bluuebunny/crossref_metadata_2025 huggingface dataset:
A multiplex real-time PCR assay for the simultaneous quantification of the major plant-parasitic nematodes in Japan
Authors: Min Yu Yu , Goto Keita , Toyota Koki , Sato Erika
Published: January 2011

Multiplex real-time PCR assays were developed to quantify multiple species of Meloidogyne incognita, Pratylenchus penetrans, Globodera rostochiensis and Heterodera glycines in soil. The probes specific for P. penetrans and H. glycines are labelled with a fluorescence molecule, FAM, and those for M. incognita and G. rostochiensis with ROX. The primers and probes are species-specific to P. penetrans, but group-specific to the other species. DNA was extracted from suspensions containing each nematode and multiplex Cycleave® PCR assays were done for pairs of P. penetrans and M. incognita, P. penetrans and G. rostochiensis, or G. rostochiensis and H. glycines. The results revealed that the target nematode, except for H. glycines, was quantified in the presence of less than 100 times that of the other nematode (competitor), but underestimated in the presence of 1000 times the competitor. Such underestimation was solved by the use of SYBR Green I real time PCR assays targeting a single species. Multiplex PCR assay for P. penetrans and M. incognita was done using environmental DNA (eDNA) extracted from a soil naturally infested with the nematodes. Results quantified both species. Multiplex assay using eDNA may enable a sensitive and simultaneous detection of P. penetrans and M. incognita or P. penetrans and G. rostochiensis in soil although caution is needed in case the existing ratio is biased to one of the species.
Numerical Simulations of Lateral Dispersion by the Relaxation of Diapycnal Mixing Events
Authors: Sundermeyer Miles A. , Lelong M-Pascale
Published: January 2011

In this second of two companion papers, numerical simulations of lateral dispersion by small-scale geostrophic motions, or vortical modes, generated by the adjustment of mixed patches following diapycnal mixing events are examined. A three-dimensional model was used to solve the Navier–Stokes equations and an advection/diffusion equation for a passive tracer. Model results were compared with theoretical predictions for vortical mode stirring with results from dye release experiments conducted over the New England continental shelf. For “weakly nonlinear” cases in which adjustment events were isolated in space and time, lateral dispersion in the model was consistent to within a constant scale factor with the parameter dependencepredicted by Sundermeyer et al., where h and L are the vertical and horizontal scales of the mixed patches, ΔN 2 is the change in stratification associated with the mixed patches, f is the Coriolis parameter, ϕ is the frequency of diapycnal mixing events, and νB is the background viscosity. The associated scale factor, assumed to be of order 1, had an actual value of about 7, although this value will depend, in an unknown way, on the assumed horizontal scale of the mixed patches, which was here held constant at close to the deformation radius. A second more energetic parameter regime was also identified in which vortical mode stirring became strongly nonlinear and the effective lateral dispersion was larger. Estimates of the relevant parameters over the New England shelf suggest that this strongly nonlinear regime is more relevant to the real ocean than the weakly nonlinear regime, at least under late summer conditions. This suggests that stirring by small-scale geostrophic motion may, under certain conditions, contribute significantly to lateral dispersion on scales of 1–10 km in the ocean.
Globalisation, Reflexivity and the Practice of Criminology
Authors: Chan Janet
Published: January 2011

This paper examines recent theorising of broader social and political trends in modern societies and discusses their implications for the practice of criminology. Globalisation has facilitated the “free trade” of criminological knowledge and ideologies and accelerated the deterritorialisation of culture and politics. Under “reflexive modernisation”, the scientific authority of criminology is being challenged, not only from within the discipline in the form of academic critique, but also from without, in the arena of law and order politics. At the same time, criminologists and criminal justice policies are increasingly being “governed” by “technologies of performance” and the “technologies of agency” as part of “reflexive government” in advanced liberal societies.
Deborah's Law: The Effects of Naming and Shaming on Sex Offenders in Australia
Authors: Ronken Carol , Lincoln Robyn
Published: January 2011

