bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide analysis of promoter architecture in Drosophila melanogaster
Authors: Hoskins Roger A. , Landolin Jane M. , Brown James B. , Sandler Jeremy E. , Takahashi Hazuki , Lassmann Timo , Yu Charles , Booth Benjamin W. , Zhang Dayu , Wan Kenneth H. , Yang Li , Boley Nathan , Andrews Justen , Kaufman Thomas C. , Graveley Brenton R. , Bickel Peter J. , Carninci Piero , Carlson Joseph W. , Celniker Susan E.
Published: December 2010

Core promoters are critical regions for gene regulation in higher eukaryotes. However, the boundaries of promoter regions, the relative rates of initiation at the transcription start sites (TSSs) distributed within them, and the functional significance of promoter architecture remain poorly understood. We produced a high-resolution map of promoters active in the Drosophila melanogaster embryo by integrating data from three independent and complementary methods: 21 million cap analysis of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) reads, and 50,000 cap-trapped expressed sequence tags (ESTs). We defined 12,454 promoters of 8037 genes. Our analysis indicates that, due to non-promoter-associated RNA background signal, previous studies have likely overestimated the number of promoter-associated CAGE clusters by fivefold. We show that TSS distributions form a complex continuum of shapes, and that promoters active in the embryo and adult have highly similar shapes in 95% of cases. This suggests that these distributions are generally determined by static elements such as local DNA sequence and are not modulated by dynamic signals such as histone modifications. Transcription factor binding motifs are differentially enriched as a function of promoter shape, and peaked promoter shape is correlated with both temporal and spatial regulation of gene expression. Our results contribute to the emerging view that core promoters are functionally diverse and control patterning of gene expression in Drosophila and mammals.
The transcriptional diversity of 25 Drosophila cell lines
Authors: Cherbas Lucy , Willingham Aarron , Zhang Dayu , Yang Li , Zou Yi , Eads Brian D. , Carlson Joseph W. , Landolin Jane M. , Kapranov Philipp , Dumais Jacqueline , Samsonova Anastasia , Choi Jeong-Hyeon , Roberts Johnny , Davis Carrie A. , Tang Haixu , van Baren Marijke J. , Ghosh Srinka , Dobin Alexander , Bell Kim , Lin Wei , Langton Laura , Duff Michael O. , Tenney Aaron E. , Zaleski Chris , Brent Michael R. , Hoskins Roger A. , Kaufman Thomas C. , Andrews Justen , Graveley Brenton R. , Perrimon Norbert , Celniker Susan E. , Gingeras Thomas R. , Cherbas Peter
Published: December 2010

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are “off” and survival/growth pathways “on.” Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common “cell line“ gene expression pattern.
Computational and experimental identification of mirtrons inDrosophila melanogasterandCaenorhabditis elegans
Authors: Chung Wei-Jen , Agius Phaedra , Westholm Jakub O. , Chen Michael , Okamura Katsutomo , Robine Nicolas , Leslie Christina S. , Lai Eric C.
Published: December 2010

Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mirtrons from theDrosophila melanogastertranscriptome. These included 17 known and six confident novel mirtrons among the top 51 candidates, and additional candidates had limited read evidence in available small RNA data. Our computational model also proved effective onCaenorhabditis elegans, for which the identification of 14 cloned mirtrons among the top 22 candidates more than tripled the number of validated mirtrons in this species. A few low-scoring introns generated mirtron-like read patterns from atypical RNA structures, but their paucity suggests that relatively few such loci were not captured by our model. Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a <8-kb region inC. elegansharboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent of evolutionary constraint.
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Authors: Niu Wei , Lu Zhi John , Zhong Mei , Sarov Mihail , Murray John I. , Brdlik Cathleen M. , Janette Judith , Chen Chao , Alves Pedro , Preston Elicia , Slightham Cindie , Jiang Lixia , Hyman Anthony A. , Kim Stuart K. , Waterston Robert H. , Gerstein Mark , Snyder Michael , Reinke Valerie
Published: December 2010

