WorldWideScience

Sample records for roi analyses revealed

  1. Return-on-Investment (ROI) Analyses of an Inpatient Lay Health Worker Model on 30-Day Readmission Rates in a Rural Community Hospital.

    Science.gov (United States)

    Cardarelli, Roberto; Bausch, Gregory; Murdock, Joan; Chyatte, Michelle Renee

    2017-07-07

    The purpose of the study was to assess the return-on-investment (ROI) of an inpatient lay health worker (LHW) model in a rural Appalachian community hospital impacting 30-day readmission rates. The Bridges to Home (BTH) study completed an evaluation in 2015 of an inpatient LHW model in a rural Kentucky hospital that demonstrated a reduction in 30-day readmission rates by 47.7% compared to a baseline period. Using the hospital's utilization and financial data, a validated ROI calculator specific to care transition programs was used to assess the ROI of the BTH model comparing 3 types of payment models including Diagnosis Related Group (DRG)-only payments, pay-for-performance (P4P) contracts, and accountable care organizations (ACOs). The BTH program had a -$0.67 ROI if the hospital had only a DRG-based payment model. If the hospital had P4P contracts with payers and 0.1% of its annual operating revenue was at risk, the ROI increased to $7.03 for every $1 spent on the BTH program. However, if the hospital was an ACO as was the case for this study's community hospital, the ROI significantly increased to $38.48 for every $1 spent on the BTH program. The BTH model showed a viable ROI to be considered by community hospitals that are part of an ACO or P4P program. A LHW care transition model may be a cost-effective alternative for impacting excess 30-day readmissions and avoiding associated penalties for hospital systems with a value-based payment model. © 2017 National Rural Health Association.

  2. Special analyses reveal coke-deposit structure

    International Nuclear Information System (INIS)

    Albright, L.F.

    1988-01-01

    A scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX) have been used to obtain information that clarifies the three mechanisms of coke formation in ethylene furnaces, and to analyze the metal condition at the exit of furnace. The results can be used to examine furnace operations and develop improved ethylene plant practices. In this first of four articles on the analyses of coke and metal samples, the coking mechanisms and coke deposits in a section of tube from an actual ethylene furnace (Furnace A) from a plant on the Texas Gulf Coast are discussed. The second articles in the series will analyze the condition of the tube metal in the same furnace. To show how coke deposition and metal condition dependent on the operating parameters of an ethylene furnace, the third article in the series will show the coke deposition in a Texas Gulf Coast furnace tube (Furnace B) that operated at shorter residence time. The fourth article discusses the metal condition in that furnace. Some recommendations, based on the analyses and findings, are offered in the fourth article that could help extend the life of ethylene furnace tubes, and also improve overall ethylene plant operations

  3. Dual-ROI radionuclide ventriculography

    International Nuclear Information System (INIS)

    Standke, R.; Hoer, G.; Kanemoto, N.; Maul, F.D.

    1981-01-01

    Accurate determination of the left ventricular activity function is the precondition for a quantitative analysis of the ventricular volume function. During the volume reduction period, extra-myocardial tissue penetrates into the ROI of the late diastole. This curve-distorting activity cannot be eliminated by a single-ROI technique. Of the multiple-ROI techniques, the dual-ROI method is the least complex and tedions and involves the least methodological error. At the time of maximum volume change rates, the curve may be distorted if the late diastolic ROI is inaccurately defined. A method is described which uses only the counting rate over the late diastolic ROI and corrects it only on the basis of the counting rate of the late systolic ROI. The time parameters remain uninfluenced by this correction method while the volumetric parameters are corrected. (orig./APR) [de

  4. The Criticality of Connecting People to Financial Results ‒ an ROI Calculation Model for Romanian FSOs

    Directory of Open Access Journals (Sweden)

    Daniela Niculescu

    2016-02-01

    Full Text Available Organisational culture and employee engagement have been the focus of recent broad-based research efforts. Adding this concern to the revealed importance of performance indicators on human capital, and that their use is getting momentum, in order to attach financial values to knowledge management assets, it becomes more and more critical to measure human capital value. Key for Romanian FSO’s managers becomes to consider that both human and financial values have a focus on adding value in every process and function in the organisation, and to perpetuate organisational profitability by the corporate culture, on the one hand, where culture is a powerful factor that helps a company to engage, on the other hand, talented people. There is a substantial concern on using ROI on Learning and Development programmes, but whilst this is still declared, Romanian FSOs do not yet have a consistent method to measure it. This study is showing the criticality of connecting people to financial results and data analysis suggests that ROI calculation has a positive impact on creating and fostering a powerful organisational culture and that employees’ awareness of ROI values within their organisation has a powerful effect on their sense of engagement. Our findings have a more practical implication for the analysed industry by shaping a formal ROI measurement mechanisms blueprint, an ROI calculation model for the Romanian FSOs, in the form of a mechanism that could be employed when considering the design of an ROI Methodology for Romanian FSOs.

  5. RFID Benefits; Looking Beyond ROI

    National Research Council Canada - National Science Library

    Guilford, Shane; Kutis, Mark C

    2005-01-01

    ...) into the logistics process that are not captured by traditional Return on Investment (ROI) analysis. The authors seek to identify some of these benefits to determine their overall contribution to the value of new technology implementation...

  6. Return on investment (ROI) proposal preparation guide

    International Nuclear Information System (INIS)

    Valero, O.J.

    1998-01-01

    The ROI Proposal Preparation Guide is a tool to assist Hanford waste generators in preparing ROI proposal forms for submittal to Department of Energy, Richland Operations Office (DOE/RL) for funding. The guide describes the requirements for submitting an ROI proposal and provides examples of completed ROI forms. The intent is to assist waste generators in identifying projects that meet the criteria, provide information necessary to complete the ROI forms, and submit a proposal that is eligible to receive funding

  7. Return on investment (ROI) proposal preparation guide

    International Nuclear Information System (INIS)

    BOOM, R.J.

    1999-01-01

    Section I: Background Return on Investment (ROI) Proposal Preparation Guide-- Over $1.9M is available to fund fiscal year (FY) 2000 waste minimization projects on the Hanford Site. This money was allocated by the US. Department of Energy Headquarters (DOE-HQ). The U.S. Department of Energy, Richland Operations (RL) and the U.S. Department of Energy, Office of River Protection (ORP) are currently seeking pollution prevention proposals from across the Hanford Site that provide a high return-on-investment (ROI) by reducing waste and associated management costs. Purpose of ROI Training The ROI Proposal Preparation Guide is a tool to assist Hanford waste generators in preparing ROI proposal forms for submittal to RL for funding. The guide describes the requirements for submitting an ROI proposal and provides examples of completed ROI forms. The intent is to assist waste generators in identifying projects that meet the criteria, provide information necessary to complete the ROI forms, and submit a proposal that is eligible to receive funding. This guide accompanies the one-hour training workshop on how to prepare and submit an ROI proposal

  8. Maximizing ROI (return on information)

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, B.

    2000-05-01

    The role and importance of managing information are discussed, underscoring the importance by quoting from the report of the International Data Corporation, according to which Fortune 500 companies lost $ 12 billion in 1999 due to inefficiencies resulting from intellectual re-work, substandard performance , and inability to find knowledge resources. The report predicts that this figure will rise to $ 31.5 billion by 2003. Key impediments to implementing knowledge management systems are identified as : the cost and human resources requirement of deployment; inflexibility of historical systems to adapt to change; and the difficulty of achieving corporate acceptance of inflexible software products that require changes in 'normal' ways of doing business. The author recommends the use of model, document and rule-independent systems with a document centered interface (DCI), employing rapid application development (RAD) and object technologies and visual model development, which eliminate these problems, making it possible for companies to maximize their return on information (ROI), and achieve substantial savings in implementation costs.

  9. Conserved regulators of nucleolar size revealed by global phenotypic analyses.

    Science.gov (United States)

    Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2013-08-20

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

  10. Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

    Science.gov (United States)

    Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2014-01-01

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

  11. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-03-01

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

  12. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  13. Measuring the ROI on Knowledge Management Systems.

    Science.gov (United States)

    Wickhorst, Vickie

    2002-01-01

    Defines knowledge management and corporate portals and provides a model that can be applied to assessing return on investment (ROI) for a knowledge management solution. Highlights include leveraging knowledge in an organization; assessing the value of human capital; and the Intellectual Capital Performance Measurement Model. (LRW)

  14. Roi Vaara tähendussõnad

    Index Scriptorium Estoniae

    2003-01-01

    10. II oli Tallinna Kunstihoones soome kunstniku Roi Vaara performance Tallinna Kunstihoone uue juhataja Reiu Tüüri, kuraatorite Andres Härmi ja Reet Varblase inauguratsiooni ning TK interneti lehekülje esitluse puhul. Uue ühtse nimekuju KU autorit Edith Parist autasustati 1934 krooniga

  15. Attention to detail helps Clarian measure ROI.

    Science.gov (United States)

    2007-01-01

    Clarian Health takes a risk and embarks on a branding strategy. Taking a multi-integrated approach, with The Heavy Weights in Indianapolis, Clarian started managing its marketing by tracking return on investment (ROI) and making the most of a CRM database. In a groundbreaking approach, it found that it was actually able to turn its marketing effort into a money-maker, leading higher-ups to see its outreach efforts as necessity.

  16. Normalisation: ROI optimal treatment planning - SNDH pattern

    International Nuclear Information System (INIS)

    Shilvat, D.V.; Bhandari, Virendra; Tamane, Chandrashekhar; Pangam, Suresh

    2001-01-01

    Dose precision maximally to the target / ROI (Region of Interest), taking care of tolerance dose of normal tissue is the aim of ideal treatment planning. This goal is achieved with advanced modalities such as, micro MLC, simulator and 3-dimensional treatment planning system. But SNDH PATTERN uses minimum available resources as, ALCYON II Telecobalt unit, CT Scan, MULTIDATA 2-dimensional treatment planning system to their maximum utility and reaches to the required precision, same as that with advance modalities. Among the number of parameters used, 'NORMALISATION TO THE ROI' will achieve the aim of the treatment planning effectively. This is dealing with an example of canal of esophagus modified treatment planning based on SNDH pattern. Results are attractive and self explanatory. By implementing SNDH pattern, the QUALITY INDEX of treatment plan will reach to greater than 90%, with substantial reduction in dose to the vital organs. Aim is to utilize the minimum available resources efficiently to achieve highest possible precision for delivering homogenous dose to ROI while taking care of tolerance dose to vital organs

  17. Practical implementation of Channelized Hotelling Observers: Effect of ROI size.

    Science.gov (United States)

    Ferrero, Andrea; Favazza, Christopher P; Yu, Lifeng; Leng, Shuai; McCollough, Cynthia H

    2017-03-01

    Fundamental to the development and application of channelized Hotelling observer (CHO) models is the selection of the region of interest (ROI) to evaluate. For assessment of medical imaging systems, reducing the ROI size can be advantageous. Smaller ROIs enable a greater concentration of interrogable objects in a single phantom image, thereby providing more information from a set of images and reducing the overall image acquisition burden. Additionally, smaller ROIs may promote better assessment of clinical patient images as different patient anatomies present different ROI constraints. To this end, we investigated the minimum ROI size that does not compromise the performance of the CHO model. In this study, we evaluated both simulated images and phantom CT images to identify the minimum ROI size that resulted in an accurate figure of merit (FOM) of the CHO's performance. More specifically, the minimum ROI size was evaluated as a function of the following: number of channels, spatial frequency and number of rotations of the Gabor filters, size and contrast of the object, and magnitude of the image noise. Results demonstrate that a minimum ROI size exists below which the CHO's performance is grossly inaccurate. The minimum ROI size is shown to increase with number of channels and be dictated by truncation of lower frequency filters. We developed a model to estimate the minimum ROI size as a parameterized function of the number of orientations and spatial frequencies of the Gabor filters, providing a guide for investigators to appropriately select parameters for model observer studies.

  18. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

    Directory of Open Access Journals (Sweden)

    Heidi G. Parker

    2017-04-01

    Full Text Available There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

  19. Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

    Science.gov (United States)

    Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

  20. Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola.

    Science.gov (United States)

    Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

    2016-01-01

    Understanding the regulation of lipid metabolism is vital for genetic engineering of canola ( Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola.

  1. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  2. Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia.

    Science.gov (United States)

    Low, V L; Lim, P E; Chen, C D; Lim, Y A L; Tan, T K; Norma-Rashid, Y; Lee, H L; Sofian-Azirun, M

    2014-06-01

    The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus. © 2013 The Royal Entomological Society.

  3. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    Science.gov (United States)

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  4. Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

    Science.gov (United States)

    da Silva Santos, Anelisie; Trigo, Tatiane Campos; de Oliveira, Tadeu Gomes; Silveira, Leandro

    2018-01-01

    Abstract The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species’ history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America. PMID:29668017

  5. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Directory of Open Access Journals (Sweden)

    Tod W Reeder

    Full Text Available Squamate reptiles (lizards and snakes are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa. Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia. These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses without considering the possible impact of molecular data on their placement.

  6. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Science.gov (United States)

    Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

  7. Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

    Science.gov (United States)

    Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

  8. Individual-based analyses reveal limited functional overlap in a coral reef fish community.

    Science.gov (United States)

    Brandl, Simon J; Bellwood, David R

    2014-05-01

    Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on

  9. Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

    Directory of Open Access Journals (Sweden)

    James J Collins

    Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

  10. Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments

    International Nuclear Information System (INIS)

    Wang, Mengcen; Qian, Yuan; Liu, Xiaoyu; Wei, Peng; Deng, Man; Wang, Lei; Wu, Huiming; Zhu, Guonian

    2017-01-01

    Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3–11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted. - Highlights: • Multiple spectroscopic analyses were applied to investigate agrochemicals transformation in environment. • Three novel compounds were isolated and identified as triafamone metabolites. • The fate and transformation pathway of triafamone in rice paddy were revealed. • Long-term consumption of the triafamone-containing brown rice is relatively safe. • Elucidation of environmental impacts by exposure to these triazine or oxazolidinedione metabolites is warranted. - Triafamone rapidly dissipates in agricultural environments

  11. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

    Science.gov (United States)

    Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

    2017-09-01

    The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

  12. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  13. Measuring Digital Signage ROI : A combination of Digital Signage and Mobile Advertising as a method for measuring Digtal Signage ROI

    OpenAIRE

    Helander, Fredrik

    2010-01-01

    Marketing has changed a lot the past decade. New modern marketing channels have been developed and marketing have become more effective. This has affected the expectations advertisers have on advertising channels. One thing advertisers increasingly expect is to be able to efficiently measure the result of advertising, the ROI. A method for measuring ROI of digital signage is in focus in this study. The measurement is enabled by a combination of digital signage and mobile advertising. First a ...

  14. Global terrestrial water storage connectivity revealed using complex climate network analyses

    Science.gov (United States)

    Sun, A. Y.; Chen, J.; Donges, J.

    2015-07-01

    Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

  15. DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms.

    Directory of Open Access Journals (Sweden)

    Bang Feng

    Full Text Available The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.

  16. DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms

    Science.gov (United States)

    Feng, Bang; Xu, Jianping; Wu, Gang; Zeng, Nian-Kai; Li, Yan-Chun; Tolgor, Bau; Kost, Gerhard W.; Yang, Zhu L.

    2012-01-01

    The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions. PMID:22629418

  17. Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

    International Nuclear Information System (INIS)

    Rumbajan, Janette Mareska; Aoki, Shigehisa; Kohashi, Kenichi; Oda, Yoshinao; Hata, Kenichiro; Saji, Tsutomu; Taguchi, Tomoaki; Tajiri, Tatsuro; Soejima, Hidenobu; Joh, Keiichiro; Maeda, Toshiyuki; Souzaki, Ryota; Mitsui, Kazumasa; Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Nishioka, Kenichi; Harada, Ryoko

    2013-01-01

    Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

  18. Robust finger vein ROI localization based on flexible segmentation.

    Science.gov (United States)

    Lu, Yu; Xie, Shan Juan; Yoon, Sook; Yang, Jucheng; Park, Dong Sun

    2013-10-24

    Finger veins have been proved to be an effective biometric for personal identification in the recent years. However, finger vein images are easily affected by influences such as image translation, orientation, scale, scattering, finger structure, complicated background, uneven illumination, and collection posture. All these factors may contribute to inaccurate region of interest (ROI) definition, and so degrade the performance of finger vein identification system. To improve this problem, in this paper, we propose a finger vein ROI localization method that has high effectiveness and robustness against the above factors. The proposed method consists of a set of steps to localize ROIs accurately, namely segmentation, orientation correction, and ROI detection. Accurate finger region segmentation and correct calculated orientation can support each other to produce higher accuracy in localizing ROIs. Extensive experiments have been performed on the finger vein image database, MMCBNU_6000, to verify the robustness of the proposed method. The proposed method shows the segmentation accuracy of 100%. Furthermore, the average processing time of the proposed method is 22 ms for an acquired image, which satisfies the criterion of a real-time finger vein identification system.

  19. Robust Finger Vein ROI Localization Based on Flexible Segmentation

    Directory of Open Access Journals (Sweden)

    Dong Sun Park

    2013-10-01

    Full Text Available Finger veins have been proved to be an effective biometric for personal identification in the recent years. However, finger vein images are easily affected by influences such as image translation, orientation, scale, scattering, finger structure, complicated background, uneven illumination, and collection posture. All these factors may contribute to inaccurate region of interest (ROI definition, and so degrade the performance of finger vein identification system. To improve this problem, in this paper, we propose a finger vein ROI localization method that has high effectiveness and robustness against the above factors. The proposed method consists of a set of steps to localize ROIs accurately, namely segmentation, orientation correction, and ROI detection. Accurate finger region segmentation and correct calculated orientation can support each other to produce higher accuracy in localizing ROIs. Extensive experiments have been performed on the finger vein image database, MMCBNU_6000, to verify the robustness of the proposed method. The proposed method shows the segmentation accuracy of 100%. Furthermore, the average processing time of the proposed method is 22 ms for an acquired image, which satisfies the criterion of a real-time finger vein identification system.

  20. Robust Finger Vein ROI Localization Based on Flexible Segmentation

    Science.gov (United States)

    Lu, Yu; Xie, Shan Juan; Yoon, Sook; Yang, Jucheng; Park, Dong Sun

    2013-01-01

    Finger veins have been proved to be an effective biometric for personal identification in the recent years. However, finger vein images are easily affected by influences such as image translation, orientation, scale, scattering, finger structure, complicated background, uneven illumination, and collection posture. All these factors may contribute to inaccurate region of interest (ROI) definition, and so degrade the performance of finger vein identification system. To improve this problem, in this paper, we propose a finger vein ROI localization method that has high effectiveness and robustness against the above factors. The proposed method consists of a set of steps to localize ROIs accurately, namely segmentation, orientation correction, and ROI detection. Accurate finger region segmentation and correct calculated orientation can support each other to produce higher accuracy in localizing ROIs. Extensive experiments have been performed on the finger vein image database, MMCBNU_6000, to verify the robustness of the proposed method. The proposed method shows the segmentation accuracy of 100%. Furthermore, the average processing time of the proposed method is 22 ms for an acquired image, which satisfies the criterion of a real-time finger vein identification system. PMID:24284769

  1. Biopsy Needle Localization and Tracking Using ROI-RK Method

    Directory of Open Access Journals (Sweden)

    Yue Zhao

    2014-01-01

    Full Text Available ROI-RK method is a biopsy needle localization and tracking method. Previous research work has proved that it has a robust performance on different series of simulated 3D US volumes. Unfortunately, in real situations, because of the strong speckle noise of the ultrasound image and the different echogenic properties of the tissues, the real 3D US volumes have more complex background than the simulated images used previously. In this paper, to adapt the ROI-RK method in real 3D US volumes, a line-filter enhancement calculation only in the ROI is added to increase the contrast between the needle and background tissue, decreasing the phenomenon of expansion of the biopsy needle due to reverberation of ultrasound in the needle. To make the ROI-RK method more stable, a self-correction system is also implemented. Real data have been acquired on an ex vivo heart of lamb. The result of the ROI-RK method shows that it is capable to localize and track the biopsy needle in real situations, and it satisfies the demand of real-time application.

  2. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

    Directory of Open Access Journals (Sweden)

    Rajini Sreenivasan

    Full Text Available BACKGROUND: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs, 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4 has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar

  3. Reproducibility of CT bone dosimetry: Operator versus automated ROI definition

    International Nuclear Information System (INIS)

    Louis, O.; Luypaert, R.; Osteaux, M.; Kalender, W.

    1988-01-01

    Intrasubject reproducibility with repeated determination of vertebral mineral density from a given set of CT images was investigated. The region of interest (ROI) in 10 patient scans was selected by four independent operators either manually or with an automated procedure separating cortical and spongeous bone, the operators being requested to interact in ROI selection. The mean intrasubject variation was found to be much lower with the automated process (0.3 to 0.6%) than with the conventional method (2.5 to 5.2%). In a second study, 10 patients were examined twice to determine the reproducibility of CT slice selection by the operator. The errors were of the same order of magnitude as in ROI selection. (orig.)

  4. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodrí guez, J. P.; Ferná ndez-Gracia, Juan; Thums, Michele; Hindell, Mark A.; Sequeira, Ana M. M.; Meekan, Mark G.; Costa, Daniel P.; Guinet, Christophe; Harcourt, R.; McMahon, Clive R.; Muelbert, Monica; Duarte, Carlos M.; Eguí luz, V. M.

    2017-01-01

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  5. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodríguez, Jorge P.

    2017-03-02

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  6. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

    Science.gov (United States)

    Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

  7. Underestimation of species richness in neotropical frogs revealed by mtDNA analyses.

    Directory of Open Access Journals (Sweden)

    Antoine Fouquet

    2007-10-01

    Full Text Available Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness.Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs.In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species.Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia

  8. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery

    DEFF Research Database (Denmark)

    Poulsen, Michael; Oh, Dong-Chan; Clardy, Jon

    2011-01-01

    and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15...... and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding...... phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest....

  9. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Directory of Open Access Journals (Sweden)

    Pengpeng Li

    Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  10. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  11. Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

  12. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

    Directory of Open Access Journals (Sweden)

    Kristina Kirschner

    2015-03-01

    Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

  13. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  14. Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean.

    Science.gov (United States)

    Chu, Shanshan; Li, Hongyan; Zhang, Xiangqian; Yu, Kaiye; Chao, Maoni; Han, Suoyi; Zhang, Dan

    2018-06-06

    Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

  15. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  16. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S; Siam, Rania; Setubal, Joã o C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvä slaiho, Heikki; Ramadan, Eman; Antunes, André ; Stingl, Ulrich; Archer, John A.C.; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  17. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Shan Goh

    Full Text Available BACKGROUND: Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS: Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50. When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS: RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

  18. Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

    DEFF Research Database (Denmark)

    Brok, J.; Thorlund, K.; Gluud, C.

    2008-01-01

    in 80% (insufficient information size). TSA(15%) and TSA(LBHIS) found that 95% and 91% had absence of evidence. The remaining nonsignificant meta-analyses had evidence of lack of effect. CONCLUSION: TSA reveals insufficient information size and potentially false positive results in many meta......OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA...

  19. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    DEFF Research Database (Denmark)

    Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria

    2015-01-01

    We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression...... of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide...

  20. Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency

    Science.gov (United States)

    Cacchiarelli, Davide; Trapnell, Cole; Ziller, Michael J.; Soumillon, Magali; Cesana, Marcella; Karnik, Rahul; Donaghey, Julie; Smith, Zachary D.; Ratanasirintrawoot, Sutheera; Zhang, Xiaolan; Ho Sui, Shannan J.; Wu, Zhaoting; Akopian, Veronika; Gifford, Casey A.; Doench, John; Rinn, John L.; Daley, George Q.; Meissner, Alexander; Lander, Eric S.; Mikkelsen, Tarjei S.

    2015-01-01

    Summary Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered reactivation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. PMID:26186193

  1. Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling.

    Science.gov (United States)

    Schluttenhofer, Craig; Pattanaik, Sitakanta; Patra, Barunava; Yuan, Ling

    2014-06-20

    To combat infection to biotic stress plants elicit the biosynthesis of numerous natural products, many of which are valuable pharmaceutical compounds. Jasmonate is a central regulator of defense response to pathogens and accumulation of specialized metabolites. Catharanthus roseus produces a large number of terpenoid indole alkaloids (TIAs) and is an excellent model for understanding the regulation of this class of valuable compounds. Recent work illustrates a possible role for the Catharanthus WRKY transcription factors (TFs) in regulating TIA biosynthesis. In Arabidopsis and other plants, the WRKY TF family is also shown to play important role in controlling tolerance to biotic and abiotic stresses, as well as secondary metabolism. Here, we describe the WRKY TF families in response to jasmonate in Arabidopsis and Catharanthus. Publically available Arabidopsis microarrays revealed at least 30% (22 of 72) of WRKY TFs respond to jasmonate treatments. Microarray analysis identified at least six jasmonate responsive Arabidopsis WRKY genes (AtWRKY7, AtWRKY20, AtWRKY26, AtWRKY45, AtWRKY48, and AtWRKY72) that have not been previously reported. The Catharanthus WRKY TF family is comprised of at least 48 members. Phylogenetic clustering reveals 11 group I, 32 group II, and 5 group III WRKY TFs. Furthermore, we found that at least 25% (12 of 48) were jasmonate responsive, and 75% (9 of 12) of the jasmonate responsive CrWRKYs are orthologs of AtWRKYs known to be regulated by jasmonate. Overall, the CrWRKY family, ascertained from transcriptome sequences, contains approximately 75% of the number of WRKYs found in other sequenced asterid species (pepper, tomato, potato, and bladderwort). Microarray and transcriptomic data indicate that expression of WRKY TFs in Arabidopsis and Catharanthus are under tight spatio-temporal and developmental control, and potentially have a significant role in jasmonate signaling. Profiling of CrWRKY expression in response to jasmonate treatment

  2. Integrative analyses reveal novel strategies in HPV11,-16 and-45 early infection

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Rossing, Maria; Andersen, Ditte

    2012-01-01

    of genes not previously implicated in HPV biology, such as the PSG family and ANKRD1, and of genes implicated in the biology of other viruses, e. g. MX1, IFI44 and DDX60. Carcinogenesis-related genes, e. g. ABL2, MGLL and CYR61, were upregulated by high-risk HPV16 and -45. The integrative analysis revealed...... the suppression of DNA repair by HPV11 and -16, and downregulation of cytoskeleton genes by all HPV types. Various signalling pathways were affected by the HPVs: IL-2 by HPV11; JAK-STAT by HPV16; and TGF-beta, NOTCH and tyrosine kinase signalling by HPV45. This study uncovered novel strategies employed by HPV...... to establish infection and promote uncontrolled growth....

  3. Categorizing words using 'frequent frames': what cross-linguistic analyses reveal about distributional acquisition strategies.

    Science.gov (United States)

    Chemla, Emmanuel; Mintz, Toben H; Bernal, Savita; Christophe, Anne

    2009-04-01

    Mintz (2003) described a distributional environment called a frame, defined as the co-occurrence of two context words with one intervening target word. Analyses of English child-directed speech showed that words that fell within any frequently occurring frame consistently belonged to the same grammatical category (e.g. noun, verb, adjective, etc.). In this paper, we first generalize this result to French, a language in which the function word system allows patterns that are potentially detrimental to a frame-based analysis procedure. Second, we show that the discontinuity of the chosen environments (i.e. the fact that target words are framed by the context words) is crucial for the mechanism to be efficient. This property might be relevant for any computational approach to grammatical categorization. Finally, we investigate a recursive application of the procedure and observe that the categorization is paradoxically worse when context elements are categories rather than actual lexical items. Item-specificity is thus also a core computational principle for this type of algorithm. Our analysis, along with results from behavioural studies (Gómez, 2002; Gómez and Maye, 2005; Mintz, 2006), provides strong support for frames as a basis for the acquisition of grammatical categories by infants. Discontinuity and item-specificity appear to be crucial features.

  4. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

    Science.gov (United States)

    Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

    2016-01-01

    Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

  6. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

    Science.gov (United States)

    Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

    2013-10-29

    Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

  7. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

    Science.gov (United States)

    Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

    2018-04-01

    The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

  8. Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

    2012-05-25

    Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).

  9. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery.

    Directory of Open Access Journals (Sweden)

    Michael Poulsen

    2011-02-01

    Full Text Available Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15 of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest.

  10. Combined metabolomic and correlation networks analyses reveal fumarase insufficiency altered amino acid metabolism.

    Science.gov (United States)

    Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

    2018-04-01

    Fumarase catalyzes the interconversion of fumarate and l-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased levels of fumarate, decreased levels of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient human umbilical vein endothelial cells (HUVEC) and negative controls. A total of 24 altered metabolites involved in seven metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, l-malic acid, l-aspartic acid, glycine and l-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. Alanine aminotransferase and glutamate dehydrogenase activities increased significantly in fumarase deficiency HUVEC. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. Copyright © 2017 John Wiley & Sons, Ltd.

  11. Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma.

    Science.gov (United States)

    Donson, Andrew M; Apps, John; Griesinger, Andrea M; Amani, Vladimir; Witt, Davis A; Anderson, Richard C E; Niazi, Toba N; Grant, Gerald; Souweidane, Mark; Johnston, James M; Jackson, Eric M; Kleinschmidt-DeMasters, Bette K; Handler, Michael H; Tan, Aik-Choon; Gore, Lia; Virasami, Alex; Gonzalez-Meljem, Jose Mario; Jacques, Thomas S; Martinez-Barbera, Juan Pedro; Foreman, Nicholas K; Hankinson, Todd C

    2017-09-01

    Pediatric adamantinomatous craniopharyngioma (ACP) is a highly solid and cystic tumor, often causing substantial damage to critical neuroendocrine structures such as the hypothalamus, pituitary gland, and optic apparatus. Paracrine signaling mechanisms driving tumor behavior have been hypothesized, with IL-6R overexpression identified as a potential therapeutic target. To identify potential novel therapies, we characterized inflammatory and immunomodulatory factors in ACP cyst fluid and solid tumor components. Cytometric bead analysis revealed a highly pro-inflammatory cytokine pattern in fluid from ACP compared to fluids from another cystic pediatric brain tumor, pilocytic astrocytoma. Cytokines and chemokines with particularly elevated concentrations in ACPs were IL-6, CXCL1 (GRO), CXCL8 (IL-8) and the immunosuppressive cytokine IL-10. These data were concordant with solid tumor compartment transcriptomic data from a larger cohort of ACPs, other pediatric brain tumors and normal brain. The majority of receptors for these cytokines and chemokines were also over-expressed in ACPs. In addition to IL-10, the established immunosuppressive factor IDO-1 was overexpressed by ACPs at the mRNA and protein levels. These data indicate that ACP cyst fluids and solid tumor components are characterized by an inflammatory cytokine and chemokine expression pattern. Further study regarding selective cytokine blockade may inform novel therapeutic interventions. © 2017 American Association of Neuropathologists, Inc. All rights reserved.

  12. Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses.

    Science.gov (United States)

    You, Xiangrong; Wang, Lingxia; Liang, Wenyu; Gai, Yonghong; Wang, Xiaoyan; Chen, Wei

    2012-02-02

    Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 18 up-regulated and 21 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohormone, cytoskeleton structure, regulation, and stress tolerance. Among these, the largest functional class was associated with primary metabolism. Down-regulated proteins were involved in photosynthesis, transcription, and translation, whereas up-regulated proteins were involved in respiration. Decreased flavonoid synthesis and up-regulated GA20ox might be involved in the floral reversion process. Up-regulated 14-3-3 proteins played a role in the regulation of floral reversion in D. longan by responding to abiotic stress. Observations via transmission electron microscopy revealed the ultrastructure changes in shedding buds undergoing floral reversion. Overall, the results provided insights into the molecular basis for the floral reversion mechanism in D. longan. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  14. Multiple Spectral Ratio Analyses Reveal Earthquake Source Spectra of Small Earthquakes and Moment Magnitudes of Microearthquakes

    Science.gov (United States)

    Uchide, T.; Imanishi, K.

    2016-12-01

    Spectral studies for macroscopic earthquake source parameters are helpful for characterizing earthquake rupture process and hence understanding earthquake source physics and fault properties. Those studies require us mute wave propagation path and site effects in spectra of seismograms to accentuate source effect. We have recently developed the multiple spectral ratio method [Uchide and Imanishi, BSSA, 2016] employing many empirical Green's function (EGF) events to reduce errors from the choice of EGF events. This method helps us estimate source spectra more accurately as well as moment ratios among reference and EGF events, which are useful to constrain the seismic moment of microearthquakes. First, we focus on earthquake source spectra. The source spectra have generally been thought to obey the omega-square model with single corner-frequency. However recent studies imply the existence of another corner frequency for some earthquakes. We analyzed small shallow inland earthquakes (3.5 multiple spectral ratio analyses. For 20000 microearthquakes in Fukushima Hamadori and northern Ibaraki prefecture area, we found that the JMA magnitudes (Mj) based on displacement or velocity amplitude are systematically below Mw. The slope of the Mj-Mw relation is 0.5 for Mj 5. We propose a fitting curve for the obtained relationship as Mw = (1/2)Mj + (1/2)(Mjγ + Mcorγ)1/γ+ c, where Mcor is a corner magnitude, γ determines the sharpness of the corner, and c denotes an offset. We obtained Mcor = 4.1, γ = 5.6, and c = -0.47 to fit the observation. The parameters are useful for characterizing the Mj-Mw relationship. This non-linear relationship affects the b-value of the Gutenberg-Richter law. Quantitative discussions on b-values are affected by the definition of magnitude to use.

  15. Comparative analyses of reproductive structures in harvestmen (opiliones reveal multiple transitions from courtship to precopulatory antagonism.

    Directory of Open Access Journals (Sweden)

    Mercedes M Burns

    Full Text Available Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers. We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.

  16. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

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    Weerachai Jaratlerdsiri

    Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

  17. What's the ROI for resolving the nursing faculty shortage?

    Science.gov (United States)

    Kowalski, Karren; Kelley, Brian M

    2013-01-01

    The nursing faculty shortage will have a fundamental impact on the ability to produce nurses. For most nursing schools and states, however, concerns about the relative merits of different solutions to the nursing faculty shortage are misplaced. Without significantly increased visibility and definition, accompanied by a clear public, private, and health care organization return on investment (ROI), proposing solutions to the nursing faculty shortage is at best premature and at worst irrelevant. There is simply too much competition for resources to expect that a vaguely defined and invisible problem with no rationale for increased investment will receive sufficient support from critical decision makers and constituencies. First must come problem definition, visibility, and ROI. Only then can the case be made for implementing solutions to the nursing faculty shortage.

