A versatile and reliable two-component system for tissue-specific gene induction in Arabidopsis

Developmental progression and differentiation of distinct cell types depend on the regulation of gene expression in space and time. Tools that allow spatial and temporal control of gene expression are crucial for the accurate elucidation of gene function. Most systems to manipulate gene expression allow control of only one factor, space or time, and currently available systems that control both temporal and spatial expression of genes have their limitations. We have developed a versatile two-component system that overcomes these limitations, providing reliable, conditional gene activation in restricted tissues or cell types. This system allows conditional tissue-specific ectopic gene expression and provides a tool for conditional cell type- or tissue-specific complementation of mutants. The chimeric transcription factor XVE, in conjunction with Gateway recombination cloning technology, was used to generate a tractable system that can efficiently and faithfully activate target genes in a variety of cell types. Six promoters/enhancers, each with different tissue specificities (including vascular tissue, trichomes, root, and reproductive cell types), were used in activation constructs to generate different expression patterns of XVE. Conditional transactivation of reporter genes was achieved in a predictable, tissue-specific pattern of expression, following the insertion of the activator or the responder T-DNA in a wide variety of positions in the genome. Expression patterns were faithfully replicated in independent transgenic plant lines. Results demonstrate that we can also induce mutant phenotypes using conditional ectopic gene expression. One of these mutant phenotypes could not have been identified using noninducible ectopic gene expression approaches.

Cluster-based network model for time-course gene expression data

We propose a model-based approach to unify clustering and network modeling using time-course gene expression data. Specifically, our approach uses a mixture model to cluster genes. Genes within the same cluster share a similar expression profile. The network is built over cluster-specific expression profiles using state-space models. We discuss the application of our model to simulated data as well as to time-course gene expression data arising from animal models on prostate cancer progression. The latter application shows that with a combined statistical/bioinformatics analyses, we are able to extract gene-to-gene relationships supported by the literature as well as new plausible relationships.

Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi) reveals large

Conifers are resistant to attack from a large number of potential herbivores or pathogens. Previous molecular and biochemical characterization of selected conifer defence systems support a model of multigenic, constitutive and induced defences that act on invading insects via physical, chemical, biochemical or ecological (multitrophic) mechanisms. However, the genomic foundation of the complex defence and resistance mechanisms of conifers is largely unknown. As part of a genomics strategy to characterize inducible defences and possible resistance mechanisms of conifers against insect herbivory, we developed a cDNA microarray building upon a new spruce (Picea spp.) expressed sequence tag resource. This first-generation spruce cDNA microarray contains 9720 cDNA elements representing c. 5500 unique genes. We used this array to monitor gene expression in Sitka spruce (Picea sitchensis) bark in response to herbivory by white pine weevils (Pissodes strobi, Curculionidae) or wounding, and in young shoot tips in response to western spruce budworm (Choristoneura occidentalis, Lepidopterae) feeding. Weevils are stem-boring insects that feed on phloem, while budworms are foliage feeding larvae that consume needles and young shoot tips. Both insect species and wounding treatment caused substantial changes of the host plant transcriptome detected in each case by differential gene expression of several thousand array elements at 1 or 2 d after the onset of treatment. Overall, there was considerable overlap among differentially expressed gene sets from these three stress treatments. Functional classification of the induced transcripts revealed genes with roles in general plant defence, octadecanoid and ethylene signalling, transport, secondary metabolism, and transcriptional regulation. Several genes involved in primary metabolic processes such as photosynthesis were down-regulated upon insect feeding or wounding, fitting with the concept of dynamic resource allocation in plant defence. Refined expression analysis using gene-specific primers and real-time PCR for selected transcripts was in agreement with microarray results for most genes tested. This study provides the first large-scale survey of insect-induced defence transcripts in a gymnosperm and provides a platform for functional investigation of plant-insect interactions in spruce. Induction of spruce genes of octadecanoid and ethylene signalling, terpenoid biosynthesis, and phenolic secondary metabolism are discussed in more detail.

Response to the apology : Queenslanders reflect : a State Library of Queensland project

On the 13th February 2008 Prime Minister Kevin Rudd made an apology to Australia’s Indigenous Peoples on behalf of the Australian Parliament. The State Library of Queensland (SLQ) with assistance from Queensland University of Technology and Queensland’s Aboriginal and Torres Strait Islander communities, has captured responses to this historic event. ‘Responses to the 2008 Apology’ is a collection of digital stories created as part of this research initiative. Until recently, digital storytelling has not generally been treated as a necessary addition to the research collections of Australian libraries. However, libraries increasingly aim to promote new literacies and active audiences as they seek innovative ways to encourage life-long learning by their users, and digital storytelling is one methodology that can contribute to these goals. The State Library of Queensland is the only Australian State Library to have undertaken a major role in the collection of digital stories. They currently lead the way with their Queensland Stories digital storytelling program. This presentation will report findings and outcomes from this research project.