Regulation of gene expression by sequence-specific transcription factors is central to developmental programs and depends on the binding of transcription factors with target sites in the genome. To date, most such analyses in Caenorhabditis elegans have focused on the interactions between a single transcription factor with one or a few select target genes. As part of the modENCODE Consortium, we have used chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq) to determine the genome-wide binding sites of 22 transcription factors (ALR-1, BLMP-1, CEH-14, CEH-30, EGL-27, EGL-5, ELT-3, EOR-1, GEI-11, HLH-1, LIN-11, LIN-13, LIN-15B, LIN-39, MAB-5, MDL-1, MEP-1, PES-1, PHA-4, PQM-1, SKN-1, and UNC-130) at diverse developmental stages. For each factor we determined candidate gene targets, both coding and non-coding. The typical binding sites of almost all factors are within a few hundred nucleotides of the transcript start site. Most factors target a mixture of coding and non-coding target genes, although one factor preferentially binds to non-coding RNA genes. We built a regulatory network among the 22 factors to determine their functional relationships to each other and found that some factors appear to act preferentially as regulators and others as target genes. Examination of the binding targets of three related HOX factors—LIN-39, MAB-5, and EGL-5—indicates that these factors regulate genes involved in cellular migration, neuronal function, and vulval differentiation, consistent with their known roles in these developmental processes. Ultimately, the comprehensive mapping of transcription factor binding sites will identify features of transcriptional networks that regulate C. elegans developmental processes.
A spatial and temporal map ofC. elegansgene expression
Authors: Spencer W. Clay , Zeller Georg , Watson Joseph D. , Henz Stefan R. , Watkins Kathie L. , McWhirter Rebecca D. , Petersen Sarah , Sreedharan Vipin T. , Widmer Christian , Jo Jeanyoung , Reinke Valerie , Petrella Lisa , Strome Susan , Von Stetina Stephen E. , Katz Menachem , Shaham Shai , Rätsch Gunnar , Miller David M.
Published: December 2010

TheC. elegansgenome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning–based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the totalC. elegansgenome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor– and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.
Genome-wide analysis of alternative splicing in Caenorhabditis elegans
Authors: Ramani Arun K. , Calarco John A. , Pan Qun , Mavandadi Sepand , Wang Ying , Nelson Andrew C. , Lee Leo J. , Morris Quaid , Blencowe Benjamin J. , Zhen Mei , Fraser Andrew G.
Published: December 2010

Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provide the most comprehensive set of annotated splice variants in C. elegans to date, and are therefore expected to facilitate focused, high resolution in vivo functional assays of AS function.
Broad chromosomal domains of histone modification patterns in C. elegans
Authors: Liu Tao , Rechtsteiner Andreas , Egelhofer Thea A. , Vielle Anne , Latorre Isabel , Cheung Ming-Sin , Ercan Sevinc , Ikegami Kohta , Jensen Morten , Kolasinska-Zwierz Paulina , Rosenbaum Heidi , Shin Hyunjin , Taing Scott , Takasaki Teruaki , Iniguez A. Leonardo , Desai Arshad , Dernburg Abby F. , Kimura Hiroshi , Lieb Jason D. , Ahringer Julie , Strome Susan , Liu X. Shirley
Published: December 2010

Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: Two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Authors: Ercan Sevinç , Lubling Yaniv , Segal Eran , Lieb Jason D.
Published: December 2010

We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic cells, adult somatic cells, and a mix of adult somatic and germ cells. In all three samples, the nucleosome occupancy of gene promoters on the X chromosome differed from autosomal promoters. While both X and autosomal promoters exhibit a typical nucleosome-depleted region upstream of transcript start sites and a well-positioned +1 nucleosome, X-linked gene promoters on average exhibit higher nucleosome occupancy relative to autosomal promoters. We show that the difference between X and autosomes does not depend on the somatic dosage compensation machinery. Instead, the chromatin difference at promoters is partly encoded by DNA sequence, because a model trained on nucleosome sequence preferences from S. cerevisiae in vitro data recapitulate nearly completely the experimentally observed difference between X and autosomal promoters. The model predictions also correlate very well with experimentally determined occupancy values genome-wide. The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline.
Chromatin signatures of the Drosophila replication program
Authors: Eaton Matthew L. , Prinz Joseph A. , MacAlpine Heather K. , Tretyakov George , Kharchenko Peter V. , MacAlpine David M.
Published: December 2010

DNA replication initiates from thousands of start sites throughout the Drosophila genome and must be coordinated with other ongoing nuclear processes such as transcription to ensure genetic and epigenetic inheritance. Considerable progress has been made toward understanding how chromatin modifications regulate the transcription program; in contrast, we know relatively little about the role of the chromatin landscape in defining how start sites of DNA replication are selected and regulated. Here, we describe the Drosophila replication program in the context of the chromatin and transcription landscape for multiple cell lines using data generated by the modENCODE consortium. We find that while the cell lines exhibit similar replication programs, there are numerous cell line-specific differences that correlate with changes in the chromatin architecture. We identify chromatin features that are associated with replication timing, early origin usage, and ORC binding. Primary sequence, activating chromatin marks, and DNA-binding proteins (including chromatin remodelers) contribute in an additive manner to specify ORC-binding sites. We also generate accurate and predictive models from the chromatin data to describe origin usage and strength between cell lines. Multiple activating chromatin modifications contribute to the function and relative strength of replication origins, suggesting that the chromatin environment does not regulate origins of replication as a simple binary switch, but rather acts as a tunable rheostat to regulate replication initiation events.
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
Authors: Berezikov Eugene , Robine Nicolas , Samsonova Anastasia , Westholm Jakub O. , Naqvi Ammar , Hung Jui-Hung , Okamura Katsutomo , Dai Qi , Bortolamiol-Becet Diane , Martin Raquel , Zhao Yongjun , Zamore Phillip D. , Hannon Gregory J. , Marra Marco A. , Weng Zhiping , Perrimon Norbert , Lai Eric C.
Published: December 2010