  18. Cloud computing and ROI a new framework for it strategy

    CERN Document Server

    Mohapatra, Sanjay

    2014-01-01

    This book develops an IT strategy for cloud computing that helps businesses evaluate their readiness for cloud services and calculate the ROI. The framework provided helps reduce risks involved in transitioning from traditional "on site" IT strategy to virtual "cloud computing." Since the advent of cloud computing, many organizations have made substantial gains implementing this innovation. Cloud computing allows companies to focus more on their core competencies, as IT enablement is taken care of through cloud services. Cloud Computing and ROI includes case studies covering retail, automobile and food processing industries. Each of these case studies have successfully implemented the cloud computing framework and their strategies are explained. As cloud computing may not be ideal for all businesses, criteria?are also offered to help determine if this strategy should be adopt.

  19. Landscape genetic analyses reveal fine-scale effects of forest fragmentation in an insular tropical bird.

    Science.gov (United States)

    Khimoun, Aurélie; Peterman, William; Eraud, Cyril; Faivre, Bruno; Navarro, Nicolas; Garnier, Stéphane

    2017-10-01

    Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order (i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then (ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea). We detected a small-scale reduction of gene flow mainly driven by land cover, with a negative impact of the nonforest matrix on landscape functional connectivity. However, matrix components did not equally constrain gene flow, as their conductivity increased with increasing structural similarity with forest habitat: urban areas and meadows had the highest resistance values whereas agricultural areas had intermediate resistance values. Our results revealed a higher performance of IBR compared to LCP in explaining gene flow, reflecting suboptimal movements across this human-modified landscape, challenging the common use of LCP to design habitat corridors and advocating for a broader use of circuit theory modelling. Finally, our results emphasize the need for an objective definition of landscape scales (landscape extent and thematic resolution) and highlight potential pitfalls associated with parameterization of resistance surfaces. © 2017 John Wiley & Sons Ltd.

  20. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  1. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  2. Water deficit mechanisms in perennial shrubs Cerasus humilis leaves revealed by physiological and proteomic analyses.

    Science.gov (United States)

    Yin, Zepeng; Ren, Jing; Zhou, Lijuan; Sun, Lina; Wang, Jiewan; Liu, Yulong; Song, Xingshun

    2016-01-01

    Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry ( Cerasus humilis ) is a good perennial plant for studying the physiological and sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants. Currently, physiological parameters were applied to investigate C. humilis response to WD. Moreover, we used two-dimensional gel electrophoresis (2DE) to identify differentially expressed proteins in C. humilis leaves subjected to WD (24 d). Furthermore, we also examined the correlation between protein and transcript levels. Several physiological parameters, including relative water content and Pn were reduced by WD. In addition, the malondialdehyde (MDA), relative electrolyte leakage (REL), total soluble sugar, and proline were increased in WD-treated C. humilis . Comparative proteomic analysis revealed 46 protein spots (representing 43 unique proteins) differentially expressed in C. humilis leaves under WD. These proteins were mainly involved in photosynthesis, ROS scavenging, carbohydrate metabolism, transcription, protein synthesis, protein processing, and nitrogen and amino acid metabolisms, respectively. WD promoted the CO 2 assimilation by increase light reaction and Calvin cycle, leading to the reprogramming of carbon metabolism. Moreover, the accumulation of osmolytes (i.e., proline and total soluble sugar) and enhancement of ascorbate-glutathione cycle and glutathione peroxidase/glutathione s-transferase pathway in leaves could minimize oxidative damage of membrane and other molecules under WD. Importantly, the regulation role of carbohydrate metabolisms (e. g. glycolysis, pentose phosphate pathways, and TCA) was enhanced. These findings provide key candidate proteins for genetic improvement of perennial plants metabolism under

  3. Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

    Science.gov (United States)

    Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

    2018-02-01

    This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

  4. Hemoglobin analyses in the Netherlands reveal more than 80 different variants including six novel ones.

    Science.gov (United States)

    van Zwieten, Rob; Veldthuis, Martijn; Delzenne, Barend; Berghuis, Jeffrey; Groen, Joke; Ait Ichou, Fatima; Clifford, Els; Harteveld, Cornelis L; Stroobants, An K

    2014-01-01

    More than 20,000 blood samples of individuals living in The Netherlands and suspected of hemolytic anemia or diabetes were analyzed by high resolution cation exchange high performance liquid chromatography (HPLC). Besides common disease-related hemoglobins (Hbs), rare variants were also detected. The variant Hbs were retrospectively analyzed by capillary zone electrophoresis (CZE) and by isoelectric focusing (IEF). For unambiguous identification, the globin genes were sequenced. Most of the 80 Hb variants detected by initial screening on HPLC were also separated by capillary electrophoresis (CE), but a few variants were only detectable with one of these methods. Some variants were unstable, had thalassemic properties or increased oxygen affinity, and some interfered with Hb A2 measurement, detection of sickle cell Hb or Hb A1c quantification. Two of the six novel variants, Hb Enschede (HBA2: c.308G  > A, p.Ser103Asn) and Hb Weesp (HBA1: c.301C > T, p.Leu101Phe), had no clinical consequences. In contrast, two others appeared clinically significant: Hb Ede (HBB: c.53A > T, p.Lys18Met) caused thalassemia and Hb Waterland (HBB: c.428C > T, pAla143Val) was related to mild polycytemia. Hb A2-Venlo (HBD: c.193G > A, p.Gly65Ser) and Hb A2-Rotterdam (HBD: c.38A > C, p.Asn13Thr) interfered with Hb A2 quantification. This survey shows that HPLC analysis followed by globin gene sequencing of rare variants is an effective method to reveal Hb variants.

  5. Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

    2014-01-01

    Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

  6. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    Science.gov (United States)

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA 2 s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA 2 s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not

  7. Comparative analyses reveal discrepancies among results of commonly used methods for Anopheles gambiaemolecular form identification

    Directory of Open Access Journals (Sweden)

    Pinto João

    2011-08-01

    Full Text Available Abstract Background Anopheles gambiae M and S molecular forms, the major malaria vectors in the Afro-tropical region, are ongoing a process of ecological diversification and adaptive lineage splitting, which is affecting malaria transmission and vector control strategies in West Africa. These two incipient species are defined on the basis of single nucleotide differences in the IGS and ITS regions of multicopy rDNA located on the X-chromosome. A number of PCR and PCR-RFLP approaches based on form-specific SNPs in the IGS region are used for M and S identification. Moreover, a PCR-method to detect the M-specific insertion of a short interspersed transposable element (SINE200 has recently been introduced as an alternative identification approach. However, a large-scale comparative analysis of four widely used PCR or PCR-RFLP genotyping methods for M and S identification was never carried out to evaluate whether they could be used interchangeably, as commonly assumed. Results The genotyping of more than 400 A. gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, highlighted discrepancies among results obtained by the different approaches due to different kinds of biases, which may result in an overestimation of MS putative hybrids, as follows: i incorrect match of M and S specific primers used in the allele specific-PCR approach; ii presence of polymorphisms in the recognition sequence of restriction enzymes used in the PCR-RFLP approaches; iii incomplete cleavage during the restriction reactions; iv presence of different copy numbers of M and S-specific IGS-arrays in single individuals in areas of secondary contact between the two forms. Conclusions The results reveal that the PCR and PCR-RFLP approaches most commonly utilized to identify A. gambiae M and S forms are not fully interchangeable as usually assumed, and highlight limits of the actual definition of the two molecular forms, which might

  8. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

    Directory of Open Access Journals (Sweden)

    Stéphane Uroz

    Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

  9. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  10. Performance of shear-wave elastography for breast masses using different region-of-interest (ROI) settings.

    Science.gov (United States)

    Youk, Ji Hyun; Son, Eun Ju; Han, Kyunghwa; Gweon, Hye Mi; Kim, Jeong-Ah

    2018-07-01

    Background Various size and shape of region of interest (ROI) can be applied for shear-wave elastography (SWE). Purpose To investigate the diagnostic performance of SWE according to ROI settings for breast masses. Material and Methods To measure elasticity for 142 lesions, ROIs were set as follows: circular ROIs 1 mm (ROI-1), 2 mm (ROI-2), and 3 mm (ROI-3) in diameter placed over the stiffest part of the mass; freehand ROIs drawn by tracing the border of mass (ROI-M) and the area of peritumoral increased stiffness (ROI-MR); and circular ROIs placed within the mass (ROI-C) and to encompass the area of peritumoral increased stiffness (ROI-CR). Mean (E mean ), maximum (E max ), and standard deviation (E SD ) of elasticity values and their areas under the receiver operating characteristic (ROC) curve (AUCs) for diagnostic performance were compared. Results Means of E mean and E SD significantly differed between ROI-1, ROI-2, and ROI-3 ( P Shear-wave elasticity values and their diagnostic performance vary based on ROI settings and elasticity indices. E max is recommended for the ROIs over the stiffest part of mass and an ROI encompassing the peritumoral area of increased stiffness is recommended for elastic heterogeneity of mass.

  11. Annotating image ROIs with text descriptions for multimodal biomedical document retrieval

    Science.gov (United States)

    You, Daekeun; Simpson, Matthew; Antani, Sameer; Demner-Fushman, Dina; Thoma, George R.

    2013-01-01

    Regions of interest (ROIs) that are pointed to by overlaid markers (arrows, asterisks, etc.) in biomedical images are expected to contain more important and relevant information than other regions for biomedical article indexing and retrieval. We have developed several algorithms that localize and extract the ROIs by recognizing markers on images. Cropped ROIs then need to be annotated with contents describing them best. In most cases accurate textual descriptions of the ROIs can be found from figure captions, and these need to be combined with image ROIs for annotation. The annotated ROIs can then be used to, for example, train classifiers that separate ROIs into known categories (medical concepts), or to build visual ontologies, for indexing and retrieval of biomedical articles. We propose an algorithm that pairs visual and textual ROIs that are extracted from images and figure captions, respectively. This algorithm based on dynamic time warping (DTW) clusters recognized pointers into groups, each of which contains pointers with identical visual properties (shape, size, color, etc.). Then a rule-based matching algorithm finds the best matching group for each textual ROI mention. Our method yields a precision and recall of 96% and 79%, respectively, when ground truth textual ROI data is used.

  12. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

    Science.gov (United States)

    Ray, Jessica L; Althammer, Julia; Skaar, Katrine S; Simonelli, Paolo; Larsen, Aud; Stoecker, Diane; Sazhin, Andrey; Ijaz, Umer Z; Quince, Christopher; Nejstgaard, Jens C; Frischer, Marc; Pohnert, Georg; Troedsson, Christofer

    2016-11-01

    In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances. © 2016 John Wiley & Sons Ltd.

  13. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

    Science.gov (United States)

    Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

    2015-05-01

    The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

  14. Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP.

    Science.gov (United States)

    Yu, Qin; Hu, Liyan; Yao, Qing; Zhu, Yongqun; Dong, Na; Wang, Da-Cheng; Shao, Feng

    2013-06-01

    Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.

  15. Revealing climate modes in steric sea levels: lessons learned from satellite geodesy, objective analyses and ocean reanalyses

    Science.gov (United States)

    Pfeffer, J.; Tregoning, P.; Purcell, A. P.

    2017-12-01

    Due to increased greenhouse gases emissions, the oceans are accumulating heat. In response to the ocean circulation and atmospheric forcing, the heat is irregularly redistributed within the oceans, causing sea level to rise at variable rates in space and time. These rates of steric expansion are extremely difficult to assess because of the sparsity of in-situ hydrographic observations available within the course of the 20th century. We compare here three methods to reconstruct the steric sea levels over the past 13, 25 and 58 years based on satellite geodesy, objective analyses and ocean reanalyses. The interannual to decadal variability of each dataset is explored with a model merging six climate indices representative of the natural variability of the ocean and climate system. Consistent regional patterns are identified for the Pacific Decadal Oscillation (PDO) and El Niño Southern Oscillation (ENSO) in all datasets at all timescales. Despite the short time coverage (13 years), the combination of satellite geodetic data (altimetry and GRACE) also reveals significant steric responses to the North Pacific Gyre Oscillation (NPGO), Indian Dipole (IOD) and Indian ocean basinwide (IOBM) mode. The richer information content in the ocean reanalyses allows us to recover the regional fingerprints of the PDO, ENSO, NPGO, IOD and IOBM, but also of the Atlantic Multidecadal Oscillation (AMO) acting over longer time scales (40 to 60 years). Therefore, ocean reanalyses, coupled with climate mode analyses, constitute innovative and promising tools to investigate the mechanisms triggering the variability of sea level rise over the past decades.

  16. Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

    Science.gov (United States)

    Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

    2018-01-01

    Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

  17. Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

    Science.gov (United States)

    Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

    1991-01-01

    Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

  18. Reinterpretation of ozone data from Base Roi Baudouin

    Science.gov (United States)

    Kelder, H.; Muller, C.

    1994-01-01

    The ozone Dobson measurements obtained in Antarctica at the Belgian 'Base Roi Baudouin' (70 deg 26 min S, 24 deg 19 min E) in 1965 and 1966 were retrieved from the KNMI (Royal Netherlands Meteorological Institute) archives in De Bilt. Despite excellent treatment at the time by the meteorologists in charge at the KNMI (Wisse and Meerburg, 1969), a study of the original observers notes was made in order to check possible seasonal ozone phenomena. No systematic anomaly in the first analysis was found; meteorological data from the site together with Brewer-Mast ozone soundings concur that the conditions did not correspond either in 1965 nor 1966 to the current ozone hole (Farman et al., 1985) situation, however, the data yields excellent correlation with stratospheric temperature and shows in 1966 a clear November maximum in opposition to an October value around 344 Dobson units.

  19. Roi Detection and Vessel Segmentation in Retinal Image

    Science.gov (United States)

    Sabaz, F.; Atila, U.

    2017-11-01

    Diabetes disrupts work by affecting the structure of the eye and afterwards leads to loss of vision. Depending on the stage of disease that called diabetic retinopathy, there are sudden loss of vision and blurred vision problems. Automated detection of vessels in retinal images is a useful study to diagnose eye diseases, disease classification and other clinical trials. The shape and structure of the vessels give information about the severity of the disease and the stage of the disease. Automatic and fast detection of vessels allows for a quick diagnosis of the disease and the treatment process to start shortly. ROI detection and vessel extraction methods for retinal image are mentioned in this study. It is shown that the Frangi filter used in image processing can be successfully used in detection and extraction of vessels.

  20. ROI DETECTION AND VESSEL SEGMENTATION IN RETINAL IMAGE

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    F. Sabaz

    2017-11-01

    Full Text Available Diabetes disrupts work by affecting the structure of the eye and afterwards leads to loss of vision. Depending on the stage of disease that called diabetic retinopathy, there are sudden loss of vision and blurred vision problems. Automated detection of vessels in retinal images is a useful study to diagnose eye diseases, disease classification and other clinical trials. The shape and structure of the vessels give information about the severity of the disease and the stage of the disease. Automatic and fast detection of vessels allows for a quick diagnosis of the disease and the treatment process to start shortly. ROI detection and vessel extraction methods for retinal image are mentioned in this study. It is shown that the Frangi filter used in image processing can be successfully used in detection and extraction of vessels.

  1. Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

    Science.gov (United States)

    Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

    2016-02-01

    Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

  2. Joint Labeling Of Multiple Regions of Interest (Rois) By Enhanced Auto Context Models.

    Science.gov (United States)

    Kim, Minjeong; Wu, Guorong; Guo, Yanrong; Shen, Dinggang

    2015-04-01

    Accurate segmentation of a set of regions of interest (ROIs) in the brain images is a key step in many neuroscience studies. Due to the complexity of image patterns, many learning-based segmentation methods have been proposed, including auto context model (ACM) that can capture high-level contextual information for guiding segmentation. However, since current ACM can only handle one ROI at a time, neighboring ROIs have to be labeled separately with different ACMs that are trained independently without communicating each other. To address this, we enhance the current single-ROI learning ACM to multi-ROI learning ACM for joint labeling of multiple neighboring ROIs (called e ACM). First, we extend current independently-trained single-ROI ACMs to a set of jointly-trained cross-ROI ACMs, by simultaneous training of ACMs for all spatially-connected ROIs to let them to share their respective intermediate outputs for coordinated labeling of each image point. Then, the context features in each ACM can capture the cross-ROI dependence information from the outputs of other ACMs that are designed for neighboring ROIs. Second, we upgrade the output labeling map of each ACM with the multi-scale representation, thus both local and global context information can be effectively used to increase the robustness in characterizing geometric relationship among neighboring ROIs. Third, we integrate ACM into a multi-atlases segmentation paradigm, for encompassing high variations among subjects. Experiments on LONI LPBA40 dataset show much better performance by our e ACM, compared to the conventional ACM.

  3. Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

    Directory of Open Access Journals (Sweden)

    Jacqueline C Lieblein-Boff

    Full Text Available Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510 were excluded. In addition, moderate correlations with xenobiotic relationships (2 or those driven by single outliers (3 were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

  4. Ancient ancestry of KFDV and AHFV revealed by complete genome analyses of viruses isolated from ticks and mammalian hosts.

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    Kimberly A Dodd

    2011-10-01

    Full Text Available BACKGROUND: Alkhurma hemorrhagic fever virus (AHFV and Kyasanur forest disease virus (KFDV cause significant human disease and mortality in Saudi Arabia and India, respectively. Despite their distinct geographic ranges, AHFV and KFDV share a remarkably high sequence identity. Given its emergence decades after KFDV, AHFV has since been considered a variant of KFDV and thought to have arisen from an introduction of KFDV to Saudi Arabia from India. To gain a better understanding of the evolutionary history of AHFV and KFDV, we analyzed the full length genomes of 16 AHFV and 3 KFDV isolates. METHODOLOGY/PRINCIPAL FINDINGS: Viral genomes were sequenced and compared to two AHFV sequences available in GenBank. Sequence analyses revealed higher genetic diversity within AHFVs isolated from ticks than human AHFV isolates. A Bayesian coalescent phylogenetic analysis demonstrated an ancient divergence of AHFV and KFDV of approximately 700 years ago. CONCLUSIONS/SIGNIFICANCE: The high sequence diversity within tick populations and the presence of competent tick vectors in the surrounding regions, coupled with the recent identification of AHFV in Egypt, indicate possible viral range expansion or a larger geographic range than previously thought. The divergence of AHFV from KFDV nearly 700 years ago suggests other AHFV/KFDV-like viruses might exist in the regions between Saudi Arabia and India. Given the human morbidity and mortality associated with these viruses, these results emphasize the importance of more focused study of these significant public health threats.

  5. Analyses in zebrafish embryos reveal that nanotoxicity profiles are dependent on surface-functionalization controlled penetrance of biological membranes.

    Science.gov (United States)

    Paatero, Ilkka; Casals, Eudald; Niemi, Rasmus; Özliseli, Ezgi; Rosenholm, Jessica M; Sahlgren, Cecilia

    2017-08-21

    Mesoporous silica nanoparticles (MSNs) are extensively explored as drug delivery systems, but in depth understanding of design-toxicity relationships is still scarce. We used zebrafish (Danio rerio) embryos to study toxicity profiles of differently surface functionalized MSNs. Embryos with the chorion membrane intact, or dechoroniated embryos, were incubated or microinjected with amino (NH 2 -MSNs), polyethyleneimine (PEI-MSNs), succinic acid (SUCC-MSNs) or polyethyleneglycol (PEG-MSNs) functionalized MSNs. Toxicity was assessed by viability and cardiovascular function. NH 2 -MSNs, SUCC-MSNs and PEG-MSNs were well tolerated, 50 µg/ml PEI-MSNs induced 100% lethality 48 hours post fertilization (hpf). Dechoroniated embryos were more sensitive and 10 µg/ml PEI-MSNs reduced viability to 5% at 96hpf. Sensitivity to PEG- and SUCC-, but not NH 2 -MSNs, was also enhanced. Typically cardiovascular toxicity was evident prior to lethality. Confocal microscopy revealed that PEI-MSNs penetrated into the embryos whereas PEG-, NH2- and SUCC-MSNs remained aggregated on the skin surface. Direct exposure of inner organs by microinjecting NH 2 -MSNs and PEI-MSNs demonstrated that the particles displayed similar toxicity indicating that functionalization affects the toxicity profile by influencing penetrance through biological barriers. The data emphasize the need for careful analyses of toxicity mechanisms in relevant models and constitute an important knowledge step towards the development of safer and sustainable nanotherapies.

  6. Combined Metabonomic and Quantitative RT-PCR Analyses Revealed Metabolic Reprogramming Associated with Fusarium graminearum Resistance in Transgenic Arabidopsis thaliana

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    Fangfang Chen

    2018-01-01

    Full Text Available Fusarium head blight disease resulting from Fusarium graminearum (FG infection causes huge losses in global production of cereals and development of FG-resistant plants is urgently needed. To understand biochemistry mechanisms for FG resistance, here, we have systematically investigated the plant metabolomic phenotypes associated with FG resistance for transgenic Arabidopsis thaliana expressing a class-I chitinase (Chi, a Fusarium-specific recombinant antibody gene (CWP2 and fused Chi-CWP2. Plant disease indices, mycotoxin levels, metabonomic characteristics, and expression levels of several key genes were measured together with their correlations. We found that A. thaliana expressing Chi-CWP2 showed higher FG resistance with much lower disease indices and mycotoxin levels than the wild-type and the plants expressing Chi or CWP2 alone. The combined metabonomic and quantitative RT-PCR analyses revealed that such FG-resistance was closely associated with the promoted biosynthesis of secondary metabolites (phenylpropanoids, alkanoids and organic osmolytes (proline, betaine, glucose, myo-inositol together with enhanced TCA cycle and GABA shunt. These suggest that the concurrently enhanced biosyntheses of the shikimate-mediated secondary metabolites and organic osmolytes be an important strategy for A. thaliana to develop and improve FG resistance. These findings provide essential biochemical information related to FG resistance which is important for developing FG-resistant cereals.

  7. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

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    Wu Shi-Fang

    2011-07-01

    Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

  8. Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis

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    Couturier Marie

    2012-02-01

    Full Text Available Abstract Background Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemicellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation. Results In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases. Conclusion This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.

  9. RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae.

    Science.gov (United States)

    Bonato, Paloma; Batista, Marcelo B; Camilios-Neto, Doumit; Pankievicz, Vânia C S; Tadra-Sfeir, Michelle Z; Monteiro, Rose Adele; Pedrosa, Fabio O; Souza, Emanuel M; Chubatsu, Leda S; Wassem, Roseli; Rigo, Liu Un

    2016-09-01

    Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO and (iii) dissipation of redox power, which in turn lead to an increase in carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. Effect of single-visit VIA and cryotherapy cervical cancer prevention program in Roi Et, Thailand: a preliminary report.

    Science.gov (United States)

    Chumworathayi, Bandit; Blumenthal, Paul D; Limpaphayom, Khunying Kobchitt; Kamsa-Ard, Supot; Wongsena, Metee; Supaatakorn, Pongsatorn

    2010-02-01

    To assess the effect of introducing visual inspection with acetic acid and cryotherapy on cervical cancer incidence rates in Roi Et province over time, between 1997 and 2006, and compare this with two nearby provinces. Data from two cancer registration units, one in Srinagarind Hospital and another in Ubon Ratchathani Cancer Center (to which all cervical cancer patients were referred from the three study provinces) were registered, extracted, combined and analyzed using a generalized estimation equation. Cervical cancer detection rates improved. These are represented by the apparent increased incidence rates in Roi Et province during the study period compared with two nearby provinces (P = 0.01), equivalent to a doubling of the previously reported age-standardized incidence ratio and three times its baseline in 2006. A single-visit approach to cervical cancer prevention in Roi Et province using visual inspection with acetic acid and cryotherapy appeared to have an effect in revealing an increased cervical cancer incidence rate by achieving higher coverage, resulting in increased case finding.

  11. The leap from ROI to SROI: Farther than expected?

    Science.gov (United States)

    Gargani, John

    2017-10-01

    Social return on investment (SROI) is a popular method for evaluating the impact that organizations have on society and the environment. It has its roots in finance, where return on investment (ROI) is used to evaluate investments. Over the past ten years, SROI has made the leap from a tool for building private wealth to one that advances the public good. Has it landed us in a better place? To answer the question, I describe the general approach to financial analysis, how it is applied to financial decisions, and how it has been adapted to evaluate impact. I then consider the strengths and weaknesses of SROI, and suggest how, by pushing beyond the constraints of financial analysis, it can give stakeholders voice and provide evidence of success from diverse perspectives. Along the way, I propose a conceptual model for value, a foundational concept in SROI that has been criticized by some as underdeveloped, and I include a technical appendix that identifies potential sources of statistical bias in SROI estimates. I conclude by acknowledging our growing need to incorporate efficiency as one of multiple success criteria and the role that SROI-properly implemented-can play. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

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    Ana Carolina Vieira Araujo

    2016-10-01

    Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

  13. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

    Science.gov (United States)

    Glicksberg, Benjamin S.; Li, Li; Badgeley, Marcus A.; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D.; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L.; Hoffman, Gabriel E.; Dan Li, Shuyu; Schadt, Eric E.; Patel, Chirag J.; Chen, Rong; Dudley, Joel T.

    2016-01-01

    Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307606

  14. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

    Science.gov (United States)

    Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T

    2016-06-15

    Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  15. Molecular analyses reveal two geographic and genetic lineages for tapeworms, Taenia solium and Taenia saginata, from Ecuador using mitochondrial DNA.

    Science.gov (United States)

    Solano, Danilo; Navarro, Juan Carlos; León-Reyes, Antonio; Benítez-Ortiz, Washington; Rodríguez-Hidalgo, Richar

    2016-12-01

    Tapeworms Taenia solium and Taenia saginata are the causative agents of taeniasis/cysticercosis. These are diseases with high medical and veterinary importance due to their impact on public health and rural economy in tropical countries. The re-emergence of T. solium as a result of human migration, the economic burden affecting livestock industry, and the large variability of symptoms in several human cysticercosis, encourage studies on genetic diversity, and the identification of these parasites with molecular phylogenetic tools. Samples collected from the Ecuadorian provinces: Loja, Guayas, Manabí, Tungurahua (South), and Imbabura, Pichincha (North) from 2000 to 2012 were performed under Maximum Parsimony analyses and haplotype networks using partial sequences of mitochondrial DNA, cytochrome oxidase subunit I (COI) and NADH subunit I (NDI), from Genbank and own sequences of Taenia solium and Taenia saginata from Ecuador. Both species have shown reciprocal monophyly, which confirms its molecular taxonomic identity. The COI and NDI genes results suggest phylogenetic structure for both parasite species from south and north of Ecuador. In T. solium, both genes gene revealed greater geographic structure, whereas in T. saginata, the variability for both genes was low. In conclusion, COI haplotype networks of T. solium suggest two geographical events in the introduction of this species in Ecuador (African and Asian lineages) and occurring sympatric, probably through the most common routes of maritime trade between the XV-XIX centuries. Moreover, the evidence of two NDI geographical lineages in T. solium from the north (province of Imbabura) and the south (province of Loja) of Ecuador derivate from a common Indian ancestor open new approaches for studies on genetic populations and eco-epidemiology. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

    Science.gov (United States)

    Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

    2016-08-12

    The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

  17. Estimating the Accuracy of the Return on Investment (ROI Performance Evaluations

    Directory of Open Access Journals (Sweden)

    Alexei Botchkarev

    2015-12-01

    Full Text Available Return on Investment (ROI is one of the most popular performance measurement and evaluation metrics. ROI analysis (when applied correctly is a powerful tool in comparing solutions and making informed decisions on the acquisitions of information systems. The purpose of this study is to provide a systematic research of the accuracy of the ROI evaluations in the context of information systems implementations. Measurements theory and error analysis, specifically propagation of uncertainties methods, were used to derive analytical expressions for ROI errors. Monte Carlo simulation methodology was used to design and deliver a quantitative experiment to model costs and returns estimating errors and calculate ROI accuracies. Spreadsheet simulation (Microsoft Excel spreadsheets enhanced with Visual Basic for Applications was used to implement Monte Carlo simulations. The main contribution of the study is that this is the first systematic effort to evaluate ROI accuracy. Analytical expressions have been derived for estimating errors of the ROI evaluations. Results of the Monte Carlo simulation will help practitioners in making informed decisions based on explicitly stated factors influencing the ROI uncertainties.

  18. A direct ROI quantification method for inherent PVE correction: accuracy assessment in striatal SPECT measurements

    Energy Technology Data Exchange (ETDEWEB)

    Vanzi, Eleonora; De Cristofaro, Maria T.; Sotgia, Barbara; Mascalchi, Mario; Formiconi, Andreas R. [University of Florence, Clinical Pathophysiology, Florence (Italy); Ramat, Silvia [University of Florence, Neurological and Psychiatric Sciences, Florence (Italy)

    2007-09-15

    The clinical potential of striatal imaging with dopamine transporter (DAT) SPECT tracers is hampered by the limited capability to recover activity concentration ratios due to partial volume effects (PVE). We evaluated the accuracy of a least squares method that allows retrieval of activity in regions of interest directly from projections (LS-ROI). An Alderson striatal phantom was filled with striatal to background ratios of 6:1, 9:1 and 28:1; the striatal and background ROIs were drawn on a coregistered X-ray CT of the phantom. The activity ratios of these ROIs were derived both with the LS-ROI method and with conventional SPECT EM reconstruction (EM-SPECT). Moreover, the two methods were compared in seven patients with motor symptoms who were examined with N-3-fluoropropyl-2-{beta}-carboxymethoxy-3-{beta}-(4-iodophenyl) (FP-CIT) SPECT, calculating the binding potential (BP). In the phantom study, the activity ratios obtained with EM-SPECT were 3.5, 5.3 and 17.0, respectively, whereas the LS-ROI method resulted in ratios of 6.2, 9.0 and 27.3, respectively. With the LS-ROI method, the BP in the seven patients was approximately 60% higher than with EM-SPECT; a linear correlation between the LS-ROI and the EM estimates was found (r = 0.98, p = 0.03). The LS-ROI PVE correction capability is mainly due to the fact that the ill-conditioning of the LS-ROI approach is lower than that of the EM-SPECT one. The LS-ROI seems to be feasible and accurate in the examination of the dopaminergic system. This approach can be fruitful in monitoring of disease progression and in clinical trials of dopaminergic drugs. (orig.)

  19. Temporal Fluctuation in North East Baltic Sea Region Cattle Population Revealed by Mitochondrial and Y-Chromosomal DNA Analyses

    Science.gov (United States)

    Niemi, Marianna; Bläuer, Auli; Iso-Touru, Terhi; Harjula, Janne; Nyström Edmark, Veronica; Rannamäe, Eve; Lõugas, Lembi; Sajantila, Antti; Lidén, Kerstin; Taavitsainen, Jussi-Pekka

    2015-01-01

    Background Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. Results Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). Conclusions The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle. PMID:25992976

  20. Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors

    International Nuclear Information System (INIS)

    Klajic, Jovana; Tost, Jörg; Kristensen, Vessela N; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise

    2013-01-01

    Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above

  1. Safety of drinking water supplies to suburban Paris: analysis and control of radioactivity at Choisy-le-Roi

    International Nuclear Information System (INIS)

    Rapinat, M.; Philipot, J.M.; Cadet, J.L.

    1990-01-01

    The Syndicat des Eaux d'Ile de France and the Compagnie des Eaux have undertaken several stringent actions, to analyse and control radioactivity at Cholsy-le-Roi, 150 KM downstream from Nogent/s/Seine:- founding in 1985 a new laboratory branch for radioactivity measurement. - adding new elements to the existing alarm network (automatic analysis of the raw water quality). - studies for the treatability of radioelements. - using protected resources (ground water). -set up of a second treated water feeder between the river Seine and the river Marne areas. Others projects are under study, such as the creation of a raw water reservoir and increasing the capacity of treated water stockage. (author)

  2. The evaluation of the automatic setting of ROI to SPECT measuring cerebral blood flow

    International Nuclear Information System (INIS)

    Mizuno, Hiroshi; Takahashi, Masaaki; Yoshioka, Katsunori

    2007-01-01

    It has been pointed out that the manual settings of region of interest (ROI) to the single-photon-emission-computed-tomography (SPECT) slice lacked objectivity when the fixed quantity value of regional cerebral blood flow (rCBF) was measured previously. Therefore, we jointly developed software Brain ROI'' with Daiichi Radioisotope Laboratories, Ltd. (DRL) that normalized an individual brain to a standard brain template by using Statistical Parametric Mapping 2 (SPM 2) of easy Z-score Imaging System ver. 3.0 (eZIS Ver. 3.0), and, ROI template was set to a specific slice. In this paper, we evaluated the accuracy of this software with ROI template that we made the useful size of the shape, in some clinical samples. As a result, the method of the automatic setting of ROI was the objectively. However, we thought that we should use the shape of ROI template without an influence of Brain atrophy. Moreover, we should see Normalizing individual brain and confirm the accuracy of normalization. When failing in normalization, we should partially correct ROI or set all by the manual operation of the operator. However, it was thought that this software was useful if the tendency was understood because the failure example was few. (author)

  3. An ROI multi-resolution compression method for 3D-HEVC

    Science.gov (United States)

    Ti, Chunli; Guan, Yudong; Xu, Guodong; Teng, Yidan; Miao, Xinyuan

    2017-09-01

    3D High Efficiency Video Coding (3D-HEVC) provides a significant potential on increasing the compression ratio of multi-view RGB-D videos. However, the bit rate still rises dramatically with the improvement of the video resolution, which will bring challenges to the transmission network, especially the mobile network. This paper propose an ROI multi-resolution compression method for 3D-HEVC to better preserve the information in ROI on condition of limited bandwidth. This is realized primarily through ROI extraction and compression multi-resolution preprocessed video as alternative data according to the network conditions. At first, the semantic contours are detected by the modified structured forests to restrain the color textures inside objects. The ROI is then determined utilizing the contour neighborhood along with the face region and foreground area of the scene. Secondly, the RGB-D videos are divided into slices and compressed via 3D-HEVC under different resolutions for selection by the audiences and applications. Afterwards, the reconstructed low-resolution videos from 3D-HEVC encoder are directly up-sampled via Laplace transformation and used to replace the non-ROI areas of the high-resolution videos. Finally, the ROI multi-resolution compressed slices are obtained by compressing the ROI preprocessed videos with 3D-HEVC. The temporal and special details of non-ROI are reduced in the low-resolution videos, so the ROI will be better preserved by the encoder automatically. Experiments indicate that the proposed method can keep the key high-frequency information with subjective significance while the bit rate is reduced.

