), accounting for between 6.1 and 40.0% of the phenotypic variance (R2), were identified using plant mortality data taken over three years in field experiments and disease severity scores taken from two greenhouse experiments. Based on annotated genic SNPs as well as synteny with soybean (Glycine max) andMedicago truncatula, candidate resistance genes were found within mapped QTL intervals. QTLMac-2explained the largest percent R2and was identified in three field and one greenhouse experiments where the QTL peak co-located with a SNP marker derived from a pectin esterase inhibitor encoding gene. Maturity effects on the expression of resistance were indicated by the co-location ofMac-6andMac-7QTLs with maturity-related senescence QTLsMat-2andMat-1, respectively. Homologs of theELF4andFLKflowering genes were found in corresponding syntenic soybean regions. Only threeMacrophominaresistance QTLs co-located with delayed drought-induced premature senescence QTLs previously mapped in the same population, suggesting that largely different genetic mechanisms mediate cowpea response to drought stress andMacrophominainfection.

Conclusion

Effective sources of host resistance were identified in this study. QTL mapping and synteny analysis identified genomic loci harboring resistance factors and revealed candidate genes with potential for further functional genomics analysis.
In vivo trafficking and immunostimulatory potential of an intranasally-administered primary dendritic cell-based vaccine
Authors: Vilekar Prachi , Awasthi Vibhudutta , Lagisetty Pallavi , King Catherine , Shankar Nathan , Awasthi Shanjana
Published: January 2011

Background

Coccidioidomycosis or Valley fever is caused by a highly virulent fungal pathogen: Coccidioides posadasii or immitis. Vaccine development against Coccidioides is of contemporary interest because a large number of relapses and clinical failures are reported with antifungal agents. An efficient Th1 response engenders protection. Thus, we have focused on developing a dendritic cell (DC)-based vaccine for coccidioidomycosis. In this study, we investigated the immunostimulatory characteristics of an intranasal primary DC-vaccine in BALB/c mouse strain that is most susceptible to coccidioidomycosis. The DCs were transfected nonvirally with Coccidioides- Ag2/PRA-cDNA. Expression of DC-markers, Ag2/PRA and cytokines were studied by flow cytometry, dot-immunoblotting and cytometric bead array methods, respectively. The T cell activation was studied by assessing the upregulation of activation markers in a DC-T cell co-culture assay. For trafficking, the DCs were co-transfected with a plasmid DNA encoding HSV1 thymidine kinase (TK) and administered intranasally into syngeneic mice. The trafficking and homing of TK-expressing DCs were monitored with positron emission tomography (PET) using 18F-FIAU probe. Based on the PET-probe accumulation in vaccinated mice, selected tissues were studied for antigen-specific response and T cell phenotypes using ELISPOT and flow cytometry, respectively.

Results

We found that the primary DCs transfected with Coccidioides-Ag2/PRA-cDNA were of immature immunophenotype, expressed Ag2/PRA and activated naïve T cells. In PET images and subsequent biodistribution, intranasally-administered DCs were found to migrate in blood, lung and thymus; lymphocytes showed generation of T effector memory cell population (TEM) and IFN-γ release.

Conclusions

In conclusion, our results demonstrate that the intranasally-administered primary DC vaccine is capable of inducing Ag2/PRA-specific T cell response. Unique approaches utilized in our study represent an attractive and novel means of producing and evaluating an autologous DC-based vaccine.
Lack of the pattern recognition molecule mannose-binding lectin increases susceptibility to influenza A virus infection
Authors: Chang Wei-Chuan , White Mitchell R , Moyo Patience , McClear Sheree , Thiel Steffen , Hartshorn Kevan L , Takahashi Kazue
Published: January 2011

Background

Mannose-binding lectin (MBL), a pattern recognition innate immune molecule, inhibits influenza A virus infectionin vitro. MBL deficiency due to gene polymorphism in humans has been associated with infection susceptibility. These clinical observations were confirmed by animal model studies, in which mice genetically lacking MBL were susceptible to certain pathogens, including herpes simplex virus 2.