Since the initial annotation of miRNAs from cloned short RNAs by the Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional miRNAs in various species. We report here a meta-analysis of short RNA data from Drosophila melanogaster, aggregating published libraries with 76 data sets that we generated for the modENCODE project. In total, we began with more than 1 billion raw reads from 187 libraries comprising diverse developmental stages, specific tissue- and cell-types, mutant conditions, and/or Argonaute immunoprecipitations. We elucidated several features of known miRNA loci, including multiple phased byproducts of cropping and dicing, abundant alternative 5′ termini of certain miRNAs, frequent 3′ untemplated additions, and potential editing events. We also identified 49 novel genomic locations of miRNA production, and 61 additional candidate loci with limited evidence for miRNA biogenesis. Although these loci broaden the Drosophila miRNA catalog, this work supports the notion that a restricted set of cellular transcripts is competent to be specifically processed by the Drosha/Dicer-1 pathway. Unexpectedly, we detected miRNA production from coding and untranslated regions of mRNAs and found the phenomenon of miRNA production from the antisense strand of known loci to be common. Altogether, this study lays a comprehensive foundation for the study of miRNA diversity and evolution in a complex animal model.
The anaphase promoting complex is required for memory function in mice
Authors: Kuczera Tanja , Stilling Roman Manuel , Hsia Hung-En , Bahari-Javan Sanaz , Irniger Stefan , Nasmyth Kim , Sananbenesi Farahnaz , Fischer Andre
Published: December 2010

Learning and memory processes critically involve the orchestrated regulation of de novo protein synthesis. On the other hand it has become clear that regulated protein degradation also plays a major role in neuronal plasticity and learning behavior. One of the key pathways mediating protein degradation is proteosomal protein destruction. The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase that targets proteins for proteosomal degradation by the 26S proteasome. While the APC/C is essential for cell cycle progression it is also expressed in postmitotic neurons where it has been implicated with axonal outgrowth and neuronal survival. In this study we addressed the role of APC/C in learning and memory function by generating mice that lack the essential subunit APC2 from excitatory neurons of the adult forebrain. Those animals are viable but exhibit a severe impairment in the ability to extinct fear memories, a process critical for the treatment of anxiety diseases such as phobia or post-traumatic stress disorder. Since deregulated protein degradation and APC/C activity has been implicated with neurodegeneration we also analyzed the effect of Apc2 deletion in a mouse model for Alzheimer's disease. In our experimental setting loss of APC2 form principle forebrain neurons did not affect the course of pathology in an Alzheimer's disease mouse model. In conclusion, our data provides genetic evidence that APC/C activity in the adult forebrain is required for cognitive function.
X-ray topography of diamond using forbidden reflections: which defects do we really see?
Authors: Shiryaev Andrei A. , Masiello Fabio , Hartwig Jurgen , Kupriyanov Igor N. , Lafford Tamzin A. , Titkov Sergey V. , Palyanov Yuri N.
Published: December 2010

Natural and synthetic diamonds with various concentrations and types of point and extended defect were investigated using X-ray topography employing allowed (111, 004) and forbidden (222) reflections. On the topographs of the forbidden reflections, weak stress fields from lattice imperfections and extended defects are readily observed. Comparison of the topographs with IR maps of the distribution of point defects suggests that certain types of point defect may increase the structure factors of the forbidden reflections.
Microstructural mapping of C60 phase transformation into disordered graphite at high pressure, using X-ray diffraction microtomography
Authors: Álvarez-Murga Michelle , Bleuet Pierre , Marques Leonel , Lepoittevin Christophe , Boudet Nathalie , Gabarino Gaston , Mezouar Mohamed , Hodeau Jean-Louis
Published: December 2010