  4. High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle

    Science.gov (United States)

    Selection Signatures (SS) assessed through analysis of genomic data are being widely studied to discover population specific regions selected via artificial or natural selection. Different methodologies have been proposed for these analyses, each having specific limitations as to the age of the sele...

  5. Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes

    NARCIS (Netherlands)

    Revuelta, M.V.; Kan, van J.A.L.; Kay, J.; Have, ten A.

    2014-01-01

    The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the

  6. Data from the Roi Removal Project, West Hawaii, 2010-2011 (NODC Accession 0082197

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In situ observations of the introduced predatory grouper roi (Cephalopholis argus) were taken within the coral reef ecosystem of Puako, northwest side of the Island...

  7. Low-Cost Small Satellite Atmospheric Rotating Solar Occultation Imager (ROI)

    Data.gov (United States)

    National Aeronautics and Space Administration — Utilizing a unique, new occultation technique involving imaging, the ROI concept will meet or exceed the quality of SAGE measurements at a small fraction of the...

  8. ROI en medios sociales: campañas de marketing en bibliotecas

    OpenAIRE

    González-Fernández-Villavicencio, Nieves

    2015-01-01

    Social media marketing must be a part of a digital marketing plan. Although marketing traditionally has been associated with obtaining an economic ROI (return on investment), it also can be measured in terms of social ROI (return on influence, return on relationships, reputation, branding, etc.). This study addresses the use of digital marketing campaigns by libraries for social profitability. Concepts related to digital marketing and social media marketing, and the way different types of org...

  9. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Science.gov (United States)

    Macovei, Anca; Faè, Matteo; Biggiogera, Marco; de Sousa Araújo, Susana; Carbonera, Daniela; Balestrazzi, Alma

    2018-01-01

    The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2) involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively) and a control (CTRL) line carrying the empty vector were investigated. Transmission electron microscopy (TEM) revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL), the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL) and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells. PMID:29868059

  10. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Directory of Open Access Journals (Sweden)

    Anca Macovei

    2018-05-01

    Full Text Available The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2 involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively and a control (CTRL line carrying the empty vector were investigated. Transmission electron microscopy (TEM revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL, the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells.

  11. The postglacial recolonization of Northern Europe by Rana arvalis as revealed by microsatellite and mitochondrial DNA analyses.

    Science.gov (United States)

    Knopp, T; Merilä, J

    2009-02-01

    The postglacial history of the moor frog (Rana arvalis) in Northern Europe was investigated with the aid of eight variable microsatellite loci and a 661 bp sequence of the mitochondrial cytochrome b gene. A division between eastern and western mitochondrial lineages was discovered, supporting two recolonization routes to Fennoscandia since the last glacial maximum. This result was corroborated by the microsatellite data, which revealed a contact zone between the two lineages in Northern Sweden. These findings add to the increasing evidence that an intraspecific genetic biodiversity founded on the existence of eastern and western clades is a common element in Fennoscandian fauna and flora.

  12. Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp.

    Science.gov (United States)

    Chen, Chao; Liu, Zhiguang; Pan, Qi; Chen, Xiao; Wang, Huihua; Guo, Haikun; Liu, Shidong; Lu, Hongfeng; Tian, Shilin; Li, Ruiqiang; Shi, Wei

    2016-05-01

    Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other populations. We found that the new population is an undescribed subspecies in the M-lineage of A. mellifera (Apis mellifera sinisxinyuan). Analyses of population history show that long-term global temperature has strongly influenced the demographic history of A. m. sinisxinyuan and its divergence from other subspecies. Further analyses comparing temperate and tropical populations identified several candidate genes related to fat body and the Hippo signaling pathway that are potentially involved in adaptation to temperate climates. Our results provide insights into the demographic history of the newly discovered A. m. sinisxinyuan, as well as the genetic basis of adaptation of A. mellifera to temperate climates at the genomic level. These findings will facilitate the selective breeding of A. mellifera to improve the survival of overwintering colonies. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

    Directory of Open Access Journals (Sweden)

    Clémentine Delan-Forino

    2014-01-01

    Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

  14. Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida.

    Science.gov (United States)

    Wu, Fengnian; Kumagai, Luci; Cen, Yijing; Chen, Jianchi; Wallis, Christopher M; Polek, MaryLou; Jiang, Hongyan; Zheng, Zheng; Liang, Guangwen; Deng, Xiaoling

    2017-08-31

    Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits "Candidatus Liberibacter asiaticus" (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes. The Californian mt-CApsy was identical to the Floridian mt-FLpsy, but different from the mitogenome (mt-GDpsy) of Guangdong, China, in 50 single nucleotide polymorphisms (SNPs). Further analyses were performed on sequences in cox1 and trnAsn regions with 100 ACPs, SNPs in nad1-nad4-nad5 locus through PCR with 252 ACP samples. All results showed the presence of a Chinese ACP cluster (CAC) and an American ACP cluster (AAC). We proposed that ACP in California was likely not introduced from China based on our current ACP collection but somewhere in America. However, more studies with ACP samples from around the world are needed. ACP mitogenome sequence analyses will facilitate ACP population research.

  15. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Science.gov (United States)

    Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

    2013-01-01

    CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  16. Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements

    Science.gov (United States)

    Egan, Jan B.; Barrett, Michael T.; Champion, Mia D.; Middha, Sumit; Lenkiewicz, Elizabeth; Evers, Lisa; Francis, Princy; Schmidt, Jessica; Shi, Chang-Xin; Van Wier, Scott; Badar, Sandra; Ahmann, Gregory; Kortuem, K. Martin; Boczek, Nicole J.; Fonseca, Rafael; Craig, David W.; Carpten, John D.; Borad, Mitesh J.; Stewart, A. Keith

    2014-01-01

    Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2. PMID:24505276

  17. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

    Directory of Open Access Journals (Sweden)

    Jan B Egan

    Full Text Available Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

  18. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Directory of Open Access Journals (Sweden)

    Takuji Oyama

    Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  19. Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

    Science.gov (United States)

    Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

    2017-08-31

    The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

  20. Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression.

    Science.gov (United States)

    Xu, Fan; Yang, Jing; Chen, Jin; Wu, Qingyuan; Gong, Wei; Zhang, Jianguo; Shao, Weihua; Mu, Jun; Yang, Deyu; Yang, Yongtao; Li, Zhiwei; Xie, Peng

    2015-04-03

    Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more responsive to current pharmacological treatment and aid in separating out depressed patients in which current antidepressants are not particularly effective. Differential co-expression analysis (DCEA) and differential regulation analysis (DRA) were applied to compare the transcriptomic profiles of peripheral blood lymphocytes from patients with two depressive subtypes: major depressive disorder (MDD) and subsyndromal symptomatic depression (SSD). Six differentially regulated genes (DRGs) (FOSL1, SRF, JUN, TFAP4, SOX9, and HLF) and 16 transcription factor-to-target differentially co-expressed gene links or pairs (TF2target DCLs) appear to be the key differential factors in MDD; in contrast, one DRG (PATZ1) and eight TF2target DCLs appear to be the key differential factors in SSD. There was no overlap between the MDD target genes and SSD target genes. Venlafaxine (Efexor™, Effexor™) appears to have a significant effect on the gene expression profile of MDD patients but no significant effect on the gene expression profile of SSD patients. DCEA and DRA revealed no apparent similarities between the differential regulatory processes underlying MDD and SSD. This bioinformatic analysis may provide novel insights that can support future antidepressant R&D efforts.

  1. Temporal analyses of Salmonellae in a headwater spring ecosystem reveals the effects of precipitation and runoff events.

    Science.gov (United States)

    Gaertner, James P; Garres, Tiffany; Becker, Jesse C; Jimenez, Maria L; Forstner, Michael R J; Hahn, Dittmar

    2009-03-01

    Sediments and water from the spring and slough arm of Spring Lake, the pristine headwaters of the San Marcos River, Texas, were analyzed for Salmonellae by culture and molecular techniques before and after three major precipitation events, each with intermediate dry periods. Polymerase chain reaction (PCR)-assisted analyses of enrichment cultures detected Salmonellae in samples after all three precipitation events, but failed to detect them immediately prior to the rainfall events. Detection among individual locations differed with respect to the precipitation event analyzed, and strains isolated were highly variable with respect to serovars. These results demonstrate that rainwater associated effects, most likely surface runoff, provide an avenue for short-term pollution of aquatic systems with Salmonellae that do not, however, appear to establish for the long-term in water nor sediments.

  2. Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

    Science.gov (United States)

    Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2017-02-22

    Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

  3. Phylogenetic and morphologic analyses of a coastal fish reveals a marine biogeographic break of terrestrial origin in the southern Caribbean.

    Directory of Open Access Journals (Sweden)

    Ricardo Betancur-R

    2010-07-01

    Full Text Available Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world.Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a approximately 2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by approximately 150 km at the Santa Marta Massif (SMM in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated approximately 0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at approximately 0.78 my.Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of additional Southern Caribbean taxa, particularly those with varying life

  4. Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

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    Yanlong Wang

    Full Text Available We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli, Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology and KEGG (Kyoto encyclopedia of genes and genomes enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species scavenging, membrane proteins and ABC (ATP binding cassette transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

  5. Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

    Directory of Open Access Journals (Sweden)

    Rémy Nicolle

    2017-11-01

    Full Text Available Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively. Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.

  6. Trophic segregation of a fish assemblage along lateral depth gradients in a subtropical coastal lagoon revealed by stable isotope analyses.

    Science.gov (United States)

    Mont'Alverne, R; Pereyra, P E R; Garcia, A M

    2016-07-01

    Stable isotopes were used to evaluate the hypothesis that fish assemblages occurring in shallow and deep areas of a large coastal lagoon are structured in partially segregated trophic modules with consumers showing contrasting reliance on benthic or pelagic food sources. The results revealed that fishes in deep areas were mainly dependent on particulate organic matter in the sediment (SOM), whereas emergent macrophytes were as important as SOM to fish consumers in shallow areas. Conceptual trophic diagrams depicting relationships among basal food sources and consumers in different regions of the lagoon highlighted the greater use of multiple basal food sources by more feeding mode functional guilds in shallow water compared with the use of predominantly benthic resources (SOM) in deep areas. The findings appear to corroborate the initial hypothesis and offer complementary perspectives in understanding the role of spatial ecology in structuring coastal ecosystem function and productivity. © 2016 The Fisheries Society of the British Isles.

  7. Comparative sequence analyses of the major quantitative trait locus phosphorus uptake 1 (Pup1) reveal a complex genetic structure.

    Science.gov (United States)

    Heuer, Sigrid; Lu, Xiaochun; Chin, Joong Hyoun; Tanaka, Juan Pariasca; Kanamori, Hiroyuki; Matsumoto, Takashi; De Leon, Teresa; Ulat, Victor Jun; Ismail, Abdelbagi M; Yano, Masahiro; Wissuwa, Matthias

    2009-06-01

    The phosphorus uptake 1 (Pup1) locus was identified as a major quantitative trait locus (QTL) for tolerance of phosphorus deficiency in rice. Near-isogenic lines with the Pup1 region from tolerant donor parent Kasalath typically show threefold higher phosphorus uptake and grain yield in phosphorus-deficient field trials than the intolerant parent Nipponbare. In this study, we report the fine mapping of the Pup1 locus to the long arm of chromosome 12 (15.31-15.47 Mb). Genes in the region were initially identified on the basis of the Nipponbare reference genome, but did not reveal any obvious candidate genes related to phosphorus uptake. Kasalath BAC clones were therefore sequenced and revealed a 278-kbp sequence significantly different from the syntenic regions in Nipponbare (145 kb) and in the indica reference genome of 93-11 (742 kbp). Size differences are caused by large insertions or deletions (INDELs), and an exceptionally large number of retrotransposon and transposon-related elements (TEs) present in all three sequences (45%-54%). About 46 kb of the Kasalath sequence did not align with the entire Nipponbare genome, and only three Nipponbare genes (fatty acid alpha-dioxygenase, dirigent protein and aspartic proteinase) are highly conserved in Kasalath. Two Nipponbare genes (expressed proteins) might have evolved by at least three TE integrations in an ancestor gene that is still present in Kasalath. Several predicted Kasalath genes are novel or unknown genes that are mainly located within INDEL regions. Our results highlight the importance of sequencing QTL regions in the respective donor parent, as important genes might not be present in the current reference genomes.

  8. Transcriptome and proteomic analyses reveal multiple differences associated with chloroplast development in the spaceflight-induced wheat albino mutant mta.

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    Kui Shi

    Full Text Available Chloroplast development is an integral part of plant survival and growth, and occurs in parallel with chlorophyll biosynthesis. However, little is known about the mechanisms underlying chloroplast development in hexaploid wheat. Here, we obtained a spaceflight-induced wheat albino mutant mta. Chloroplast ultra-structural observation showed that chloroplasts of mta exhibit abnormal morphology and distribution compared to wild type. Photosynthetic pigments content was also significantly decreased in mta. Transcriptome and chloroplast proteome profiling of mta and wild type were done to identify differentially expressed genes (DEGs and proteins (DEPs, respectively. In total 4,588 DEGs including 1,980 up- and 2,608 down-regulated, and 48 chloroplast DEPs including 15 up- and 33 down-regulated were identified in mta. Classification of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. Besides, transcription factors such as PIF3, GLK and MYB which might participate in those pathways were also identified. The correlation analysis between DEGs and DEPs revealed that the transcript-to-protein in abundance was functioned into photosynthesis and chloroplast relevant groups. Real time qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in mta. Together, our results suggest that the molecular mechanism for albino leaf color formation in mta is a thoroughly regulated and complicated process. The combined analysis of transcriptome and proteome afford comprehensive information for further research on chloroplast development mechanism in wheat. And spaceflight provides a potential means for mutagenesis in crop breeding.

  9. Trophic structure of mesopelagic fishes in the Gulf of Mexico revealed by gut content and stable isotope analyses

    Science.gov (United States)

    McClain-Counts, Jennifer P.; Demopoulos, Amanda W.J.; Ross, Steve W.

    2017-01-01

    Mesopelagic fishes represent an important component of the marine food web due to their global distributions, high abundances and ability to transport organic material throughout a large part of the water column. This study combined stable isotope (SIAs) and gut content analyses (GCAs) to characterize the trophic structure of mesopelagic fishes in the North-Central Gulf of Mexico. Additionally, this study examined whether mesopelagic fishes utilized chemosynthetic energy from cold seeps. Specimens were collected (9–25 August 2007) over three deep (>1,000 m) cold seeps at discrete depths (surface to 1,503 m) over the diurnal cycle. GCA classified 31 species (five families) of mesopelagic fishes into five feeding guilds: piscivores, large crustacean consumers, copepod consumers, generalists and mixed zooplanktivores. However, these guilds were less clearly defined based on stable isotope mixing model (MixSIAR) results, suggesting diets may be more mixed over longer time periods (weeks–months) and across co-occurring species. Copepods were likely important for the majority of mesopelagic fishes, consistent with GCA (this study) and previous literature. MixSIAR results also identified non-crustacean prey items, including salps and pteropods, as potentially important prey items for mesopelagic fishes, including those fishes not analysed in GCA (Sternoptyx spp. and Melamphaidae). Salps and other soft-bodied species are often missed in GCAs. Mesopelagic fishes had δ13C results consistent with particulate organic matter serving as the baseline organic carbon source, fueling up to three trophic levels. Fishes that undergo diel vertical migration were depleted in 15N relative to weak migrators, consistent with depth-specific isotope trends in sources and consumers, and assimilation of 15N-depleted organic matter in surface waters. Linear correlations between fish size and δ15N values suggested ontogenetic changes in fish diets for several species. While there was

  10. Least-squares dual characterization for ROI assessment in emission tomography

    International Nuclear Information System (INIS)

    Ben Bouallègue, F; Mariano-Goulart, D; Crouzet, J F; Dubois, A; Buvat, I

    2013-01-01

    Our aim is to describe an original method for estimating the statistical properties of regions of interest (ROIs) in emission tomography. Drawn upon the works of Louis on the approximate inverse, we propose a dual formulation of the ROI estimation problem to derive the ROI activity and variance directly from the measured data without any image reconstruction. The method requires the definition of an ROI characteristic function that can be extracted from a co-registered morphological image. This characteristic function can be smoothed to optimize the resolution-variance tradeoff. An iterative procedure is detailed for the solution of the dual problem in the least-squares sense (least-squares dual (LSD) characterization), and a linear extrapolation scheme is described to compensate for sampling partial volume effect and reduce the estimation bias (LSD-ex). LSD and LSD-ex are compared with classical ROI estimation using pixel summation after image reconstruction and with Huesman's method. For this comparison, we used Monte Carlo simulations (GATE simulation tool) of 2D PET data of a Hoffman brain phantom containing three small uniform high-contrast ROIs and a large non-uniform low-contrast ROI. Our results show that the performances of LSD characterization are at least as good as those of the classical methods in terms of root mean square (RMS) error. For the three small tumor regions, LSD-ex allows a reduction in the estimation bias by up to 14%, resulting in a reduction in the RMS error of up to 8.5%, compared with the optimal classical estimation. For the large non-specific region, LSD using appropriate smoothing could intuitively and efficiently handle the resolution-variance tradeoff. (paper)

  11. Least-squares dual characterization for ROI assessment in emission tomography

    Science.gov (United States)

    Ben Bouallègue, F.; Crouzet, J. F.; Dubois, A.; Buvat, I.; Mariano-Goulart, D.

    2013-06-01

    Our aim is to describe an original method for estimating the statistical properties of regions of interest (ROIs) in emission tomography. Drawn upon the works of Louis on the approximate inverse, we propose a dual formulation of the ROI estimation problem to derive the ROI activity and variance directly from the measured data without any image reconstruction. The method requires the definition of an ROI characteristic function that can be extracted from a co-registered morphological image. This characteristic function can be smoothed to optimize the resolution-variance tradeoff. An iterative procedure is detailed for the solution of the dual problem in the least-squares sense (least-squares dual (LSD) characterization), and a linear extrapolation scheme is described to compensate for sampling partial volume effect and reduce the estimation bias (LSD-ex). LSD and LSD-ex are compared with classical ROI estimation using pixel summation after image reconstruction and with Huesman's method. For this comparison, we used Monte Carlo simulations (GATE simulation tool) of 2D PET data of a Hoffman brain phantom containing three small uniform high-contrast ROIs and a large non-uniform low-contrast ROI. Our results show that the performances of LSD characterization are at least as good as those of the classical methods in terms of root mean square (RMS) error. For the three small tumor regions, LSD-ex allows a reduction in the estimation bias by up to 14%, resulting in a reduction in the RMS error of up to 8.5%, compared with the optimal classical estimation. For the large non-specific region, LSD using appropriate smoothing could intuitively and efficiently handle the resolution-variance tradeoff.

  12. Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China

    KAUST Repository

    Abd El Ghany, Moataz

    2016-05-25

    Human infections with Salmonella enterica subspecies enterica serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14 Salmonella Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of S. Senftenberg, designated SC1 and SC2, harboring variations in Salmonella pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures. Although the two variants shared the same serotype, the SC2 isolates of sequence type 14 (ST14) harbored intact SPI-1 and -2 and hence were characterized by possessing efficient invasion capabilities. In contrast, the SC1 isolates had structural deletion patterns in both SPI-1 and -2 that correlated with an impaired capacity to invade cultured human cells and also the year of their isolation. These atypical SC1 isolates also lacked the capacity to produce hydrogen sulfide. These findings highlight the emergence of atypical Salmonella Senftenberg variants in China and provide genetic validation that variants lacking SPI-1 and regions of SPI-2, which leads to impaired invasion capacity, can still cause clinical disease. These data have identified an emerging public health concern and highlight the need to strengthen surveillance to detect the prevalence and transmission of nontyphoidal Salmonella species.

  13. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

    Science.gov (United States)

    Chen, Chih-Yu; Shi, Wenqiang; Balaton, Bradley P; Matthews, Allison M; Li, Yifeng; Arenillas, David J; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Brown, Carolyn J; Wasserman, Wyeth W

    2016-11-18

    Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

  14. Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

    Science.gov (United States)

    Lee, Hong-Won; Kyung, Taeyoon; Yoo, Janghyun; Kim, Tackhoon; Chung, Chaeuk; Ryu, Ji Young; Lee, Hanki; Park, Kihyun; Lee, Sangkyu; Jones, Walton D.; Lim, Dae-Sik; Hyeon, Changbong; Do Heo, Won; Yoon, Tae-Young

    2013-01-01

    Co-immunoprecipitation (co-IP) has become a standard technique, but its protein-band output provides only static, qualitative information about protein–protein interactions. Here we demonstrate a real-time single-molecule co-IP technique that generates real-time videos of individual protein–protein interactions as they occur in unpurified cell extracts. By analysing single Ras–Raf interactions with a 50-ms time resolution, we have observed transient intermediates of the protein–protein interaction and determined all the essential kinetic rates. Using this technique, we have quantified the active fraction of native Ras proteins in xenograft tumours, normal tissue and cancer cell lines. We demonstrate that the oncogenic Ras mutations selectively increase the active-Ras fraction by one order of magnitude, without affecting total Ras levels or single-molecule signalling kinetics. Our approach allows us to probe the previously hidden, dynamic aspects of weak protein–protein interactions. It also suggests a path forward towards precision molecular diagnostics at the protein–protein interaction level. PMID:23422673

  15. Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development.

    Science.gov (United States)

    da Silva, Danielle Costenaro; da Silveira Falavigna, Vítor; Fasoli, Marianna; Buffon, Vanessa; Porto, Diogo Denardi; Pappas, Georgios Joannis; Pezzotti, Mario; Pasquali, Giancarlo; Revers, Luís Fernando

    2016-01-01

    The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.

  16. Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

    Directory of Open Access Journals (Sweden)

    Li Chuan

    2012-05-01

    Full Text Available Abstract Background Little is known about the potential of Brachypodium distachyon as a model for low temperature stress responses in Pooideae. The ice recrystallization inhibition protein (IRIP genes, fructosyltransferase (FST genes, and many C-repeat binding factor (CBF genes are Pooideae specific and important in low temperature responses. Here we used comparative analyses to study conservation and evolution of these gene families in B. distachyon to better understand its potential as a model species for agriculturally important temperate grasses. Results Brachypodium distachyon contains cold responsive IRIP genes which have evolved through Brachypodium specific gene family expansions. A large cold responsive CBF3 subfamily was identified in B. distachyon, while CBF4 homologs are absent from the genome. No B. distachyon FST gene homologs encode typical core Pooideae FST-motifs and low temperature induced fructan accumulation was dramatically different in B. distachyon compared to core Pooideae species. Conclusions We conclude that B. distachyon can serve as an interesting model for specific molecular mechanisms involved in low temperature responses in core Pooideae species. However, the evolutionary history of key genes involved in low temperature responses has been different in Brachypodium and core Pooideae species. These differences limit the use of B. distachyon as a model for holistic studies relevant for agricultural core Pooideae species.

  17. Analyses of Dynein Heavy Chain Mutations Reveal Complex Interactions Between Dynein Motor Domains and Cellular Dynein Functions

    Science.gov (United States)

    Sivagurunathan, Senthilkumar; Schnittker, Robert R.; Razafsky, David S.; Nandini, Swaran; Plamann, Michael D.; King, Stephen J.

    2012-01-01

    Cytoplasmic dynein transports cargoes for a variety of crucial cellular functions. However, since dynein is essential in most eukaryotic organisms, the in-depth study of the cellular function of dynein via genetic analysis of dynein mutations has not been practical. Here, we identify and characterize 34 different dynein heavy chain mutations using a genetic screen of the ascomycete fungus Neurospora crassa, in which dynein is nonessential. Interestingly, our studies show that these mutations segregate into five different classes based on the in vivo localization of the mutated dynein motors. Furthermore, we have determined that the different classes of dynein mutations alter vesicle trafficking, microtubule organization, and nuclear distribution in distinct ways and require dynactin to different extents. In addition, biochemical analyses of dynein from one mutant strain show a strong correlation between its in vitro biochemical properties and the aberrant intracellular function of that altered dynein. When the mutations were mapped to the published dynein crystal structure, we found that the three-dimensional structural locations of the heavy chain mutations were linked to particular classes of altered dynein functions observed in cells. Together, our data indicate that the five classes of dynein mutations represent the entrapment of dynein at five separate points in the dynein mechanochemical and transport cycles. We have developed N. crassa as a model system where we can dissect the complexities of dynein structure, function, and interaction with other proteins with genetic, biochemical, and cell biological studies. PMID:22649085

  18. Transcriptomic and Functional Analyses Reveal That PpGLK1 Regulates Chloroplast Development in Peach (Prunus persica

    Directory of Open Access Journals (Sweden)

    Min Chen

    2018-01-01

    Full Text Available Peach is an ideal species for fruit tree research because of its small, fully sequenced genome. Chloroplast development is dependent on the tight cooperation between the nuclear and plastid genomes, and is regulated by GLK transcription factors. In this work, the pigment content was monitored and the chloroplast-to-chromoplast conversion during the fruit ripening was visualized by transmission electron microscopy. Localization and expression analyses showed that PpGLK1 was located in the nucleus and expressed mainly in the leaves and fruit skin. A transcriptome analysis showed that PpGLK1 and its target genes were significantly differentially expressed in ripening peach fruit skin. PpGLK1 silencing affected chlorophyll accumulation in peach leaves and fruits. Overexpression of PpGLK1 rescued the phenotypes of the Arabidopsis Atglk1Atglk2 double mutant and the tomato uniform ripening mutant. The results of a yeast two-hybrid analysis showed that PpGLK1 is autoactivated and that PpGLK1 (301-542 a.a. interacted with PpARF5. Together, our results indicate that PpGLK1 regulates chloroplast development in green tissues in peach. Therefore, it may be a promising target gene for improving the production and quality of peach by genetic engineering and breeding approaches.

  19. NMR spectroscopic and bioinformatic analyses of the LTBP1 C-terminus reveal a highly dynamic domain organisation.

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    Ian B Robertson

    Full Text Available Proteins from the LTBP/fibrillin family perform key structural and functional roles in connective tissues. LTBP1 forms the large latent complex with TGFβ and its propeptide LAP, and sequesters the latent growth factor to the extracellular matrix. Bioinformatics studies suggest the main structural features of the LTBP1 C-terminus are conserved through evolution. NMR studies were carried out on three overlapping C-terminal fragments of LTBP1, comprising four domains with characterised homologues, cbEGF14, TB3, EGF3 and cbEGF15, and three regions with no homology to known structures. The NMR data reveal that the four domains adopt canonical folds, but largely lack the interdomain interactions observed with homologous fibrillin domains; the exception is the EGF3-cbEGF15 domain pair which has a well-defined interdomain interface. (15N relaxation studies further demonstrate that the three interdomain regions act as flexible linkers, allowing a wide range of motion between the well-structured domains. This work is consistent with the LTBP1 C-terminus adopting a flexible "knotted rope" structure, which may facilitate cell matrix interactions, and the accessibility to proteases or other factors that could contribute to TGFβ activation.

  20. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

    Directory of Open Access Journals (Sweden)

    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  1. Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation.

    Science.gov (United States)

    Bargiela, Rafael; Herbst, Florian-Alexander; Martínez-Martínez, Mónica; Seifert, Jana; Rojo, David; Cappello, Simone; Genovese, María; Crisafi, Francesca; Denaro, Renata; Chernikova, Tatyana N; Barbas, Coral; von Bergen, Martin; Yakimov, Michail M; Ferrer, Manuel; Golyshin, Peter N

    2015-10-01

    Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi-enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large-scale chronic pollution is yet to be defined, particularly in anaerobic and micro-aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen-depleted petroleum-polluted sediments. © 2015 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Metaproteomics and metabolomics analyses of chronically petroleum‐polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

    Science.gov (United States)

    Bargiela, Rafael; Herbst, Florian‐Alexander; Martínez‐Martínez, Mónica; Seifert, Jana; Rojo, David; Cappello, Simone; Genovese, María; Crisafi, Francesca; Denaro, Renata; Chernikova, Tatyana N.; Barbas, Coral; von Bergen, Martin; Yakimov, Michail M.; Golyshin, Peter N.

    2015-01-01

    Crude oil is one of the most important natural assets for humankind, yet it is a major environmental pollutant, notably in marine environments. One of the largest crude oil polluted areas in the word is the semi‐enclosed Mediterranean Sea, in which the metabolic potential of indigenous microbial populations towards the large‐scale chronic pollution is yet to be defined, particularly in anaerobic and micro‐aerophilic sites. Here, we provide an insight into the microbial metabolism in sediments from three chronically polluted marine sites along the coastline of Italy: the Priolo oil terminal/refinery site (near Siracuse, Sicily), harbour of Messina (Sicily) and shipwreck of MT Haven (near Genoa). Using shotgun metaproteomics and community metabolomics approaches, the presence of 651 microbial proteins and 4776 metabolite mass features have been detected in these three environments, revealing a high metabolic heterogeneity between the investigated sites. The proteomes displayed the prevalence of anaerobic metabolisms that were not directly related with petroleum biodegradation, indicating that in the absence of oxygen, biodegradation is significantly suppressed. This suppression was also suggested by examining the metabolome patterns. The proteome analysis further highlighted the metabolic coupling between methylotrophs and sulphate reducers in oxygen‐depleted petroleum‐polluted sediments. PMID:26201687

  3. SNP analyses of growth factor genes EGF, TGF{beta}-1, and HGF reveal haplotypic association of EGF with autism

    Energy Technology Data Exchange (ETDEWEB)

    Toyoda, Takao; Thanseem, Ismail; Kawai, Masayoshi; Sekine, Yoshimoto [Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Nakamura, Kazuhiko; Anitha, Ayyappan; Suda, Shiro [Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Yamada, Kazuo [Laboratory of Molecular Psychiatry, RIKEN Brain Science Institute, Saitama (Japan); Tsujii, Masatsugu [Faculty of Sociology, Chukyo University, Toyota, Aichi (Japan); [The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu (Japan); Iwayama, Yoshimi; Hattori, Eiji; Toyota, Tomoko; Yoshikawa, Takeo [Laboratory of Molecular Psychiatry, RIKEN Brain Science Institute, Saitama (Japan); Miyachi, Taishi; Tsuchiya, Kenji; Sugihara, Gen-ichi; Matsuzaki, Hideo [The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu (Japan); Iwata, Yasuhide; Suzuki, Katsuaki [Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Mori, Norio [Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); [The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Graduate School of Medicine, Osaka University (Japan); Ouchi, Yasuomi [The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu (Japan); [The Positron Medical Center, Hamamatsu Medical Center, Hamamatsu (Japan); Sugiyama, Toshiro [Aichi Children' s Health and Medical Center, Obu, Aichi (Japan); Takei, Nori [The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu (Japan)

    2007-09-07

    Autism is a pervasive neurodevelopmental disorder diagnosed in early childhood. Growth factors have been found to play a key role in the cellular differentiation and proliferation of the central and peripheral nervous systems. Epidermal growth factor (EGF) is detected in several regions of the developing and adult brain, where, it enhances the differentiation, maturation, and survival of a variety of neurons. Transforming growth factor-{beta} (TGF{beta}) isoforms play an important role in neuronal survival, and the hepatocyte growth factor (HGF) has been shown to exhibit neurotrophic activity. We examined the association of EGF, TGF{beta}1, and HGF genes with autism, in a trio association study, using DNA samples from families recruited to the Autism Genetic Resource Exchange; 252 trios with a male offspring scored for autism were selected for the study. Transmission disequilibrium test revealed significant haplotypic association of EGF with autism. No significant SNP or haplotypic associations were observed for TGF{beta}1 or HGF. Given the role of EGF in brain and neuronal development, we suggest a possible role of EGF in the pathogenesis of autism.

  4. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection

    Directory of Open Access Journals (Sweden)

    Dongxu Xing

    2017-02-01

    Full Text Available The silkworm Bombyx mori is an economically important species. White muscardine caused by Beauveria bassiana is the main fungal disease in sericulture, and understanding the silkworm responses to B. bassiana infection is of particular interest. Herein, we investigated the molecular mechanisms underlying these responses in two silkworm strains Haoyue (HY, sensitive to B. bassiana and Kang 8 (K8, resistant to B. bassiana using an RNA-seq approach. For each strain, three biological replicates for immersion treatment, two replicates for injection treatment and three untreated controls were collected to generate 16 libraries for sequencing. Differentially expressed genes (DEGs between treated samples and untreated controls, and between the two silkworm strains, were identified. DEGs and the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG pathways of the two strains exhibited an obvious difference. Several genes encoding cuticle proteins, serine proteinase inhibitors (SPI and antimicrobial peptides (AMP and the drug metabolism pathway involved in toxin detoxification were considered to be related to the resistance of K8 to B. bassiana. These results revealed insight into the resistance and susceptibility of two silkworm strains against B. bassiana infection and provided a roadmap for silkworm molecular breeding to enhance its resistance to B. bassiana.

  5. RNA-Seq Analyses for Two Silkworm Strains Reveals Insight into Their Susceptibility and Resistance to Beauveria bassiana Infection.

    Science.gov (United States)

    Xing, Dongxu; Yang, Qiong; Jiang, Liang; Li, Qingrong; Xiao, Yang; Ye, Mingqiang; Xia, Qingyou

    2017-02-10

    The silkworm Bombyx mori is an economically important species. White muscardine caused by Beauveria bassiana is the main fungal disease in sericulture, and understanding the silkworm responses to B. bassiana infection is of particular interest. Herein, we investigated the molecular mechanisms underlying these responses in two silkworm strains Haoyue (HY, sensitive to B. bassiana ) and Kang 8 (K8, resistant to B. bassiana ) using an RNA-seq approach. For each strain, three biological replicates for immersion treatment, two replicates for injection treatment and three untreated controls were collected to generate 16 libraries for sequencing. Differentially expressed genes (DEGs) between treated samples and untreated controls, and between the two silkworm strains, were identified. DEGs and the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the two strains exhibited an obvious difference. Several genes encoding cuticle proteins, serine proteinase inhibitors (SPI) and antimicrobial peptides (AMP) and the drug metabolism pathway involved in toxin detoxification were considered to be related to the resistance of K8 to B. bassiana. These results revealed insight into the resistance and susceptibility of two silkworm strains against B. bassiana infection and provided a roadmap for silkworm molecular breeding to enhance its resistance to B. bassiana .