Community notification laws for sex offenders are now widespread in the USA and there is considerable interest in introducing ,them in Australia. Along with these public moves to name and shame, there has been a parallel increase in private forms of naming and shaming through “outing” of sex offenders. This article examines both public and private notification to conclude from the few studies available that they fail to achieve their goals and lead to significant unintended consequences. The article analyses The Australian Paedophile and Sex Offender Index (Coddington, 1997), a prime exemplar of the private domain of notification, to explore a range of variables (offender demographics, offence details, sentences, previous convictions and victimology) and concludes that it is unrepresentative and has criminogenic potential. The article summarises direct consequences of notification actions that include possibilities for vigilantism, effects on treatment and rehabilitation, and displacement. Finally, it examines the theoretical frameworks in which notification laws have been couched — restorative justice and criminological notions of shame and degradation — to conclude that notification laws are not supported by these theoretical paradigms
Self-Harm in Western Australian Prisons: Differences Between Prisoners Who Have Self-Harmed and Those Who Have Not
Authors: Dear Greg E. , Thomson Donald M. , Howells Kevin , Hall Guy J.
Published: January 2011

This is the second of two studies that examined self-harm in Western Australian prisons. Data were collected from 71 prisoners who had self-harmed in the previous three days and 71 comparison prisoners for whom there was no evidence of ever having self-harmed in prison. The groups were matched on age, sex, race, custodial status (remanded or sentenced) and placement within the prison. Measures across three –domains (personal background, perceptions of the prison experience and psychological functioning) were administered in a structured interview. The self-harm group reported a significantly greater level of distress, disorder or vulnerability on almost every measure. On no measure did they report lower distress or dysfunction. Two main implications for preventing self-harm are discussed. First, prison authorities need to develop more effective methods for identifying distressed prisoners. Second, strategies should be implemented to minimize prisoners' vulnerability to distress.
Rejection by the Social Order and Delinquent Orientation
Authors: Rathus Spencer A. , Siegel Larry J. , Ruppert Carol-Ann
Published: January 2011

It has been argued that once adolescents are labelled as delinquent, they are systematically rejected by the social order. Thus they should develop antagonism towards the criminal justice system, increased tolerance for proscribed activities, and short-sighted hedonism. These assertions were formulated as null hypotheses, and a comparison of the attitudes of delinquents and non-delinquents, through semantic differential technique, resulted in failure to accept the null hypotheses. Thus, the existence of the predicted attitudes were verified empirically, but it was pointed out that their origins must be confirmed through longitudinal research.
Custody and Conflict: An Organizational Study of Prison Officers' Roles and Attitudes
Authors: Williams Trevor A
Published: January 2011

The study reports on survey research into prison officers' attitudes in the Western Australian Department of Corrections. Drawing on research on a variety of organizations, which provides evidence for the prevalence of “occupational orientations” or “task orientations” among employees, the research tested for significant and systematic relationships between prison officers' attitudes and the characteristics of their organizational roles and role problems. Three commonly observed attitudes of prison officers are their reliance on disciplinary authority, their negative stereotyping of inmates, and their antagonism towards non-custodial staff. The research findings support the hypothesis that such attitudes are directly related to the primary task of prison officers as confining inmates in custody and the conflict with inmates which arises from performing the custodial task. The characteristics and demands of the work itself evidently comprise an important variable in explaining prison officers' attitudes, whereas in most published research on prisons this factor is largely neglected.
Insider trading as an aspect of white collar crime
Authors: Polk Kenneth , Weston William
Published: January 2011

This discussion examines the criminal laws regarding insider trading of the United States, the United Kingdom and Australia. It points out that successful prosecutions in the United States have been aided by the provision of a civil penalty which has both a lower level of proof and potentially much higher financial penalties than exist under current Australian law. Several case studies on insider trading drawn from the United States are described to show how the criminal procedures developed there in the 1980s have resulted in several successful prosecutions. An argument is developed that these US procedures are effective because they address the nature of insider trading as a network of individuals motivated by self interest, where that self interest leads some individuals to cooperate with prosecutors in order to reduce their individual liability. Specific recommendations of proposed Australian legislation are then reviewed.
Lawyers and Police: An Uneasy Marriage in the National Crime Authority's Fight against Organised Crime
Authors: Corns Chris
Published: January 2011