An extended use of synchrotron-based X-ray diffraction microtomography (XRD-µCT) to study simultaneously the phase distribution and microstructure in phase-transformation processes is proposed. This three-dimensional non-invasive imaging approach has been applied to understand the phase transformation of C60 rhombohedral polymer (C60R) into disordered graphite (DG) at high pressure and high temperature. The heterogeneous sample was synthesized (5 GPa, 1100 K) using a Paris–Edinburgh cell and selective image reconstructions were achieved for all different phases present in this sample. The XRD-µCT analysis evidences elongated DG domains with a fiber texture where nested (002)DGplanes show ±70° preferential orientation relative to the compression axis. In contrast C60R domains are found to be small and spotty, preferentially in the middle of the sample. The parent and product phases are mutually interpenetrative and exhibit a crystallographic relationship. This study evidences that formation of (002)DGplanes occurs parallel to {111}C60Cpseudo-cubic planes. Among these four possible alignments, uniaxial pressure favors one [111]C60Cdirection. Transmission electron microscopy observations validate these nondestructive XRD-µCT results.
Involvement of STAP‐2 in Brk‐mediated phosphorylation and activation of STAT5 in breast cancer cells
Authors: Ikeda Osamu , Mizushima Akihiro , Sekine Yuichi , Yamamoto Chikako , Muromoto Ryuta , Nanbo Asuka , Oritani Kenji , Yoshimura Akihiko , Matsuda Tadashi
Published: December 2010

Signal‐transducing adaptor protein (STAP)‐2 is a recently identified adaptor protein that contains Pleckstrin homology and Src homology 2‐like domains, and is also known to be a substrate of breast tumor kinase (Brk). In a previous study, we found that STAP‐2 upregulated Brk‐mediated activation of signal transducer and activator of transcription (STAT) 3 in breast cancer cells. Here, we examined the involvement of STAP‐2 in Brk‐mediated STAT5 activation in breast cancer cells. Ectopic expression of STAP‐2 induced Brk‐mediated transcriptional activity of STAT5. Furthermore, STAP‐2‐knockdown in T47D breast cancer cells induced a marked decrease in proliferation that was as strong as that after Brk‐ or STAT5b‐knockdown. Regarding the mechanism, the Pleckstrin homology domain of STAP‐2 is likely to participate in the process by which Brk phosphorylates and activates STAT5. Taken together, our findings provide insights toward the development of novel therapeutic strategies as well as novel prognostic values in breast carcinomas. (Cancer Sci 2011; 102: 756–761)
Associations ofCYP2A6genotype with smoking behaviors in southern China
Authors: Liu Tao , David Sean P. , Tyndale Rachel F. , Wang Hui , Zhou Qian , Ding Peng , He Yan‐Hui , Yu Xue‐Qing , Chen Wei , Crump Casey , Wen Xiao‐Zhong , Chen Wei‐Qing
Published: December 2010

Aims To investigate the association ofCYP2A6genetic polymorphisms with smoking‐related phenotypes in Chinese smokers.

Design Case‐only genetic association study.

Setting Southern China.

Participants A total of 1328 Han Chinese smokers who participated in a community‐based chronic disease screening project in Guangzhou and Zhuhai from 2006 to 2007.

Measurements All participants answered a structured questionnaire about socio‐demographic status and smoking behaviors and informative alleles were genotyped for the cytochrome P450 2A6 (CYP2A6) gene (CYP2A6*4,*5,*7,*9and *10).

Findings The frequencies ofCYP2A6*4, *5, *7, *9and *10alleles were 8.5, 1.2, 6.3, 13.5 and 2.4%, which corresponded to 48.9, 15.4, 24.2 and 11.5% of participants being classified as normal, intermediate, slow and poor metabolizers, respectively. Multivariate analyses in male smokers demonstrated that compared with normal metabolizers, poor metabolizers reported smoking fewer cigarettes per day [adjusted odds ratio (OR) = 0.49; 95% confidence interval (CI): 0.32–0.76], started smoking regularly later in life (adjusted OR = 1.55; 95% CI: 1.06–2.26) and, among former smokers, reported smoking for a shorter duration prior to quitting (adjusted OR = 0.33; 95% CI: 0.12–0.94). However, poor metabolizers were less likely to quit smoking and remain abstinent than normal metabolizers (adjusted OR = 0.54; 95% CI: 0.34–0.86).

Conclusions Reduced metabolism function of cytochrome P450 2A6 in smokers appears to be associated with fewer cigarettes smoked, later initiation of smoking regularly, shorter smoking duration and lower likelihood of smoking cessation.
Alcohol‐related discussions in health care—a population view
Authors: Mäkelä Pia , Havio Marjaliisa , Seppä Kaija
Published: December 2010

Aims  The present study aimed to evaluate the frequency and the target group of alcohol screening and brief interventions in health‐care settings and how well this level of activity reflects public opinion.

Design  A general population survey.

Setting and participants  A random sample of Finns aged 15–69 years with a 74% response rate (n = 2725).

