The Paediatric Rheumatology International Trials Organisation provisional criteria for the evaluation of response to therapy in juvenile dermatomyositis.

Objective To develop a provisional definition for the evaluation of response to therapy in juvenile dermatomyositis (DM) based on the Paediatric Rheumatology International Trials Organisation juvenile DM core set of variables. Methods Thirty-seven experienced pediatric rheumatologists from 27 countries achieved consensus on 128 difficult patient profiles as clinically improved or not improved using a stepwise approach (patient's rating, statistical analysis, definition selection). Using the physicians' consensus ratings as the “gold standard measure,” chi-square, sensitivity, specificity, false-positive and-negative rates, area under the receiver operating characteristic curve, and kappa agreement for candidate definitions of improvement were calculated. Definitions with kappa values >0.8 were multiplied by the face validity score to select the top definitions. Results The top definition of improvement was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 1 of the remaining worsening by more than 30%, which cannot be muscle strength. The second-highest scoring definition was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 2 of the remaining worsening by more than 25%, which cannot be muscle strength (definition P1 selected by the International Myositis Assessment and Clinical Studies group). The third is similar to the second with the maximum amount of worsening set to 30%. This indicates convergent validity of the process. Conclusion We propose a provisional data-driven definition of improvement that reflects well the consensus rating of experienced clinicians, which incorporates clinically meaningful change in core set variables in a composite end point for the evaluation of global response to therapy in juvenile DM.

The mitochondrial and autosomal mutation landscapes of prostate cancer

BACKGROUND: Prostate cancer (PCa) is the most common cancer in men. PCa is strongly age associated; low death rates in surveillance cohorts call into question the widespread use of surgery, which leads to overtreatment and a reduction in quality of life. There is a great need to increase the understanding of tumor characteristics in the context of disease progression.

OBJECTIVE: To perform the first multigenome investigation of PCa through analysis of both autosomal and mitochondrial DNA, and to integrate exome sequencing data, and RNA sequencing and copy-number alteration (CNA) data to investigate how various different tumor characteristics, commonly analyzed separately, are interconnected.

DESIGN, SETTING, AND PARTICIPANTS: Exome sequencing was applied to 64 tumor samples from 55 PCa patients with varying stage and grade. Integrated analysis was performed on a core set of 50 tumors from which exome sequencing, CNA, and RNA sequencing data were available.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Genes, mutated at a significantly higher rate relative to a genomic background, were identified. In addition, mitochondrial and autosomal mutation rates were correlated to CNAs and proliferation, assessed as a cell cycle gene expression signature.

RESULTS AND LIMITATIONS: Genes not previously reported to be significantly mutated in PCa, such as cell division cycle 27 homolog (Saccharomyces cerevisiae) (CDC27), myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), lysine (K)-specific demethylase 6A (KDM6A), and kinesin family member 5A (KIF5A) were identified. The mutation rate in the mitochondrial genome was 55 times higher than that of the autosomes. Multilevel analysis demonstrated a tight correlation between high reactive-oxygen exposure, chromosomal damage, high proliferation, and in parallel, a transition from multiclonal indolent primary PCa to monoclonal aggressive disease. As we only performed targeted sequence analysis; copy-number neutral rearrangements recently described for PCa were not accounted for.

CONCLUSIONS: The mitochondrial genome displays an elevated mutation rate compared to the autosomal chromosomes. By integrated analysis, we demonstrated that different tumor characteristics are interconnected, providing an increased understanding of PCa etiology.

DNA microarray profiling of genes differentially regulated by the histone deacetylase inhibitors vorinostat and LBH589 in colon cancer cell lines

BACKGROUND: Despite the significant progress made in colon cancer chemotherapy, advanced disease remains largely incurable and novel efficacious chemotherapies are urgently needed. Histone deacetylase inhibitors (HDACi) represent a novel class of agents which have demonstrated promising preclinical activity and are undergoing clinical evaluation in colon cancer. The goal of this study was to identify genes in colon cancer cells that are differentially regulated by two clinically advanced hydroxamic acid HDACi, vorinostat and LBH589 to provide rationale for novel drug combination partners and identify a core set of HDACi-regulated genes.