A central feature of new law enforcement agencies, established specifically to combat organised crime in Australia, is their use of internal multi-disciplinary investigation teams. This strategy can be seen as mirroring the structure and modus operandi of the targeted criminal activity. One of the first law enforcement agencies in Australia to 'collectivise' legal and policing skills has been the National Crime Authority. However, aspects of the legal and police 'sub-cultures' are structurally and ideologically inconsistent creating the potential for significant intra-organisational conflict. This article explores the nature and significance of 'cultural clashes' between lawyers and police within the National Crime Authority, and describes a number of unique legal problems arising from the cross-jurisdictional deployment of police officers on secondment to the National Crime Authority. The article argues that in the context of organised crime, sub-cultural dimensions of law enforcement has been a neglected area within criminological research and policy making. The article argues that organisational sub-cultures have limited the capacity of law enforcement agencies to fulfil their junctions and suggests a number of reforms.
Women Doing a Man's Job: Female Prison Officers Working in a Male Prison
Authors: Farnworth Louise
Published: January 2011

This article concerns the integration difficulties of female prison officers working in the traditionally male prison environment at Pentridge Prison. Because the role of prison officer is highly male-stereotyped, it was believed that the integration problems experienced by female prison officers working in male prisons would be accentuated. A semi-structured interview research methodology was used to collect data from 24 female and 21 male prison officers. The findings suggested that the job of a prison officer at Pentridge was highly male-stereotyped, which created several integration difficulties for female officers. However, while female officers may have performed the job differently, they were not disadvantaged promotionally indicating that the organisation recognised them as competent prison officers.
Greedy, Needy, or Troubled? High School and University Students' Natural and Induced Views of Shopstealers
Authors: Lawrence Jeanette A , Hore Philippa
Published: January 2011

Adolescents and university students processed comprehension packages designed to induce them to adopt schemas for categorising shoplifters as either “greedy”, “needy” or “troubled” persons. Adolescents' subsequent views of shoplifters, measured on a Shop Stealing Attitude Questionnaire (SSAQ) were related to schema conditions in expected ways, demonstrating the influence of the comprehension packages. Subjects who processed the package claiming that shopstealers are greedy displayed tougher attitudes to shopstealers, with higher mean Greed and Condemn Scale scores. Subjects who processed packages claiming that shopstealers are either needy or troubled displayed more lenient attitudes with higher Need and Troubled Scale Scores. Younger adolescents showed harsher views, while older adolescents and all females were more understanding of offenders' circumstances and motives. Schema inducing comprehension packages, subjects' ages, and SSAQ measured views were weakly predictive of penalties assigned to offenders in sample cases. Finding? support general trends of younger adolescents'punitiveness in relation to a specific offence, but indicate the difficulties of inexperienced penalisers in assigning penalties.
Beyond the Regulatory State
Authors: Grabosky P N
Published: January 2011

The traditional view of regulation as essentially a governmental function has become outmoded. Regulatory enforcement, and state activity generally, are diminishing. In their place, a devolution of control is occurring which entails the harnessing of private institutions and energies in furtherance of regulatory policy. This paper describes some of these new regulatory forms, and suggests that new private or hybrid regulatory orderings may emerge which are more stringent, yet more subtle, and ultimately more palatable to the target of regulation than conventional state control.
Dangerousness, Risk and Technologies of Power
Authors: Pratt John
Published: January 2011

This paper provides a critical examination of the prevalence of dangerous offender legislation in modern criminal justice systems. The debate about this has been dominated by issues of ethics and effectiveness. Here, though, I want to examine the significance of this legislation and some of the theoretical issues that this raises. This involves discussion of the way in which ‘dangerousness’ as a social construct has changed historically and similarly the mode of its calibration. Ultimately, the dangerousness legislation today involves the use of a largely unnoticed strategy of control — actuarialism; and seems more likely to have an effect on the behaviour of potential victims of crime rather than dangerous offenders themselves.
The Prosecution of Child Sexual Assault: A Survey of NSW DPP Solicitors
Authors: Cashmor Judy
Published: January 2011

Over the last decade, there has been a number of changes in the law and in courtroom procedures in relation to the prosecution of child sexual assault. These changes were intended to ease the restrictions on the admission of children's evidence and to make the experience of testifying less stressful for child witnesses. Court statistics on the outcome of child sexual assault prosecutions and the results of a survey by the NSW Office of the Director of Public Prosecutions (DPP) of prosecuted cases of child sexual assault in New South Wales were examined to throw some light on the way such prosecutions and the child witnesses involved were dealt with in the criminal justice system. One of the major concerns was that while some reforms have allowed more and younger children to give evidence, full advantage has not been taken of other reforms to ease children's experience at court.
Sex, Contagion, Control: Prison Officers vs Condoms in New South Wales Gaols
Authors: Cregar Jan , Kippax Susan , Crawford June
Published: January 2011