Results

We demonstrate that MBL is present in the lung of naïve healthy wild type (WT) mice and that MBL null mice are more susceptible to IAV infection. Administration of recombinant human MBL (rhMBL) reverses the infection phenotype, confirming that the infection susceptibility is MBL-mediated. The anti-viral mechanisms of MBL include activation of the lectin complement pathway and coagulation, requiring serum factors. White blood cells (WBCs) in the lung increase in WT mice compared with MBL null mice on day 1 post-infection. In contrast, apoptotic macrophages (MΦs) are two-fold higher in the lung of MBL null mice compared with WT mice. Furthermore, MBL deficient macrophages appear to be susceptible to apoptosisin vitro. Lastly, soluble factors, which are associated with lung injury, are increased in the lungs of MBL null mice during IAV infection. These results suggest that MBL plays a key role against IAV infection.

Conclusion

MBL plays a key role in clearing IAV and maintaining lung homeostasis. In addition, our findings also suggest that MBL deficiency maybe a risk factor in IAV infection and MBL may be a useful adjunctive therapy for IAV infection.
MicroDSC study of Staphylococcus epidermidis growth
Authors: Zaharia Dragos C , Iancu Cezar , Steriade Alexandru T , Muntean Alexandru A , Balint Octavian , Popa Vlad T , Popa Mircea I , Bogdan Miron A
Published: January 2011

Background

A microcalorimetric study was carried out using a Staphylococcus epidermidis population to determine the reproducibility of bacterial growth and the variability of the results within certain experimental parameters (temperature, bacterial concentration, sample thermal history). Reproducibility tests were performed as series of experiments within the same conditions using either freshly prepared populations or samples kept in cold storage. In both cases, the samples were obtained by serial dilution from a concentrated TSB bacterial inoculum incubated overnight.

Results

The results show that experiments are fairly reproducible and that specimens can be preserved at low temperatures (1 - 2°C) at least 4 days. The thermal signal variations at different temperatures and initial bacterial concentrations obey a set of rules that we identified.

Conclusion

Our study adds to the accumulating data and confirms available results of isothermal microcalorimetry applications in microbiology and can be used to standardize this method for either research or clinical setting.
Eukaryotic signaling pathways targeted by Salmonella effector protein AvrA in intestinal infection in vivo
Authors: Liu Xingyin , Lu Rong , Xia Yinglin , Wu Shaoping , Sun Jun
Published: January 2011

Background

The Salmonella AvrA gene is present in 80% of Salmonella enterica serovar strains. AvrA protein mimics the activities of some eukaryotic proteins and uses these activities to the pathogen's advantage by debilitating the target cells, such as intestinal epithelial cells. Therefore, it is important to understand how AvrA works in targeting eukaryotic signaling pathways in intestinal infection in vivo. In this study, we hypothesized that AvrA interacts with multiple stress pathways in eukaryotic cells to manipulate the host defense system. A whole genome approach combined with bioinformatics assays was used to investigate the in vivo genetic responses of the mouse colon to Salmonella with or without AvrA protein expression in the early stage (8 hours) and late stage (4 days). Specifically, we examined the gene expression profiles in mouse colon as it responded to pathogenic Salmonella stain SL1344 (with AvrA expression) or SB1117 (without AvrA expression).

Results

We identified the eukaryotic targets of AvrA and the cell signaling pathways regulated by AvrA in vivo. We found that pathways, such as mTOR, NF-kappaB, platelet-derived growth factors, vascular endothelial growth factor, oxidative phosphorylation, and mitogen-activated protein kinase signaling are specifically regulated by AvrA in vivo and are associated with inflammation, anti-apoptosis, and proliferation. At the early stage of Salmonella infection, AvrA mainly targeted pathways related to nuclear receptor signaling and oxidative phosphorylation. At the late stage of Salmonella infection, AvrA is associated with interferon-gamma responses.