METHODS: HCT116 and HT29 colon cancer cells were treated with LBH589 or vorinostat and growth inhibition, acetylation status and apoptosis were analyzed in response to treatment using MTS, Western blotting and flow cytometric analyses. In addition, gene expression was analyzed using the Illumina Human-6 V2 BeadChip array and Ingenuity Pathway Analysis.

RESULTS: Treatment with either vorinostat or LBH589 rapidly induced histone acetylation, cell cycle arrest and inhibited the growth of both HCT116 and HT29 cells. Bioinformatic analysis of the microarray profiling revealed significant similarity in the genes altered in expression following treatment with the two HDACi tested within each cell line. However, analysis of genes that were altered in expression in the HCT116 and HT29 cells revealed cell-line-specific responses to HDACi treatment. In addition a core cassette of 11 genes modulated by both vorinostat and LBH589 were identified in both colon cancer cell lines analyzed.

CONCLUSION: This study identified HDACi-induced alterations in critical genes involved in nucleotide metabolism, angiogenesis, mitosis and cell survival which may represent potential intervention points for novel therapeutic combinations in colon cancer. This information will assist in the identification of novel pathways and targets that are modulated by HDACi, providing much-needed information on HDACi mechanism of action and providing rationale for novel drug combination partners. We identified a core signature of 11 genes which were modulated by both vorinostat and LBH589 in a similar manner in both cell lines. These core genes will assist in the development and validation of a common gene set which may represent a molecular signature of HDAC inhibition in colon cancer.

A Classificação Internacional de Funcionalidade, Incapacidade e Saúde : um modelo multidimensional e multideterminado da funcionalidade em idosos assistidos na Rede