Since the beginning of the HIV/AIDS epidemic, public health experts have identified prison populations as a target for preventive strategies in order to minimise transmission of HIV among the general community. Public opinion favours supplying condoms to prisoners, but this was successfully resisted by prison officers in New South Wales for eight years.

This paper examines expert and community opinions, HIV/AIDS and prison policies, public and correctional discourse, and statements made by prison officers' union representatives. It offers an account of the prison officers' success in blocking condom distribution, based on three major discursive themes emerging from the analysis.
Psychometric Prediction of Recividism: Utility of the Risk Needs Inventory
Authors: Cumberland Andrew K , Boyle Gregory J
Published: January 2011

The efficacy of psychometric measures of recidivism is an important issue. Accordingly, the present study examines: (1)the predictive (criterion-related) validity of the Risk Needs Inventory (RNI); (2) whether RNI scores alone are better predictors than are scores moderated by Community Corrections Officers (professional override principle); and (3) whether inclusion of age and marital status as independent variables improves predictive validity. It was found that RNI total and risk category scores for both the unadjusted and override conditions significantly predicted both number and severity of reoffences for in-program and total recidivism measures. Age predicted number and severity of reoffences (inversely), but generally did not add significantly to the variance accounted for by the RNI items. While the RNI appears to have some utility, the prediction of recidivism remains a complex psychometric issue. However, it is likely that use of the RNI provides a more structured/objective assessment of recidivism risk. Although the variance accounted for is small (8–15%), nonetheless, use of the RNI results in correct classification of the majority of offenders. In addition, use of professional override would appear to be essential in order to differentiate between the reoffending behaviours of medium and high risk groups.
Re-forming Justice: The Potential of Maori Processes
Authors: Tauri Juan , Morris Allison
Published: January 2011

There have been a number of calls for the implementation of a separate Maori justice system. This paper examines these calls and the practicalities of moving in this direction by drawing from two pieces of research: first, an exploratory study of the views of more than 50 Maori elders on how Maori communities dealt with offenders in the recent past and how Maori justice practices might work in the modern context; and, second, an examination of the philosophy and practice of family group conferences. The paper concludes that Maori justice processes have the potential not only to provide solutions to the over-representation of Maori in the criminal justice system, but also to re-form conventional justice systems. It advocates a reconciliation of Maori and Pakeha justice systems.
Sentencing the Multiple Offender: Towards Detailed Sentencing Statistics for Armed Robbers
Authors: Lovegrove Austin
Published: January 2011

Recently, Lovegrove developed a decision model describing how judges in Victoria apply the totality principle to determine sentences for offenders convicted on multiple counts. The model, taking the form of a set of working rules, is empirically based but springs from the legal analyses of Thomas and Ashworth. This article describes a new study in which this conceptual framework is used to analyse archival sentencing data in order to show quantitatively the relationship between the effective (head) sentence determined for a case and the component sentences fixed for its comprising counts. The sample comprised 69 multiple-count cases in which armed robbery was the principal offence. They were selected from cases heard in the Victorian Court of Criminal Appeal between 1985 and 1994 (inclusive). The theoretical significance of this work is that it uses archival data to quantify an algebraic model — reciprocal function — representing the judges' approach to this sentencing problem. The practical product of this study is a method for developing, for the assistance of judges, detailed sentencing statistics: these could be used to generate an effective sentence from the sentences fixed for counts comprising a case, according to sentencing practice.
Judicial Sentencing Policy, Criminological Expertise and Public Opinion
Authors: Lovegrove Austin
Published: January 2011

The first part of this article asks whether judicial sentencing can be regarded as founded on a well-informed policy. An analysis of the character of sentencing policy as it is to be found in sentencing judgments, the criminological basis of this policy and an assessment of the public's knowledge of and participation in the development of judicial sentencing policy demonstrates a negative answer is required. A case is then made for the judicial development of a more comprehensive and criminologically well-founded policy and for appropriate community involvement in this process. Finally, a scheme is proposed to facilitate these two outcomes: judicial sentencing policy could then be regarded as well informed.
Moral Tales: Representations of Child Abuse in the Quality and Tabloid Media
Authors: Wilczynski Ania , Sinclair Kate
Published: January 2011