Nuclear localization of NPR1 is required for activation of PR gene expression

Systemic acquired resistance (SAR) is a broad-spectrum resistance in plants that involves the upregulation of a battery of pathogenesis-related (PR) genes. NPR1 is a key regulator in the signal transduction pathway that leads to SAR. Mutations in NPR1 result in a failure to induce PR genes in systemic tissues and a heightened susceptibility to pathogen infection, whereas overexpression of the NPR1 protein leads to increased induction of the PR genes and enhanced disease resistance. We analyzed the subcellular localization of NPR1 to gain insight into the mechanism by which this protein regulates SAR. An NPR1–green fluorescent protein fusion protein, which functions the same as the endogenous NPR1 protein, was shown to accumulate in the nucleus in response to activators of SAR. To control the nuclear transport of NPR1, we made a fusion of NPR1 with the glucocorticoid receptor hormone binding domain. Using this steroid-inducible system, we clearly demonstrate that nuclear localization of NPR1 is essential for its activity in inducing PR genes.

Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR–1 gene

The Arabidopsis thaliana NPR1 has been shown to be a key regulator of gene expression during the onset of a plant disease-resistance response known as systemic acquired resistance. The npr1 mutant plants fail to respond to systemic acquired resistance-inducing signals such as salicylic acid (SA), or express SA-induced pathogenesis-related (PR) genes. Using NPR1 as bait in a yeast two-hybrid screen, we identified a subclass of transcription factors in the basic leucine zipper protein family (AHBP-1b and TGA6) and showed that they interact specifically in yeast and in vitro with NPR1. Point mutations that abolish the NPR1 function in A. thaliana also impair the interactions between NPR1 and the transcription factors in the yeast two-hybrid assay. Furthermore, a gel mobility shift assay showed that the purified transcription factor protein, AHBP-1b, binds specifically to an SA-responsive promoter element of the A. thaliana PR-1 gene. These data suggest that NPR1 may regulate PR-1 gene expression by interacting with a subclass of basic leucine zipper protein transcription factors.

Molecular analysis of the myosin gene family in Arabidopsis thaliana

Myosin is believed to act as the molecular motor for many actin-based motility processes in eukaryotes. It is becoming apparent that a single species may possess multiple myosin isoforms, and at least seven distinct classes of myosin have been identified from studies of animals, fungi, and protozoans. The complexity of the myosin heavy-chain gene family in higher plants was investigated by isolating and characterizing myosin genomic and cDNA clones from Arabidopsis thaliana. Six myosin-like genes were identified from three polymerase chain reaction (PCR) products (PCR1, PCR11, PCR43) and three cDNA clones (ATM2, MYA2, MYA3). Sequence comparisons of the deduced head domains suggest that these myosins are members of two major classes. Analysis of the overall structure of the ATM2 and MYA2 myosins shows that they are similar to the previously-identified ATM1 and MYA1 myosins, respectively. The MYA3 appears to possess a novel tail domain, with five IQ repeats, a six-member imperfect repeat, and a segment of unique sequence. Northern blot analyses indicate that some of the Arabidopsis myosin genes are preferentially expressed in different plant organs. Combined with previous studies, these results show that the Arabidopsis genome contains at least eight myosin-like genes representing two distinct classes.

Preparing library staff for research support services at QUT

INTRODUCTION: Queensland University of Technology (QUT) Library is partnering with High Performance Computing (HPC) services and the Division of Research and Commercialisation to develop and deliver a range of integrated research support services and systems designed to enhance the research capabilities of the University. Existing and developing research support services include - support for publishing strategies including open access, bibliographic citation and ranking services, research data management, use of online collaboration tools, online survey tools, quantitative and qualitative data analysis, content management and storage solutions. In order to deliver timely and effective research referral and support services, it is imperative that library staff maintain their awareness of, and develop expertise in new eResearch methods and technologies. ---------- METHODS: In 2009/10 QUT Library initiated an online survey for support staff and researchers and a series of focus groups for researchers aimed at gaining a better understanding of current and future eresearch practices and skills. These would better inform the development of a research skills training program and the development of new research support services. The Library and HPC also implemented a program of seminars and workshops designed to introduce key library staff to a broad range of eresearch concepts and technologies. Feedback was obtained after each training session. A number of new services were implemented throughout 2009 and 2010. ---------- RESULTS: Key findings of the survey and focus groups are related to the development of the staff development program. Feedback from program attendees is provided and evaluated. The staff development program is assessed in terms of its success to support the implementation of new research support services. --------- CONCLUSIONS QUT Library has embarked on an ambitious awareness and skills development program to assist Library staff transition a period of rapid change and broadening scope for the Library. Successes and challenges of the program are discussed. A number of recommendations are made in retrospect and also looking forward to the future training needs of Library staff to support the University’s future research goals.

Becoming “Librarian 2.0” : the skills, knowledge, and attributes required by library and information science professionals in a Web 2.0 world (and beyond)

In 2005, Stephen Abram, vice president of Innovation at SirsiDynix, challenged library and information science (LIS) professionals to start becoming “librarian 2.0.” In the last few years, discussion and debate about the “core competencies” needed by librarian 2.0 have appeared in the “biblioblogosphere” (blogs written by LIS professionals). However, beyond these informal blog discussions few systematic and empirically based studies have taken place. This article will discuss a research project that fills this gap. Funded by the Australian Learning and Teaching Council, the project identifies the key skills, knowledge, and attributes required by “librarian 2.0.” Eighty-one members of the Australian LIS profession participated in a series of focus groups. Eight themes emerged as being critical to “librarian 2.0”: technology, communication, teamwork, user focus, business savvy, evidence based practice, learning and education, and personal traits. This article will provide a detailed discussion on each of these themes. The study’s findings also suggest that “librarian 2.0” is a state of mind, and that the Australian LIS profession is undergoing a significant shift in “attitude.”