Conclusion

Both early and late phases of the host response exhibit remarkable specificity for the AvrA+ Salmonella. Our studies provide new insights into the eukaryotic molecular cascade that combats Salmonella-associated intestinal infection in vivo.
A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines
Authors: Aoki Kazuma , Harashima Akira , Sano Miho , Yokoi Takahide , Nakamura Shuji , Kibata Masayoshi , Hirose Tetsuro
Published: January 2011

Background

Postgenomic transcriptome analyses have identified large numbers of noncoding (nc)RNAs in mammalian cells. However, the biological function of long ncRNAs in mammalian cells remains largely unknown. Our recent expression profiling of selected human long ncRNAs revealed that a majority were expressed in an organ-specific manner, suggesting their function was linked to specific physiological phenomena in each organ. We investigated the characteristics and function of ncRNAs that were specifically expressed in the thymus, the site of T-cell selection and maturation.

Results

Expression profiling of 10 thymus-specific ncRNAs in 17 T-cell leukemia cell lines derived from various stages of T-cell maturation revealed that HIT14168 ncRNA, named Thy-ncR1, was specifically expressed in cell lines derived from stage III immature T cells in which the neighbouring CD1 gene cluster is also specifically activated. The Thy-ncR1 precursor exhibited complex alternative splicing patterns and differential usage of the 5' terminus leading to the production of an estimated 24 isoforms, which were predominantly located in the cytoplasm. Selective RNAi knockdown of each Thy-ncR1 isoform demonstrated that microfibril-associated glycoprotein 4 (MFAP4) mRNA was negatively regulated by two major Thy-ncR1 isoforms. Intriguingly, the MFAP4 mRNA level was controlled by a hUPF1-dependent mRNA degradation pathway in the cytoplasm distinct from nonsense-mediated decay.

Conclusions

This study identified Thy-ncR1 ncRNA to be specifically expressed in stage III immature T cells in which the neighbouring CD1 gene cluster was activated. Complex alternative splicing produces multiple Thy-ncR1 isoforms. Two major Thy-ncR1 isoforms are cytoplasmic riboregulators that suppress the expression of MFAP4 mRNA, which is degraded by an uncharacterized hUPF1-dependent pathway.
Antillatoxin is a sodium channel activator that displays unique efficacy in heterologously expressed rNav1.2, rNav1.4 and rNav1.5 alpha subunits
Authors: Cao Zhengyu , Gerwick William H , Murray Thomas F
Published: January 2011

Background

Antillatoxin (ATX) is a structurally unique lipopeptide produced by the marine cyanobacteriumLyngbya majuscula. ATX activates voltage-gated sodium channel α-subunits at an undefined recognition site and stimulates sodium influx in neurons. However, the pharmacological properties and selectivity of ATX on the sodium channel α-subunits were not fully characterized.

Results

In this study, we characterized the pharmacological properties and selectivity of ATX in cells heterologously expressing rNav1.2, rNav1.4 or rNav1.5 α-subunits by using the Na+selective fluorescent dye, sodium-binding benzofuran isophthalate. ATX produced sodium influx in cells expressing each sodium channel α-subunit, whereas two other sodium channel activators, veratridine and brevetoxin-2, were without effect. The ATX potency at rNav1.2, rNav1.4 and rNav1.5 did not differ significantly. Similarly, there were no significant differences in the efficacy for ATX-induced sodium influx between rNav1.2, rNav1.4 and rNav1.5 α-subunits. ATX also produced robust Ca2+influx relative to other sodium channel activators in the calcium-permeable DEAA mutant of rNav1.4 α-subunit. Finally, we demonstrated that the 8-demethyl-8,9-dihydro-antillatoxin analog was less efficacious and less potent in stimulating sodium influx.

Conclusions

ATX displayed a unique efficacy with respect to stimulation of sodium influx in cells expressing rNav1.2, rNav1.4 and rNav1.5 α-subunits. The efficacy of ATX was distinctive inasmuch as it was not shared by activators of neurotoxin sites 2 and 5 on VGSC α-subunits. Given the unique pharmacological properties of ATX interaction with sodium channel α-subunits, decoding the molecular determinants and mechanism of action of antillatoxin may provide further insight into sodium channel gating mechanisms.