Measurements  Frequency counts were used to evaluate the level of activity. Logistic regression models were used to examine which groups were asked and advised about alcohol use and which groups considered it useful.

Findings  More than 90% had positive attitudes towards being asked about their alcohol use. Of those who had been in contact with health care (n = 2062) in the 12 months before the survey, 33.3% had been asked about their alcohol use, being most often men, young, heavy drinkers and those of high socio‐economic status. Thirty‐seven per cent of those who had been asked were given advice, being most often heavy drinkers and those with a normal body mass index. However, 50% of heavy drinkers who had been asked about their alcohol use had not been advised about it. Of those who had been advised, 71.9% considered it useful, especially older subjects, and also including heavy episodic drinkers, although less than others.

Conclusions  In Finland, the frequency of health‐care professionals asking and giving advice on alcohol is relatively low. However, public opinion towards these discussions is positive. Our results encourage the support and uptake of systematic screenings and brief interventions in health‐care settings.
Outcomes of a decision support prompt in community pharmacy‐dispensing software to promote step‐down of proton pump inhibitor therapy
Authors: Curtain Colin , Peterson Gregory M. , Tenni Peter , Bindoff Ivan K. , Williams Mackenzie
Published: December 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Computerized clinical decision support has been increasingly utilized in hospital and general‐practice settings where it may improve prescribing practice. Little investigation has been undertaken using computerized decision support in the community pharmacy setting. Proton pump inhibitors are expensive and often prescribed in dosages above recommended guidelines.

WHAT THIS STUDY ADDS

• This study adds justification for the use of computerized decision support in community pharmacy. It highlights the promotion of improved prescribing of proton pump inhibitors through patient empowerment.

AIM To evaluate the effect of a computerized decision support prompt regarding high‐dose proton pump inhibitor (PPI) therapy on prescribing and medication costs.

METHODS A prompt activated on dispensing high‐dose esomeprazole or pantoprazole was implemented in 73 of 185 pharmacies. Anonymized prescription data and a patient survey were used to determine changes in prescribing and associated medication costs.

RESULTS The pharmacist‐recorded PPI intervention rate per 100 high‐dose PPI prescriptions was 1.67 for the PPI prompt group and 0.17 for the control group (P < 0.001). During the first 28 days of the trial, 196 interventions resulted in 34 instances of PPI step‐down, with 28 of these occurring in PPI prompt pharmacies. Cost savings attributable to the prompt were AUD 7.98 (£4.95) per month per PPI prompt pharmacy compared with AUD 1.05 (£0.65) per control pharmacy.

CONCLUSION The use of electronic decision support prompts in community pharmacy practice can promote the quality use of medicines.
Basic ecological theory can inform habitat restoration for woodland birds
Authors: Huth Neil , Possingham Hugh P.
Published: December 2010

1. Extensive clearing of native vegetation for agriculture has severely impacted upon Australia’s biodiversity. Environmental tree planting, forestry and restoration of existing remnant patches provide ways for improving the matrix habitat value between larger conservation areas. However, improved guidelines are required to inform land managers on appropriate ways to design these areas when resources for habitat improvement are limited.

2. We developed a simple habitat suitability model for woodland birds from two basic observations of ecology: (i) the species–area relationship and (ii) the relationship between bird species richness and vegetation structural diversity. The model provides a suite of species–area relationships for habitats of different structural diversity. Data from across Australia were used in developing the model to ensure its generality.

3. A single species–area relationship for patches from 2 ha to 16 million ha was estimated for high‐quality habitat patches using data from across mainland Australia. When this was combined with information on habitat complexity, the resultant species richness model was able to adequately describe the variation in woodland bird species richness within patches of various sizes (1–500 ha) in an independent data set from the Australian Capital Territory.

4. The results from the model suggest that for small patches of high quality, increases in patch size or quality reap benefits whereas the marginal return in species richness for increasing patch size is almost negligible for low quality patches above 10 ha or high quality patches of 20 ha. For small patches of low quality, there is little benefit in increasing patch area and so quality should be improved. These results agree with recommendations obtained using various other techniques.

5. Synthesis and applications. Investigation of the relationships embedded in the model provided similar recommendations for habitat restoration as determined by more detailed methods. The success of a simple combination of ecological principles linking area, structure and species richness supports the notion that existing basic theory can provide a sufficient basis for informing habitat restoration.
The potential of parasitoid Hymenoptera as bioindicators of arthropod diversity in agricultural grasslands
Authors: Anderson Annette , McCormack Stephen , Helden Alvin , Sheridan Helen , Kinsella Anne , Purvis Gordon
Published: December 2010

1. As measuring biodiversity in its entirety is impractical, there is a need for bioindicators. This study tested the hypothesis that parasitoid Hymenoptera are potential bioindicators that provide a useful means to assess the wider biodiversity of arthropod populations in agro‐ecosystems. There are a range of theoretical arguments to support such a claim, including the high trophic position of these taxa within the arthropod communities in which they occur, and the unique nature of their biological relationships with the majority of terrestrial arthropod groups.