RESUMO: Os estudos sobre a funcionalidade da população idosa têm uma representação importante naquilo que é o atual conhecimento da demografia do mundo. Portugal posiciona-se e perspetiva-se como pertencendo aos países mais envelhecidos, possuindo uma rede de cuidados pós-agudos – a Rede Nacional de Cuidados Continuados Integrados (RNCCI)– que assiste uma parcela importante dessa população. Os aspetos conceptuais da funcionalidade de acordo com a OMS e operacionalizados pela Classificação Internacional de Funcionalidade (CIF), não mereceram até agora suficiente aplicabilidade no nosso país, inviabilizando a possibilidade de oferecermos contributos para a sua operacionalização. Da mesma forma, também os Core Sets da Classificação não têm sido sujeitos a processos de validação que contemplem amostras portuguesas, mantendo-se desconhecimento da especificidade dos fatores contextuais na nossa população. O presente estudo tem como objetivos conhecer a evolução da funcionalidade dos idosos assistidos na RNCCI na região do Algarve nas unidades de convalescença e média duração, validar o Core Set Geriátrico da OMS e propor uma versão abreviada da sua modalidade abrangente, no contexto destes cuidados. A amostra constituída por 451 idosos, dos quais 62,1% eram mulheres, revelou na pré-morbilidade níveis favoráveis de funcionalidade, com exceção para as Atividades Domésticas. Contudo, os mais idosos (≥ 85 anos), os indivíduos sem escolaridade, as mulheres e os viúvos/solteiros apresentaram mais casos desfavoráveis quando comparados com os seus pares. Na evolução da funcionalidade observámos melhorias significativas em todos os domínios avaliados, com diferenças relativamente à idade e à escolaridade; apesar dos resultados positivos os mais idosos e os indivíduos sem escolaridade apresentaram níveis inferiores de evolução. No entanto, a funcionalidade alcançada revelou ficar com resultados significativamente inferiores na comparação com aquela que os indivíduos possuíam na pré-morbilidade. Os modelos de regressão revelaram que as Funções Mentais, a Perceção do Estado de Saúde e a atividade Usar o Telefone, foram as variáveis que melhor explicaram os outcomes da funcionalidade alcançada. A validação do Core Set Geriátrico foi possível na maioria das categorias, sendo que foi no componente das Funções do Corpo onde esse processo revelou maior fragilidade. As Funções Neuromusculoesqueléticas e Relacionadas com o Movimento foram aquelas que registaram em ambos os momentos avaliativos frequências mais elevadas de deficiência, enquanto no componente Atividades & Participação isso ocorreu na atividade Utilização dos Movimentos Finos da Mão. Os capítulos Apoios e Relacionamentos e Atitudes foram considerados os Fatores Ambientais mais Facilitadores mas também com maior impacto Barreira. A proposta para o Core Set Geriátrico Abreviado resultou das categorias independentes que explicaram os modelos da funcionalidade alcançada e cujo resultado engloba um conjunto de 27 categorias, com um enfoque importante no componente Atividades/Participação de onde se destacam os domínios da Mobilidade e dos Auto Cuidados. A funcionalidade dos indivíduos e das populações deve ser considerada uma variável incontornável da Saúde Pública, cuja avaliação deve refletir uma abordagem biopsicossocial, apoiada na Classificação Internacional de Funcionalidade. A operacionalização da Classificação a partir dos Core Sets necessita de pesquisa mais aprofundada relativamente às caraterísticas psicométricas dos seus qualificadores e dos seus processos de validação.-----------ABSTRACT: The studies about the functioning of the elderly play an important role on what the present knowledge of the demography in the world is. Portugal figures high on the most aged countries, having a network of post-acute care - the National Network of Integrated Continuous Care (RNCCI) - which assists a large part of that population. The conceptual aspects of functioning according to WHO and operated by the International Classification of Functioning (ICF), have been insufficiently addressed concerning its adequate applicability in our country, hindering the contributions of its operation. In the same way, also the Core Sets of the Classification have not been subjected to validation procedures that include portuguese samples, keeping the unawareness of specificity of the contextual factors in our population. The objectives of the present study were to know the evolution of the functioning of the elderly assisted in the RNCCI in the Algarve region in units of convalescence and average duration, validate the WHO Geriatric Core Set and propose an abridged version of this comprehensive core set in this healthcare context. The sample was composed by 451 elderly people, of which 62.1% were women, they showed favourable levels in functioning in the pre-morbid state, except for Domestic Activities. However, the oldest (≥ 85 years), the individuals with no education, women and widowed/ unmarried showed more unfavourable cases when compared to their peers. In the evolution of functioning we observed significant improvements in all domains assessed, with diferences with respect to age and education. In spite of positive results, the oldest and the individuals with no education showed lower levels of evolution. However, the functioning achieved showed significantly lower results when compared to the those observed in pre-morbidity state. Regression models reveal that Mental Functions, the Perceived Health Status and the Use of the Phone activity, were the variables that better explain the functioning of the outcomes achieved. The validation of the Geriatric Core Set of ICF was possible in most categories, and Body Functions was the component where this process showed greatest weakness. Neuromusculoskeletal and Movement-Related Functions experienced in both evaluation times with higher rates of disability, while in the Activities & Participation component this occurred in the Fine Hand Use activity. The Support and Relationships and Attitudes chapters were considered the Environmental Factors most Facilitators but also with greater impact Barrier. The proposal for the Brief Geriatric Core Set has resulted from the independent categories that explained the regression models of functioning and includes a set of 27 categories, with na important emphasis on Activities & Participation component where we can highlight the areas of Mobility and Self Care domains. The functioning of individuals and populations should be considered as an unavoidable variable of Public Health, of which the assessment should reflect a biopsychosocial approach, based on the International Classification of Functioning. The operationalization of the Classification from the Core Sets requires further research regarding the psychometric characteristics of their qualifiers and their validation procedure.