  6. Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types

    Science.gov (United States)

    Xia, Zheng; Donehower, Lawrence A; Cooper, Thomas A.; Neilson, Joel R.; Wheeler, David A.; Wagner, Eric J.; Li, Wei

    2015-01-01

    Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumor/normal pairs across 7 tumor types, DaPars reveals 1,346 genes with recurrent and tumor-specific APAs. Most APA genes (91%) have shorter 3′ UTRs in tumors that can avoid miRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumor proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′ UTR shortening across multiple tumor types. PMID:25409906

  7. Cytogenetic analyses of Azadirachtin reveal absence of genotoxicity but marked antiproliferative effects in human lymphocytes and CHO cells in vitro.

    Science.gov (United States)

    Mosesso, Pasquale; Bohm, Lothar; Pepe, Gaetano; Fiore, Mario; Carpinelli, Alice; Gäde, Gerd; Nagini, Siddavaram; Ottavianelli, Alessandro; Degrassi, Francesca

    2012-09-18

    In this work we have examined the genotoxic potential of the bioinsecticide Azadirachtin A (AZA) and its influence on cell proliferation on human lymphocytes and Chinese Hamster ovary (CHO) cells. AZA genotoxicity was assessed by the analysis of chromosomal aberrations and sister chromatid exchanges (SCEs) in the absence and presence of rat liver S9 metabolism. Primary DNA damage was also investigated by means of the comet assay. The results obtained clearly indicate that AZA is not genotoxic in mammalian cells. On the other hand, AZA proved to interfere with cell cycle progression as shown by modulation of frequencies of first (M1) and second division (M2) metaphases detected by 5-Bromo-2'-deoxyuridine labeling. Accumulation of M1 metaphases were more pronounced in human lymphocytes. In the transformed CHO cell line, however, significant increases of multinucleated interphases and polyploid cells were observed at long treatment time. At higher dose-levels, the incidence of polyploidy was close to 100%. Identification of spindle structure and number of centrosomes by fluorescent immunostaining with α- and γ-tubulin antibodies revealed aberrant mitoses exhibiting multipolar spindles with several centrosomal signals. These findings suggest that AZA can act either through a stabilizing activity of microtubules or by inhibition of Aurora A, since both mechanisms are able to generate genetically unstable polyploid cells with multipolar spindles and multinucleated interphases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  8. Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge

    Directory of Open Access Journals (Sweden)

    Simon J. McIlroy

    2017-06-01

    Full Text Available Anaerobic digestion for biogas production is reliant on the tightly coupled synergistic activities of complex microbial consortia. Members of the uncultured A6 phylotype, within the phylum Chloroflexi, are among the most abundant genus-level-taxa of mesophilic anaerobic digester systems treating primary and surplus sludge from wastewater treatment plants, yet are known only by their 16S rRNA gene sequence. This study applied metagenomics to obtain a complete circular genome (2.57 Mbp from a representative of the A6 taxon. Preliminary annotation of the genome indicates these organisms to be anaerobic chemoorganoheterotrophs with a fermentative metabolism. Given their observed abundance, they are likely important primary fermenters in digester systems. Application of fluorescence in situ hybridisation probes designed in this study revealed their morphology to be short filaments present within the flocs. The A6 were sometimes co-located with the filamentous Archaea Methanosaeta spp. suggesting potential undetermined synergistic relationships. Based on its genome sequence and morphology we propose the species name Brevefilum fermentans gen. nov. sp. nov.

  9. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Directory of Open Access Journals (Sweden)

    Ayaka Yamamuro

    Full Text Available Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2 (based on the projected area of the anode. In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  10. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Science.gov (United States)

    Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2014-01-01

    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  11. SNP analyses of growth factor genes EGF, TGFβ-1, and HGF reveal haplotypic association of EGF with autism

    International Nuclear Information System (INIS)

    Toyoda, Takao; Nakamura, Kazuhiko; Yamada, Kazuo; Thanseem, Ismail; Anitha, Ayyappan; Suda, Shiro; Tsujii, Masatsugu; Iwayama, Yoshimi; Hattori, Eiji; Toyota, Tomoko; Miyachi, Taishi; Iwata, Yasuhide; Suzuki, Katsuaki; Matsuzaki, Hideo; Kawai, Masayoshi; Sekine, Yoshimoto; Tsuchiya, Kenji; Sugihara, Gen-ichi; Ouchi, Yasuomi; Sugiyama, Toshiro; Takei, Nori; Yoshikawa, Takeo; Mori, Norio

    2007-01-01

    Autism is a pervasive neurodevelopmental disorder diagnosed in early childhood. Growth factors have been found to play a key role in the cellular differentiation and proliferation of the central and peripheral nervous systems. Epidermal growth factor (EGF) is detected in several regions of the developing and adult brain, where, it enhances the differentiation, maturation, and survival of a variety of neurons. Transforming growth factor-β (TGFβ) isoforms play an important role in neuronal survival, and the hepatocyte growth factor (HGF) has been shown to exhibit neurotrophic activity. We examined the association of EGF, TGFβ1, and HGF genes with autism, in a trio association study, using DNA samples from families recruited to the Autism Genetic Resource Exchange; 252 trios with a male offspring scored for autism were selected for the study. Transmission disequilibrium test revealed significant haplotypic association of EGF with autism. No significant SNP or haplotypic associations were observed for TGFβ1 or HGF. Given the role of EGF in brain and neuronal development, we suggest a possible role of EGF in the pathogenesis of autism

  12. Paleogenetic analyses reveal unsuspected phylogenetic affinities between mice and the extinct Malpaisomys insularis, an endemic rodent of the Canaries.

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    Marie Pagès

    Full Text Available BACKGROUND: The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14(th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae. Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. CONCLUSION/SIGNIFICANCE: This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse.

  13. RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

    Science.gov (United States)

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-01-01

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

  14. Multiproxy analyses of Lake Allos reveal synchronicity and divergence in geosystem dynamics during the Lateglacial/Holocene in the Alps

    Science.gov (United States)

    Cartier, Rosine; Brisset, Elodie; Guiter, Frédéric; Sylvestre, Florence; Tachikawa, Kazuyo; Anthony, Edward J.; Paillès, Christine; Bruneton, Hélène; Bard, Edouard; Miramont, Cécile

    2018-04-01

    Palaeoenvironmental reconstructions of ecosystem responses to external forcing are generally limited by the difficulty of understanding the geosystem as a whole, because of the complex interactions between ecological compartments. Therefore, identifying which geosystem compartments or proxies co-vary is a prerequisite in unravelling the propagation of disturbances (e.g. climatic or anthropogenic) from one compartment to another. A multiproxy study of a continuous 13,500-year sedimentary profile cored in Lake Allos (European Alps, 2200 m a.s.l) was carried out on the basis of high-resolution sedimentological, geochemical, and botanical analyses, as well as determination of aquatic biotic proxies (diatoms, ostracods). These multiproxy datasets are rare at these high altitudes. Major changes occurred in the course of the palaeoenvironmental history of this alpine watershed at 12,000, 8600, 7200 and 3000 cal. BP. During the Holocene, two main transitions were recorded in all the ecological compartments (8600 and 3000 cal. BP), but the period 4500-3000 cal. BP stands out because of major changes that concerned only the lacustrine ecosystem. The frequent switches in lake level might correspond to the 4.2 ka climatic event. Proximity of this alpine lake to climatically-sensitive thresholds (ice-cover, thermal stratification, hydrological balance) may have amplified climatic signals in the lake ecosystem. This study illustrates the difficulties inherent to the use of common intra-Holocene stratigraphical limits, given that ecological compartments are likely to have different responses to forcing factors depending on the characteristics of the watershed and its capacity to accommodate disturbances.

  15. Correlation analyses revealed global microRNA-mRNA expression associations in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Wang, Lan; Zhu, Jiang; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Xiao-Wei; Xia, Wei; Xie, Fang-Fei; He, Pei; Bing, Peng-Fei; Qiu, Ying-Hua; Lin, Xiang; Lu, Xin; Zhang, Lei; Yi, Neng-Jun; Zhang, Yong-Hong; Lei, Shu-Feng

    2018-02-01

    MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study. We predicted and achieved 861 miRNA-mRNA pairs (65 miRNAs, 412 mRNAs) using multiple bioinformatics programs, and found global negative miRNA-mRNA correlations in PBMC from all 46 study subjects. Among the 861 pairs of correlations, 19.5% were significant (P correlation network was complex and highlighted key miRNAs/genes in PBMC. Some miRNAs, such as hsa-miR-29a, hsa-miR-148a, regulate a cluster of target genes. Some genes, e.g., TNRC6A, are regulated by multiple miRNAs. The identified genes tend to be enriched in molecular functions of DNA and RNA binding, and biological processes such as protein transport, regulation of translation and chromatin modification. The results provided a global view of the miRNA-mRNA expression correlation profile in human PBMCs, which would facilitate in-depth investigation of biological functions of key miRNAs/mRNAs and better understanding of the pathogenesis underlying PBMC-related diseases.

  16. Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Xie, Fang-Fei; Deng, Fei-Yan; Wu, Long-Fei; Mo, Xing-Bo; Zhu, Hong; Wu, Jian; Guo, Yu-Fan; Zeng, Ke-Qin; Wang, Ming-Jun; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Lu, Xin; Zhang, Yong-Hong; Lei, Shu-Feng

    2018-01-01

    DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1 ) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P correlation (R T4  > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

  17. Structure and Principal Components Analyses Reveal an Intervarietal Fusion in Malaysian Mistletoe Fig (Ficus deltoidea Jack Populations

    Directory of Open Access Journals (Sweden)

    Birifdzi Zimisuhara

    2015-06-01

    Full Text Available Genetic structure and biodiversity of the medicinal plant Ficus deltoidea have rarely been scrutinized. To fill these lacunae, five varieties, consisting of 30 F. deltoidea accessions were collected across the country and studied on the basis of molecular and morphological data. Molecular analysis of the accessions was performed using nine Inter Simple Sequence Repeat (ISSR markers, seven of which were detected as polymorphic markers. ISSR-based clustering generated four clusters supporting the geographical distribution of the accessions to some extent. The Jaccard’s similarity coefficient implied the existence of low diversity (0.50–0.75 in the studied population. STRUCTURE analysis showed a low differentiation among the sampling sites, while a moderate varietal differentiation was unveiled with two main populations of F. deltoidea. Our observations confirmed the occurrence of gene flow among the accessions; however, the highest degree of this genetic interference was related to the three accessions of FDDJ10, FDTT16 and FDKT25. These three accessions may be the genetic intervarietal fusion points of the plant’s population. Principal Components Analysis (PCA relying on quantitative morphological characteristics resulted in two principal components with Eigenvalue >1 which made up 89.96% of the total variation. The cluster analysis performed by the eight quantitative characteristics led to grouping the accessions into four clusters with a Euclidean distance ranged between 0.06 and 1.10. Similarly, a four-cluster dendrogram was generated using qualitative traits. The qualitative characteristics were found to be more discriminating in the cluster and PCA analyses, while ISSRs were more informative on the evolution and genetic structure of the population.

  18. Analytical pyrolysis and stable isotope analyses reveal past environmental changes in coralloid speleothems from Easter Island (Chile).

    Science.gov (United States)

    Miller, Ana Z; De la Rosa, José M; Jiménez-Morillo, Nicasio T; Pereira, Manuel F C; González-Pérez, José A; Calaforra, José M; Saiz-Jimenez, Cesareo

    2016-08-26

    This study comprises an innovative approach based on the combination of chromatography (analytical pyrolysis and pyrolysis compound-specific isotope analysis (Py-CSIA)), light stable isotopes, microscopy and mineralogy analyses to characterize the internal layering of coralloid speleothems from the Ana Heva lava tube in Easter Island (Chile). This multidisciplinary proxy showed that the speleothems consist of banded siliceous materials of low crystallinity with different mineralogical compositions and a significant contribution of organic carbon. Opal-A constitutes the outermost grey layer of the coralloids, whereas calcite and amorphous Mg hydrate silicate are the major components of the inner whitish and honey-brown layers, respectively. The differences found in the mineralogical, elemental, molecular and isotopic composition of these distinct coloured layers are related to environmental changes during speleothem development. Stable isotopes and analytical pyrolysis suggested alterations in the water regime, pointing to wetter conditions during the formation of the Ca-rich layer and a possible increase in the amount of water dripping into the cave. The trend observed for δ(15)N values suggested an increase in the average temperature over time, which is consistent with the so-called climate warming during the Holocene. The pyrolysis compound-specific isotope analysis of each speleothem layer showed a similar trend with the bulk δ(13)C values pointing to the appropriateness of direct Py-CSIA in paleoenvironmental studies. The δ(13)C values for n-alkanes reinforced the occurrence of a drastic environmental change, indicating that the outermost Opal layer was developed under drier and more arid environmental conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Spliced leader-based analyses reveal the effects of polycyclic aromatic hydrocarbons on gene expression in the copepod Pseudodiaptomus poplesia.

    Science.gov (United States)

    Zhuang, Yunyun; Yang, Feifei; Xu, Donghui; Chen, Hongju; Zhang, Huan; Liu, Guangxing

    2017-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are a group of toxic and carcinogenic pollutants that can adversely affect the development, growth and reproduction of marine organisms including copepods. However, knowledge on the molecular mechanisms regulating the response to PAH exposure in marine planktonic copepods is limited. In this study, we investigated the survival and gene expression of the calanoid copepod Pseudodiaptomus poplesia upon exposure to two PAHs, 1, 2-dimethylnaphthalene (1, 2-NAPH) and pyrene. Acute toxicity responses resulted in 96-h LC 50 of 788.98μgL -1 and 54.68μgL -1 for 1, 2-NAPH and pyrene, respectively. Using the recently discovered copepod spliced leader as a primer, we constructed full-length cDNA libraries from copepods exposed to sublethal concentrations and revealed 289 unique genes of diverse functions, including stress response genes and novel genes previously undocumented for this species. Eighty-three gene families were specifically expressed in PAH exposure libraries. We further analyzed the expression of seven target genes by reverse transcription-quantitative PCR in a time-course test with three sublethal concentrations. These target genes have primary roles in detoxification, oxidative defense, and signal transduction, and include different forms of glutathione S-transferase (GST), glutathione peroxidases (GPX), peroxiredoxin (PRDX), methylmalonate-semialdehyde dehydrogenase (MSDH) and ras-related C3 botulinum toxin substrate (RAC1). Expression stability of seven candidate reference genes were evaluated and the two most stable ones (RPL15 and RPS20 for 1, 2-NAPH exposure, RPL15 and EF1D for pyrene exposure) were used to normalize the expression levels of the target genes. Significant upregulation was detected in GST-T, GST-DE, GPX4, PRDX6 and RAC1 upon 1, 2-NAPH exposure, and GST-DE and MSDH upon pyrene exposure. These results indicated that the oxidative stress was induced and that signal transduction might be affected by PAH

  20. Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations.

    Science.gov (United States)

    Reem, Nathan T; Chen, Han-Yi; Hur, Manhoi; Zhao, Xuefeng; Wurtele, Eve Syrkin; Li, Xu; Li, Ling; Zabotina, Olga

    2018-03-01

    This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.

  1. Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance.

    Science.gov (United States)

    Sapeta, Helena; Lourenço, Tiago; Lorenz, Stefan; Grumaz, Christian; Kirstahler, Philipp; Barros, Pedro M; Costa, Joaquim Miguel; Sohn, Kai; Oliveira, M Margarida

    2016-02-01

    Jatropha curcas, a multipurpose plant attracting a great deal of attention due to its high oil content and quality for biofuel, is recognized as a drought-tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, using a combined approach of transcriptional profiling and morphophysiological characterization during a period of water-withholding (49 d) followed by rewatering (7 d). Morphophysiological measurements showed that J. curcas plants present different adaptation strategies to withstand moderate and severe drought. Therefore, RNA sequencing was performed for samples collected under moderate and severe stress followed by rewatering, for both roots and leaves. Jatropha curcas transcriptomic analysis revealed shoot- and root-specific adaptations across all investigated conditions, except under severe stress, when the dramatic transcriptomic reorganization at the root and shoot level surpassed organ specificity. These changes in gene expression were clearly shown by the down-regulation of genes involved in growth and water uptake, and up-regulation of genes related to osmotic adjustments and cellular homeostasis. However, organ-specific gene variations were also detected, such as strong up-regulation of abscisic acid synthesis in roots under moderate stress and of chlorophyll metabolism in leaves under severe stress. Functional validation further corroborated the differential expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  2. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

    Science.gov (United States)

    Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

    2012-01-01

    Background Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/Significance The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in

  3. Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium.

    Science.gov (United States)

    Liu, Yang; Zhang, Hai-Liang; Guo, He-Rong; Xie, Li; Zeng, Rui-Zhen; Zhang, Xiang-Qian; Zhang, Zhi-Sheng

    2017-01-01

    Cymbidium , one of the most important orchid genera in horticulture, can be classified into epiphytic and terrestrial species. Generally, epiphytic Cymbidium seedlings can be easily propagated by tissue culture, but terrestrial seedlings are difficult to propagate. To date, the molecular mechanisms underlying the differences in the ease with which terrestrial and epiphytic cymbidiums can be propagated are largely unknown. Using RNA-sequencing, quantitative reverse transcription PCR and enzyme-linked immunosorbent assay, Cymbidium 'Xiaofeng' (CXF), which can be efficiently micropropagated, and terrestrial Cymbidium sinense 'Qijianbaimo' (CSQ), which has a low regeneration ability, were used to explore the molecular mechanisms underlying the micropropagation ability of Cymbidium species. To this end, 447 million clean short reads were generated, and 31,264 annotated unigenes were obtained from 10 cDNA libraries. A total of 1,290 differentially expressed genes (DEGs) were identified between CXF and CSQ during shoot induction. Gene ontology (GO) enrichment analysis indicated that the DEGs were significantly enriched in auxin pathway-related GO terms. Further analysis demonstrated that YUC and GH3 family genes, which play crucial roles in the regulation of auxin/IAA (indole-3-acetic acid) metabolism, acted quickly in response to shoot induction culture in vitro and were closely correlated with variation in shoot regeneration between CXF and CSQ. In addition, the study showed that IAA accumulated rapidly and significantly during shoot induction in CXF compared to that in CSQ; in contrast, no significant changes in other hormones were observed between CXF and CSQ. Furthermore, shoot regeneration in CXF was inhibited by a yucasin-auxin biosynthesis inhibitor, indicating that increased IAA level is required for high-frequency shoot regeneration in CXF. In conclusion, our study revealed that YUC-mediated auxin biogenesis is involved in shoot regeneration from rhizome in

  4. Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2017-10-01

    Full Text Available Cymbidium, one of the most important orchid genera in horticulture, can be classified into epiphytic and terrestrial species. Generally, epiphytic Cymbidium seedlings can be easily propagated by tissue culture, but terrestrial seedlings are difficult to propagate. To date, the molecular mechanisms underlying the differences in the ease with which terrestrial and epiphytic cymbidiums can be propagated are largely unknown. Using RNA-sequencing, quantitative reverse transcription PCR and enzyme-linked immunosorbent assay, Cymbidium ‘Xiaofeng’ (CXF, which can be efficiently micropropagated, and terrestrial Cymbidium sinense ‘Qijianbaimo’ (CSQ, which has a low regeneration ability, were used to explore the molecular mechanisms underlying the micropropagation ability of Cymbidium species. To this end, 447 million clean short reads were generated, and 31,264 annotated unigenes were obtained from 10 cDNA libraries. A total of 1,290 differentially expressed genes (DEGs were identified between CXF and CSQ during shoot induction. Gene ontology (GO enrichment analysis indicated that the DEGs were significantly enriched in auxin pathway-related GO terms. Further analysis demonstrated that YUC and GH3 family genes, which play crucial roles in the regulation of auxin/IAA (indole-3-acetic acid metabolism, acted quickly in response to shoot induction culture in vitro and were closely correlated with variation in shoot regeneration between CXF and CSQ. In addition, the study showed that IAA accumulated rapidly and significantly during shoot induction in CXF compared to that in CSQ; in contrast, no significant changes in other hormones were observed between CXF and CSQ. Furthermore, shoot regeneration in CXF was inhibited by a yucasin-auxin biosynthesis inhibitor, indicating that increased IAA level is required for high-frequency shoot regeneration in CXF. In conclusion, our study revealed that YUC-mediated auxin biogenesis is involved in shoot

  5. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

    Directory of Open Access Journals (Sweden)

    Ouyang Shu

    2005-09-01

    Full Text Available Abstract Background The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. Results All available ESTs and Expressed Transcripts (ETs, 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana, were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. Conclusion Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.

  6. Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures

    Directory of Open Access Journals (Sweden)

    Schriemer David C

    2010-11-01

    Full Text Available Abstract Background Papaver somniferum (opium poppy is the source for several pharmaceutical benzylisoquinoline alkaloids including morphine, the codeine and sanguinarine. In response to treatment with a fungal elicitor, the biosynthesis and accumulation of sanguinarine is induced along with other plant defense responses in opium poppy cell cultures. The transcriptional induction of alkaloid metabolism in cultured cells provides an opportunity to identify components of this process via the integration of deep transcriptome and proteome databases generated using next-generation technologies. Results A cDNA library was prepared for opium poppy cell cultures treated with a fungal elicitor for 10 h. Using 454 GS-FLX Titanium pyrosequencing, 427,369 expressed sequence tags (ESTs with an average length of 462 bp were generated. Assembly of these sequences yielded 93,723 unigenes, of which 23,753 were assigned Gene Ontology annotations. Transcripts encoding all known sanguinarine biosynthetic enzymes were identified in the EST database, 5 of which were represented among the 50 most abundant transcripts. Liquid chromatography-tandem mass spectrometry (LC-MS/MS of total protein extracts from cell cultures treated with a fungal elicitor for 50 h facilitated the identification of 1,004 proteins. Proteins were fractionated by one-dimensional SDS-PAGE and digested with trypsin prior to LC-MS/MS analysis. Query of an opium poppy-specific EST database substantially enhanced peptide identification. Eight out of 10 known sanguinarine biosynthetic enzymes and many relevant primary metabolic enzymes were represented in the peptide database. Conclusions The integration of deep transcriptome and proteome analyses provides an effective platform to catalogue the components of secondary metabolism, and to identify genes encoding uncharacterized enzymes. The establishment of corresponding transcript and protein databases generated by next-generation technologies in a

  7. Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures.

    Science.gov (United States)

    Desgagné-Penix, Isabel; Khan, Morgan F; Schriemer, David C; Cram, Dustin; Nowak, Jacek; Facchini, Peter J

    2010-11-18

    Papaver somniferum (opium poppy) is the source for several pharmaceutical benzylisoquinoline alkaloids including morphine, the codeine and sanguinarine. In response to treatment with a fungal elicitor, the biosynthesis and accumulation of sanguinarine is induced along with other plant defense responses in opium poppy cell cultures. The transcriptional induction of alkaloid metabolism in cultured cells provides an opportunity to identify components of this process via the integration of deep transcriptome and proteome databases generated using next-generation technologies. A cDNA library was prepared for opium poppy cell cultures treated with a fungal elicitor for 10 h. Using 454 GS-FLX Titanium pyrosequencing, 427,369 expressed sequence tags (ESTs) with an average length of 462 bp were generated. Assembly of these sequences yielded 93,723 unigenes, of which 23,753 were assigned Gene Ontology annotations. Transcripts encoding all known sanguinarine biosynthetic enzymes were identified in the EST database, 5 of which were represented among the 50 most abundant transcripts. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) of total protein extracts from cell cultures treated with a fungal elicitor for 50 h facilitated the identification of 1,004 proteins. Proteins were fractionated by one-dimensional SDS-PAGE and digested with trypsin prior to LC-MS/MS analysis. Query of an opium poppy-specific EST database substantially enhanced peptide identification. Eight out of 10 known sanguinarine biosynthetic enzymes and many relevant primary metabolic enzymes were represented in the peptide database. The integration of deep transcriptome and proteome analyses provides an effective platform to catalogue the components of secondary metabolism, and to identify genes encoding uncharacterized enzymes. The establishment of corresponding transcript and protein databases generated by next-generation technologies in a system with a well-defined metabolite profile facilitates

  8. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

  9. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    Science.gov (United States)

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  10. Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

  11. Medical Ultrasound Video Coding with H.265/HEVC Based on ROI Extraction.

    Science.gov (United States)

    Wu, Yueying; Liu, Pengyu; Gao, Yuan; Jia, Kebin

    2016-01-01

    High-efficiency video compression technology is of primary importance to the storage and transmission of digital medical video in modern medical communication systems. To further improve the compression performance of medical ultrasound video, two innovative technologies based on diagnostic region-of-interest (ROI) extraction using the high efficiency video coding (H.265/HEVC) standard are presented in this paper. First, an effective ROI extraction algorithm based on image textural features is proposed to strengthen the applicability of ROI detection results in the H.265/HEVC quad-tree coding structure. Second, a hierarchical coding method based on transform coefficient adjustment and a quantization parameter (QP) selection process is designed to implement the otherness encoding for ROIs and non-ROIs. Experimental results demonstrate that the proposed optimization strategy significantly improves the coding performance by achieving a BD-BR reduction of 13.52% and a BD-PSNR gain of 1.16 dB on average compared to H.265/HEVC (HM15.0). The proposed medical video coding algorithm is expected to satisfy low bit-rate compression requirements for modern medical communication systems.

  12. Medical Ultrasound Video Coding with H.265/HEVC Based on ROI Extraction.

    Directory of Open Access Journals (Sweden)

    Yueying Wu

    Full Text Available High-efficiency video compression technology is of primary importance to the storage and transmission of digital medical video in modern medical communication systems. To further improve the compression performance of medical ultrasound video, two innovative technologies based on diagnostic region-of-interest (ROI extraction using the high efficiency video coding (H.265/HEVC standard are presented in this paper. First, an effective ROI extraction algorithm based on image textural features is proposed to strengthen the applicability of ROI detection results in the H.265/HEVC quad-tree coding structure. Second, a hierarchical coding method based on transform coefficient adjustment and a quantization parameter (QP selection process is designed to implement the otherness encoding for ROIs and non-ROIs. Experimental results demonstrate that the proposed optimization strategy significantly improves the coding performance by achieving a BD-BR reduction of 13.52% and a BD-PSNR gain of 1.16 dB on average compared to H.265/HEVC (HM15.0. The proposed medical video coding algorithm is expected to satisfy low bit-rate compression requirements for modern medical communication systems.

  13. Return on investment. What is ROI and how to use it.

    Science.gov (United States)

    Cotter, Steve

    2014-08-01

    Formulated and interpreted correctly, ROI tools and techniques can be very useful for EMS managers when evaluating various competing projects and initiatives within the organization. More so, decision makers and elected bodies responsible for approving the financial support of these initiatives are demanding that they be presented with a more complete picture of the return for any dollars allocated under ever-tightening financial considerations that all organizations face today. ROI can be a powerful tool in supporting your organization when competing for limited dollars.

  14. The hands-on project office guaranteeing ROI and on-time delivery

    CERN Document Server

    Kesner, Richard M

    2003-01-01

    THE THREE PILLARS OF IT DELIVERY - PROBLEM RESOLUTION, SERVICE REQUESTS, AND PROJECTSIntroduction The Business Context The Internal Economy for Investing in IT Services and ProjectsThe Three Pillars of IT Delivery Managing Service DeliveryManaging Project Commitments IT Metrics and Reporting Tools THE PROJECT MANAGEMENT OFFICE BUSINESS MODELIntroduction: Revisiting the IT Organization IT Service and Project Delivery RolesThe Role of the Project Management Office: Measuring its ROI The PMO Value Proposition: An Initial ROI Estimate ALIGNMENT AND PLANNING - DOING THE RIGHT THINGS Introduction Ge

  15. Comparative proteomic analyses reveal that FlbA down-regulates gliT expression and SOD activity in Aspergillus fumigatus.

    Science.gov (United States)

    Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young-Hwan; Yu, Jae-Hyuk

    2013-07-11

    FlbA is a regulator of G-protein signaling protein that plays a central role in attenuating heterotrimeric G-protein mediated vegetative growth signaling in Aspergillus. The deletion of flbA (∆flbA) in the opportunistic human pathogen Aspergillus fumigatus results in accelerated cell death and autolysis in submerged culture. To further investigate the effects of ∆flbA on intracellular protein levels we carried out 2-D proteome analyses of 2-day old submerged cultures of ∆flbA and wild type (WT) strains and observed 160 differentially expressed proteins. Via nano-LC-ESI-MS/MS analyses, we revealed the identity of 10 and 2 proteins exhibiting high and low level accumulation, respectively, in ∆flbA strain. Notably, the GliT protein is accumulated at about 1800-fold higher levels in ∆flbA than WT. Moreover, GliT is secreted at high levels from ∆flbA strain, whereas Sod1 (superoxide dismutase) is secreted at a higher level in WT. Northern blot analyses reveal that ∆flbA results in elevated accumulation of gliT mRNA. Consequently, ∆flbA strain exhibits enhanced tolerance to gliotoxin toxicity. Finally, ∆flbA strain displayed enhanced SOD activity and elevated resistance to menadione and paraquat. In summary, FlbA-mediated signaling control negatively affects cellular responses associated with detoxification of reactive oxygen species and of exogenous gliotoxin in A. fumigatus. Regulator of G protein Signaling (RGS) proteins play crucial roles in fundamental biological processes in filamentous fungi. FlbA is the first studied filamentous fungal RGS protein, yet much remains to be understood about its roles in the opportunistic human pathogen Aspergillus fumigatus. In the present study, we examined the effects of the deletion of flbA using comprehensive analyses of the intra- and extracellular proteomes of A. fumigatus wild type and the flbA deletion mutant. Via MS analyses, we identified 10 proteins exhibiting high level accumulation in the flbA deletion

  16. SU-F-J-19: Robust Region-Of-Interest (ROI) for Consistent Registration On Deteriorated Surface Images

    Energy Technology Data Exchange (ETDEWEB)

    Kang, H; Malin, M; Chmura, S; Hasan, Y; Al-Hallaq, H [The Department of Radiation and Cellular Oncology, The University of Chicago Medicine, Chicago, IL (United States)

    2016-06-15

    Purpose: For African-American patients receiving breast radiotherapy with a bolus, skin darkening can affect the surface visualization when using optical imaging for daily positioning and gating at deep-inspiration breath holds (DIBH). Our goal is to identify a region-of-interest (ROI) that is robust against deteriorating surface image quality due to skin darkening. Methods: We study four patients whose post-mastectomy surfaces are imaged daily with AlignRT (VisionRT, UK) for DIBH radiotherapy and whose surface image quality is degraded toward the end of treatment. To simulate the effects of skin darkening, surfaces from the first ten fractions of each patient are systematically degraded by 25–35%, 40–50% and 65–75% of the total area of the clinically used ROI-ipsilateral-chestwall. The degraded surfaces are registered to the reference surface in six degrees-of-freedom. To identify a robust ROI, three additional reference ROIsROI-chest+abdomen, ROI-bilateral-chest and ROI-extended-ipsilateral-chestwall are created and registered to the degraded surfaces. Differences in registration using these ROIs are compared to that using ROI-ipsilateral-chestwall. Results: For three patients, the deviations in the registrations to ROI-ipsilateral-chestwall are > 2.0, 3.1 and 7.9mm on average for 25–35%, 40–50% and 65–75% degraded surfaces, respectively. Rotational deviations reach 11.1° in pitch. For the last patient, registration is consistent to within 2.6mm even on the 65–75% degraded surfaces, possibly because the surface topography has more distinct features. For ROI-bilateral-chest and ROI-extended-ipsilateral-chest registrations deviate in a similar pattern. However, registration on ROI-chest+abdomen is robust to deteriorating image qualities to within 4.2mm for all four patients. Conclusion: Registration deviations using ROI-ipsilateral-chestwall can reach 9.8mm on the 40–50% degraded surfaces. Caution is required when using AlignRT for patients

  17. Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Mark H.; Qian, Weijun; Wang, Haixing; Petyuk, Vladislav A.; Bloom, Joshua S.; Sforza, Daniel M.; Lacan, Goran; Liu, Dahai; Khan, Arshad H.; Cantor, Rita M.; Bigelow, Diana J.; Melega, William P.; Camp, David G.; Smith, Richard D.; Smith, Desmond J.

    2008-02-10

    The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson disease (PD) are not completely understood. Here we use mass spectrometry and microarrays to study the proteomic and transcriptomic changes in the striatum of two mouse models of PD, induced by the distinct neurotoxins 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Proteomic analyses resulted in the identification and relative quantification of 912 proteins with two or more unique peptides and 85 proteins with significant abundance changes following neurotoxin treatment. Similarly, microarray analyses revealed 181 genes with significant changes in mRNA following neurotoxin treatment. The combined protein and gene list provides a clearer picture of the potential mechanisms underlying neurodegeneration observed in PD. Functional analysis of this combined list revealed a number of significant categories, including mitochondrial dysfunction, oxidative stress response and apoptosis. Additionally, codon usage and miRNAs may play an important role in translational control in the striatum. These results constitute one of the largest datasets integrating protein and transcript changes for these neurotoxin models with many similar endpoint phenotypes but distinct mechanisms.

  18. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  19. Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

    Science.gov (United States)

    Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

    2017-11-28

    We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

  20. Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis.

    Directory of Open Access Journals (Sweden)

    Jason Abernathy

    Full Text Available Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

  1. Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

    Science.gov (United States)

    Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

    2016-10-03

    FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

  2. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855 (Mollusca, Ommastrephidae in the eastern tropical Atlantic.

    Directory of Open Access Journals (Sweden)

    Véronique Merten

    Full Text Available In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855 (Cephalopoda, Ommastrephidae is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding were combined with stable isotope data (∂15N and ∂13C of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp., but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae, crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and

  3. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic.

    Science.gov (United States)

    Merten, Véronique; Christiansen, Bernd; Javidpour, Jamileh; Piatkowski, Uwe; Puebla, Oscar; Gasca, Rebeca; Hoving, Henk-Jan T

    2017-01-01

    In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from

  4. Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

    Science.gov (United States)

    Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

    2014-01-01

    ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

  5. Proteomic and physiological analyses reveal the role of exogenous spermidine on cucumber roots in response to Ca(NO3)2 stress.