2. A survey of 48 commercial farms was conducted and Generalized Linear Models used to investigate relationships between six taxa—parasitoid Hymenoptera, Coleoptera, Hemiptera, Diptera, Araneae and plants (species richness and sward height)—in agricultural grasslands. As well as relationships between these groups, the relationship of each individual group to the overall biodiversity of all other arthropod groups was explored.

3. Both abundance (r2 = 0·58) and taxon richness (r2 = 0·54) of parasitoid Hymenoptera had stronger relationships with overall arthropod taxon richness than any other arthropod group investigated. Parasitoid abundance also had a positive relationship with species richness of Coleoptera (r2 = 0·23) and Hemiptera (r2 = 0·47).

4. An historical data set demonstrated how the relationship between parasitoid abundance and overall arthropod taxon richness changes over the growing season. July, when the relationship was strongest, is potentially the most useful time to sample.

5. For use in routine monitoring, it is important that an effort be made to understand the seasonal influence on the relationship in the context being studied. Equal sampling effort must be made for all sites being compared and sites should be sampled as close together in the season as is possible.

6. Synthesis and applications. We show that, within agricultural grasslands, both the abundance and taxon richness of parasitoid Hymenoptera are more closely related with overall arthropod diversity than any other arthropod group investigated. The use of parasitoid abundance provides a simple and practicable monitoring tool for tracking change in wider arthropod diversity in agro‐ecosystems.
Species‐specific tree growth responses to 9 years of CO2 enrichment at the alpine treeline
Authors: Dawes Melissa A. , Hättenschwiler Stephan , Bebi Peter , Hagedorn Frank , Handa Ira Tanya , Körner Christian , Rixen Christian
Published: December 2010

1. Using experimental atmospheric CO2 enrichment, we tested for tree growth stimulation at the high‐elevation treeline, where there is overwhelming evidence that low temperature inhibits growth despite an adequate carbon supply. We exposed Larix decidua (European larch) and Pinus mugo ssp. uncinata (mountain pine) to 9 years of free‐air CO2 enrichment (FACE) in an in situ experiment at treeline in the Swiss Alps (2180 m a.s.l.).

2. Accounting for pre‐treatment vigour of individual trees, tree ring increments throughout the experimental period were larger in Larix growing under elevated CO2 but not in Pinus. The magnitude of the CO2 response in Larix ring width varied over time, with a significant stimulation occurring in treatment years 3–7 (marginal in year 6).

3. After 9 years of treatment, leaf canopy cover, stem basal area and total new shoot production were overall greater in Larix trees growing under elevated CO2, whereas Pinus showed no such cumulative growth response. The Larix ring width response in years 3–7 could have caused the cumulative CO2 effect on tree size even if no further stimulation occurred, so it remains unclear if responsiveness was sustained over the longer term.

4. Larix ring width was stimulated more by elevated CO2 in years with relatively high spring temperatures and an early snowmelt date, suggesting that temperatures were less limiting in these years and greater benefit was gained from extra carbon assimilated under elevated CO2. The magnitude of CO2 stimulation was also larger after relatively high temperatures and high solar radiation in the preceding growing season, perhaps reflecting gains due to larger carbon reserves.

5. Synthesis. Contrasting above‐ground growth responses of two treeline tree species to elevated CO2 concentrations suggest that Larix will have a competitive advantage over less responsive species, such as co‐occurring Pinus, under future CO2 concentrations. Stimulation of Larix growth might be especially pronounced in a future warmer climate.
Seagrass genotypic diversity increases disturbance response via complementarity and dominance
Authors: Randall Hughes A. , Stachowicz John J.
Published: December 2010

1. Genetic diversity, like species diversity, can enhance resistance or resilience to perturbation. However, we know little about how disturbance intensity affects this relationship or what mechanisms underlie the positive effects of genetic diversity.

2. We experimentally tested the independent and interactive effects of seagrass genotypic diversity (two levels) and disturbance (three levels) on seagrass biomass in a 2‐year field experiment.

3. Our results indicate that genotypic diversity enhances seagrass resilience from experimental biomass removal, but only at the highest level of disturbance; in the absence of disturbance, monocultures out‐perform polycultures over the short term.