Les déterminants biopsychosociaux de la réadaptation de travailleurs accidentés du travail

Malgré des années de recherches sur la douleur et les incapacités chroniques, peu de conclusions claires émergent quant aux facteurs de risque les plus pertinents. La majorité des auteurs s’entendent toutefois sur un fait, les troubles musculo-squelettiques et l’adaptation à leurs nombreuses conséquences est un processus complexe, multidimensionnel et déterminé par l’interaction de facteurs biopsychosociaux. Deux articles sont présentés avec comme objectifs généraux d’identifier les déterminants importants de l’ajustement à un trouble musculo-squelettique. Le premier article consiste en une recension des écrits systématique visant à résumer tous les facteurs pronostiques biopsychosociaux de l’ajustement multidimensionnel aux troubles musculo-squelettiques et examinant leur pertinence à déterminer ces divers indicateurs d’ajustement, principalement la participation au travail, les limitations fonctionnelles, la douleur, la qualité de la vie, la détresse psychologique et la rechute. Les 105 études prospectives recensées et correspondant aux critères d’inclusion et d’exclusion ont été analysés et chaque association significative a été résumée. Par la suite, 68 études qui ont inclus des facteurs sociodémographiques, biologiques, psychologiques et sociaux ont été analysées séparément. Leur qualité méthodologique a été évaluée, un niveau d’évidence a par la suite été établi pour chaque association entre les facteurs de risque et les diverses variables de résultats. Les divergences dans ces associations entre les différentes phases de chronicité ont également été identifiées. Un niveau d’évidence élevée a été découvert concernant le rôle des attentes de rétablissement, certaines pratiques de gestion intégrées de l’incapacité, les stratégies d’adaptation (coping), la somatisation, la comorbidité, la durée de l’épisode symptomatique et un niveau modéré d’évidence a été découvert pour les comportements de douleur. Lorsque vient le temps de prédire les divers indicateurs d’ajustement de sujets souffrant de troubles musculo-squelettiques, chacun tend à être associé à des facteurs de risque différents. Peu de différences ont été relevées lorsque les phases de chronicité ont été prises en compte. Ces résultats confirment la nature biopsychosociale de l’ajustement aux troubles musculo-squelettiques bien que les facteurs psychosociaux semblent être prédominants. Le second article est une étude prospective avec un suivi de 2 et 8 mois. Elle a été menée auprès de 62 travailleurs accidentés, principalement en phase de chronicité et prestataires d’indemnités de revenu de la CSST (Commission en Santé et Sécurité du Travail du Québec). L’objectif de cette étude était d’identifier les déterminants de l’engagement actif dans un processus de retour a travail par opposition à l’incapacité chronique, tout en adoptant une approche biopsychosociale. Cet objectif a été poursuivi en faisant l’étude, d’une part, de la pertinence de facteurs de risque ayant déjà fait l’objet d’études mais pour lesquelles aucun consensus n’est atteint quant à leur utilité prédictive et d’autre part, de certains facteurs de risque négligés, voire, même omis de ce domaine de recherche. Suite à des analyses multivariées, le genre, les attentes de rétablissement en terme de capacité à retourner au travail et l’importance du travail ont été identifiés comme des déterminants de l’incapacité chronique liée au travail. Après 8 mois, l’âge, la consolidation médicale, les symptômes traumatiques, le support au travail et l’importance du travail ont été également identifiés comme des déterminants d’incapacité chronique liée au travail. Ces résultats démontrent l’importance d’aborder l’étude de l’incapacité chronique et de la réinsertion professionnelle selon une perspective multidimensionnelle. Ces résultats corroborent également les conclusions de notre recension des écrits, puisque les facteurs psychosociaux ont été identifiés comme étant des déterminants importants dans cette étude.

Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism

Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting thatmost effectors represent species-specific adaptations.

Heterozygosity and diversity analysis using mapped single nucelotide polymorphisms in a faba bean inbreeding programme

The aim of this study was to convert existing faba bean (Vicia faba L.) single nucleotide polymorphism (SNP) markers from cleaved amplification polymorphic sequences and SNaPshot® formats, which are expensive and time-consuming, to the more convenient KBiosciences competitive allele‐specific PCR (KASP) assay format. Out of 80 assays designed, 75 were validated, though a core set of 67 of the most robust markers is recommended for further use. The 67 best KASP SNP assays were used across two generations of single seed descent to detect unintended outcrossing and to track and quantify loss of heterozygosity, a capability that will significantly increase the efficiency and performance of pure line production and maintenance. This same set of assays was also used to examine genetic relationships between the 67 members of the partly inbred panel, and should prove useful for line identification and diversity studies in the future.