    Science.gov (United States)

    Du, Jing; Guo, Shirong; Sun, Jin; Shu, Sheng

    2018-05-01

    The mechanism of exogenous Spd-induced Ca(NO 3 ) 2 stress tolerance in cucumber was studied by proteomics and physiological analyses. Protein-protein interaction network revealed 13 key proteins involved in Spd-induced Ca(NO 3 ) 2 stress resistance. Ca(NO 3 ) 2 stress is one of the major reasons for secondary salinization that limits cucumber plant development in greenhouse. The conferred protective role of exogenous Spd on cucumber in response to Ca(NO 3 ) 2 stress cues involves changes at the cellular and physiological levels. To investigate the molecular foundation of exogenous Spd in Ca(NO 3 ) 2 stress tolerance, a proteomic approach was performed in our work. After a 9 days period of Ca(NO 3 ) 2 stress and/or exogenous Spd, 71 differential protein spots were confidently identified. The resulting proteins were enriched in seven different categories of biological processes, including protein metabolism, carbohydrate and energy metabolism, ROS homeostasis and stress defense, cell wall related, transcription, others and unknown. Protein metabolism (31.2%), carbohydrate and energy metabolism (15.6%), ROS homeostasis and stress defense (32.5%) were the three largest functional categories in cucumber root and most of them were significantly increased by exogenous Spd. The Spd-responsive protein interaction network revealed 13 key proteins, whose accumulation changes could be critical for Spd-induced resistance; all 13 proteins were upregulated by Spd at transcriptional and protein levels in response to Ca(NO 3 ) 2 stress. Furthermore, accumulation of antioxidant enzymes, non-enzymatic antioxidant and polyamines, along with reduction of H 2 O 2 and MDA, were detected after exogenous Spd application during Ca(NO 3 ) 2 stress. The results of these proteomic and physiological analyses in cucumber root may facilitate a better understanding of the underlying mechanism of Ca(NO 3 ) 2 stress tolerance mediated by exogenous Spd.

  6. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    Science.gov (United States)

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-xian; Reiter, Russel J.; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-01-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. PMID:25225478

  8. Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

    Science.gov (United States)

    Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

    2012-11-02

    HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

  9. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin.

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-Xian; Reiter, Russel J; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-02-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  10. Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Directory of Open Access Journals (Sweden)

    Eunyoung Seo

    2016-08-01

    Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  11. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

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    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  12. Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

    Science.gov (United States)

    Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

    2013-01-01

    The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

  13. The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    Directory of Open Access Journals (Sweden)

    Arzu Coleri Cihan

    2012-03-01

    Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

  14. Multi-ROI Association and Tracking With Belief Functions: Application to Traffic Sign Recognition

    OpenAIRE

    Boumediene , Mohammed; Lauffenburger , Jean-Philippe; Daniel , Jérémie; Cudel , Christophe; Ouamri , Abdelaziz

    2014-01-01

    International audience; —This paper presents an object tracking algorithm using belief functions applied to vision-based traffic sign recognition systems. This algorithm tracks detected sign candidates over time in order to reduce false positives due to data fusion formalization. In the first stage, regions of interest (ROIs) are detected and combined using the transferable belief model semantics. In the second stage, the local pignistic probability algorithm generates the associations maximi...

  15. Diffusion-weighted magnetic resonance imaging in the characterization of testicular germ cell neoplasms: Effect of ROI methods on apparent diffusion coefficient values and interobserver variability

    Energy Technology Data Exchange (ETDEWEB)

    Tsili, Athina C., E-mail: a_tsili@yahoo.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Ntorkou, Alexandra, E-mail: alexdorkou@hotmail.com [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Astrakas, Loukas, E-mail: astrakas@uoi.gr [Department of Medical Physics, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Xydis, Vasilis, E-mail: vxydis@cc.uoi.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Tsampalas, Stavros, E-mail: stamp@gmail.com [Department of Urology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Sofikitis, Nikolaos, E-mail: akrosnin@hotmail.com [Department of Urology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece); Argyropoulou, Maria I., E-mail: margyrop@cc.uoi.gr [Department of Clinical Radiology, Medical School, University of Ioannina, University Campus, 45110, Ioannina (Greece)

    2017-04-15

    Highlights: • Seminomas have lower mean ADC compared to NSGCNs. • Round ROI is accurate in characterizing TGCNS. • ROI shape has no significant effect on interobserver variability. - Abstract: Introduction: To evaluate the difference in apparent diffusion coefficient (ADC) measurements at diffusion-weighted (DW) magnetic resonance imaging of differently shaped regions-of-interest (ROIs) in testicular germ cell neoplasms (TGCNS), the diagnostic ability of differently shaped ROIs in differentiating seminomas from nonseminomatous germ cell neoplasms (NSGCNs) and the interobserver variability. Materials and methods: Thirty-three TGCNs were retrospectively evaluated. Patients underwent MR examinations, including DWI on a 1.5-T MR system. Two observers measured mean tumor ADCs using four distinct ROI methods: round, square, freehand and multiple small, round ROIs. The interclass correlation coefficient was analyzed to assess interobserver variability. Statistical analysis was used to compare mean ADC measurements among observers, methods and histologic types. Results: All ROI methods showed excellent interobserver agreement, with excellent correlation (P < 0.001). Multiple, small ROIs provided the lower mean ADC in TGCNs. Seminomas had lower mean ADC compared to NSGCNs for each ROI method (P < 0.001). Round ROI proved the most accurate method in characterizing TGCNS. Conclusion: Interobserver variability in ADC measurement is excellent, irrespective of the ROI shape. Multiple, small round ROIs and round ROI proved the more accurate methods for ADC measurement in the characterization of TGCNs and in the differentiation between seminomas and NSGCNs, respectively.

  16. Oil palm fresh fruit bunch ripeness classification based on rule- based expert system of ROI image processing technique results

    International Nuclear Information System (INIS)

    Alfatni, M S M; Shariff, A R M; Marhaban, M H; Shafie, S B; Saaed, O M B; Abdullah, M Z; BAmiruddin, M D

    2014-01-01

    There is a processing need for a fast, easy and accurate classification system for oil palm fruit ripeness. Such a system will be invaluable to farmers and plantation managers who need to sell their oil palm fresh fruit bunch (FFB) for the mill as this will avoid disputes. In this paper,a new approach was developed under the name of expert rules-based systembased on the image processing techniques results of thethree different oil palm FFB region of interests (ROIs), namely; ROI1 (300x300 pixels), ROI2 (50x50 pixels) and ROI3 (100x100 pixels). The results show that the best rule-based ROIs for statistical colour feature extraction with k-nearest neighbors (KNN) classifier at 94% were chosen as well as the ROIs that indicated results higher than the rule-based outcome, such as the ROIs of statistical colour feature extraction with artificial neural network (ANN) classifier at 94%, were selected for further FFB ripeness inspection system

  17. Application of a semi-automatic ROI setting system for brain PET images to animal PET studies

    International Nuclear Information System (INIS)

    Kuge, Yuji; Akai, Nobuo; Tamura, Koji

    1998-01-01

    ProASSIST, a semi-automatic ROI (region of interest) setting system for human brain PET images, has been modified for use with the canine brain, and the performance of the obtained system was evaluated by comparing the operational simplicity for ROI setting and the consistency of ROI values obtained with those by a conventional manual procedure. Namely, we created segment maps for the canine brain by making reference to the coronal section atlas of the canine brain by Lim et al., and incorporated them into the ProASSIST system. For the performance test, CBF (cerebral blood flow) and CMRglc (cerebral metabolic rate in glucose) images in dogs with or without focal cerebral ischemia were used. In ProASSIST, brain contours were defined semiautomatically. In the ROI analysis of the test image, manual modification of the contour was necessary in half cases examined (8/16). However, the operation was rather simple so that the operation time per one brain section was significantly shorter than that in the manual operation. The ROI values determined by the system were comparable with those by the manual procedure, confirming the applicability of the system to these animal studies. The use of the system like the present one would also merit the more objective data acquisition for the quantitative ROI analysis, because no manual procedure except for some specifications of the anatomical features is required for ROI setting. (author)

  18. Feeding biology of the introduced fish roi, and its impact on Hawaiian reef fishes, January 2004 and January 2005, (NODC Accession 0002172)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Feeding biology of the introduced fish roi (Cephalopholis argus), and its impact on Hawaiian reef fishes and fisheries between January 2004 and January 2005. Roi...

  19. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

    Science.gov (United States)

    Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

    2017-04-12

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

  20. Transcriptome, expression, and activity analyses reveal a vital heat shock protein 70 in the stress response of stony coral Pocillopora damicornis.

    Science.gov (United States)

    Zhang, Yidan; Zhou, Zhi; Wang, Lingui; Huang, Bo

    2018-02-12

    Coral bleaching occurs worldwide with increasing frequencies and intensities, which is caused by the stress response of stony coral to environmental change, especially increased sea surface temperature. In the present study, transcriptome, expression, and activity analyses were employed to illustrate the underlying molecular mechanisms of heat shock protein 70 (HSP70) in the stress response of coral to environmental changes. The domain analyses of assembled transcripts revealed 30 HSP70 gene contigs in stony coral Pocillopora damicornis. One crucial HSP70 (PdHSP70) was observed, whose expressions were induced by both elevated temperature and ammonium after expression difference analysis. The complete complementary DNA (cDNA) sequence of PdHSP70 was identified, which encoded a polypeptide of 650 amino acids with a molecular weight of 71.93 kDa. The deduced amino acid sequence of PdHSP70 contained a HSP70 domain (from Pro8 to Gly616), and it shared the highest similarity (95%) with HSP70 from Stylophora pistillata. The expression level of PdHSP70 gene increased significantly at 12 h, and returned to the initial level at 24 h after the stress of high temperature (32 °C). The cDNA fragment encoding the mature peptide of PdHSP70 was recombined and expressed in the prokaryotic expression system. The ATPase activity of recombinant PdHSP70 protein was determined, and it did not change significantly in a wide range of temperature from 25 to 40 °C. These results collectively suggested that PdHSP70 was a vital heat shock protein 70 in the stony coral P. damicornis, whose mRNA expression could be induced by diverse environmental stress and whose activity could remain stable under heat stress. PdHSP70 might be involved in the regulation of the bleaching owing to heat stress in the stony coral P. damicornis.

  1. Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

    Directory of Open Access Journals (Sweden)

    Alexander Lichius

    Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

  2. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

    Science.gov (United States)

    Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

    2018-02-01

    Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

  3. Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii

    Directory of Open Access Journals (Sweden)

    Johnson David R

    2011-11-01

    opposite effect and decreased after perturbation with PEG8000. Conclusions A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

  4. Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

    Science.gov (United States)

    King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

    2006-12-01

    Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

  5. Possible Factors Promoting Car Evacuation in the 2011 Tohoku Tsunami Revealed by Analysing a Large-Scale Questionnaire Survey in Kesennuma City

    Directory of Open Access Journals (Sweden)

    Fumiyasu Makinoshima

    2017-11-01

    Full Text Available Excessive car evacuation can cause severe traffic jams that can lead to large numbers of casualties during tsunami disasters. Investigating the possible factors that lead to unnecessary car evacuation can ensure smoother tsunami evacuations and mitigate casualty damages in future tsunami events. In this study, we quantitatively investigated the possible factors that promote car evacuation, including both necessary and unnecessary usages, by statistically analysing a large amount of data on actual tsunami evacuation behaviours surveyed in Kesennuma, where devastating damage occurred during the 2011 Tohoku Tsunami. A straightforward statistical analysis revealed a high percentage of car evacuations (approx. 50%; however, this fraction includes a high number of unnecessary usage events that were distinguished based on mode choice reasons. In addition, a binary logistic regression was conducted to quantitatively evaluate the effects of several factors and to identify the dominant factor that affected evacuation mode choice. The regression results suggested that the evacuation distance was the dominant factor for choosing car evacuation relative to other factors, such as age and sex. The cross-validation test of the regression model demonstrated that the considered factors were useful for decision making and the prediction of evacuation mode choice in the target area.

  6. Divergent Significance of Bone Mineral Density Changes in Aging Depending on Sites and Sex Revealed through Separate Analyses of Bone Mineral Content and Area

    Directory of Open Access Journals (Sweden)

    Yasumoto Matsui

    2012-01-01

    Full Text Available Bone mineral density (aBMD is equivalent to bone mineral content (BMC divided by area. We rechecked the significance of aBMD changes in aging by examining BMC and area separately. Subjects were 1167 community-dwelling Japanese men and women, aged 40–79 years. ABMDs of femoral neck and lumbar spine were assessed by DXA twice, at 6-year intervals. The change rates of BMC and area, as well as aBMD, were calculated and described separately by the age stratum and by sex. In the femoral neck region, aBMDs were significantly decreased in all age strata by an increase in area as well as BMC loss in the same pattern in both sexes. In the lumbar spine region, aBMDs decreased until the age of 60 in women, caused by the significant BMC decrease accompanying the small area change. Very differently in men, aBMDs increased after their 50s due to BMC increase, accompanied by an area increase. Separate analyses of BMC and area change revealed that the significance of aBMD changes in aging was very divergent among sites and between sexes. This may explain in part the dissociation of aBMD change and bone strength, suggesting that we should be more cautious when interpreting the meaning of aBMD change.

  7. Influence of ROI selection on Resting Functional Connectivity: An Individualized Approach for Resting fMRI Analysis

    Directory of Open Access Journals (Sweden)

    William Seunghyun Sohn

    2015-08-01

    Full Text Available The differences in how our brain is connected are often thought to reflect the differences in our individual personalities and cognitive abilities. Individual differences in brain connectivity has long been recognized in the neuroscience community however it has yet to manifest itself in the methodology of resting state analysis. This is evident as previous studies use the same region of interest (ROIs for all subjects. In this paper we demonstrate that the use of ROIs which are standardized across individuals leads to inaccurate calculations of functional connectivity. We also show that this problem can be addressed by taking an individualized approach by using subject-specific ROIs. Finally we show that ROI selection can affect the way we interpret our data by showing different changes in functional connectivity with ageing.

  8. Cephalopholis argus fish census and assemblage data from the West Hawaii Roi Removal Project 2010-2012 (NODC Accession 0099263)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project examined the results of the field manipulative experiment that has been set up to test the ecological effects of introduced roi on reef fish...

  9. Examining Brain Morphometry Associated with Self-Esteem in Young Adults Using Multilevel-ROI-Features-Based Classification Method

    Directory of Open Access Journals (Sweden)

    Bo Peng

    2017-05-01

    Full Text Available Purpose: This study is to exam self-esteem related brain morphometry on brain magnetic resonance (MR images using multilevel-features-based classification method.Method: The multilevel region of interest (ROI features consist of two types of features: (i ROI features, which include gray matter volume, white matter volume, cerebrospinal fluid volume, cortical thickness, and cortical surface area, and (ii similarity features, which are based on similarity calculation of cortical thickness between ROIs. For each feature type, a hybrid feature selection method, comprising of filter-based and wrapper-based algorithms, is used to select the most discriminating features. ROI features and similarity features are integrated by using multi-kernel support vector machines (SVMs with appropriate weighting factor.Results: The classification performance is improved by using multilevel ROI features with an accuracy of 96.66%, a specificity of 96.62%, and a sensitivity of 95.67%. The most discriminating ROI features that are related to self-esteem spread over occipital lobe, frontal lobe, parietal lobe, limbic lobe, temporal lobe, and central region, mainly involving white matter and cortical thickness. The most discriminating similarity features are distributed in both the right and left hemisphere, including frontal lobe, occipital lobe, limbic lobe, parietal lobe, and central region, which conveys information of structural connections between different brain regions.Conclusion: By using ROI features and similarity features to exam self-esteem related brain morphometry, this paper provides a pilot evidence that self-esteem is linked to specific ROIs and structural connections between different brain regions.

  10. Cerebral blood flow SPET in transient global amnesia with automated ROI analysis by 3DSRT

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Ryo [Division of Nuclear Medicine, Nishi-Kobe Medical Center, Kohjidai 5-7-1, 651-2273, Nishi-ku, Kobe-City, Hyogo (Japan); Matsuda, Hiroshi [Department of Radiology, National Center Hospital for Mental, Nervous and Muscular Disorders, National Center of Neurology and Psychiatry, Tokyo (Japan); Yoshioka, Katsunori [Daiichi Radioisotope Laboratories, Ltd., Tokyo (Japan); Yonekura, Yoshiharu [Biomedical Imaging Research Center, University of Fukui, Fukui (Japan)

    2004-04-01

    The aim of this study was to determine the areas involved in episodes of transient global amnesia (TGA) by calculation of cerebral blood flow (CBF) using 3DSRT, fully automated ROI analysis software which we recently developed. Technetium-99m l,l-ethyl cysteinate dimer single-photon emission tomography ({sup 99m}Tc-ECD SPET) was performed during and after TGA attacks on eight patients (four men and four women; mean study interval, 34 days). The SPET images were anatomically standardized using SPM99 followed by quantification of 318 constant ROIs, grouped into 12 segments (callosomarginal, precentral, central, parietal, angular, temporal, posterior cerebral, pericallosal, lenticular nucleus, thalamus, hippocampus and cerebellum), in each hemisphere to calculate segmental CBF (sCBF) as the area-weighted mean value for each of the respective 12 segments based on the regional CBF in each ROI. Correlation of the intra- and post-episodic sCBF of each of the 12 segments of the eight patients was estimated by scatter-plot graphical analysis and Pearson's correlation test with Fisher's Z-transformation. For the control, {sup 99m}Tc-ECD SPET was performed on eight subjects (three men and five women) and repeated within 1 month; the correlation between the first and second sCBF values of each of the 12 segments was evaluated in the same way as for patients with TGA. Excellent reproducibility between the two sCBF values was found in all 12 segments of the control subjects. However, a significant correlation between intra- and post-episodic sCBF was not shown in the thalamus or angular segments of TGA patients. The present study was preliminary, but at least suggested that thalamus and angular regions are closely involved in the symptoms of TGA. (orig.)

  11. Cerebral blood flow SPET in transient global amnesia with automated ROI analysis by 3DSRT

    International Nuclear Information System (INIS)

    Takeuchi, Ryo; Matsuda, Hiroshi; Yoshioka, Katsunori; Yonekura, Yoshiharu

    2004-01-01

    The aim of this study was to determine the areas involved in episodes of transient global amnesia (TGA) by calculation of cerebral blood flow (CBF) using 3DSRT, fully automated ROI analysis software which we recently developed. Technetium-99m l,l-ethyl cysteinate dimer single-photon emission tomography ( 99m Tc-ECD SPET) was performed during and after TGA attacks on eight patients (four men and four women; mean study interval, 34 days). The SPET images were anatomically standardized using SPM99 followed by quantification of 318 constant ROIs, grouped into 12 segments (callosomarginal, precentral, central, parietal, angular, temporal, posterior cerebral, pericallosal, lenticular nucleus, thalamus, hippocampus and cerebellum), in each hemisphere to calculate segmental CBF (sCBF) as the area-weighted mean value for each of the respective 12 segments based on the regional CBF in each ROI. Correlation of the intra- and post-episodic sCBF of each of the 12 segments of the eight patients was estimated by scatter-plot graphical analysis and Pearson's correlation test with Fisher's Z-transformation. For the control, 99m Tc-ECD SPET was performed on eight subjects (three men and five women) and repeated within 1 month; the correlation between the first and second sCBF values of each of the 12 segments was evaluated in the same way as for patients with TGA. Excellent reproducibility between the two sCBF values was found in all 12 segments of the control subjects. However, a significant correlation between intra- and post-episodic sCBF was not shown in the thalamus or angular segments of TGA patients. The present study was preliminary, but at least suggested that thalamus and angular regions are closely involved in the symptoms of TGA. (orig.)

  12. Les marbriers des Bâtiments du roi : organisation et réalisations

    Directory of Open Access Journals (Sweden)

    Sophie Mouquin

    2012-09-01

    Full Text Available Matériau noble, symbole de beauté, de pouvoir et d’éternité, le marbre est sous l’Ancien Régime, et particulièrement sous le règne de Louis XIV et la Régence, un matériau royal. Toutes les maisons royales reçoivent pavements, lambris et cheminées réalisés dans des marbres aux couleurs vives, provenant pour la plupart de carrières du royaume. Leur origine répond ainsi à la politique royale du marbre français que les directeurs des Bâtiments du roi s’efforcent de mettre en place et de consolider. Tous ces travaux ont leurs artisans : Derbais, Dezègre, Pasquier, Ménard, Mathaut, Lisquy, Tarlé, Trouard, etc., autant de noms indissociables des réalisations marbrières dans les maisons royales, mais si souvent oubliés. Ils jouent pourtant, dans ce domaine, un rôle de premier plan à tous niveaux, de la carrière au chantier. L’exposé présente l’organisation de ce corps de métier, sa place au sein des Bâtiments du roi et son rôle dans la politique marbrière. Il s’appuie sur les principales réalisations versaillaises, comme l’appartement des bains, l’escalier des Ambassadeurs, l’escalier de la Reine, la galerie des Glaces, le salon d’Hercule, les cheminées et les lambris des appartements du Roi et de la Reine. Il évoquera le chantier des jardins avec le bosquet de la Colonnade et d’autres bosquets.

  13. A multilevel-ROI-features-based machine learning method for detection of morphometric biomarkers in Parkinson's disease.

    Science.gov (United States)

    Peng, Bo; Wang, Suhong; Zhou, Zhiyong; Liu, Yan; Tong, Baotong; Zhang, Tao; Dai, Yakang

    2017-06-09

    Machine learning methods have been widely used in recent years for detection of neuroimaging biomarkers in regions of interest (ROIs) and assisting diagnosis of neurodegenerative diseases. The innovation of this study is to use multilevel-ROI-features-based machine learning method to detect sensitive morphometric biomarkers in Parkinson's disease (PD). Specifically, the low-level ROI features (gray matter volume, cortical thickness, etc.) and high-level correlative features (connectivity between ROIs) are integrated to construct the multilevel ROI features. Filter- and wrapper- based feature selection method and multi-kernel support vector machine (SVM) are used in the classification algorithm. T1-weighted brain magnetic resonance (MR) images of 69 PD patients and 103 normal controls from the Parkinson's Progression Markers Initiative (PPMI) dataset are included in the study. The machine learning method performs well in classification between PD patients and normal controls with an accuracy of 85.78%, a specificity of 87.79%, and a sensitivity of 87.64%. The most sensitive biomarkers between PD patients and normal controls are mainly distributed in frontal lobe, parental lobe, limbic lobe, temporal lobe, and central region. The classification performance of our method with multilevel ROI features is significantly improved comparing with other classification methods using single-level features. The proposed method shows promising identification ability for detecting morphometric biomarkers in PD, thus confirming the potentiality of our method in assisting diagnosis of the disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer).

    Science.gov (United States)

    Drews, Anna; Strandh, Maria; Råberg, Lars; Westerdahl, Helena

    2017-06-26

    The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non

  15. Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

    Directory of Open Access Journals (Sweden)

    Xiaoyan Yue

    2018-05-01

    Full Text Available Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP, Chinese white pear (CWP, Chinese sand pear (CSP, and Ussurian pear (UP, but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR markers and two non-coding chloroplast DNA (cpDNA regions (trnL-trnF and accD-psaI. High levels of genetic diversity were detected for both nSSRs (HE = 0.744 and cpDNAs (Hd = 0.792. The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a JPs; (b cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be

  16. Family-based Association Analyses of Imputed Genotypes Reveal Genome-Wide Significant Association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

    Science.gov (United States)

    Herold, Christine; Hooli, Basavaraj V.; Mullin, Kristina; Liu, Tian; Roehr, Johannes T; Mattheisen, Manuel; Parrado, Antonio R.; Bertram, Lars; Lange, Christoph; Tanzi, Rudolph E.

    2015-01-01

    The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1 and PSEN2 cause a subset of early-onset familial Alzheimer's disease (EOFAD). On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ε4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3,500 subjects from 1,070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value = 3.98·10−08), rs1347297 in the gene OSBPL6 (P-value = 4.53·10−08), and rs1513625 near PDCL3 (P-value = 4.28·10−08). In addition, rs72953347 in OSBPL6 (P-value = 6.36·10−07) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value: 4.76·10−07; rs62400067, P-value: 3.54·10−07). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance. PMID:26830138

  17. An alternative to γ histograms for ROI-based quantitative dose comparisons

    International Nuclear Information System (INIS)

    Dvorak, P

    2009-01-01

    An alternative to gamma (γ) histograms for ROI-based quantitative comparisons of dose distributions using the γ concept is proposed. The method provides minimum values of dose difference and distance-to-agreement such that a pre-set fraction of the region of interest passes the γ test. Compared to standard γ histograms, the method provides more information in terms of pass rate per γ calculation. This is achieved at negligible additional calculation cost and without loss of accuracy. The presented method is proposed as a useful and complementary alternative to standard γ histograms, increasing both the quantity and quality of information for use in acceptance or rejection decisions. (note)

  18. Diabetes and Obesity as Independent Risk Factors for Osteoporosis: Updated Results from the ROIS/EMEROS Registry in a Population of Five Thousand Post-Menopausal Women Living in a Region Characterized by Heavy Environmental Pressure.

    Science.gov (United States)

    Neglia, Cosimo; Argentiero, Alberto; Chitano, Giovanna; Agnello, Nadia; Ciccarese, Roberta; Vigilanza, Antonella; Pantile, Valerio; Argentiero, Domenico; Quarta, Raffaele; Rivezzi, Matteo; Di Tanna, Gian Luca; Di Somma, Carolina; Migliore, Alberto; Iolascon, Giovanni; Gimigliano, Francesca; Distante, Alessandro; Piscitelli, Prisco

    2016-11-01

    Objectives : We aimed to analyze bone mineralization and the effect of different risk factors for osteoporosis in postmenopausal women. Methods : We found 4909 postmenopausal subjects within ≥10,000 records from the ROIS/EMEROS (Ionian and Salento Osteoporosis Registry/Euro Mediterranean Registry of Osteoporosis) registry, a population study carried out in an area characterized by heavy environmental pressure between Brindisi and Taranto from 2009 to 2016. All subjects were assessed via phalangeal quantitative ultrasound (QUS) to evaluate their bone mineralization (assessed via amplitude dependent speed of sound (AD-SoS)) and the association between demineralization and the presence of other conditions or risk factors. Results : Mean age was 64 ± 9.5 years and mean body mass index (BMI) was 28.7 ± 3.5 kg/m². Pearson correlation analyses revealed a negative association between bone mineralization (AD-SoS) and BMI ( p osteoporosis (adjusted for age, physical activity, and the use of drugs known to increase the risk of fractures) in subjects with diabetes and obesity: 1.39 (confidence interval (CI): 1.05-1.83) and 1.46 (CI: 1.20-1.78), respectively. A statistically significant linear trend of higher ORs of osteoporosis was found for increasing values of BMI. Conclusions : Our study confirmed the high impact of obesity and type 1 and type 2 diabetes on osteoporosis.

  19. Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya.

    Science.gov (United States)

    Khanal, Laxman; Chalise, Mukesh K; He, Kai; Acharya, Bipin K; Kawamoto, Yoshi; Jiang, Xuelong

    2018-03-01

    Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion. © 2018 Wiley Periodicals, Inc.

  20. Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

    Science.gov (United States)

    Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

    2013-10-01

    Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

  1. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  2. Effects of ROI definition and reconstruction method on quantitative outcome and applicability in a response monitoring trial

    International Nuclear Information System (INIS)

    Krak, Nanda C.; Boellaard, R.; Hoekstra, Otto S.; Hoekstra, Corneline J.; Twisk, Jos W.R.; Lammertsma, Adriaan A.

    2005-01-01

    Quantitative measurement of tracer uptake in a tumour can be influenced by a number of factors, including the method of defining regions of interest (ROIs) and the reconstruction parameters used. The main purpose of this study was to determine the effects of different ROI methods on quantitative outcome, using two reconstruction methods and the standard uptake value (SUV) as a simple quantitative measure of FDG uptake. Four commonly used methods of ROI definition (manual placement, fixed dimensions, threshold based and maximum pixel value) were used to calculate SUV (SUV [MAN] , SUV 15 mm , SUV 50 , SUV 75 and SUV max , respectively) and to generate ''metabolic'' tumour volumes. Test-retest reproducibility of SUVs and of ''metabolic'' tumour volumes and the applicability of ROI methods during chemotherapy were assessed. In addition, SUVs calculated on ordered subsets expectation maximisation (OSEM) and filtered back-projection (FBP) images were compared. ROI definition had a direct effect on quantitative outcome. On average, SUV [MAN] , SUV 15 mm , SUV 50 and SUV 75 , were respectively 48%, 27%, 34% and 15% lower than SUV max when calculated on OSEM images. No statistically significant differences were found between SUVs calculated on OSEM and FBP reconstructed images. Highest reproducibility was found for SUV 15 mm and SUV [MAN] (ICC 0.95 and 0.94, respectively) and for ''metabolic'' volumes measured with the manual and 50% threshold ROIs (ICC 0.99 for both). Manual, 75% threshold and maximum pixel ROIs could be used throughout therapy, regardless of changes in tumour uptake or geometry. SUVs showed the same trend in relative change in FDG uptake after chemotherapy, irrespective of the ROI method used. The method of ROI definition has a direct influence on quantitative outcome. In terms of simplicity, user-independence, reproducibility and general applicability the threshold-based and fixed dimension methods are the best ROI methods. Threshold methods are in

  3. Study of regional cerebral blood flow in obsessive compulsive disorder patients with SPM and ROI method

    International Nuclear Information System (INIS)

    Li Peiyong; Jiang Xufeng; Zhang Liying; Guo Wanhua; Zhu Chengmo

    2002-01-01

    Objective: To investigate the alternations in regional cerebral blood flow (rCBF) in obsessive compulsive disorder (OCD) patients using statistical parametric mapping (SPM). Methods: rCBF measurements using 99 Tc m -ethyl cysteinate dimer (ECD) SPECT was performed on 14 OCD patients and 23 age-matched healthy volunteers. The rCBF distribution was compared between these two groups with SPM under the conditions of increased and decreased perfusion, and with regions of interest (ROIs) using cerebral template. P value was set at 0.01 level. Results: SPM analysis showed that rCBF decreased in cerebral areas including bilateral putamen, superior temporal gyrus and precuneus, and right orbital gyrus, superior and middle frontal gyrus, and left temporo-occipital lobule and superior parietal gyrus, and vermis. rCBF was also increased in left inferior frontal gyrus and posterior cingulate gyrus. With ROIs method, rCBF was decreased in right anterior frontal, temporo-parietal lobule and left temporo-occipital lobule. Conclusions: The study supports the viewpoint that rCBF abnormality of fronto-striatal circuits is involved in OCD patients. SPM method is a forceful tool in analyzing cerebral regional characters

  4. Computerized analysis of mammographic parenchymal patterns for assessing breast cancer risk: Effect of ROI size and location

    International Nuclear Information System (INIS)

    Li Hui; Giger, Maryellen L.; Huo Zhimin; Olopade, Olufunmilayo I.; Lan Li; Weber, Barbara L.; Bonta, Ioana

    2004-01-01

    The long-term goal of our research is to develop computerized radiographic markers for assessing breast density and parenchymal patterns that may be used together with clinical measures for determining the risk of breast cancer and assessing the response to preventive treatment. In our earlier studies, we found that women at high risk tended to have dense breasts with mammographic patterns that were coarse and low in contrast. With our method, computerized texture analysis is performed on a region of interest (ROI) within the mammographic image. In our current study, we investigate the effect of ROI size and ROI location on the computerized texture features obtained from 90 subjects (30 BRCA1/BRCA2 gene-mutation carriers and 60 age-matched women deemed to be at low risk for breast cancer). Mammograms were digitized at 0.1 mm pixel size and various ROI sizes were extracted from different breast regions in the craniocaudal (CC) view. Seventeen features, which characterize the density and texture of the parenchymal patterns, were extracted from the ROIs on these digitized mammograms. Stepwise feature selection and linear discriminant analysis were applied to identify features that differentiate between the low-risk women and the BRCA1/BRCA2 gene-mutation carriers. ROC analysis was used to assess the performance of the features in the task of distinguishing between these two groups. Our results show that there was a statistically significant decrease in the performance of the computerized texture features, as the ROI location was varied from the central region behind the nipple. However, we failed to show a statistically significant decrease in the performance of the computerized texture features with decreasing ROI size for the range studied

  5. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Kwang-Soo, E-mail: shinks@dju.kr [Division of Life Science, Daejeon University, Daejeon, 300-716 (Korea, Republic of); Kim, Young Hwan [Biomedical Omics Team, Korea Basic Science Institute (KBSI), Ohcang, 368-883 (Korea, Republic of); Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 305-333 (Korea, Republic of); Yu, Jae-Hyuk, E-mail: jyu1@wisc.edu [Departments of Bacteriology and Genetics, The University of Wisconsin–Madison, Madison, WI, 53706 (United States)

    2015-07-31

    The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus.

  6. Medulloblastoma in China: clinicopathologic analyses of SHH, WNT, and non-SHH/WNT molecular subgroups reveal different therapeutic responses to adjuvant chemotherapy.

    Directory of Open Access Journals (Sweden)

    Zhen-Yu Zhang

    Full Text Available Medulloblastoma (MB is one of the most common primary central nervous system tumors in children. Data is lacking of a large cohort of medulloblastoma patients in China. Also, our knowledge on the sensitivity of different molecular subgroups of MB to adjuvant radiation therapy (RT or chemotherapy (CHT is still limited. The authors performed a retrospective study of 173 medulloblastoma patients treated at two institutions from 2002 to 2011. Formalin-fixed paraffin embedded (FFPE tissues were available in all the cases and sections were stained to classify histological and molecular subgroups. Univariate and multivariate analyses were used to investigate prognostic factors. Of 173 patients, there were 118 children and 55 adults, 112 males and 61 females. Estimated 5-year overall survival (OS rates for all patients, children and adults were 52%, 48% and 63%, respectively. After multivariate analysis, postoperative primary radiation therapy (RT and chemotherapy (CHT were revealed as favorable prognostic factors influencing OS and EFS. Postoperative primary chemotherapy (CHT was found significantly improving the survival of children (p<0.001 while it was not a significant prognostic factor for adult patients. Moreover, patients in WNT subtype had better OS (p = 0.028 than others (SHH and Non-SHH/WNT subtypes given postoperative adjuvant therapies. Postoperative primary RT was found to be a strong prognostic factor influencing the survival in all histological and molecular subgroups (p<0.001. Postoperative primary CHT was found significantly to influence the survival of classic medulloblastoma (CMB (OS p<0.001, EFS p<0.001, SHH subgroup (OS p = 0.020, EFS p = 0.049 and WNT subgroup (OS p = 0.003, EFS p = 0.016 but not in desmoplastic/nodular medulloblastoma (DMB (OS p = 0.361, EFS p = 0.834 and Non-SHH/WNT subgroup (OS p = 0.127, EFS p = 0.055. Our study showed postoperative primary CHT significantly influence the

  7. Holocene climate variability in arid Central Asia as revealed from high-resolution sedimentological and geochemical analyses of laminated sediments from Lake Chatyr Kol (Central Tian Shan, Kyrgyzstan)

    Science.gov (United States)

    Lauterbach, S.; Plessen, B.; Dulski, P.; Mingram, J.; Prasad, S.