4. Following recovery from the planned experimental disturbance, a natural macroalgal bloom caused a loss of seagrass shoots in our plots. In this case polycultures lost fewer shoots than monocultures (i.e. were more resistant to the disturbance), and this positive effect of genetic diversity persisted until the end of the experiment (1 year in total, including 6 months after all plots had recovered to pre‐disturbance densities). At the end of the 2‐year experiment, polycultures had higher shoot density and above‐ground biomass than monocultures.

5. The positive effects of diversity on shoot density and biomass were caused by both trait‐independent complementarity (TIC; due to differential resource use among clones) and positive dominance (due to one genotype achieving high density in both monoculture and polyculture).

6.
Synthesis. Our results confirm that genetic diversity, like species diversity, can influence disturbance response and does so via similar mechanisms. They also highlight that over longer time frames, these effects are likely to result from a complex mix of dominance and complementarity mechanisms that depend on the traits of the specific taxa involved and the response variables of interest.
Interregional variation in the floristic recovery of post‐agricultural forests
Authors: De Frenne Pieter , Baeten Lander , Graae Bente J. , Brunet Jörg , Wulf Monika , Orczewska Anna , Kolb Annette , Jansen Ivy , Jamoneau Aurélien , Jacquemyn Hans , Hermy Martin , Diekmann Martin , De Schrijver An , De Sanctis Michele , Decocq Guillaume , Cousins Sara A. O. , Verheyen Kris
Published: December 2010

1. Worldwide, the floristic composition of temperate forests bears the imprint of past land use for decades to centuries as forests regrow on agricultural land. Many species, however, display significant interregional variation in their ability to (re)colonize post‐agricultural forests. This variation in colonization across regions and the underlying factors remain largely unexplored.

2. We compiled data on 90 species and 812 species × study combinations from 18 studies across Europe that determined species’ distribution patterns in ancient (i.e. continuously forested since the first available land use maps) and post‐agricultural forests. The recovery rate (RR) of species in each landscape was quantified as the log‐response ratio of the percentage occurrence in post‐agricultural over ancient forest and related to the species‐specific life‐history traits and local (soil characteristics and light availability) and regional factors (landscape properties as habitat availability, time available for colonization, and climate).

3. For the herb species, we demonstrate a strong (interactive) effect of species’ life‐history traits and forest habitat availability on the RR of post‐agricultural forest. In graminoids, however, none of the investigated variables were significantly related to the RR.

4. The better colonizing species that mainly belonged to the short‐lived herbs group showed the largest interregional variability. Their recovery significantly increased with the amount of forest habitat within the landscape, whereas, surprisingly, the time available for colonization, climate, soil characteristics and light availability had no effect.

5. Synthesis. By analysing 18 independent studies across Europe, we clearly showed for the first time on a continental scale that the recovery of short‐lived forest herbs increased with the forest habitat availability in the landscape. Small perennial forest herbs, however, were generally unsuccessful in colonizing post‐agricultural forest – even in relatively densely forested landscapes. Hence, our results stress the need to avoid ancient forest clearance to preserve the typical woodland flora.
Neuroadaptation of GABAergic transmission in the central amygdala during chronic morphine treatment
Authors: Bajo Michal , Roberto Marisa , Madamba Samuel G. , Siggins George Robert
Published: December 2010

We investigated possible alterations of pharmacologically‐isolated, evoked GABAAinhibitory postsynaptic potentials (eIPSPs) and miniature GABAAinhibitory postsynaptic currents (mIPSCs) in the rat central amygdala (CeA) elicited by acute application of µ‐opioid receptor (MOR) agonists (DAMGO and morphine; 1 µM) and by chronic morphine treatment with morphine pellets. The acute activation of MORs decreased the amplitudes of eIPSPs, increased paired‐pulse facilitation (PPF) of eIPSPs and decreased the frequency (but not the amplitude) of mIPSCs in a majority of CeA neurons, suggesting that acute MOR‐dependent modulation of this GABAergic transmission is mediated predominantly via presynaptic inhibition of GABA release. We observed no significant changes in the membrane properties, eIPSPs, PPF or mIPSCs of CeA neurons during chronic morphine treatment compared to CeA of naïve or sham rats. Superfusion of the MOR antagonist CTOP (1 µM) increased the mean amplitude of eIPSPs in a majority of CeA neurons to the same degree in both naïve/sham and morphine‐treated rats, suggesting a tonic activation of MORs in both conditions. Superfusion of DAMGO decreased eIPSP amplitudes and the frequency of mIPSCs equally in both naïve/sham and morphine‐treated rats but decreased the amplitude of mIPSCs only in morphine treated rats, an apparent postsynaptic action. Our combined findings suggest the development of tolerance of the CeA GABAergic system to inhibitory effects of acute activation of MORs on presynaptic GABA release and possible alteration of MOR‐dependent postsynaptic mechanisms that may represent important neuroadaptations of the GABAergic and MOR systems during chronic morphine treatment.
Effect of methamphetamine dependence on heart rate variability
Authors: Henry Brook L. , Minassian Arpi , Perry William
Published: December 2010

