Plant genomics – a way forward?

This report was presented at the UK Organic Research 2002 Conference. Diseases of plants cause significant losses in crop yield and quality. Plants contain a battery of genes whose role is to prevent pathogens invading. Their effective use in crop plants is very important in crop production and especially in chemical free cropping systems. Such genes are introduced into crop varieties by plant breeding. The new science of genomics may enable scientists to recognise all the resistance genes present in a plant. This will eventually allow plant breeders to more precisely and rapidly select useful resistant plants in their breeding programmes. Furthermore, genomics could enable effective deployment of these genes in cropping systems, so providing more durable resistance

From bench to bountiful harvests : a road map for the next decade of Arabidopsis research

In the face of an increasing world population and climate instability, the demands for food and fuel will continue to rise. Plant science will be crucial to help meet these exponentially increasing requirements for food and fuel supplies. Fundamental plant research will play a major role in providing key advances in our understanding of basic plant processes that can then flow into practical advances through knowledge sharing and collaborations. The model plant Arabidopsis thaliana has played a major role in our understanding of plant biology, and the Arabidopsis community has developed many tools and resources to continue building on this knowledge. Drawing from previous experience of internationally coordinated projects, The international Arabidopsis community, represented by the Multinational Arabidopsis Steering Committee (MASC), has drawn up a road map for the next decade of Arabidopsis research to inform scientists and decision makers on the future foci of Arabidopsis research within the wider plant science landscape. This article provides a summary of the MASC road map

Graphite core brick crack detection through automated load trace analysis

This presentation looks at graphite core brick crack detection through automated load trace analysi

MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using fluorescence activated cell sorting

Changes in gene expression form a crucial part of the plant response to infection. In the last decade, whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant Arabidopsis thaliana and a diverse range of pathogens. However, with some pathogens such as downy mildew caused by the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis (Hpa), whole-leaf profiling may fail to capture the complete Arabidopsis response encompassing responses of non-infected as well as infected cells within the leaf. Highly localized expression changes that occur in infected cells may be diluted by the comparative abundance of non-infected cells. Furthermore, local and systemic Hpa responses of a differing nature may become conflated. To address this we applied the technique of Fluorescence Activated Cell Sorting (FACS), typically used for analyzing plant abiotic responses, to the study of plant-pathogen interactions. We isolated haustoriated (Hpa-proximal) and non-haustoriated (Hpa-distal) cells from infected seedling samples using FACS, and measured global gene expression. When compared with an uninfected control, 278 transcripts were identified as significantly differentially expressed, the vast majority of which were differentially expressed specifically in Hpa-proximal cells. By comparing our data to previous, whole organ studies, we discovered many highly locally regulated genes that can be implicated as novel in the Hpa response, and that were uncovered for the first time using our sensitive FACS technique

The impact of citrate introduction at UK syringe exchange programmes: a retrospective cohort study in Cheshire and Merseyside, UK

<p>Abstract</p> <p>Background</p> <p>In 2003, it became legal in the UK for syringe exchange programmes (SEPs) to provide citrate to injecting drug users to solubilise heroin. Little work has been undertaken on the effect of policy change on SEP function. Here, we examine whether the introduction of citrate in Cheshire and Merseyside SEPs has altered the number of heroin/crack injectors accessing SEPs, the frequency at which heroin/crack injectors visited SEPs and the number of syringes dispensed.</p> <p>Methods</p> <p>Eleven SEPs in Cheshire and Merseyside commenced citrate provision in 2003. SEP-specific data for the six months before and six months after citrate was introduced were extracted from routine monitoring systems relating to heroin and crack injectors. Analyses compared all individuals attending pre and post citrate and matched analyses only those individuals attending in both periods (defined as 'longitudinal attenders'). Non-parametric tests were used throughout.</p> <p>Results</p> <p>Neither new (first seen in either six months period) nor established clients visited SEPs more frequently post citrate. New clients collected significantly less syringes per visit post citrate, than pre citrate (14.5,10.0; z = 1.992, P < 0.05). Matched pair analysis showed that the median number of visits for 'longitudinal attenders' (i.e. those who attended in both pre and post citrate periods) increased from four pre citrate to five post citrate (z = 2.187, P < 0.05) but the number of syringes collected remained unchanged. These changes were not due to seasonal variation or other changes in service configuration.</p> <p>Conclusion</p> <p>The introduction of citrate did not negatively affect SEP attendance. 'Longitudinal attenders' visited SEPs more frequently post citrate, providing staff with greater opportunity for intervention and referral. As the number of syringes they collected each visit remained unchanged the total number of clean syringes made available to this group of injectors increased very slightly between the pre and post citrate periods. However, new clients collected significantly less syringes post citrate than pre citrate, possibly due to staff concerns regarding the amount of citrate (and thus syringes) to dispense safely to new clients. These concerns should not be allowed to negatively impact on the number of syringes dispensed.</p

Constraining the nuclear equation of state at subsaturation densities

Only one third of the nucleons in $^{208}$Pb occupy the saturation density area. Consequently nuclear observables related to average properties of nuclei, such as masses or radii, constrain the equation of state (EOS) not at saturation density but rather around the so-called crossing density, localised close to the mean value of the density of nuclei: $\rho\simeq$0.11 fm$^{-3}$. This provides an explanation for the empirical fact that several EOS quantities calculated with various functionals cross at a density significantly lower than the saturation one. The third derivative M of the energy at the crossing density is constrained by the giant monopole resonance (GMR) measurements in an isotopic chain rather than the incompressibility at saturation density. The GMR measurements provide M=1110 $\pm$ 70 MeV (6% uncertainty), whose extrapolation gives K$_\infty$=230 $\pm$ 40 MeV (17% uncertainty).Comment: 4 pages, 4 figure

Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research

The \u3ci\u3ePseudomonas syringae\u3c/i\u3e type III effector HopD1 suppresses effector-triggered immunity, localizes to the endoplasmic reticulum, and targets the Arabidopsis transcription factor NTL9

Pseudomonas syringae type III effectors are known to suppress plant immunity to promote bacterial virulence. However, the activities and targets of these effectors are not well understood. We used genetic, molecular, and cell biology methods to characterize the activities, localization, and target of the HopD1 type III effector in Arabidopsis. HopD1 contributes to P. syringae virulence in Arabidopsis and reduces effector-triggered immunity (ETI) responses but not pathogen-associated molecular pattern-triggered immunity (PTI) responses. Plants expressing HopD1 supported increased growth of ETI-inducing P. syringae strains compared with wild-type Arabidopsis. We show that HopD1 interacts with the membrane-tethered Arabidopsis transcription factor NTL9 and demonstrate that this interaction occurs at the endoplasmic reticulum (ER). A P. syringae hopD1 mutant and ETI-inducing P. syringae strains exhibited enhanced growth on Arabidopsis ntl9 mutant plants. Conversely, growth of P. syringae strains was reduced in plants expressing a constitutively active NTL9 derivative, indicating that NTL9 is a positive regulator of plant immunity. Furthermore, HopD1 inhibited the induction of NTL9-regulated genes during ETI but not PTI. HopD1 contributes to P. syringae virulence in part by targeting NTL9, resulting in the suppression of ETI responses but not PTI responses and the promotion of plant pathogenicity

CATMA: a complete Arabidopsis GST database

The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a complete reannotation of the genome using uniform parameters. The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.or