    2013-12-01

    A pronounced trend from a predominantly wet climate during the early Holocene towards significantly drier conditions since the mid-Holocene, mainly attributed to the weakening of the Asian summer monsoon (ASM), is documented in numerous palaeoclimate records from the monsoon-influenced parts of Asia, e.g. the Tibetan Plateau and north- and southeastern China. In contrast, climate in the adjacent regions of mid-latitude arid Central Asia, located north and northwest of the Tibetan Plateau, is supposed to have been characterized by pronounced dry conditions during the early Holocene, wet conditions during the mid-Holocene and a rather moderate drying during the late Holocene, which is mainly attributed to the complex interplay between the mid-latitude Westerlies and the ASM. However, although mid-latitude Central Asia thus might represent a key region for the understanding of teleconnections between the ASM system and the Westerlies, knowledge about past climate development in this region is still ambiguous due to the limited number of high-resolution palaeoclimate records. Hence, new well-dated and highly resolved palaeoclimate records from this region are expected to provide important information about spatio-temporal changes in the regional interplay between Westerlies and ASM and thus aid the understanding of global climate teleconnections. As a part of the project CADY (Central Asian Climate Dynamics), aiming at reconstructing past climatic and hydrological variability in Central Asia, a sediment core of about 6.25 m length has been recovered from alpine Lake Chatyr Kol (40°36' N, 75°14' E, 3530 m a. s. l., surface area ~170 km2, maximum depth ~20 m), located in the Central Tian Shan of Kyrgyzstan. Sediment microfacies analysis on large-scale petrographic thin sections reveals continuously sub-mm scale laminated sediments throughout the record except for the uppermost ca. 60 cm. Microsedimentological characterization of these laminae, which are most probably

  8. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

    International Nuclear Information System (INIS)

    Shin, Kwang-Soo; Kim, Young Hwan; Yu, Jae-Hyuk

    2015-01-01

    The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus

  9. Gradual aridification of the Sahara during the last 11,000 years revealed by plant wax δD analyses of Lake Yoa (Chad)

    Science.gov (United States)

    Rethemeyer, Janet; Kröpelin, Stefan; Karls, Jens; Thienemann, Matthias; Melles, Martin; Schefuß, Enno

    2014-05-01

    It is still an ongoing debate whether the transition of the last 'green Sahara' period to today's large desert during the Holocene, the African Humid Period (AHP), was a progressive or an abrupt change in hydrological conditions. Several climate records mainly from East Africa suggest a rapid decline of moisture availability at the end of the AHP including new data from a marine sequence off the Horn of Africa (Tierney & deMenocal, 2013). Other archives including sedimentological, geochemical and palynological data from the central North African Lakes Chad and Lake Yoa point to a gradual rather than an abrupt transition near 5,000 years ago (Amaral et al., 2013; Kröpelin et al., 2008). The discrepancy of the available paleo-hydrological reconstructions underline the importance of proxy parameters directly related to hydrological conditions for accurate assessment of continental rainfall changes. Here, we present the first molecular-isotopic data from Lake Yoa documenting the hydrologic evolution over the entire Holocene. Compound-specific carbon and hydrogen isotope analyses were performed on long-chain n-alkanes. Our data indicate relative high but variable contributions of plant-derived long-chain n-alkanes carrying a distinct leaf-wax signature, i.e., a high Carbon Preference Index (CPI). A trend towards higher CPI values since 7,300 years ago suggests declining soil degradation and vegetation cover under increasingly drier conditions. In parallel, the average-chain-length of the long-chain n-alkanes increases gradually towards the present implying higher relative contributions from grasses. Compound-specific carbon isotope data confirm this finding, indicating a mixed C3/C4 contribution in the early and mid-Holocene changing towards a C4-grass dominated vegetation in the late Holocene. Most importantly, compound-specific hydrogen isotope data reveal a continuous increase from 8,100 years ago towards the present, reflecting a gradual aridification. The large

  10. A Joint Watermarking and ROI Coding Scheme for Annotating Traffic Surveillance Videos

    Directory of Open Access Journals (Sweden)

    Su Po-Chyi

    2010-01-01

    Full Text Available We propose a new application of information hiding by employing the digital watermarking techniques to facilitate the data annotation in traffic surveillance videos. There are two parts in the proposed scheme. The first part is the object-based watermarking, in which the information of each vehicle collected by the intelligent transportation system will be conveyed/stored along with the visual data via information hiding. The scheme is integrated with H.264/AVC, which is assumed to be adopted by the surveillance system, to achieve an efficient implementation. The second part is a Region of Interest (ROI rate control mechanism for encoding traffic surveillance videos, which helps to improve the overall performance. The quality of vehicles in the video will be better preserved and a good rate-distortion performance can be attained. Experimental results show that this potential scheme works well in traffic surveillance videos.

  11. Implementasi CMMI dalam Sebuah Organisasi Pengembang Software untuk Mencapai Return on Investment (ROI yang Diinginkan

    Directory of Open Access Journals (Sweden)

    Ikrar Adinata Arin

    2012-06-01

    Full Text Available The main mechanism to achieve a level of maturity in the organization of software developers is always focused, structured and consistent in carrying out work procedures of a quality standard applied. This article offers readers an approach and discourse of using CMMI (Capability Maturity Model Integrated concept thatgives a positive impact on development of organizational business in a software developer. The goals of CMMI are getting the best product quality, increasing productivity, reducing operational costs as well as software development period and increasing customer’s satisfaction. Nevertheless, a leader of the organization shouldalso be able to take important decisions to be consistent with the estimated time of desired return on investment (ROI.

  12. Shifting from region of interest (ROI) to voxel-based analysis in human brain mapping

    International Nuclear Information System (INIS)

    Astrakas, Loukas G.; Argyropoulou, Maria I.

    2010-01-01

    Current clinical studies involve multidimensional high-resolution images containing an overwhelming amount of structural and functional information. The analysis of such a wealth of information is becoming increasingly difficult yet necessary in order to improve diagnosis, treatment and healthcare. Voxel-wise analysis is a class of modern methods of image processing in the medical field with increased popularity. It has replaced manual region of interest (ROI) analysis and has provided tools to make statistical inferences at voxel level. The introduction of voxel-based analysis software in all modern commercial scanners allows clinical use of these techniques. This review will explain the main principles, advantages and disadvantages behind these methods of image analysis. (orig.)

  13. The fast iris image clarity evaluation based on Tenengrad and ROI selection

    Science.gov (United States)

    Gao, Shuqin; Han, Min; Cheng, Xu

    2018-04-01

    In iris recognition system, the clarity of iris image is an important factor that influences recognition effect. In the process of recognition, the blurred image may possibly be rejected by the automatic iris recognition system, which will lead to the failure of identification. Therefore it is necessary to evaluate the iris image definition before recognition. Considered the existing evaluation methods on iris image definition, we proposed a fast algorithm to evaluate the definition of iris image in this paper. In our algorithm, firstly ROI (Region of Interest) is extracted based on the reference point which is determined by using the feature of the light spots within the pupil, then Tenengrad operator is used to evaluate the iris image's definition. Experiment results show that, the iris image definition algorithm proposed in this paper could accurately distinguish the iris images of different clarity, and the algorithm has the merit of low computational complexity and more effectiveness.

  14. Recovery from optic neuritis: an ROI-based analysis of LGN and visual cortical areas

    DEFF Research Database (Denmark)

    Korsholm, Kirsten; Madsen, Kristoffer Hougaard; Frederiksen, Jette L

    2007-01-01

    in the ROIs and compared activation during monocular stimulation of the affected and unaffected eye. In the acute phase the activation of LGN during visual stimulation of the affected eye was significantly reduced (P difference in LGN activation between...... the affected and unaffected eye diminished during recovery, and after 180 days the difference was no longer significant (P = 0.59). The decreased difference during recovery was mainly due to an increase in the fMRI signal when stimulating the affected eye, but included a component of a decreasing fMRI signal...... from LGN when stimulating the unaffected eye. In LOC, V1 and V2 activation during visual stimulation of the affected eye in the acute phase was significantly reduced (P difference diminished with no significant differences left after 180...

  15. Single-shot full resolution region-of-interest (ROI) reconstruction in image plane digital holographic microscopy

    Science.gov (United States)

    Singh, Mandeep; Khare, Kedar

    2018-05-01

    We describe a numerical processing technique that allows single-shot region-of-interest (ROI) reconstruction in image plane digital holographic microscopy with full pixel resolution. The ROI reconstruction is modelled as an optimization problem where the cost function to be minimized consists of an L2-norm squared data fitting term and a modified Huber penalty term that are minimized alternately in an adaptive fashion. The technique can provide full pixel resolution complex-valued images of the selected ROI which is not possible to achieve with the commonly used Fourier transform method. The technique can facilitate holographic reconstruction of individual cells of interest from a large field-of-view digital holographic microscopy data. The complementary phase information in addition to the usual absorption information already available in the form of bright field microscopy can make the methodology attractive to the biomedical user community.

  16. Distribution-analytical techniques in the study of AD/HD: Delta plot analyses reveal deficits in response inhibition that are eliminated by methylphenidate treatment

    NARCIS (Netherlands)

    Ridderinkhof, K.R.; Scheres, A.; Oosterlaan, J.; Sergeant, J.A.

    2005-01-01

    The authors highlight the utility of distribution-analytical techniques in the study of individual differences and clinical disorders. Cognitive deficits associated with attention-deficit/hyperactivity disorder (AD/HD) were examined by using delta-plot analyses of performance data (reaction time and

  17. Community microrespirometry and molecular analyses reveal a diverse energy economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin.

    Science.gov (United States)

    Murphy, Caitlin N; Dodsworth, Jeremy A; Babbitt, Aaron B; Hedlund, Brian P

    2013-05-01

    Microrespirometry showed that several organic and inorganic electron donors stimulated oxygen consumption in two ∼80°C springs. Sediment and planktonic communities were structurally and functionally distinct, and quantitative PCR revealed catabolically distinct subpopulations of Thermocrinis. This study suggests that a variety of chemolithotrophic metabolisms operate simultaneously in these springs.

  18. Automated PET-only quantification of amyloid deposition with adaptive template and empirically pre-defined ROI

    Science.gov (United States)

    Akamatsu, G.; Ikari, Y.; Ohnishi, A.; Nishida, H.; Aita, K.; Sasaki, M.; Yamamoto, Y.; Sasaki, M.; Senda, M.

    2016-08-01

    Amyloid PET is useful for early and/or differential diagnosis of Alzheimer’s disease (AD). Quantification of amyloid deposition using PET has been employed to improve diagnosis and to monitor AD therapy, particularly in research. Although MRI is often used for segmentation of gray matter and for spatial normalization into standard Montreal Neurological Institute (MNI) space where region-of-interest (ROI) template is defined, 3D MRI is not always available in clinical practice. The purpose of this study was to examine the feasibility of PET-only amyloid quantification with an adaptive template and a pre-defined standard ROI template that has been empirically generated from typical cases. A total of 68 subjects who underwent brain 11C-PiB PET were examined. The 11C-PiB images were non-linearly spatially normalized to the standard MNI T1 atlas using the same transformation parameters of MRI-based normalization. The automatic-anatomical-labeling-ROI (AAL-ROI) template was applied to the PET images. All voxel values were normalized by the mean value of cerebellar cortex to generate the SUVR-scaled images. Eleven typical positive images and eight typical negative images were normalized and averaged, respectively, and were used as the positive and negative template. Positive and negative masks which consist of voxels with SUVR  ⩾1.7 were extracted from both templates. Empirical PiB-prone ROI (EPP-ROI) was generated by subtracting the negative mask from the positive mask. The 11C-PiB image of each subject was non-rigidly normalized to the positive and negative template, respectively, and the one with higher cross-correlation was adopted. The EPP-ROI was then inversely transformed to individual PET images. We evaluated differences of SUVR between standard MRI-based method and PET-only method. We additionally evaluated whether the PET-only method would correctly categorize 11C-PiB scans as positive or negative. Significant correlation was observed between the SUVRs

  19. Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range.

    Science.gov (United States)

    Fernández-Mazuecos, Mario; Vargas, Pablo

    2013-06-01

    · The role of Quaternary climatic shifts in shaping the distribution of Linaria elegans, an Iberian annual plant, was investigated using species distribution modelling and molecular phylogeographical analyses. Three hypotheses are proposed to explain the Quaternary history of its mountain ring range. · The distribution of L. elegans was modelled using the maximum entropy method and projected to the last interglacial and to the last glacial maximum (LGM) using two different paleoclimatic models: the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC). Two nuclear and three plastid DNA regions were sequenced for 24 populations (119 individuals sampled). Bayesian phylogenetic, phylogeographical, dating and coalescent-based population genetic analyses were conducted. · Molecular analyses indicated the existence of northern and southern glacial refugia and supported two routes of post-glacial recolonization. These results were consistent with the LGM distribution as inferred under the CCSM paleoclimatic model (but not under the MIROC model). Isolation between two major refugia was dated back to the Riss or Mindel glaciations, > 100 kyr before present (bp). · The Atlantic distribution of inferred refugia suggests that the oceanic (buffered)-continental (harsh) gradient may have played a key and previously unrecognized role in determining Quaternary distribution shifts of Mediterranean plants. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  20. Integrated Marketing Communications (IMC) Variables That Influence Perceived Return on Investment (ROI) in Higher Education: Chief Marketing Officers' Perceptions

    Science.gov (United States)

    King, Adrienne L.

    2013-01-01

    This study examines the relationship of the level of Integrated Marketing Communications (IMC) implementation, level of open systems and change in state appropriations on perceived return on investment (ROI) in U.S. public higher education institutions (HEIs). Designed to provide HEI leaders with data to more accurately determine the best IMC…

  1. Lib-Value: Values, Outcomes, and Return on Investment of Academic Libraries, Phase III: ROI of the Syracuse University Library

    Science.gov (United States)

    Kingma, Bruce; McClure, Kathleen

    2015-01-01

    This study measures the return on investment (ROI) of the Syracuse University library. Faculty and students at Syracuse University were surveyed using contingent valuation methodology to measure their willingness to pay in time and money for the services of the academic library. Their travel time and use of the online library was measured to…

  2. Reliability evaluation of I-123 ADAM SPECT imaging using SPM software and AAL ROI methods

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Bang-Hung [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Tsai, Sung-Yi [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Imaging Medical, St.Martin De Porres Hospital, Chia-Yi, Taiwan (China); Wang, Shyh-Jen [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Su, Tung-Ping; Chou, Yuan-Hwa [Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan (China); Chen, Chia-Chieh [Institute of Nuclear Energy Research, Longtan, Taiwan (China); Chen, Jyh-Cheng, E-mail: jcchen@ym.edu.tw [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China)

    2011-08-21

    The level of serotonin was regulated by serotonin transporter (SERT), which is a decisive protein in regulation of serotonin neurotransmission system. Many psychiatric disorders and therapies were also related to concentration of cerebral serotonin. I-123 ADAM was the novel radiopharmaceutical to image SERT in brain. The aim of this study was to measure reliability of SERT densities of healthy volunteers by automated anatomical labeling (AAL) method. Furthermore, we also used statistic parametric mapping (SPM) on a voxel by voxel analysis to find difference of cortex between test and retest of I-123 ADAM single photon emission computed tomography (SPECT) images. Twenty-one healthy volunteers were scanned twice with SPECT at 4 h after intravenous administration of 185 MBq of {sup 123}I-ADAM. The image matrix size was 128x128 and pixel size was 3.9 mm. All images were obtained through filtered back-projection (FBP) reconstruction algorithm. Region of interest (ROI) definition was performed based on the AAL brain template in PMOD version 2.95 software package. ROI demarcations were placed on midbrain, pons, striatum, and cerebellum. All images were spatially normalized to the SPECT MNI (Montreal Neurological Institute) templates supplied with SPM2. And each image was transformed into standard stereotactic space, which was matched to the Talairach and Tournoux atlas. Then differences across scans were statistically estimated on a voxel by voxel analysis using paired t-test (population main effect: 2 cond's, 1 scan/cond.), which was applied to compare concentration of SERT between the test and retest cerebral scans. The average of specific uptake ratio (SUR: target/cerebellum-1) of {sup 123}I-ADAM binding to SERT in midbrain was 1.78{+-}0.27, pons was 1.21{+-}0.53, and striatum was 0.79{+-}0.13. The cronbach's {alpha} of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2

  3. Towards equitable access to medicines for the rural poor: analyses of insurance claims reveal rural pharmacy initiative triggers price competition in Kyrgyzstan.

    Science.gov (United States)

    Waning, Brenda; Maddix, Jason; Tripodis, Yorghos; Laing, Richard; Leufkens, Hubert Gm; Gokhale, Manjusha

    2009-12-14

    A rural pharmacy initiative (RPI) designed to increase access to medicines in rural Kyrgyzstan created a network of 12 pharmacies using a revolving drug fund mechanism in 12 villages where no pharmacies previously existed. The objective of this study was to determine if the establishment of the RPI resulted in the unforeseen benefit of triggering medicine price competition in pre-existing (non-RPI) private pharmacies located in the region. We conducted descriptive and multivariate analyses on medicine insurance claims data from Kyrgyzstan's Mandatory Health Insurance Fund for the Jumgal District of Naryn Province from October 2003 to December 2007. We compared average quarterly medicine prices in competitor pharmacies before and after the introduction of the rural pharmacy initiative in October 2004 to determine the RPI impact on price competition. Descriptive analyses suggest competitors reacted to RPI prices for 21 of 30 (70%) medicines. Competitor medicine prices from the quarter before RPI introduction to the end of the study period decreased for 17 of 30 (57%) medicines, increased for 4 of 30 (13%) medicines, and remained unchanged for 9 of 30 (30%) medicines. Among the 9 competitor medicines with unchanged prices, five initially decreased in price but later reverted back to baseline prices. Multivariate analyses on 19 medicines that met sample size criteria confirm these findings. Fourteen of these 19 (74%) competitor medicines changed significantly in price from the quarter before RPI introduction to the quarter after RPI introduction, with 9 of 19 (47%) decreasing in price and 5 of 19 (26%) increasing in price. The RPI served as a market driver, spurring competition in medicine prices in competitor pharmacies, even when they were located in different villages. Initiatives designed to increase equitable access to medicines in rural regions of developing and transitional countries should consider the potential to leverage medicine price competition as a means

  4. Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

    Science.gov (United States)

    Dyer, Betsey D.; Kahn, Michael J.; LeBlanc, Mark D.

    2008-01-01

    Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results. PMID:19054742

  5. RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

    DEFF Research Database (Denmark)

    Salleh, M. S.; Mazzoni, G.; Höglund, J. K.

    2017-01-01

    -throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate...... genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency....... On average, 57 million reads (short reads or short mRNA sequences ...

  6. The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (Haliotis tuberculata), Revealed by Combined Mitochondrial and Nuclear Marker Analyses.

    Science.gov (United States)

    Roussel, Valérie; Van Wormhoudt, Alain

    2017-04-01

    The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea-probably before the separation of the two lineages-and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the

  7. Biochemical and full genome sequence analyses of clinical Vibrio cholerae isolates in Mexico reveals the presence of novel V. cholerae strains.

    Science.gov (United States)

    Díaz-Quiñonez, José Alberto; Hernández-Monroy, Irma; Montes-Colima, Norma Angélica; Moreno-Pérez, María Asunción; Galicia-Nicolás, Adriana Guadalupe; López-Martínez, Irma; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ortíz-Alcántara, Joanna María; Garcés-Ayala, Fabiola; Ramírez-González, José Ernesto

    2016-05-01

    The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the four strains obtained in this study confirmed the presence of Pathogenicity Islands VPI-1 and -2, VSP-1 and -2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  8. Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types.

    Science.gov (United States)

    Knudsen, Gitte M; Nielsen, Jesper Boye; Marvig, Rasmus L; Ng, Yin; Worning, Peder; Westh, Henrik; Gram, Lone

    2017-08-01

    Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long-term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time-based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18-0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  9. Language pathway tracking: comparing nTMS-based DTI fiber tracking with a cubic ROIs-based protocol.

    Science.gov (United States)

    Negwer, Chiara; Sollmann, Nico; Ille, Sebastian; Hauck, Theresa; Maurer, Stefanie; Kirschke, Jan S; Ringel, Florian; Meyer, Bernhard; Krieg, Sandro M

    2017-03-01

    OBJECTIVE Diffusion tensor imaging (DTI) fiber tracking (FT) has been widely used in glioma surgery in recent years. It can provide helpful information about subcortical structures, especially in patients with eloquent space-occupying lesions. This study compared the newly developed navigated transcranial magnetic stimulation (nTMS)-based DTI FT of language pathways with the most reproducible protocol for language pathway tractography, using cubic regions of interest (ROIs) for the arcuate fascicle. METHODS Thirty-seven patients with left-sided perisylvian lesions underwent language mapping by repetitive nTMS. DTI FT was performed using the cubic ROIs-based protocol and the authors' nTMS-based DTI FT approach. The same minimal fiber length and fractional anisotropy were chosen (50 mm and 0.2, respectively). Both protocols were performed with standard clinical tractography software. RESULTS Both methods visualized language-related fiber tracts (i.e., corticonuclear tract, arcuate fascicle, uncinate fascicle, superior longitudinal fascicle, inferior longitudinal fascicle, arcuate fibers, commissural fibers, corticothalamic fibers, and frontooccipital fascicle) in all 37 patients. Using the cubic ROIs-based protocol, 39.9% of these language-related fiber tracts were detected in the examined patients, as opposed to 76.0% when performing nTMS-based DTI FT. For specifically tracking the arcuate fascicle, however, the cubic ROIs-based approach showed better results (97.3% vs 75.7% with nTMS-based DTI FT). CONCLUSIONS The cubic ROIs-based protocol was designed for arcuate fascicle tractography, and this study shows that it is still useful for this intention. However, superior results were obtained using the nTMS-based DTI FT for visualization of other language-related fiber tracts.

  10. Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

    Science.gov (United States)

    Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

    2008-03-01

    Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

  11. Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits

    Science.gov (United States)

    Marcelletti, Simone; Scortichini, Marco

    2015-01-01

    The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches. PMID:26147218

  12. Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata.

    Directory of Open Access Journals (Sweden)

    Ting Guo

    Full Text Available Fungal species of Armillaria, which can act as plant pathogens and/or symbionts of the Chinese traditional medicinal herb Gastrodia elata ("Tianma", are ecologically and economically important and have consequently attracted the attention of mycologists. However, their taxonomy has been highly dependent on morphological characterization and mating tests. In this study, we phylogenetically analyzed Chinese Armillaria samples using the sequences of the internal transcribed spacer region, translation elongation factor-1 alpha gene and beta-tubulin gene. Our data revealed at least 15 phylogenetic lineages of Armillaria from China, of which seven were newly discovered and two were recorded from China for the first time. Fourteen Chinese biological species of Armillaria, which were previously defined based on mating tests, could be assigned to the 15 phylogenetic lineages identified herein. Seven of the 15 phylogenetic lineages were found to be disjunctively distributed in different continents of the Northern Hemisphere, while eight were revealed to be endemic to certain continents. In addition, we found that seven phylogenetic lineages of Armillaria were used for the cultivation of Tianma, only two of which had been recorded to be associated with Tianma previously. We also illustrated that G. elata f. glauca ("Brown Tianma" and G. elata f. elata ("Red Tianma", two cultivars of Tianma grown in different regions of China, form symbiotic relationships with different phylogenetic lineages of Armillaria. These findings should aid the development of Tianma cultivation in China.

  13. Towards equitable access to medicines for the rural poor: analyses of insurance claims reveal rural pharmacy initiative triggers price competition in Kyrgyzstan

    Directory of Open Access Journals (Sweden)

    Leufkens Hubert GM

    2009-12-01

    Full Text Available Abstract Background A rural pharmacy initiative (RPI designed to increase access to medicines in rural Kyrgyzstan created a network of 12 pharmacies using a revolving drug fund mechanism in 12 villages where no pharmacies previously existed. The objective of this study was to determine if the establishment of the RPI resulted in the unforeseen benefit of triggering medicine price competition in pre-existing (non-RPI private pharmacies located in the region. Methods We conducted descriptive and multivariate analyses on medicine insurance claims data from Kyrgyzstan's Mandatory Health Insurance Fund for the Jumgal District of Naryn Province from October 2003 to December 2007. We compared average quarterly medicine prices in competitor pharmacies before and after the introduction of the rural pharmacy initiative in October 2004 to determine the RPI impact on price competition. Results Descriptive analyses suggest competitors reacted to RPI prices for 21 of 30 (70% medicines. Competitor medicine prices from the quarter before RPI introduction to the end of the study period decreased for 17 of 30 (57% medicines, increased for 4 of 30 (13% medicines, and remained unchanged for 9 of 30 (30% medicines. Among the 9 competitor medicines with unchanged prices, five initially decreased in price but later reverted back to baseline prices. Multivariate analyses on 19 medicines that met sample size criteria confirm these findings. Fourteen of these 19 (74% competitor medicines changed significantly in price from the quarter before RPI introduction to the quarter after RPI introduction, with 9 of 19 (47% decreasing in price and 5 of 19 (26% increasing in price. Conclusions The RPI served as a market driver, spurring competition in medicine prices in competitor pharmacies, even when they were located in different villages. Initiatives designed to increase equitable access to medicines in rural regions of developing and transitional countries should consider the

  14. A localization algorithm of adaptively determining the ROI of the reference circle in image

    Science.gov (United States)

    Xu, Zeen; Zhang, Jun; Zhang, Daimeng; Liu, Xiaomao; Tian, Jinwen

    2018-03-01

    Aiming at solving the problem of accurately positioning the detection probes underwater, this paper proposed a method based on computer vision which can effectively solve this problem. The theory of this method is that: First, because the shape information of the heat tube is similar to a circle in the image, we can find a circle which physical location is well known in the image, we set this circle as the reference circle. Second, we calculate the pixel offset between the reference circle and the probes in the picture, and adjust the steering gear through the offset. As a result, we can accurately measure the physical distance between the probes and the under test heat tubes, then we can know the precise location of the probes underwater. However, how to choose reference circle in image is a difficult problem. In this paper, we propose an algorithm that can adaptively confirm the area of reference circle. In this area, there will be only one circle, and the circle is the reference circle. The test results show that the accuracy of the algorithm of extracting the reference circle in the whole picture without using ROI (region of interest) of the reference circle is only 58.76% and the proposed algorithm is 95.88%. The experimental results indicate that the proposed algorithm can effectively improve the efficiency of the tubes detection.

  15. [Buffon, the director of 'Jardin du Roi' in the 1700s].

    Science.gov (United States)

    Jeune, Bernard; Petersen, Hans Christian

    2008-01-01

    Buffon and Linné were the two greatest naturalists of the 1700s. As they were both born in 1707, their 300 anniversaries were therefore celebrated in France and Sweden. At the celebration meeting at the University of Bourgogne in Dijon - The Buffon Legacy - September 3-6, 2007, we presented the following paper: "Buffon and the longevity of species". In the present paper the life and work of Buffon is introduced on the basis of recent literature, including Jacques Roger's famous biography. Among non-biologists Buffon has nearly been forgotten, even though in the 1700s he was considered to be at the same level as the most famous French thinkers of the Enlightenment - Montesquieu, Voltaire, Rousseau and Diderot. His largest contributions were the publication of his comprehensive "Histoire naturelle" and his long and significant leadership of "Jardin du Roi", which he built up to become one of the best scientific institutions of Europe. Buffon's scientific contributions wereas overshadowed by those of Linné, as it was his classification system, which became dominant all overn Europe. Buffon's student Lamarck and later Darwin contributed by pushing Buffon in oblivion of history, even though Darwin valued him highly. However, in recent decades Buffon is experiencing a renaissance in connection with the increasing interest in biological anthropology, biogeography, ethology, and ecology, as well as on account of his modern species concept.

  16. Bias in tensor based morphometry Stat-ROI measures may result in unrealistic power estimates.

    Science.gov (United States)

    Thompson, Wesley K; Holland, Dominic

    2011-07-01

    A series of reports have recently appeared using tensor based morphometry statistically-defined regions of interest, Stat-ROIs, to quantify longitudinal atrophy in structural MRIs from the Alzheimer's Disease Neuroimaging Initiative (ADNI). This commentary focuses on one of these reports, Hua et al. (2010), but the issues raised here are relevant to the others as well. Specifically, we point out a temporal pattern of atrophy in subjects with Alzheimer's disease and mild cognitive impairment whereby the majority of atrophy in two years occurs within the first 6 months, resulting in overall elevated estimated rates of change. Using publicly-available ADNI data, this temporal pattern is also found in a group of identically-processed healthy controls, strongly suggesting that methodological bias is corrupting the measures. The resulting bias seriously impacts the validity of conclusions reached using these measures; for example, sample size estimates reported by Hua et al. (2010) may be underestimated by a factor of five to sixteen. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Career satisfaction and work-life balance of specialist orthodontists within the UK/ROI.

    Science.gov (United States)

    Al-Junaid, S M; Hodges, S J; Petrie, A; Cunningham, S J

    2017-07-07

    Objectives To investigate factors affecting career satisfaction and work-life balance in specialist orthodontists in the UK/ROI.Design and setting Prospective questionnaire-based study.Subjects and methods The questionnaire was sent to specialist orthodontists who were members of the British Orthodontic Society.Results Orthodontists reported high levels of career satisfaction (median score 90/100). Career satisfaction was significantly higher in those who exhibited: i) satisfaction with working hours; ii) satisfaction with the level of control over their working day; iii) ability to manage unexpected home events; and iv) confidence in how readily they managed patient expectations. The work-life balance score was lower than the career satisfaction score but the median score was 75/100. Work-life balance scores were significantly affected by the same four factors, but additionally were higher in those who worked part-time.Conclusions Orthodontists in this study were highly satisfied with their career and the majority responded that they would choose orthodontics again. Work-life balance scores were lower than career satisfaction scores but still relatively high. It is important for the profession to consider ways of maintaining, or improving, career satisfaction and work-life balance; including maintaining flexibility of working hours and ensuring that all clinicians have ready access to appropriate training courses throughout their careers (for example, management of patient expectations).

  18. Coastal groundwater exchange on a small Pacific atoll island: Roi Namur, Republic of the Marshall Islands

    Science.gov (United States)

    Oberle, Ferdinand K. J.; Swarzenski, Peter W.; Storlazzi, Curt

    2017-04-01

    Atoll islands, most of which only average 1-2 meters above today's sea level, provide a tremendous natural laboratory in which to study and better understand the intensifying impacts of high rates of sea-level rise on tropical reef-lined islands globally due to their unique geologic structure and limited water supply. Groundwater resources of atolls are typically minimal due to the low elevation and small surface area of the islands and are also subject to recurring droughts, and more frequent, storm-driven seawater overwash events. Although groundwater is the principal means of freshwater storage on atoll islands and is a major factor in determining the overall sustainability of island communities, hydrological data on how an aquifer will response to changes in sea-level rise or storm-driven overwash remain limited. We here present high-resolution time series hydrogeological and geochemical data to determine the role of the atoll's carbonate geology, land use, and atmospheric and oceanographic forcing in driving coastal groundwater exchange on the island of Roi Namur on Kwajalein Atoll in the Republic of the Marshall Islands. This information can provide new estimates on the recovery and resilience of coastal groundwater resources on such islands to expected climate change-driven perturbations.

  19. cDNA analyses of CAPN3 enhance mutation detection and reveal a low prevalence of LGMD2A patients in Denmark

    DEFF Research Database (Denmark)

    Duno, M.; Sveen, M.L.; Schwartz, M.

    2008-01-01

    Calpainopathy or limb-girdle muscular dystrophy type 2A (LGMD2A) is generally recognized as the most prevalent form of recessive LGMD and is caused by mutations in the CAPN3 gene. Out of a cohort of 119 patients fulfilling clinical criteria for LGMD2, referred to our neuromuscular clinic, 46 were....... In three other, only one heterozygous mutation could be identified on the genomic level; however, CAPN3 cDNA analyses demonstrated homozygosity for the mutant allele, indicating the presence of an unidentified allele that somehow compromise correct CAPN3 RNA processing. In the three remaining patients...... origin, indicating a five- to sixfold lower prevalence in Denmark compared to other European countries. A total of 16 different CAPN3 mutations were identified, of which 5 were novel. The present study demonstrates the value of cDNA analysis for CAPN3 in LGMD2A patients and indicates that calpainopathy...

  20. Effect of scatter and attenuation correction in ROI analysis of brain perfusion scintigraphy. Phantom experiment and clinical study in patients with unilateral cerebrovascular disease

    Energy Technology Data Exchange (ETDEWEB)

    Bai, J. [Keio Univ., Tokyo (Japan). 21st Century Center of Excellence Program; Hashimoto, J.; Kubo, A. [Keio Univ., Tokyo (Japan). Dept. of Radiology; Ogawa, K. [Hosei Univ., Tokyo (Japan). Dept. of Electronic Informatics; Fukunaga, A.; Onozuka, S. [Keio Univ., Tokyo (Japan). Dept. of Neurosurgery

    2007-07-01

    The aim of this study was to evaluate the effect of scatter and attenuation correction in region of interest (ROI) analysis of brain perfusion single-photon emission tomography (SPECT), and to assess the influence of selecting the reference area on the calculation of lesion-to-reference count ratios. Patients, methods: Data were collected from a brain phantom and ten patients with unilateral internal carotid artery stenosis. A simultaneous emission and transmission scan was performed after injecting {sup 123}I-iodoamphetamine. We reconstructed three SPECT images from common projection data: with scatter correction and nonuniform attenuation correction, with scatter correction and uniform attenuation correction, and with uniform attenuation correction applied to data without scatter correction. Regional count ratios were calculated by using four different reference areas (contralateral intact side, ipsilateral cerebellum, whole brain and hemisphere). Results: Scatter correction improved the accuracy of measuring the count ratios in the phantom experiment. It also yielded marked difference in the count ratio in the clinical study when using the cerebellum, whole brain or hemisphere as the reference. Difference between nonuniform and uniform attenuation correction was not significant in the phantom and clinical studies except when the cerebellar reference was used. Calculation of the lesion-to-normal count ratios referring the same site in the contralateral hemisphere was not dependent on the use of scatter correction or transmission scan-based attenuation correction. Conclusion: Scatter correction was indispensable for accurate measurement in most of the ROI analyses. Nonuniform attenuation correction is not necessary when using the reference area other than the cerebellum. (orig.)