Although child abuse is a favourite topic for media stories, there has been little research on how the media portrays such issues. The present research examined the media construction of child abuse in a comprehensive sample of all 1302 reports on the subject during 1995 in a representative quality and tabloid newspaper in NSW. It was found that: the focus was on ‘hard news’ reports of individual cases and the most atypical and sensational ‘child abuse horror stories’; irony or incongruity between the offence and the offender was emphasised; child abuse was popular as a topic for ‘soft news’ (human interest) media stories; criminal justice agencies were the predominant sources used for the stories; child abusers were individualised and demonised by the press and used to promote ‘law and order’ agendas; and there was little coverage of the social causes of abuse and prevention issues. Although both the quality and tabloid press demonstrated these features, there were some marked differences between the coverage in the two sources, such as a much greater emphasis on individual cases in the tabloid press.
Evaluation of Immunohistochemical Fine Sectioning for Sentinel Lymph Node Biopsy in Oral Squamous Cell Carcinoma
Authors: Jefferson Gina D. , Sollaccio David , Gomez‐Fernandez Carmen R. , Civantos Francisco
Published: January 2011

Objective

To determine the level of sentinel lymph node sectioning necessary to accurately detect nodal micrometastasis.

Study Design

Cross‐sectional.

Setting

Tertiary care university medical center.

Subjects and Methods

Fine sections of oral squamous cell carcinoma sentinel lymph nodes previously sectioned at 2‐mm intervals in a prospective clinical trial were reexamined. The results yielded from prior hematoxylin and eosin and immunohistochemical staining were compared with results following exhaustive serial sectioning at 150‐µm intervals using identical staining methods. These experimental findings were compared with pathologic results of immediate completion selective neck dissection, previously recorded prospectively.

Results

Reexamination of 35 sentinel nodes at 150‐µm intervals has not revealed any missed micrometastatic disease at 2‐mm intervals used initially. Both comparisons of 150‐µm sectioning analysis to the original 2‐mm section samples and to the neck dissection pathology reports demonstrate a 100% negative predictive value.

Conclusion

These data suggest that sentinel lymph node sectioning at 2‐mm intervals for oral carcinoma using hematoxylin and eosin staining and then immunohistochemical analysis maximizes efficiency, accuracy, and expenditure for the detection of micrometastasis.
Aberrant interferon-signaling is associated with aggressive chronic lymphocytic leukemia
Authors: Tomic Jelena , Lichty Brian , Spaner David E.
Published: January 2011

The type I interferons (IFNs) normally suppress tumor growth by phosphorylating and activating the signal transducer and activator of transcription 1 (STAT1), but also briefly activate STAT3, which promotes cell growth. In chronic lymphocytic leukemia (CLL) cells, the duration of IFN-mediated STAT3 phosphorylation was found to exhibit significant interpatient variability and was prolonged in cells with high risk features, such as 11q− and 17p− deletions involving ataxia telangiectasia mutated (ATM) and p53. This aberrant signaling pattern was associated with a paradoxical increase in cell size and number in response to IFN and similar alterations in IFN-signaling and responses were seen in cell lines that developed in the absence of p53 or ATM. However, direct inhibition of p53 or ATM failed to cause these changes, and CLL cells with aggressive clinical features were found to also express high levels of reactive oxygen species (ROS), which decrease tyrosine phosphatase activity. Prolonged IFN-mediated STAT3 phosphorylation and lowered phosphatase activity could be reversed by antioxidants. These findings suggest that increased ROS levels may corrupt IFN-signaling processes in aggressive CLL cells, causing IFN to be used as a growth factor rather than a tumor suppressor. Antioxidants or STAT3 kinase inhibitors might improve the outcome of IFN therapy in CLL by restoring normal signaling.
Systemic perturbation of cytokine and chemokine networks in Erdheim-Chester disease: a single-center series of 37 patients
Authors: Arnaud Laurent , Gorochov Guy , Charlotte Frédéric , Lvovschi Virginie , Parizot Christophe , Larsen Martin , Ghillani-Dalbin Pascale , Hervier Baptiste , Kahn Jean-Emmanuel , Deback Claire , Musset Lucile , Amoura Zahir , Haroche Julien
Published: January 2011