Methamphetamine (METH) is an increasing popular and highly addictive stimulant associated with autonomic nervous system (ANS) dysfunction, cardiovascular pathology and neurotoxicity. Heart rate variability (HRV) has been used to assess autonomic function and predict mortality in cardiac disorders and drug intoxication, but has not been characterized in METH use. We recorded HRV in a sample of currently abstinent individuals with a history of METH dependence compared to age‐ and gender‐matched drug‐free comparison subjects. HRV was assessed using time domain, frequency domain, and non‐linear entropic analyses in 17 previously METH‐dependent and 21 drug‐free comparison individuals during a 5 minute rest period. The METH‐dependent group demonstrated significant reduction in HRV, reduced parasympathetic activity, and diminished heartbeat complexity relative to comparison participants. More recent METH use was associated with increased sympathetic tone. Chronic METH exposure may be associated with decreased HRV, impaired vagal function, and reduction in heart rate complexity as assessed by multiple methods of analysis. We discuss and review evidence that impaired HRV may be related to the cardiotoxic or neurotoxic effects of prolonged METH use.
The endocannabinoid system modulates the valence of the emotion associated to food ingestion
Authors: Méndez‐Díaz Mónica , Rueda‐Orozco Pavel Ernesto , Ruiz‐Contreras Alejandra Evelyn , Prospéro‐García Oscar
Published: December 2010

Endocannabinoids (eCBs) are mediators of the homeostatic and hedonic systems that modulate food ingestion. Hence, eCBs, by regulating the hedonic system, may be modulating the valence of the emotion associated to food ingestion (positive: pleasant or negative: unpleasant). Our first goal was to demonstrate that palatable food induces conditioned place preference (CPP), hence a positive‐valence emotion. Additionally, we analyzed if this CPP is blocked by AM251, inducing a negative valence emotion, meaning avoiding the otherwise pursued compartment. The second goal was to demonstrate that CPP induced by regular food would be strengthened by the simultaneous administration of anandamide or oleamide, and if such, CPP is blocked by AM251. Finally, we tested the capacity of eCBs (without food) to induce CPP. Our results indicate that rats readily developed CPP to palatable food, which was blocked by AM251. The CPP induced by regular food was strengthened by eCBs and blocked by AM251. Finally, oleamide, unlike anandamide, induced CPP. These results showed that eCBs mediate the positive valence (CPP) of the emotion associated to food ingestion. It was also observed that the blockade of the CB1 receptor causes a loss of correlation between food and CPP (negative valence: avoidance). These data further support the role of eCBs as regulators of the hedonic value of food.
Repeated exposure to moderate doses of ethanol augments hippocampal glutamate neurotransmission by increasing release
Authors: Chefer Vladimir , Meis Jennifer , Wang Grace , Kuzmin Alexander , Bakalkin Georgy , Shippenberg Toni
Published: December 2010

The present study used conventional and quantitative microdialysis to assess glutamatergic and GABAergic neurotransmission in the hippocampal CA3 area of the rat following a moderate‐dose ethanol treatment regimen. Male Wistar rats received 3.4 g/kg of ethanol or water for 6 days via gastric gavage. Microdialysis experiments commenced 2 days later. Basal and depolarization‐induced glutamate overflow were significantly elevated in ethanol‐treated animals. Basal and depolarization‐induced gamma‐aminobutyric acid (GABA) overflow were unaltered. Quantitative no‐net‐flux microdialysis was used to determine if changes in dialysate glutamate levels following ethanol administration are due to an increase in release or a decrease in uptake. To confirm the validity of this method for quantifying basal glutamate dynamics, extracellular concentrations of glutamate and the extraction fraction, which reflects changes in analyte clearance, were quantified in response to retro‐dialysis of the glutamate uptake blocker trans‐pyrrolidine‐2,4‐dicarboxylic acid (tPDC). tPDC significantly decreased the extraction fraction for glutamate, resulting in augmented extracellular glutamate concentrations. Repeated ethanol administration did not alter the glutamate extraction fraction. However, extracellular glutamate concentrations were significantly elevated, indicating that glutamate release is increased as a consequence of repeated ethanol administration. These data demonstrate that repeated bouts of moderate ethanol consumption alter basal glutamate dynamics in the CA3 region of the dorsal hippocampus. Basal glutamate release is augmented, whereas glutamate uptake is unchanged. Furthermore, they suggest that dysregulation of glutamate transmission in this region may contribute to the previously documented deficits in cognitive function associated with moderate dose ethanol use.