  1. Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

    Science.gov (United States)

    Ngugi, David Kamanda; Stingl, Ulrich

    2012-01-01

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium. PMID:23185592

  2. TRANSCRIPTOME ANALYSES REVEAL DIFFERENTIAL GENE EXPRESSION PATTERNS BETWEEN THE LIFE-CYCLE STAGES OF EMILIANIA HUXLEYI (HAPTOPHYTA) AND REFLECT SPECIALIZATION TO DIFFERENT ECOLOGICAL NICHES(1).

    Science.gov (United States)

    Rokitta, Sebastian D; de Nooijer, Lennart J; Trimborn, Scarlett; de Vargas, Colomban; Rost, Björn; John, Uwe

    2011-08-01

    Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 μm diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit. © 2011 Phycological Society of America.

  3. Combined analyses of the ITS loci and the corresponding 16S rRNA genes reveal high micro- and macrodiversity of SAR11 populations in the Red Sea.

    KAUST Repository

    Ngugi, David

    2012-11-20

    Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24 °C throughout the year, and a remarkable uniform temperature (~22 °C) and salinity (~41 psu) from the mixed layer (~200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea\\'s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium.

  4. Transcriptome-wide mega-analyses reveal joint dysregulation of immunologic genes and transcription regulators in brain and blood in schizophrenia.

    Science.gov (United States)

    Hess, Jonathan L; Tylee, Daniel S; Barve, Rahul; de Jong, Simone; Ophoff, Roel A; Kumarasinghe, Nishantha; Tooney, Paul; Schall, Ulrich; Gardiner, Erin; Beveridge, Natalie Jane; Scott, Rodney J; Yasawardene, Surangi; Perera, Antionette; Mendis, Jayan; Carr, Vaughan; Kelly, Brian; Cairns, Murray; Tsuang, Ming T; Glatt, Stephen J

    2016-10-01

    The application of microarray technology in schizophrenia research was heralded as paradigm-shifting, as it allowed for high-throughput assessment of cell and tissue function. This technology was widely adopted, initially in studies of postmortem brain tissue, and later in studies of peripheral blood. The collective body of schizophrenia microarray literature contains apparent inconsistencies between studies, with failures to replicate top hits, in part due to small sample sizes, cohort-specific effects, differences in array types, and other confounders. In an attempt to summarize existing studies of schizophrenia cases and non-related comparison subjects, we performed two mega-analyses of a combined set of microarray data from postmortem prefrontal cortices (n=315) and from ex-vivo blood tissues (n=578). We adjusted regression models per gene to remove non-significant covariates, providing best-estimates of transcripts dysregulated in schizophrenia. We also examined dysregulation of functionally related gene sets and gene co-expression modules, and assessed enrichment of cell types and genetic risk factors. The identities of the most significantly dysregulated genes were largely distinct for each tissue, but the findings indicated common emergent biological functions (e.g. immunity) and regulatory factors (e.g., predicted targets of transcription factors and miRNA species across tissues). Our network-based analyses converged upon similar patterns of heightened innate immune gene expression in both brain and blood in schizophrenia. We also constructed generalizable machine-learning classifiers using the blood-based microarray data. Our study provides an informative atlas for future pathophysiologic and biomarker studies of schizophrenia. Published by Elsevier B.V.

  5. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    DEFF Research Database (Denmark)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.

    2015-01-01

    organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10ºC. Multivariate statistical analysis of the bacterial diversity data (DNA......The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78º......N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable...

  6. Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus and other eukaryote species revealed by nucleotide and amino acid sequence analyses

    Directory of Open Access Journals (Sweden)

    Andréia B. Poletto

    2008-01-01

    Full Text Available Actin-encoding cDNAs of Nile tilapia (Oreochromis niloticus were isolated by RT-PCR using total RNA samples of different tissues and further characterized by nucleotide sequencing and in silico amino acid (aa sequence analysis. Comparisons among the actin gene sequences of O. niloticus and those of other species evidenced that the isolated genes present a high similarity to other fish and other vertebrate actin genes. The highest nucleotide resemblance was observed between O. niloticus and O. mossambicus a-actin and b-actin genes. Analysis of the predicted aa sequences revealed two distinct types of cytoplasmic actins, one cardiac muscle actin type and one skeletal muscle actin type that were expressed in different tissues of Nile tilapia. The evolutionary relationships between the Nile tilapia actin genes and diverse other organisms is discussed.

  7. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    Science.gov (United States)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-01-01

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

  8. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  9. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence.

    Directory of Open Access Journals (Sweden)

    Dawoon Chung

    2014-11-01

    Full Text Available The Aspergillus fumigatus sterol regulatory element binding protein (SREBP SrbA belongs to the basic Helix-Loop-Helix (bHLH family of transcription factors and is crucial for antifungal drug resistance and virulence. The latter phenotype is especially striking, as loss of SrbA results in complete loss of virulence in murine models of invasive pulmonary aspergillosis (IPA. How fungal SREBPs mediate fungal virulence is unknown, though it has been suggested that lack of growth in hypoxic conditions accounts for the attenuated virulence. To further understand the role of SrbA in fungal infection site pathobiology, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq was used to identify genes under direct SrbA transcriptional regulation in hypoxia. These results confirmed the direct regulation of ergosterol biosynthesis and iron uptake by SrbA in hypoxia and revealed new roles for SrbA in nitrate assimilation and heme biosynthesis. Moreover, functional characterization of an SrbA target gene with sequence similarity to SrbA identified a new transcriptional regulator of the fungal hypoxia response and virulence, SrbB. SrbB co-regulates genes involved in heme biosynthesis and demethylation of C4-sterols with SrbA in hypoxic conditions. However, SrbB also has regulatory functions independent of SrbA including regulation of carbohydrate metabolism. Loss of SrbB markedly attenuates A. fumigatus virulence, and loss of both SREBPs further reduces in vivo fungal growth. These data suggest that both A. fumigatus SREBPs are critical for hypoxia adaptation and virulence and reveal new insights into SREBPs' complex role in infection site adaptation and fungal virulence.

  10. Diabetes and Obesity as Independent Risk Factors for Osteoporosis: Updated Results from the ROIS/EMEROS Registry in a Population of Five Thousand Post-Menopausal Women Living in a Region Characterized by Heavy Environmental Pressure

    Directory of Open Access Journals (Sweden)

    Cosimo Neglia

    2016-11-01

    Full Text Available Objectives: We aimed to analyze bone mineralization and the effect of different risk factors for osteoporosis in postmenopausal women. Methods: We found 4909 postmenopausal subjects within ≥10,000 records from the ROIS/EMEROS (Ionian and Salento Osteoporosis Registry/Euro Mediterranean Registry of Osteoporosis registry, a population study carried out in an area characterized by heavy environmental pressure between Brindisi and Taranto from 2009 to 2016. All subjects were assessed via phalangeal quantitative ultrasound (QUS to evaluate their bone mineralization (assessed via amplitude dependent speed of sound (AD-SoS and the association between demineralization and the presence of other conditions or risk factors. Results: Mean age was 64 ± 9.5 years and mean body mass index (BMI was 28.7 ± 3.5 kg/m2. Pearson correlation analyses revealed a negative association between bone mineralization (AD-SoS and BMI (p < 0.001. By using multivariate logistic regression analysis, we observed significant values of odds ratios (ORs of osteoporosis (adjusted for age, physical activity, and the use of drugs known to increase the risk of fractures in subjects with diabetes and obesity: 1.39 (confidence interval (CI: 1.05–1.83 and 1.46 (CI: 1.20–1.78, respectively. A statistically significant linear trend of higher ORs of osteoporosis was found for increasing values of BMI. Conclusions: Our study confirmed the high impact of obesity and type 1 and type 2 diabetes on osteoporosis.

  11. Controls on the long term earthquake behavior of an intraplate fault revealed by U-Th and stable isotope analyses of syntectonic calcite veins

    Science.gov (United States)

    Williams, Randolph; Goodwin, Laurel; Sharp, Warren; Mozley, Peter

    2017-04-01

    U-Th dates on calcite precipitated in coseismic extension fractures in the Loma Blanca normal fault zone, Rio Grande rift, NM, USA, constrain earthquake recurrence intervals from 150-565 ka. This is the longest direct record of seismicity documented for a fault in any tectonic environment. Combined U-Th and stable isotope analyses of these calcite veins define 13 distinct earthquake events. These data show that for more than 400 ka the Loma Blanca fault produced earthquakes with a mean recurrence interval of 40 ± 7 ka. The coefficient of variation for these events is 0.40, indicating strongly periodic seismicity consistent with a time-dependent model of earthquake recurrence. Stochastic statistical analyses further validate the inference that earthquake behavior on the Loma Blanca was time-dependent. The time-dependent nature of these earthquakes suggests that the seismic cycle was fundamentally controlled by a stress renewal process. However, this periodic cycle was punctuated by an episode of clustered seismicity at 430 ka. Recurrence intervals within the earthquake cluster were as low as 5-11 ka. Breccia veins formed during this episode exhibit carbon isotope signatures consistent with having formed through pronounced degassing of a CO2 charged brine during post-failure, fault-localized fluid migration. The 40 ka periodicity of the long-term earthquake record of the Loma Blanca fault is similar in magnitude to recurrence intervals documented through paleoseismic studies of other normal faults in the Rio Grande rift and Basin and Range Province. We propose that it represents a background rate of failure in intraplate extension. The short-term, clustered seismicity that occurred on the fault records an interruption of the stress renewal process, likely by elevated fluid pressure in deeper structural levels of the fault, consistent with fault-valve behavior. The relationship between recurrence interval and inferred fluid degassing suggests that pore fluid pressure

  12. An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies

    Science.gov (United States)

    Broughton, Mary C.; Davidson, Jane W.

    2016-01-01

    Musicians' expressive bodily movements can influence observers' perception of performance. Furthermore, individual differences in observers' music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies—one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers' perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players' bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the types and locations of actions

  13. An expressive bodily movement repertoire for marimba performance, revealed through observers’ Laban effort-shape analyses, and allied musical features: two case studies

    Directory of Open Access Journals (Sweden)

    Mary C Broughton

    2016-08-01

    Full Text Available Musicians’ expressive bodily movements can influence observers’ perception of performance. Furthermore, individual differences in observers’ music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies – one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers’ perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players’ bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the

  14. An Expressive Bodily Movement Repertoire for Marimba Performance, Revealed through Observers' Laban Effort-Shape Analyses, and Allied Musical Features: Two Case Studies.

    Science.gov (United States)

    Broughton, Mary C; Davidson, Jane W

    2016-01-01

    Musicians' expressive bodily movements can influence observers' perception of performance. Furthermore, individual differences in observers' music and motor expertise can shape how they perceive and respond to music performance. However, few studies have investigated the bodily movements that different observers of music performance perceive as expressive, in order to understand how they might relate to the music being produced, and the particular instrument type. In this paper, we focus on marimba performance through two case studies-one solo and one collaborative context. This study aims to investigate the existence of a core repertoire of marimba performance expressive bodily movements, identify key music-related features associated with the core repertoire, and explore how observers' perception of expressive bodily movements might vary according to individual differences in their music and motor expertise. Of the six professional musicians who observed and analyzed the marimba performances, three were percussionists and experienced marimba players. Following training, observers implemented the Laban effort-shape movement analysis system to analyze marimba players' bodily movements that they perceived as expressive in audio-visual recordings of performance. Observations that were agreed by all participants as being the same type of action at the same location in the performance recording were examined in each case study, then across the two studies. A small repertoire of bodily movements emerged that the observers perceived as being expressive. Movements were primarily allied to elements of the music structure, technique, and expressive interpretation, however, these elements appeared to be interactive. A type of body sway movement and more localized sound generating actions were perceived as expressive. These movements co-occurred and also appeared separately. Individual participant data revealed slightly more variety in the types and locations of actions

  15. Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy.

    Science.gov (United States)

    Sheng, Xihui; Wang, Ligang; Ni, Hemin; Wang, Lixian; Qi, Xiaolong; Xing, Shuhan; Guo, Yong

    2016-01-01

    The molecular mechanism regulated by microRNAs (miRNAs) that underlies postnatal hypertrophy of skeletal muscle is complex and remains unclear. Here, the miRNAomes of longissimus dorsi muscle collected at five postnatal stages (60, 120, 150, 180, and 210 days after birth) from Large White (commercial breed) and Min pigs (indigenous breed of China) were analyzed by Illumina sequencing. We identified 734 miRNAs comprising 308 annotated miRNAs and 426 novel miRNAs, of which 307 could be considered pig-specific. Comparative analysis between two breeds suggested that 60 and 120 days after birth were important stages for skeletal muscle hypertrophy and intramuscular fat accumulation. A total of 263 miRNAs were significantly differentially expressed between two breeds at one or more developmental stages. In addition, the differentially expressed miRNAs between every two adjacent developmental stages in each breed were determined. Notably, ssc-miR-204 was significantly more highly expressed in Min pig skeletal muscle at all postnatal stages compared with its expression in Large White pig skeletal muscle. Based on gene ontology and KEGG pathway analyses of its predicted target genes, we concluded that ssc-miR-204 may exert an impact on postnatal hypertrophy of skeletal muscle by regulating myoblast proliferation. The results of this study will help in elucidating the mechanism underlying postnatal hypertrophy of skeletal muscle modulated by miRNAs, which could provide valuable information for improvement of pork quality and human myopathy.

  16. Morphological and Genetic Analyses of the Invasive Forest Pathogen Phytophthora austrocedri Reveal that Two Clonal Lineages Colonized Britain and Argentina from a Common Ancestral Population.

    Science.gov (United States)

    Henricot, Béatrice; Pérez-Sierra, Ana; Armstrong, April C; Sharp, Paul M; Green, Sarah

    2017-12-01

    Phytophthora austrocedri is causing widespread mortality of Austrocedrus chilensis in Argentina and Juniperus communis in Britain. The pathogen has also been isolated from J. horizontalis in Germany. Isolates from Britain, Argentina, and Germany are homothallic, with no clear differences in the dimensions of sporangia, oogonia, or oospores. Argentinian and German isolates grew faster than British isolates across a range of media and had a higher temperature tolerance, although most isolates, regardless of origin, grew best at 15°C and all isolates were killed at 25°C. Argentinian and British isolates caused lesions when inoculated onto both A. chilensis and J. communis; however, the Argentinian isolate caused longer lesions on A. chilensis than on J. communis and vice versa for the British isolate. Genetic analyses of nuclear and mitochondrial loci showed that all British isolates are identical. Argentinian isolates and the German isolate are also identical but differ from the British isolates. Single-nucleotide polymorphisms are shared between the British and Argentinian isolates. We concluded that British isolates and Argentinian isolates conform to two distinct clonal lineages of P. austrocedri founded from the same as-yet-unidentified source population. These lineages should be recognized and treated as separate risks by international plant health legislation.

  17. Comparative proteomic and metabolomic analyses reveal mechanisms of improved cold stress tolerance in bermudagrass (Cynodon dactylon (L.) Pers.) by exogenous calcium.

    Science.gov (United States)

    Shi, Haitao; Ye, Tiantian; Zhong, Bao; Liu, Xun; Chan, Zhulong

    2014-11-01

    As an important second messenger, calcium is involved in plant cold stress response, including chilling (Cynodon dactylon (L.) Pers.). Physiological analyses showed that CaCl2 treatment alleviated the reactive oxygen species (ROS) burst and cell damage triggered by chilling stress, via activating antioxidant enzymes, non-enzymatic glutathione antioxidant pool, while EGTA treatment had the opposite effects. Additionally, comparative proteomic analysis identified 51 differentially expressed proteins that were enriched in redox, tricarboxylicacid cycle, glycolysis, photosynthesis, oxidative pentose phosphate pathway, and amino acid metabolisms. Consistently, 42 metabolites including amino acids, organic acids, sugars, and sugar alcohols were regulated by CaCl2 treatment under control and cold stress conditions, further confirming the common modulation of CaCl2 treatment in carbon metabolites and amino acid metabolism. Taken together, this study reported first evidence of the essential and protective roles of endogenous and exogenous calcium in bermudagrass response to cold stress, partially via activation of the antioxidants and modulation of several differentially expressed proteins and metabolic homeostasis in the process of cold acclimation. © 2014 Institute of Botany, Chinese Academy of Sciences.

  18. The regulatory mechanism of fruit ripening revealed by analyses of direct targets of the tomato MADS-box transcription factor RIPENING INHIBITOR

    Science.gov (United States)

    Fujisawa, Masaki; Ito, Yasuhiro

    2013-01-01

    The developmental process of ripening is unique to fleshy fruits and a key factor in fruit quality. The tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN), one of the earliest-acting ripening regulators, is required for broad aspects of ripening, including ethylene-dependent and -independent pathways. However, our knowledge of direct RIN target genes has been limited, considering the broad effects of RIN on ripening. In a recent work published in The Plant Cell, we identified 241 direct RIN target genes by chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip) and transcriptome analysis. Functional classification of the targets revealed that RIN participates in the regulation of many biological processes including well-known ripening processes such as climacteric ethylene production and lycopene accumulation. In addition, we found that ethylene is required for the full expression of RIN and several RIN-targeting transcription factor genes at the ripening stage. Here, based on our recently published findings and additional data, we discuss the ripening processes regulated by RIN and the interplay between RIN and ethylene. PMID:23518588

  19. Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

    Science.gov (United States)

    Sibout, Richard; Proost, Sebastian; Hansen, Bjoern Oest; Vaid, Neha; Giorgi, Federico M; Ho-Yue-Kuang, Severine; Legée, Frédéric; Cézart, Laurent; Bouchabké-Coussa, Oumaya; Soulhat, Camille; Provart, Nicholas; Pasha, Asher; Le Bris, Philippe; Roujol, David; Hofte, Herman; Jamet, Elisabeth; Lapierre, Catherine; Persson, Staffan; Mutwil, Marek

    2017-08-01

    While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  20. Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family.

    Science.gov (United States)

    Afrache, Hassnae; Pontarotti, Pierre; Abi-Rached, Laurent; Olive, Daniel

    2017-06-01

    The butyrophilin 3 (BTN3) receptors are implicated in the T lymphocytes regulation and present a wide plasticity in mammals. In order to understand how these genes have been diversified, we studied their evolution and show that the three human BTN3 are the result of two successive duplications in Primates and that the three genes are present in Hominoids and the Old World Monkey groups. A thorough phylogenetic analysis reveals a concerted evolution of BTN3 characterized by a strong and recurrent homogenization of the region encoding the signal peptide and the immunoglobulin variable (IgV) domain in Hominoids, where the sequences of BTN3A1 or BTN3A3 are replaced by BTN3A2 sequence. In human, the analysis of the diversity of these genes in 1683 individuals representing 26 worldwide populations shows that the three genes are polymorphic, with more than 46 alleles for each gene, and marked by extreme homogenization of the IgV sequences. The same analysis performed for the BTN2 genes shows also a concerted evolution; however, it is not as strong and recurrent as for BTN3. This study shows that BTN3 receptors are marked by extreme concerted evolution at the IgV domain and that BTN3A2 plays a central role in this evolution.

  1. Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

    Science.gov (United States)

    Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

    2014-01-01

    Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

  2. DNA sequence analyses reveal co-occurrence of novel haplotypes of Fasciola gigantica with F. hepatica in South Africa and Zimbabwe.

    Science.gov (United States)

    Mucheka, Vimbai T; Lamb, Jennifer M; Pfukenyi, Davies M; Mukaratirwa, Samson

    2015-11-30

    The aim of this study was to identify and determine the genetic diversity of Fasciola species in cattle from Zimbabwe, the KwaZulu-Natal and Mpumalanga provinces of South Africa and selected wildlife hosts from Zimbabwe. This was based on analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS1 and 2) and mitochondrial cytochrome oxidase 1 (CO1) regions. The sample of 120 flukes was collected from livers of 57 cattle at 4 abattoirs in Zimbabwe and 47 cattle at 6 abattoirs in South Africa; it also included three alcohol-preserved duiker, antelope and eland samples from Zimbabwe. Aligned sequences (ITS 506 base pairs and CO1 381 base pairs) were analyzed by neighbour-joining, maximum parsimony and Bayesian inference methods. Phylogenetic trees revealed the presence of Fasciola gigantica in cattle from Zimbabwe and F. gigantica and Fasciola hepatica in the samples from South Africa. F. hepatica was more prevalent (64%) in South Africa than F. gigantica. In Zimbabwe, F. gigantica was present in 99% of the samples; F. hepatica was found in only one cattle sample, an antelope (Hippotragus niger) and a duiker (Sylvicapra grimmia). This is the first molecular confirmation of the identity Fasciola species in Zimbabwe and South Africa. Knowledge on the identity and distribution of these liver flukes at molecular level will allow disease surveillance and control in the studied areas. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain.

    Directory of Open Access Journals (Sweden)

    Ruben Pérez

    Full Text Available Canine parvovirus (CPV, a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population and a major recombinant strain (86.7%. The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity.

  4. Phylogenetic and Genome-Wide Deep-Sequencing Analyses of Canine Parvovirus Reveal Co-Infection with Field Variants and Emergence of a Recent Recombinant Strain

    Science.gov (United States)

    Pérez, Ruben; Calleros, Lucía; Marandino, Ana; Sarute, Nicolás; Iraola, Gregorio; Grecco, Sofia; Blanc, Hervé; Vignuzzi, Marco; Isakov, Ofer; Shomron, Noam; Carrau, Lucía; Hernández, Martín; Francia, Lourdes; Sosa, Katia; Tomás, Gonzalo; Panzera, Yanina

    2014-01-01

    Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity. PMID:25365348

  5. Genome-wide identification, phylogeny, and expression analyses of the 14-3-3 family reveal their involvement in the development, ripening and abiotic stress response in banana

    Directory of Open Access Journals (Sweden)

    meiying li

    2016-09-01

    Full Text Available Plant 14-3-3 proteins act as critical components of various cellular signaling processes and play an important role in regulating multiple physiological processes. However, less information is known about the 14-3-3 gene family in banana. In this study, 25 14-3-3 genes were identified from the banana genome. Based on the evolutionary analysis, banana 14-3-3 proteins were clustered into ε and non-ε groups. Conserved motif analysis showed that all identified banana 14-3-3 genes had the typical 14-3-3 motif. The gene structure of banana 14-3-3 genes showed distinct class-specific divergence between the ε group and the non-ε group. Most banana 14-3-3 genes showed strong transcript accumulation changes during fruit development and postharvest ripening in two banana varieties, indicating that they might be involved in regulating fruit development and ripening. Moreover, some 14-3-3 genes also showed great changes after osmotic, cold, and salt treatments in two banana varieties, suggested their potential role in regulating banana response to abiotic stress. Taken together, this systemic analysis reveals the involvement of banana 14-3-3 genes in fruit development, postharvest ripening, and response to abiotic stress and provides useful information for understanding the functions of 14-3-3 genes in banana.

  6. SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus

    Science.gov (United States)

    Li, Bing; Tian, Xiaofang; Wang, Chunlan; Zeng, Xu; Xing, Yongmei; Ling, Hong; Yin, Wanqiang; Tian, Lixia; Meng, Zhixia; Zhang, Jihui; Guo, Shunxing

    2017-01-01

    Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.

  7. Structure-Function Analyses of a Caffeic Acid O-Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference[W][OA

    Science.gov (United States)

    Louie, Gordon V.; Bowman, Marianne E.; Tu, Yi; Mouradov, Aidyn; Spangenberg, German; Noel, Joseph P.

    2010-01-01

    Lignin forms from the polymerization of phenylpropanoid-derived building blocks (the monolignols), whose modification through hydroxylation and O-methylation modulates the chemical and physical properties of the lignin polymer. The enzyme caffeic acid O-methyltransferase (COMT) is central to lignin biosynthesis. It is often targeted in attempts to engineer the lignin composition of transgenic plants for improved forage digestibility, pulping efficiency, or utility in biofuel production. Despite intensive investigation, the structural determinants of the regiospecificity and substrate selectivity of COMT remain poorly defined. Reported here are x-ray crystallographic structures of perennial ryegrass (Lolium perenne) COMT (Lp OMT1) in open conformational state, apo- and holoenzyme forms and, most significantly, in a closed conformational state complexed with the products S-adenosyl-l-homocysteine and sinapaldehyde. The product-bound complex reveals the post-methyl-transfer organization of COMT’s catalytic groups with reactant molecules and the fully formed phenolic-ligand binding site. The core scaffold of the phenolic ligand forges a hydrogen-bonding network involving the 4-hydroxy group that anchors the aromatic ring and thereby permits only metahydroxyl groups to be positioned for transmethylation. While distal from the site of transmethylation, the propanoid tail substituent governs the kinetic preference of ryegrass COMT for aldehydes over alcohols and acids due to a single hydrogen bond donor for the C9 oxygenated moiety dictating the preference for an aldehyde. PMID:21177481

  8. Structure-function analyses of a caffeic acid O-methyltransferase from perennial ryegrass reveal the molecular basis for substrate preference.

    Science.gov (United States)

    Louie, Gordon V; Bowman, Marianne E; Tu, Yi; Mouradov, Aidyn; Spangenberg, German; Noel, Joseph P

    2010-12-01

    Lignin forms from the polymerization of phenylpropanoid-derived building blocks (the monolignols), whose modification through hydroxylation and O-methylation modulates the chemical and physical properties of the lignin polymer. The enzyme caffeic acid O-methyltransferase (COMT) is central to lignin biosynthesis. It is often targeted in attempts to engineer the lignin composition of transgenic plants for improved forage digestibility, pulping efficiency, or utility in biofuel production. Despite intensive investigation, the structural determinants of the regiospecificity and substrate selectivity of COMT remain poorly defined. Reported here are x-ray crystallographic structures of perennial ryegrass (Lolium perenne) COMT (Lp OMT1) in open conformational state, apo- and holoenzyme forms and, most significantly, in a closed conformational state complexed with the products S-adenosyl-L-homocysteine and sinapaldehyde. The product-bound complex reveals the post-methyl-transfer organization of COMT's catalytic groups with reactant molecules and the fully formed phenolic-ligand binding site. The core scaffold of the phenolic ligand forges a hydrogen-bonding network involving the 4-hydroxy group that anchors the aromatic ring and thereby permits only metahydroxyl groups to be positioned for transmethylation. While distal from the site of transmethylation, the propanoid tail substituent governs the kinetic preference of ryegrass COMT for aldehydes over alcohols and acids due to a single hydrogen bond donor for the C9 oxygenated moiety dictating the preference for an aldehyde.

  9. Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis.

    Science.gov (United States)

    Wei, Tao; Deng, Kejun; Wang, Hongbin; Zhang, Lipeng; Wang, Chunguo; Song, Wenqin; Zhang, Yong; Chen, Chengbin

    2018-03-12

    In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT) and AtDREB1A -expressing transgenic plants using RNA-sequencing (RNA-seq). Using cluster analysis, we identified 3904 differentially expressed genes (DEGs). Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the 'signal transduction mechanisms' category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation, DEGs associated with "ribosome", "plant hormone signal transduction", photosynthesis", "plant-pathogen interaction", "glycolysis/gluconeogenesis" and "carbon fixation" are hypothesized to perform major functions in drought resistance in AtDREB1A -expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

  10. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    International Nuclear Information System (INIS)

    Bao, Guanhui; Dong, Hongjun; Zhu, Yan; Mao, Shaoming; Zhang, Tianrui; Zhang, Yanping; Chen, Zugen; Li, Yin

    2014-01-01

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance

  11. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  12. Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia

    Science.gov (United States)

    Graw, Frederik; Leitner, Thomas; Ribeiro, Ruy M.

    2012-01-01

    Injecting drug users (IDU) are a driving force for the spread of HIV-1 in Latvia and other Baltic States, accounting for a majority of cases. However, in recent years, heterosexual cases have increased disproportionately. It is unclear how the changes in incidence patterns in Latvia can be explained, and how important IDU are for the heterosexual sub-epidemic. We introduce a novel epidemic model and use phylogenetic analyses in parallel to examine the spread of HIV-1 in Latvia between 1987 and 2010. Using a hybrid framework with a mean-field description for the susceptible population and an agent-based model for the infecteds, we track infected individuals and follow transmission histories dynamically formed during the simulation. The agent-based simulations and the phylogenetic analysis show that more than half of the heterosexual transmissions in Latvia were caused by IDU, which sustain the heterosexual epidemic. Indeed, we find that heterosexual clusters are characterized by short transmission chains with up to 63% of the chains dying out after the first introduction. In the simulations, the distribution of transmission chain sizes follows a power law distribution, which is confirmed by the phylogenetic data. Our models indicate that frequent introductions reduced the extinction probability of an autonomously spreading heterosexual HIV-1 epidemic, which now has the potential to dominate the spread of the overall epidemic in the future. Furthermore, our model shows that social heterogeneity of the susceptible population can explain the shift in HIV-1 incidence in Latvia over the course of the epidemic. Thus, the decrease in IDU incidence may be due to local heterogeneities in transmission, rather than the implementation of control measures. Increases in susceptibles, through social or geographic movement of IDU, could lead to a boost in HIV-1 infections in this risk group. Targeting individuals that bridge social groups would help prevent further spread of the

  13. Comparative genomic and proteomic analyses of Clostridium acetobutylicum Rh8 and its parent strain DSM 1731 revealed new understandings on butanol tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Guanhui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); University of Chinese Academy of Sciences, Beijing (China); Dong, Hongjun; Zhu, Yan; Mao, Shaoming [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Zhang, Tianrui [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin (China); Zhang, Yanping [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China); Chen, Zugen [Department of Human Genetics, School of Medicine, University of California, Los Angeles, CA 90095 (United States); Li, Yin, E-mail: yli@im.ac.cn [CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing (China)

    2014-08-08

    Highlights: • Genomes of a butanol tolerant strain and its parent strain were deciphered. • Comparative genomic and proteomic was applied to understand butanol tolerance. • None differentially expressed proteins have mutations in its corresponding genes. • Mutations in ribosome might be responsible for the global difference of proteomics. - Abstract: Clostridium acetobutylicum strain Rh8 is a butanol-tolerant mutant which can tolerate up to 19 g/L butanol, 46% higher than that of its parent strain DSM 1731. We previously performed comparative cytoplasm- and membrane-proteomic analyses to understand the mechanism underlying the improved butanol tolerance of strain Rh8. In this work, we further extended this comparison to the genomic level. Compared with the genome of the parent strain DSM 1731, two insertion sites, four deletion sites, and 67 single nucleotide variations (SNVs) are distributed throughout the genome of strain Rh8. Among the 67 SNVs, 16 SNVs are located in the predicted promoters and intergenic regions; while 29 SNVs are located in the coding sequence, affecting a total of 21 proteins involved in transport, cell structure, DNA replication, and protein translation. The remaining 22 SNVs are located in the ribosomal genes, affecting a total of 12 rRNA genes in different operons. Analysis of previous comparative proteomic data indicated that none of the differentially expressed proteins have mutations in its corresponding genes. Rchange Algorithms analysis indicated that the mutations occurred in the ribosomal genes might change the ribosome RNA thermodynamic characteristics, thus affect the translation strength of these proteins. Take together, the improved butanol tolerance of C. acetobutylicum strain Rh8 might be acquired through regulating the translational process to achieve different expression strength of genes involved in butanol tolerance.

  14. Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode).

    Science.gov (United States)

    Alkharouf, Nadim W; Klink, Vincent P; Chouikha, Imed B; Beard, Hunter S; MacDonald, Margaret H; Meyer, Susan; Knap, Halina T; Khan, Rana; Matthews, Benjamin F

    2006-09-01

    Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.

  15. Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation

    Science.gov (United States)

    Hou, Junjie; Zhang, Chengqian; Xue, Peng; Wang, Jifeng; Chen, Xiulan; Guo, Xiaojing; Yang, Fuquan

    2017-01-01

    Ovarian cancer is one of the most common cancer among women in the world, and chemotherapy remains the principal treatment for patients. However, drug resistance is a major obstacle to the effective treatment of ovarian cancers and the underlying mechanism is not clear. An increased understanding of the mechanisms that underline the pathogenesis of drug resistance is therefore needed to develop novel therapeutics and diagnostic. Herein, we report the comparative analysis of the doxorubicin sensitive OVCAR8 cells and its doxorubicin-resistant variant NCI/ADR-RES cells using integrated global proteomics and N-glycoproteomics. A total of 1525 unique N-glycosite-containing peptides from 740 N-glycoproteins were identified and quantified, of which 253 N-glycosite-containing peptides showed significant change in the NCI/ADR-RES cells. Meanwhile, stable isotope labeling by amino acids in cell culture (SILAC) based comparative proteomic analysis of the two ovarian cancer cells led to the quantification of 5509 proteins. As about 50% of the identified N-glycoproteins are low-abundance membrane proteins, only 44% of quantified unique N-glycosite-containing peptides had corresponding protein expression ratios. The comparison and calibration of the N-glycoproteome versus the proteome classified 14 change patterns of N-glycosite-containing peptides, including 8 up-regulated N-glycosite-containing peptides with the increased glycosylation sites occupancy, 35 up-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy, 2 down-regulated N-glycosite-containing peptides with the decreased glycosylation sites occupancy, 46 down-regulated N-glycosite-containing peptides with the unchanged glycosylation sites occupancy. Integrated proteomic and N-glycoproteomic analyses provide new insights, which can help to unravel the relationship of N-glycosylation and multidrug resistance (MDR), understand the mechanism of MDR, and discover the new diagnostic and

  16. Genome-Wide Transcription and Functional Analyses Reveal Heterogeneous Molecular Mechanisms Driving Pyrethroids Resistance in the Major Malaria Vector Anopheles funestus Across Africa.