Computer Theorem Proving and HoTT

Theorem-proving is a one-player game. The history of computer programs being the players goes back to 1956 and the ‘LT’ LOGIC THEORY MACHINE of Newell, Shaw and Simon. In game-playing terms, the ‘initial position’ is the core set of axioms chosen for the particular logic and the ‘moves’ are the rules of inference. Now, the Univalent Foundations Program at IAS Princeton and the resulting ‘HoTT’ book on Homotopy Type Theory have demonstrated the success of a new kind of experimental mathematics using computer theorem proving.

Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales

Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II of APG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diversity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller ""unplaced"" groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rps16 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees. Consistent with more weakly supported results from previous studies, our analyses support the monophyly of the four major clades and the relationships among them. Most importantly, Asterales are inferred to be sister to a clade containing Apiales and Dipsacales. Paracryphiaceae is consistently placed sister to the Dipsacales. However, the exact relationships of Bruniaceae, Columelliaceae, and an Escallonia clade depended upon the dataset. Areas of poor resolution in combined analyses may be partly explained by conflict between the coding and non-coding data partitions. We discuss the implications of these results for our understanding of campanulid phylogeny and evolution, paying special attention to how our findings bear on character evolution and biogeography in Dipsacales.

RQF publication quality measures: methodoligical issues

The Research Quality Framework uses Thomson-ISI citation benchmarks as its main set of objective measures of research quality. The Thomson-ISI measures rely on identifying a core set of journals in which the major publications for a discipline are to be found. The core for a discipline is determined by applying a nontransparent process that is partly based on Bradford’s Law (1934). Yet Bradford was not seeking measures about quality of publications or journals. How valid then is it to base measures of publication quality on Bradford’s Law? We explore this by returning to Bradford’s Law and subsequent related research asking ‘what is Bradford’s Law really about?’ We go further, and ask ‘does Bradford’s Law apply in Information Systems?’ We use data from John Lamp’s internationally respected Index of Information Systems Journals to explore the latter question. We have found that Information Systems may have a core of journals only a subset of which is also in the list of Thomson-ISI journals. There remain many unanswered questions about the RQF metrics based on Thomson-ISI and their applicability to information systems.

Broadband : benefits and problems

The striving of nations to build a broadband-based information society is paralleled by individuals striving to improve their personal lot and by organisations seeking a competitive advantage—all supposedly to be achieved via broadband. However, the social and economic impact of broadband may be surrounded in controversies. This paper argues that these controversies need to be identified and addressed if public policy decisions about broadband are to be made with confidence. While literature on broadband abounds, it is rarely directed at the impact of broadband on social and personal issues. Rather, that literature typically focuses on broadband's economic aspects, but with poor benefit identification and measure difficulties, the findings tend to be steeped in rhetoric. Largely, what we are left with is literature on the impact of narrowband Internet. While research on the Internet abounds, its findings are typically indeterminate and often disputed. The paper works with literature on broadband and extrapolates from the literature on narrowband with its disputed impacts to identify possible impacts of broadband. In so doing it identifies a core set of controversies regarding broadband at the national, individual and organisational levels. It then calls for diversity of analysis of possible broadband outcomes. Only with such analysis will it be possible to place the likely broadband future in the context of broader national, individual and organisational aspirations.

Diabetes MILES - Australia (Management and Impact for Long-Term Empowerment and Success) : methods and sample characteristics of a national survey of the psychological aspects of living with type 1 or type 2 diabetes in Australian adults

Background Successful management of diabetes requires attention to the behavioural, psychological and social aspects of this progressive condition. The Diabetes MILES (Management and Impact for Long-term Empowerment and Success) Study is an international collaborative. Diabetes MILES-Australia, the first Diabetes MILES initiative to be undertaken, was a national survey of adults living with type 1 or type 2 diabetes in Australia. The aim of this study was to gather data that will provide insights into how Australians manage their diabetes, the support they receive and the impact of diabetes on their lives, as well as to use the data to validate new diabetes outcome measures.