Immunopathogenesis of Erdheim-Chester disease (ECD), a rare non–Langerhans cell histiocytosis, is poorly known. In previous studies, various cytokines were detected in ECD lesions, presumably orchestrating lesional histiocyte recruitment. Because ECD lesions are frequently associated with systemic symptoms, we postulated that underlying global immune perturbations might also be revealed. We quantitatively analyzed 23 cytokines in serum samples obtained from a large single-center cohort of 37 patients with ECD, and studied the impact of treatment on cytokine production. IL-6, IL-12, interferon-α (IFN-α), and monocyte chemotactic protein-1 (MCP-1) levels were significantly higher in untreated patients than in controls, whereas interferon-γ (IFN-γ) inducible protein 10, IL-12, MCP-1, and IL-1 receptor antagonist were found significantly increased in IFN-α–treated patients. A biomathematical approach was used to rationalize multiparameter data, to generate new hypotheses, and identify global control pathways. Interestingly, cytokine profiles proved to be particularly stable at the individual level, and an “ECD signature” further distinguished patients from controls, based on their production of IFN-α, IL-12, MCP-1, IL-4, and IL-7. Altogether, our data underline the systemic immune Th-1–oriented perturbation associated with this condition and provide clues for the choice of more focused therapeutic agents in this rare disease with noncodified therapeutic management.
Genetic diversity of selected genes that are potentially economically important in feral sheep of New Zealand
Authors: McKenzie Grant W , Abbott Johanna , Zhou Huitong , Fang Qian , Merrick Norma , Forrest Rachel H , Sedcole J Richard , Hickford Jonathan G
Published: January 2011

Background

Feral sheep are considered to be a source of genetic variation that has been lost from their domestic counterparts through selection.

Methods

This study investigates variation in the genes KRTAP1-1, KRT33, ADRB3 and DQA2 in Merino-like feral sheep populations from New Zealand and its offshore islands. These genes have previously been shown to influence wool, lamb survival and animal health.

Results

All the genes were polymorphic, but no new allele was identified in the feral populations. In some of these populations, allele frequencies differed from those observed in commercial Merino sheep and other breeds found in New Zealand. Heterozygosity levels were comparable to those observed in other studies on feral sheep. Our results suggest that some of the feral populations may have been either inbred or outbred over the duration of their apparent isolation.

Conclusion

The variation described here allows us to draw some conclusions about the likely genetic origin of the populations and selective pressures that may have acted upon them, but they do not appear to be a source of new genetic material, at least for these four genes.
The complexity of gene expression dynamics revealed by permutation entropy
Authors: Sun Xiaoliang , Zou Yong , Nikiforova Victoria , Kurths Jürgen , Walther Dirk
Published: January 2011

Background

High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity.

Results

Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes.

Conclusions

We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data.
MBAT: A scalable informatics system for unifying digital atlasing workflows
Authors: Lee Daren , Ruffins Seth , Ng Queenie , Sane Nikhil , Anderson Steve , Toga Arthur
Published: January 2011

Background

Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data.

Results

The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data.

Conclusions

MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows.
Galaxy CloudMan: delivering cloud compute clusters
Authors: Afgan Enis , Baker Dannon , Coraor Nate , Chapman Brad , Nekrutenko Anton , Taylor James
Published: January 2011

Background

Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists.

Results

We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs.

Conclusions

The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.
DNA damage-induced translocation of S100A11 into the nucleus regulates cell proliferation
Authors: Gorsler Theresa , Murzik Ulrike , Ulbricht Tobias , Hentschel Julia , Hemmerich Peter , Melle Christian
Published: January 2011

Background

Proteins are able to react in response to distinct stress stimuli by alteration of their subcellular distribution. The stress-responsive protein S100A11 belongs to the family of multifunctional S100 proteins which have been implicated in several key biological processes. Previously, we have shown that S100A11 is directly involved in DNA repair processes at damaged chromatin in the nucleus. To gain further insight into the underlying mechanism subcellular trafficking of S100A11 in response to DNA damage was analyzed.

Results

We show that DNA damage induces a nucleolin-mediated translocation of S100A11 from the cytoplasm into the nucleus. This translocation is impeded by inhibition of the phosphorylation activity of PKCα. Translocation of S100A11 into the nucleus correlates with an increased cellular p21 protein level. Depletion of nucleolin by siRNA severely impairs translocation of S100A11 into the nucleus resulting in a decreased p21 protein level. Additionally, cells lacking nucleolin showed a reduced colony forming capacity.

Conclusions

These observations suggest that regulation of the subcellular distribution of S100A11 plays an important role in the DNA damage response and p21-mediated cell cycle control.
A sensitive and bright single-cell resolution live imaging reporter of Wnt/ß-catenin signaling in the mouse
Authors: Ferrer-Vaquer Anna , Piliszek Anna , Tian Guangnan , Aho Robert J , Dufort Daniel , Hadjantonakis Anna-Katerina
Published: January 2011

Background

Understanding the dynamic cellular behaviors and underlying molecular mechanisms that drive morphogenesis is an ongoing challenge in biology. Live imaging provides the necessary methodology to unravel the synergistic and stereotypical cell and molecular events that shape the embryo. Genetically-encoded reporters represent an essential tool for live imaging. Reporter strains can be engineered by placingcis-regulatory elements of interest to direct the expression of a desired reporter gene. In the case of canonical Wnt signaling, also referred to as Wnt/β-catenin signaling, since the downstream transcriptional response is well understood, reporters can be designed that reflect sites of active Wnt signaling, as opposed to sites of gene transcription, as is the case with many fluorescent reporters. However, even though several transgenic Wnt/β-catenin reporter strains have been generated, to date, none provides the single-cell resolution favored for live imaging studies.

Results

We have placed six copies of a TCF/Lef responsive element and anhsp68minimal promoter in front of a fluorescent protein fusion comprising human histone H2B to GFP and used it to generate a strain of mice that would report Wnt/β-catenin signaling activity. Characterization of developmental and adult stages of the resultingTCF/Lef:H2B-GFPstrain revealed discrete and specific expression of the transgene at previously characterized sites of Wnt/β-catenin signaling. In support of the increased sensitivity of theTCF/Lef:H2B-GFPreporter, additional sites of Wnt/β-catenin signaling not documented with other reporters but identified through genetic and embryological analysis were observed. Furthermore, the sub-cellular localization of the reporter minimized reporter perdurance, and allowed visualization and tracking of individual cells within a cohort, so facilitating the detailed analysis of cell behaviors and signaling activity during morphogenesis.

Conclusion

By combining the Wnt activity read-out efficiency of multimerized TCF/Lef DNA binding sites, together with the high-resolution imaging afforded by subcellularly-localized fluorescent fusion proteins such as H2B-GFP, we have created a mouse transgenic line that faithfully recapitulates Wnt signaling activity at single-cell resolution. TheTCF/Lef:H2B-GFPreporter represents a unique tool for live imaging thein vivoprocesses triggered by Wnt/β-catenin signaling, and thus should help the formulation of a high-resolution understanding of the serial events that define the morphogenetic process regulated by this signaling pathway.
Incomplete concerted evolution and reproductive isolation at the rDNA locus uncovers nine cryptic species within Anopheles longirostrisfrom Papua New Guinea
Authors: Alquezar David E , Hemmerter Stephane , Cooper Robert D , Beebe Nigel W
Published: January 2011

Background

Nuclear ribosomal DNA (rDNA) genes and transcribed spacers are highly utilized as taxonomic markers in metazoans despite the lack of a cohesive understanding of their evolution. Here we follow the evolution of the rDNA second internal transcribed spacer (ITS2) and the mitochondrial DNA cytochrome oxidase I subunit in the malaria mosquito Anopheles longirostris from Papua New Guinea (PNG). This morphospecies inhabits a variety of ecological environments indicating that it may comprise a complex of morphologically indistinguishable species. Using collections from over 70 sites in PNG, the mtDNA was assessed via direct DNA sequencing while the ITS2 was assessed at three levels - crude sequence variation through restriction digest, intragenomic copy variant organisation (homogenisation) through heteroduplex analysis and DNA sequencing via cloning.