Methods The survey was designed to include a core set of self-report measures, as well as modules specific to diabetes type or management regimens. Other measures or items were included in only half of the surveys. Cognitive debriefing interviews with 20 participants ensured the survey content was relevant and easily understood. In July 2011, the survey was posted to 15,000 adults (aged 18-70 years) with type 1 or type 2 diabetes selected randomly from the National Diabetes Services Scheme (NDSS) database. An online version of the survey was advertised nationally. A total of 3,338 eligible Australians took part; most (70.4%) completed the postal survey. Respondents of both diabetes types and genders, and of all ages, were adequately represented in both the postal and online survey sub-samples. More people with type 2 diabetes than type 1 diabetes took part in Diabetes MILES-Australia (58.8% versus 41.2%). Most respondents spoke English as their main language, were married/in a de facto relationship, had at least a high school education, were occupied in paid work, had an annual household income > $AUS40,000, and lived in metropolitan areas.

Discussion A potential limitation of the study is the under-representation of respondents from culturally and linguistically diverse backgrounds (including Aboriginal and Torres Strait Islander origin). Diabetes MILES-Australia represents a major achievement in the study of diabetes in Australia, where for the first time, the focus is on psychosocial and behavioural aspects of this condition at a national level.

Wireless sensor networks for heritage object deformation detection and tracking algorithm

Deformation is the direct cause of heritage object collapse. It is significant to monitor and signal the early warnings of the deformation of heritage objects. However, traditional heritage object monitoring methods only roughly monitor a simple-shaped heritage object as a whole, but cannot monitor complicated heritage objects, which may have a large number of surfaces inside and outside. Wireless sensor networks, comprising many small-sized, low-cost, low-power intelligent sensor nodes, are more useful to detect the deformation of every small part of the heritage objects. Wireless sensor networks need an effective mechanism to reduce both the communication costs and energy consumption in order to monitor the heritage objects in real time. In this paper, we provide an effective heritage object deformation detection and tracking method using wireless sensor networks (EffeHDDT). In EffeHDDT, we discover a connected core set of sensor nodes to reduce the communication cost for transmitting and collecting the data of the sensor networks. Particularly, we propose a heritage object boundary detecting and tracking mechanism. Both theoretical analysis and experimental results demonstrate that our EffeHDDT method outperforms the existing methods in terms of network traffic and the precision of the deformation detection.

Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection

Invasive phytoplasmas wreak havoc on coconut palms worldwide, leading to high loss of income, food insecurity and extreme poverty of farmers in producing countries. Phytoplasmas as strictly biotrophic insect-transmitted bacterial pathogens instigate distinct changes in developmental processes and defence responses of the infected plants and manipulate plants to their own advantage; however, little is known about the cellular and molecular mechanisms underlying host–phytoplasma interactions. Further, phytoplasma-mediated transcriptional alterations in coconut palm genes have not yet been identified. This study evaluated the whole transcriptome profiles of naturally infected leaves of Cocos nucifera ecotype Malayan Red Dwarf in response to yellow decline phytoplasma from group 16SrXIV, using RNA-Seq technique. Transcriptomics-based analysis reported here identified genes involved in coconut innate immunity. The number of down-regulated genes in response to phytoplasma infection exceeded the number of genes up-regulated. Of the 39,873 differentially expressed unigenes, 21,860 unigenes were suppressed and 18,013 were induced following infection. Comparative analysis revealed that genes associated with defence signalling against biotic stimuli were significantly overexpressed in phytoplasma-infected leaves versus healthy coconut leaves. Genes involving cell rescue and defence, cellular transport, oxidative stress, hormone stimulus and metabolism, photosynthesis reduction, transcription and biosynthesis of secondary metabolites were differentially represented. Our transcriptome analysis unveiled a core set of genes associated with defence of coconut in response to phytoplasma attack, although several novel defence response candidate genes with unknown function have also been identified. This study constitutes valuable sequence resource for uncovering the resistance genes and/or susceptibility genes which can be used as genetic tools in disease resistance breeding.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.