Results

Genetic evaluation of over 300 individuals revealed that A. longirostris comprises eight ITS2 PCR-RFLP genotypes and nine ITS2 heteroduplex genotypes showing distinct copy variant organization profiles after PCR amplification. Seven of these nine genotypes were found to be sympatric with other genotypes. Phylogenetic analysis of cloned ITS2 PCR products and mtDNA COI confirmed all nine clades with evidence of reproductive isolation at the rDNA locus. Compensatory base changes in the ITS2 secondary structure or in pseudoknots were absent when closely related species were assessed. Individuals from each ITS2 genotype showed the same copy variant heteroduplex profile suggesting that the rDNA array is fixed within each genotype.

Conclusion

The centromere-proximal position of the rDNA array in Anopheles mosquitoes has probably reduced interchromosomal recombination leaving intrachromosomal events responsible for the observed pattern of concerted evolution we see in these mosquitoes. The stability of these intragenomic ITS2 copy variants within individuals and interbreeding populations suggests that rDNA is moving as a single evolutionary unit through natural populations to fixation and has provided a complementary diagnostic tool to the restriction digest for studying genetic discontinuities and species boundaries. In this, the utility of the ITS2 as a universal taxonomic marker is probably contingent on several factors pertaining to spacer dimensions and the genomic location of the rDNA array with respect to recombination and proximity to regions potentially under selection.
Genomic mapping of social behavior traits in a F2 cross derived from mice selectively bred for high aggression
Authors: Nehrenberg Derrick L , Wang Shiliang , Buus Ryan J , Perkins James , de Villena Fernando Pardo-Manuel , Pomp Daniel
Published: January 2011

Background

Rapid response to selection was previously observed in mice selected for high levels of inter-male aggression based on number of attacks displayed in a novel social interaction test after isolation housing. Attack levels in this high aggression line (NC900) increased significantly within just four generations of selective breeding, suggesting the presence of a locus with large effect. We conducted an experiment using a small (n ≈ 100) F2 cross between the ICR-derived, non-inbred NC900 strain and the low aggression inbred strain C57BL/6J, genotyped for 154 fully informative SNPs, to determine if a locus with large effect controls the high-aggression selection trait. A second goal was to use high density SNP genotyping (n = 549,000) in the parental strains to characterize residual patterns of heterozygosity within NC900, and evaluate regions that are identical by descent (IBD) between NC900 and C57BL/6J, to determine what impacts these may have on accuracy and resolution of quantitative trait locus (QTL) mapping in the F2 cross.

Results

No evidence for a locus with major effect on aggressive behavior in mice was identified. However, several QTL with genomewide significance were mapped for aggression on chromosomes 7 and 19 and other social behavior traits on chromosomes 4, 7, 14, and 19. High density genotyping revealed that 28% of the genome is still segregating among the six NC900 females used to originate the F2 cross, and that segregating regions are present on every chromosome but are of widely different sizes. Regions of IBD between NC900 and C57BL/6J are found on every chromosome but are most prominent on chromosomes 10, 16 and X. No significant differences were found for amounts of heterozygosity or prevalence of IBD in QTL regions relative to global analysis.

Conclusions

While no major gene was identified to explain the rapid selection response in the NC900 line, transgressive variation (i.e. where the allele from the C57BL/6J increased attack levels) and a significant role for dominant gene action were hallmarks of the genetic architecture for aggressive behavior uncovered in this study. The high levels of heterozygosity and the distribution of minor allele frequency observed in the NC900 population suggest that maintenance of heterozygosity may have been under selection in this line.
De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq
Authors: Mizrachi Eshchar , Hefer Charles A , Ranik Martin , Joubert Fourie , Myburg Alexander A
Published: January 2011

Background

De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a Eucalyptus tree species (E. grandis) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.

Results

We present an extensive expressed gene catalog for a commercially grown E. grandis × E. urophylla hybrid clone constructed using only Illumina mRNA-Seq technology and de novo assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any Eucalyptus tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions.

Conclusions

De novo assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in Eucalyptus and other non-model organisms. The transcriptome resource (Eucspresso, http://eucspresso.bi.up.ac.za/) generated by this study will be of value for genomic analysis of woody biomass production in Eucalyptus and for comparative genomic analysis of growth and development in woody and herbaceous plants.