    Science.gov (United States)

    Riveron, Jacob M; Ibrahim, Sulaiman S; Mulamba, Charles; Djouaka, Rousseau; Irving, Helen; Wondji, Murielle J; Ishak, Intan H; Wondji, Charles S

    2017-06-07

    Pyrethroid resistance in malaria vector, An. funestus is increasingly reported across Africa, threatening the sustainability of pyrethroid-based control interventions, including long lasting insecticidal nets (LLINs). Managing this problem requires understanding of the molecular basis of the resistance from different regions of the continent, to establish whether it is being driven by a single or independent selective events. Here, using a genome-wide transcription profiling of pyrethroid resistant populations from southern (Malawi), East (Uganda), and West Africa (Benin), we investigated the molecular basis of resistance, revealing strong differences between the different African regions. The duplicated cytochrome P450 genes ( CYP6P9a and CYP6P9b ) which were highly overexpressed in southern Africa are not the most upregulated in other regions, where other genes are more overexpressed, including GSTe2 in West (Benin) and CYP9K1 in East (Uganda). The lack of directional selection on both CYP6P9a and CYP6P9b in Uganda in contrast to southern Africa further supports the limited role of these genes outside southern Africa. However, other genes such as the P450 CYP9J11 are commonly overexpressed in all countries across Africa. Here, CYP9J11 is functionally characterized and shown to confer resistance to pyrethroids and moderate cross-resistance to carbamates (bendiocarb). The consistent overexpression of GSTe2 in Benin is coupled with a role of allelic variation at this gene as GAL4-UAS transgenic expression in Drosophila flies showed that the resistant 119F allele is highly efficient in conferring both DDT and permethrin resistance than the L119. The heterogeneity in the molecular basis of resistance and cross-resistance to insecticides in An. funestus populations throughout sub-Saharan African should be taken into account in designing resistance management strategies. Copyright © 2017 Riveron et al.

  17. Compositional and expression analyses of the glideosome during the Plasmodium life cycle reveal an additional myosin light chain required for maximum motility.

    Science.gov (United States)

    Green, Judith L; Wall, Richard J; Vahokoski, Juha; Yusuf, Noor A; Ridzuan, Mohd A Mohd; Stanway, Rebecca R; Stock, Jessica; Knuepfer, Ellen; Brady, Declan; Martin, Stephen R; Howell, Steven A; Pires, Isa P; Moon, Robert W; Molloy, Justin E; Kursula, Inari; Tewari, Rita; Holder, Anthony A

    2017-10-27

    Myosin A (MyoA) is a Class XIV myosin implicated in gliding motility and host cell and tissue invasion by malaria parasites. MyoA is part of a membrane-associated protein complex called the glideosome, which is essential for parasite motility and includes the MyoA light chain myosin tail domain-interacting protein (MTIP) and several glideosome-associated proteins (GAPs). However, most studies of MyoA have focused on single stages of the parasite life cycle. We examined MyoA expression throughout the Plasmodium berghei life cycle in both mammalian and insect hosts. In extracellular ookinetes, sporozoites, and merozoites, MyoA was located at the parasite periphery. In the sexual stages, zygote formation and initial ookinete differentiation precede MyoA synthesis and deposition, which occurred only in the developing protuberance. In developing intracellular asexual blood stages, MyoA was synthesized in mature schizonts and was located at the periphery of segmenting merozoites, where it remained throughout maturation, merozoite egress, and host cell invasion. Besides the known GAPs in the malaria parasite, the complex included GAP40, an additional myosin light chain designated essential light chain (ELC), and several other candidate components. This ELC bound the MyoA neck region adjacent to the MTIP-binding site, and both myosin light chains co-located to the glideosome. Co-expression of MyoA with its two light chains revealed that the presence of both light chains enhances MyoA-dependent actin motility. In conclusion, we have established a system to study the interplay and function of the three glideosome components, enabling the assessment of inhibitors that target this motor complex to block host cell invasion. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and gamma-rays.

    Science.gov (United States)

    Kimura, Shinzo; Ishidou, Emi; Kurita, Sakiko; Suzuki, Yoshiteru; Shibato, Junko; Rakwal, Randeep; Iwahashi, Hitoshi

    2006-07-21

    Ionizing radiation (IR) is the most enigmatic of genotoxic stress inducers in our environment that has been around from the eons of time. IR is generally considered harmful, and has been the subject of numerous studies, mostly looking at the DNA damaging effects in cells and the repair mechanisms therein. Moreover, few studies have focused on large-scale identification of cellular responses to IR, and to this end, we describe here an initial study on the transcriptional responses of the unicellular genome model, yeast (Saccharomyces cerevisiae strain S288C), by cDNA microarray. The effect of two different IR, X-rays, and gamma (gamma)-rays, was investigated by irradiating the yeast cells cultured in YPD medium with 50 Gy doses of X- and gamma-rays, followed by resuspension of the cells in YPD for time-course experiments. The samples were collected for microarray analysis at 20, 40, and 80 min after irradiation. Microarray analysis revealed a time-course transcriptional profile of changed gene expressions. Up-regulated genes belonged to the functional categories mainly related to cell cycle and DNA processing, cell rescue defense and virulence, protein and cell fate, and metabolism (X- and gamma-rays). Similarly, for X- and gamma-rays, the down-regulated genes belonged to mostly transcription and protein synthesis, cell cycle and DNA processing, control of cellular organization, cell fate, and C-compound and carbohydrate metabolism categories, respectively. This study provides for the first time a snapshot of the genome-wide mRNA expression profiles in X- and gamma-ray post-irradiated yeast cells and comparatively interprets/discusses the changed gene functional categories as effects of these two radiations vis-à-vis their energy levels.

  19. Structure-function analyses reveal the molecular architecture and neutralization mechanism of a bacterial HEPN-MNT toxin-antitoxin system.

    Science.gov (United States)

    Jia, Xuanyan; Yao, Jianyun; Gao, Zengqiang; Liu, Guangfeng; Dong, Yu-Hui; Wang, Xiaoxue; Zhang, Heng

    2018-05-04

    Toxin-antitoxin (TA) loci in bacteria are small genetic modules that regulate various cellular activities, including cell growth and death. The two-gene module encoding a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and a cognate MNT (minimal nucleotidyltransferase) domain have been predicted to represent a novel type II TA system prevalent in archaea and bacteria. However, the neutralization mechanism and cellular targets of the TA family remain unclear. The toxin SO_3166 having a HEPN domain and its cognate antitoxin SO_3165 with an MNT domain constitute a typical type II TA system that regulates cell motility and confers plasmid stability in the bacterium Shewanella oneidensis Here, we report the crystal structure and solution conformation of the SO_3166-SO_3165 pair, representing the first complex structures in this TA family. The structures revealed that SO_3165 and SO_3166 form a tight heterooctamer (at a 2:6 ratio), an organization that is very rare in other TA systems. We also observed that SO_3166 dimerization enables the formation of a deep cleft at the HEPN-domain interface harboring a composite R X 4-6H active site that functions as an RNA-cleaving RNase. SO_3165 bound SO_3166 mainly through its two α-helices (α2 and α4), functioning as molecular recognition elements. Moreover, their insertion into the SO_3166 cleft sterically blocked the R X 4-6H site or narrowed the cleft to inhibit RNA substrate binding. Structure-based mutagenesis confirmed the important roles of these α-helices in SO_3166 binding and inhibition. Our structure-function analysis provides first insights into the neutralization mechanism of the HEPN-MNT TA family. © 2018 Jia et al.

  20. Proteomic and Metabolomic Analyses Reveal Contrasting Anti-Inflammatory Effects of an Extract of Mucor Racemosus Secondary Metabolites Compared to Dexamethasone.

    Science.gov (United States)

    Meier, Samuel M; Muqaku, Besnik; Ullmann, Ronald; Bileck, Andrea; Kreutz, Dominique; Mader, Johanna C; Knasmüller, Siegfried; Gerner, Christopher

    2015-01-01

    Classical drug assays are often confined to single molecules and targeting single pathways. However, it is also desirable to investigate the effects of complex mixtures on complex systems such as living cells including the natural multitude of signalling pathways. Evidence based on herbal medicine has motivated us to investigate potential beneficial health effects of Mucor racemosus (M rac) extracts. Secondary metabolites of M rac were collected using a good-manufacturing process (GMP) approved production line and a validated manufacturing process, in order to obtain a stable product termed SyCircue (National Drug Code USA: 10424-102). Toxicological studies confirmed that this product does not contain mycotoxins and is non-genotoxic. Potential effects on inflammatory processes were investigated by treating stimulated cells with M rac extracts and the effects were compared to the standard anti-inflammatory drug dexamethasone on the levels of the proteome and metabolome. Using 2D-PAGE, slight anti-inflammatory effects were observed in primary white blood mononuclear cells, which were more pronounced in primary human umbilical vein endothelial cells (HUVECs). Proteome profiling based on nLC-MS/MS analysis of tryptic digests revealed inhibitory effects of M rac extracts on pro-inflammatory cytoplasmic mediators and secreted cytokines and chemokines in these endothelial cells. This finding was confirmed using targeted proteomics, here treatment of stimulated cells with M rac extracts down-regulated the secretion of IL-6, IL-8, CXCL5 and GROA significantly. Finally, the modulating effects of M rac on HUVECs were also confirmed on the level of the metabolome. Several metabolites displayed significant concentration changes upon treatment of inflammatory activated HUVECs with the M rac extract, including spermine and lysophosphatidylcholine acyl C18:0 and sphingomyelin C26:1, while the bulk of measured metabolites remained unaffected. Interestingly, the effects of M rac

  1. Genome-Wide Transcription and Functional Analyses Reveal Heterogeneous Molecular Mechanisms Driving Pyrethroids Resistance in the Major Malaria Vector Anopheles funestus Across Africa

    Science.gov (United States)

    Riveron, Jacob M.; Ibrahim, Sulaiman S.; Mulamba, Charles; Djouaka, Rousseau; Irving, Helen; Wondji, Murielle J.; Ishak, Intan H.; Wondji, Charles S.

    2017-01-01

    Pyrethroid resistance in malaria vector, An. funestus is increasingly reported across Africa, threatening the sustainability of pyrethroid-based control interventions, including long lasting insecticidal nets (LLINs). Managing this problem requires understanding of the molecular basis of the resistance from different regions of the continent, to establish whether it is being driven by a single or independent selective events. Here, using a genome-wide transcription profiling of pyrethroid resistant populations from southern (Malawi), East (Uganda), and West Africa (Benin), we investigated the molecular basis of resistance, revealing strong differences between the different African regions. The duplicated cytochrome P450 genes (CYP6P9a and CYP6P9b) which were highly overexpressed in southern Africa are not the most upregulated in other regions, where other genes are more overexpressed, including GSTe2 in West (Benin) and CYP9K1 in East (Uganda). The lack of directional selection on both CYP6P9a and CYP6P9b in Uganda in contrast to southern Africa further supports the limited role of these genes outside southern Africa. However, other genes such as the P450 CYP9J11 are commonly overexpressed in all countries across Africa. Here, CYP9J11 is functionally characterized and shown to confer resistance to pyrethroids and moderate cross-resistance to carbamates (bendiocarb). The consistent overexpression of GSTe2 in Benin is coupled with a role of allelic variation at this gene as GAL4-UAS transgenic expression in Drosophila flies showed that the resistant 119F allele is highly efficient in conferring both DDT and permethrin resistance than the L119. The heterogeneity in the molecular basis of resistance and cross-resistance to insecticides in An. funestus populations throughout sub-Saharan African should be taken into account in designing resistance management strategies. PMID:28428243

  2. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos

    Science.gov (United States)

    Wang, Xinyi; Liu, Denghui; He, Dajian; Suo, Shengbao; Xia, Xian; He, Xiechao; Han, Jing-Dong J.; Zheng, Ping

    2017-01-01

    Preimplantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell-fate commitment. The molecular basis of these processes remains obscure in primates in which there is a high rate of embryo wastage. Thus, understanding the factors involved in genome reprogramming and ZGA might help reproductive success during this susceptible period of early development and generate induced pluripotent stem cells with greater efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution. By using RNA-seq in single and pooled oocytes and embryos, we defined the transcriptome throughout preimplantation development in rhesus monkey. In comparison to archival human and mouse data, we found that the transcriptome dynamics of monkey oocytes and embryos were very similar to those of human but very different from those of mouse. We identified several classes of maternal and zygotic genes, whose expression peaks were highly correlated with the time frames of genome reprogramming, ZGA, and cell-fate commitment, respectively. Importantly, comparison of the ZGA-related network modules among the three species revealed less robust surveillance of genomic instability in primate oocytes and embryos than in rodents, particularly in the pathways of DNA damage signaling and homology-directed DNA double-strand break repair. This study highlights the utility of monkey models to better understand the molecular basis for genome reprogramming, ZGA, and genomic stability surveillance in human early embryogenesis and may provide insights for improved homologous recombination-mediated gene editing in monkey. PMID:28223401

  3. Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex.

    Science.gov (United States)

    Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

    2014-10-24

    The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Novel Binding Motif and New Flexibility Revealed by Structural Analyses of a Pyruvate Dehydrogenase-Dihydrolipoyl Acetyltransferase Subcomplex from the Escherichia coli Pyruvate Dehydrogenase Multienzyme Complex*

    Science.gov (United States)

    Arjunan, Palaniappa; Wang, Junjie; Nemeria, Natalia S.; Reynolds, Shelley; Brown, Ian; Chandrasekhar, Krishnamoorthy; Calero, Guillermo; Jordan, Frank; Furey, William

    2014-01-01

    The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly. PMID:25210042

  5. Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

    Science.gov (United States)

    Malone, Kerri M.; Rue-Albrecht, Kévin; Magee, David A.; Conlon, Kevin; Schubert, Olga T.; Nalpas, Nicolas C.; Browne, John A.; Smyth, Alicia; Gormley, Eamonn; Aebersold, Ruedi; MacHugh, David E.; Gordon, Stephen V.

    2018-01-01

    Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection. PMID:29557774

  6. Comparative Transcriptome Analyses Reveal Potential Mechanisms of Enhanced Drought Tolerance in Transgenic Salvia Miltiorrhiza Plants Expressing AtDREB1A from Arabidopsis

    Directory of Open Access Journals (Sweden)

    Tao Wei

    2018-03-01

    Full Text Available In our previous study, drought-resistant transgenic plants of Salvia miltiorrhiza were produced via overexpression of the transcription factor AtDREB1A. To unravel the molecular mechanisms underpinning elevated drought tolerance in transgenic plants, in the present study we compared the global transcriptional profiles of wild-type (WT and AtDREB1A-expressing transgenic plants using RNA-sequencing (RNA-seq. Using cluster analysis, we identified 3904 differentially expressed genes (DEGs. Compared with WT plants, 423 unigenes were up-regulated in pRD29A::AtDREB1A-31 before drought treatment, while 936 were down-regulated and 1580 and 1313 unigenes were up- and down-regulated after six days of drought. COG analysis revealed that the ‘signal transduction mechanisms’ category was highly enriched among these DEGs both before and after drought stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG annotation, DEGs associated with “ribosome”, “plant hormone signal transduction”, photosynthesis”, “plant-pathogen interaction”, “glycolysis/gluconeogenesis” and “carbon fixation” are hypothesized to perform major functions in drought resistance in AtDREB1A-expressing transgenic plants. Furthermore, the number of DEGs associated with different transcription factors increased significantly after drought stress, especially the AP2/ERF, bZIP and MYB protein families. Taken together, this study substantially expands the transcriptomic information for S. miltiorrhiza and provides valuable clues for elucidating the mechanism of AtDREB1A-mediated drought tolerance in transgenic plants.

  7. Aznar, Hanotin, and May (eds., À la place du roi. Vice-rois, gouverneurs et ambassadeurs dans les monarchies française et espanole (Casa de Velázquez, 2014

    Directory of Open Access Journals (Sweden)

    Lisandra Estevez

    2016-06-01

    Full Text Available The French and Spanish courts were two of the most powerful cultural and political institutions in seventeenth-century Europe.  Both rivals and allies, the French and Spanish crowns were bound by disputes and diplomacy.  This anthology examines the Gallic and Iberian court systems from a comparative approach, filling an important lacuna in early modern political studies and diplomatic history.  It is based on the proceedings of a seminar held at the Casa de Velázquez, Madrid in June 2010. Edited by Daniel Aznar, Guillaume Hanotin and Niels F. May, À la place du roi. Vice-rois, gouverneurs et ambassadeurs dans les monarchies française et espanole (XVIe-XVIIIe siècles unites ten essays by leading scholars of seventeenth-century French and Spanish history.

  8. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

    Science.gov (United States)

    Laing, Chad R; Buchanan, Cody; Taboada, Eduardo N; Zhang, Yongxiang; Karmali, Mohamed A; Thomas, James E; Gannon, Victor Pj

    2009-06-29

    accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

  9. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

    Directory of Open Access Journals (Sweden)

    Karmali Mohamed A

    2009-06-01

    methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

  10. Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Men, Yujie; Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa; Liu, Shuang-Jiang

    2017-02-10

    ABSTRACT

    The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions.

    IMPORTANCEThe key

  11. Molecular analyses reveal an abundant diversity of ticks and rickettsial agents associated with wild birds in two regions of primary Brazilian Atlantic Rainforest.

    Science.gov (United States)

    Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; McIntosh, Douglas

    2017-06-01

    Brazilian wild birds are recognized as frequent and important hosts for immature stages of more than half of the 32 recognized species of Amblyomma ticks recorded in that country. Several species of Amblyomma harbor rickettsial agents, including members of the spotted fever group (SFG). Most studies on this topic relied primarily on morphological characterization and reported large portions of the collected ticks at the genus rather than species level. Clearly, this factor may have contributed to an underestimation of tick diversity and distribution and makes comparisons between studies difficult. The current investigation combined morphological and molecular analyses to assess the diversity of ticks and rickettsial agents associated with wild birds, captured in two regions of native Atlantic rainforest, in the state of Rio de Janeiro, Brazil. A total of 910 birds were captured, representing two orders, 34 families and 106 species, among which 93 specimens (10.2%), were parasitized by 138 immature ticks (60 larvae and 78 nymphs), representing 10 recognized species of the genus Amblyomma; together with two reasonably well classified haplotypes (Amblyomma sp. haplotype Nazaré and Amblyomma sp. strain USNTC 6792). Amplification by PCR and sequencing of rickettsial genes (htrA, gltA, ompA and ompB), demonstrated the presence of Rickettsia DNA in 48 (34%) of the ticks. Specifically, Rickettsia bellii was detected in a single larva and a single nymph of A. aureolatum; R. amblyomatis was found in 16 of 37 A. longirostre and was recorded for the first time in three nymphs of A. calcaratum; R. rhipicephali was detected in 9 (47%) of 19 Amblyomma sp. haplotype Nazaré ticks. The remaining ticks were infected with genetic variants of R. parkeri, namely strain ApPR in 12 A. parkeri and seven Amblyomma sp. haplotype Nazaré ticks, with the strain NOD found in two specimens of A. nodosum. Interestingly, a single larvae of A. ovale was shown to be infected with the emerging

  12. A framework supporting the development of a Grid portal for analysis based on ROI.

    Science.gov (United States)

    Ichikawa, K; Date, S; Kaishima, T; Shimojo, S

    2005-01-01

    In our research on brain function analysis, users require two different simultaneous types of processing: interactive processing to a specific part of data and high-performance batch processing to an entire dataset. The difference between these two types of processing is in whether or not the analysis is for data in the region of interest (ROI). In this study, we propose a Grid portal that has a mechanism to freely assign computing resources to the users on a Grid environment according to the users' two different types of processing requirements. We constructed a Grid portal which integrates interactive processing and batch processing by the following two mechanisms. First, a job steering mechanism controls job execution based on user-tagged priority among organizations with heterogeneous computing resources. Interactive jobs are processed in preference to batch jobs by this mechanism. Second, a priority-based result delivery mechanism that administrates a rank of data significance. The portal ensures a turn-around time of interactive processing by the priority-based job controlling mechanism, and provides the users with quality of services (QoS) for interactive processing. The users can access the analysis results of interactive jobs in preference to the analysis results of batch jobs. The Grid portal has also achieved high-performance computation of MEG analysis with batch processing on the Grid environment. The priority-based job controlling mechanism has been realized to freely assign computing resources to the users' requirements. Furthermore the achievement of high-performance computation contributes greatly to the overall progress of brain science. The portal has thus made it possible for the users to flexibly include the large computational power in what they want to analyze.

  13. Automatic feature learning using multichannel ROI based on deep structured algorithms for computerized lung cancer diagnosis.

    Science.gov (United States)

    Sun, Wenqing; Zheng, Bin; Qian, Wei

    2017-10-01

    This study aimed to analyze the ability of extracting automatically generated features using deep structured algorithms in lung nodule CT image diagnosis, and compare its performance with traditional computer aided diagnosis (CADx) systems using hand-crafted features. All of the 1018 cases were acquired from Lung Image Database Consortium (LIDC) public lung cancer database. The nodules were segmented according to four radiologists' markings, and 13,668 samples were generated by rotating every slice of nodule images. Three multichannel ROI based deep structured algorithms were designed and implemented in this study: convolutional neural network (CNN), deep belief network (DBN), and stacked denoising autoencoder (SDAE). For the comparison purpose, we also implemented a CADx system using hand-crafted features including density features, texture features and morphological features. The performance of every scheme was evaluated by using a 10-fold cross-validation method and an assessment index of the area under the receiver operating characteristic curve (AUC). The observed highest area under the curve (AUC) was 0.899±0.018 achieved by CNN, which was significantly higher than traditional CADx with the AUC=0.848±0.026. The results from DBN was also slightly higher than CADx, while SDAE was slightly lower. By visualizing the automatic generated features, we found some meaningful detectors like curvy stroke detectors from deep structured schemes. The study results showed the deep structured algorithms with automatically generated features can achieve desirable performance in lung nodule diagnosis. With well-tuned parameters and large enough dataset, the deep learning algorithms can have better performance than current popular CADx. We believe the deep learning algorithms with similar data preprocessing procedure can be used in other medical image analysis areas as well. Copyright © 2017. Published by Elsevier Ltd.

  14. The regulation mechanisms of soluble starch and glycerol for production of azaphilone pigments in Monascus purpureus FAFU618 as revealed by comparative proteomic and transcriptional analyses.

    Science.gov (United States)

    Huang, Zi-Rui; Zhou, Wen-Bin; Yang, Xue-Ling; Tong, Ai-Jun; Hong, Jia-Li; Guo, Wei-Ling; Li, Tian-Tian; Jia, Rui-Bo; Pan, Yu-Yang; Lin, Jun; Lv, Xu-Cong; Liu, Bin

    2018-04-01

    Monascus spp. have been used for thousands of years as a traditional food additive in China. This mold can produce many different types of commercially valuable secondary metabolites of biological activity. Soluble starch and glycerol are the two principal carbon sources universally utilized by Monascus for the production of beneficial metabolites. In this study, the effects and regulation mechanisms of soluble starch and glycerol for M. purpureus FAFU618 on Monascus azaphilone pigments (MonAzPs) were investigated through ultra-performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF-MS/MS), comparative proteomics and quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR). The production of intracellular and extracellular pigments was significantly different between the soluble starch group (SSG) and glycerol group (GCG). Additionally, the components of intracellular pigments revealed by UPLC-QTOF-MS/MS showed that Monascin and Ankaflavin increased significantly in the GCG, while Rubropunctatin and Monascorubrin increased in the SSG. Differentially expressed proteins of mycelia between SSG and GCG were analyzed by two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF MS. We identified 27 proteins with statistically altered expression, of which 18 proteins associated with the EMP (glycolytic pathway), translation, energy generation, proteolysis, etc. were up-regulated, and 9 proteins, including ribosomal proteins, heat shock proteins (HSPs) and others, were down-regulated in GCG. Meanwhile, the expression levels of MonAzP biosynthetic genes were also analyzed by RT-qPCR, and the results showed that mppA, mppC, mppR1 and mppR2 were down-regulated, whereas genes MpPKS5, MpFasA2, MpFasB2, mppB, mppD and mppE were up-regulated. Collectively, these findings illustrate that the regulation of MonAzPs is not only closely related to the expression levels of certain proteins in the polyketide synthesis pathway

  15. Ludwig, un roi sur la lune : l’histoire d’un roi fou jouée par des comédien.ne.s en situation de handicap mental

    Directory of Open Access Journals (Sweden)

    Marie Astier

    2017-12-01

    Full Text Available Ludwig, un roi sur la lune, spectacle mis en scène par Madeleine Louarn avec les comédien.ne.s professionnels en situation de handicap mental de l’Atelier Catalyse et présenté lors de la dernière édition du Festival d’Avignon n’est pas une reconstitution historique de la vie de Louis II de Bavière, roi du XIXe siècle diagnostiqué paranoïaque et destitué pour être interné, mais une tentative de transcrire théâtralement la perception du monde d’un homme amoureux de l’Art, de la nature et des hommes, mais qui devait être Roi. Ce n’est ni un personnage ni des comédien.ne.s « handicapé.e.s » que nous sommes invités à voir, mais les visions de Ludwig incarnées par des comédien.ne.s qui se trouvent être en situation de handicap mental. Dans ce spectacle, la « folie » devenue plus tard « handicap mental » apparaît sous les traits de la non-conformité bien plus que sous ceux de la pathologie.

  16. Mid- to Late Holocene climate development in Central Asia as revealed from multi-proxy analyses of sediments from Lake Son Kol (Kyrgyzstan)

    Science.gov (United States)

    Lauterbach, Stefan; Dulski, Peter; Gleixner, Gerd; Hettler-Riedel, Sabine; Mingram, Jens; Plessen, Birgit; Prasad, Sushma; Schwalb, Antje; Schwarz, Anja; Stebich, Martina; Witt, Roman

    2013-04-01

    A mid-Holocene shift from predominantly wet to significantly drier climate conditions, attributed to the weakening of the Asian summer monsoon (ASM), is documented in numerous palaeoclimate records from the monsoon-influenced parts of Asia, e.g. the Tibetan Plateau and north- and southeastern China. In contrast, Holocene climate development in the arid regions of mid-latitude Central Asia, located north and northwest of the Tibetan Plateau, is less well-constrained but supposed to have been influenced by a complex interaction between the mid-latitude Westerlies and the ASM. Hence, well-dated and highly resolved palaeoclimate records from Central Asia might provide important information about spatio-temporal changes in the regional interplay between Westerlies and ASM and thus aid the understanding of global climate teleconnections. As a part of the project CADY (Central Asian Climate Dynamics), aiming at reconstructing past climatic and hydrological variability in Central Asia, several sediment cores were recovered from alpine Lake Son Kol (41° 48'N, 75° 12'E, 3016 m a. s. l.) in the Central Tian Shan of Kyrgyzstan. A radiocarbon-dated sediment sequence of 154.5 cm length, covering approximately the last 6000 years, was investigated by using a multi-proxy approach, including sedimentological, (bio)geochemical, isotopic and micropalaeontological analyses. Preliminary proxy data indicate hydrologically variable but predominantly wet conditions until ca. 5100 cal. a BP, characterized by the deposition of finely laminated organic-carbonatic sediments. In contrast to monsoonal Asia, where a distinct trend towards drier conditions is observed since the mid-Holocene, the hydrologically variable interval at Lake Son Kol was apparently followed by an only short-term dry episode between ca. 5100 and 4200 cal. a BP. This is characterized by a higher δD of the C29 n-alkanes, probably reflecting increased evapotranspiration. Also pollen, diatom and ostracod data point

  17. Wavelet-based compression with ROI coding support for mobile access to DICOM images over heterogeneous radio networks.

    Science.gov (United States)

    Maglogiannis, Ilias; Doukas, Charalampos; Kormentzas, George; Pliakas, Thomas

    2009-07-01

    Most of the commercial medical image viewers do not provide scalability in image compression and/or region of interest (ROI) encoding/decoding. Furthermore, these viewers do not take into consideration the special requirements and needs of a heterogeneous radio setting that is constituted by different access technologies [e.g., general packet radio services (GPRS)/ universal mobile telecommunications system (UMTS), wireless local area network (WLAN), and digital video broadcasting (DVB-H)]. This paper discusses a medical application that contains a viewer for digital imaging and communications in medicine (DICOM) images as a core module. The proposed application enables scalable wavelet-based compression, retrieval, and decompression of DICOM medical images and also supports ROI coding/decoding. Furthermore, the presented application is appropriate for use by mobile devices activating in heterogeneous radio settings. In this context, performance issues regarding the usage of the proposed application in the case of a prototype heterogeneous system setup are also discussed.

  18. MEASURES OF EFFICIENCY AND INVESTMENTS RETURN: AN STUDY OF BRAZILIAN ELECTRICITY DISTRIBUTORS WITH DATA ENVELOPMENT ANALYSIS, MALMQUIST INDEX AND ROI

    Directory of Open Access Journals (Sweden)

    Valter Saurin

    2013-03-01

    Full Text Available This paper aims to determine, in a group of companies from the Brazilian electric sector, if there is a relationship between the return on investment (ROI and the concept of efficiency estimated by the method Data Envelopment Analysis (DEA, as well as evaluating the growth of productivity based on Malmquist Index (Fare et al, 1996. The hypothesis is that firms that had return on investment higher during certain period of time are those employed their resources efficiently in getting their outputs (DEA efficient. The input (1 Products (5 DEA model correspond to the operating cost (I, the network length (km, the number of consumers and the market billed high, medium and low voltage, respectively. The sample consisted of 31 companies of Brazilian electricity distribution and timing of the study was from 2007 to 2009. We calculated the Malmquist index (M0, represented by the change in total factor productivity (TFPC, which is composed by the evolution of technical efficiency (EC and the change in the technological frontier (TC of the companies were also determined ROI for each period. We calculated the correlation between the TFPC, TC, EC, score the DEA and the ROI for the period 2007 to 2009. The results showed a positive correlation, although weak, between efficiency change and the indexes mentioned above, rejecting the initial hypothesis

  19. A comparison between the conventional manual ROI method and an automatic algorithm for semiquantitative analysis of SPECT studies

    International Nuclear Information System (INIS)

    Pagan, L; Novi, B; Guidarelli, G; Tranfaglia, C; Galli, S; Lucchi, G; Fagioli, G

    2011-01-01

    In this study, the performance of a free software for automatic segmentation of striatal SPECT brain studies (BasGanV2 - www.aimn.it) and a standard manual Region Of Interest (ROI) method were compared. The anthropomorphic Alderson RSD phantom, filled with solutions at different concentration of 123 I-FP-CIT with Caudate-Putamen to Background ratios between 1 and 8.7 and Caudate to Putamen ratios between 1 and 2, was imaged on a Philips-Irix triple head gamma camera. Images were reconstructed using filtered back-projection and processed with both BasGanV2, that provides normalized striatal uptake values on volumetric anatomical ROIs, and a manual method, based on average counts per voxel in ROIs drawn in a three-slice section. Caudate-Putamen/Background and Caudate/Putamen ratios obtained with the two methods were compared with true experimental ratios. Good correlation was found for each method; BasGanV2, however, has higher R index (BasGan R mean = 0.95, p mean = 0.89, p 123 I-FP-CIT SPECT data with, moreover, the advantage of the availability of a control subject's database.

  20. Detecting high spatial variability of ice shelf basal mass balance, Roi Baudouin Ice Shelf, Antarctica

    Directory of Open Access Journals (Sweden)

    S. Berger

    2017-11-01

    Full Text Available Ice shelves control the dynamic mass loss of ice sheets through buttressing and their integrity depends on the spatial variability of their basal mass balance (BMB, i.e. the difference between refreezing and melting. Here, we present an improved technique – based on satellite observations – to capture the small-scale variability in the BMB of ice shelves. As a case study, we apply the methodology to the Roi Baudouin Ice Shelf, Dronning Maud Land, East Antarctica, and derive its yearly averaged BMB at 10 m horizontal gridding. We use mass conservation in a Lagrangian framework based on high-resolution surface velocities, atmospheric-model surface mass balance and hydrostatic ice-thickness fields (derived from TanDEM-X surface elevation. Spatial derivatives are implemented using the total-variation differentiation, which preserves abrupt changes in flow velocities and their spatial gradients. Such changes may reflect a dynamic response to localized basal melting and should be included in the mass budget. Our BMB field exhibits much spatial detail and ranges from −14.7 to 8.6 m a−1 ice equivalent. Highest melt rates are found close to the grounding line where the pressure melting point is high, and the ice shelf slope is steep. The BMB field agrees well with on-site measurements from phase-sensitive radar, although independent radar profiling indicates unresolved spatial variations in firn density. We show that an elliptical surface depression (10 m deep and with an extent of 0.7 km × 1.3 km lowers by 0.5 to 1.4 m a−1, which we tentatively attribute to a transient adaptation to hydrostatic equilibrium. We find evidence for elevated melting beneath ice shelf channels (with melting being concentrated on the channel's flanks. However, farther downstream from the grounding line, the majority of ice shelf channels advect passively (i.e. no melting nor refreezing toward the ice shelf front. Although the absolute, satellite

  1. Usefulness of a three-dimensional stereotaxic ROI template on anatomically standardised {sup 99m}Tc-ECD SPET

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Ryo [Department of Internal Medicine, Division of Nuclear Medicine, Nishi-Kobe Medical Center, Kobe (Japan); Yonekura, Yoshiharu [Biomedical Imaging Research Center, Fukui Medical University, Fukui (Japan); Matsuda, Hiroshi [Department of Radiology, National Center Hospital for Mental, Tokyo (Japan); Konishi, Junji [Department of Nuclear Medicine and Diagnostic Imaging, Graduate School of Medicine, Kyoto University, Kyoto (Japan)

    2002-03-01

    We have constructed a three-dimensional stereotaxic ROI template (3DSRT) on anatomically standardised cerebral blood flow (CBF) single-photon emission tomography (SPET) images to objectively estimate regional CBF (rCBF). The 3DSRT is composed of 259 regions of interest (ROIs) in 11 segments (1, superior frontal; 2, middle and inferior frontal; 3, primary sensorimotor; 4, parietal; 5, angular; 6, temporal; 7, occipital; 8, pericallosal; 9, lenticular nucleus; 10, thalamus; 11, hippocampus) on each side. We measured the rCBF values of the 518 ROIs and calculated the area-weighted average (segmental CBF; sCBF) of the 22 segments based on the rCBF in each ROI. We compared vascular reserve before and after revascularisation surgery using sCBF on anatomically standardised resting and acetazolamide (Acz)-challenged CBF SPET images, which were obtained using an equal-volume-split dual-injection single-day protocol [resting and vascular reserve (RVR) method] in 13 patients who had not suffered any major stroke but did have significant cerebrovascular stenosis. Prior to the evaluation, we examined the sCBF values of 16 subjects with various cerebrovascular conditions (8, normal; 3, lacunar infarction; 2, chronic infarction; 2, meningioma; 1, aneurysm) using physiological saline instead of Acz (placebo study) in order to confirm the reproducibility of the RVR method. In the placebo study we observed excellent linearity (y=1.444+0.964x) between the 352 pairs of baseline (x) and post-placebo (y) sCBF values in the 16 subjects, irrespective of the segment location. In all of the 13 patients, estimation of sCBF demonstrated impaired vascular reserve pre-operatively and improved vascular reserve postoperatively. We conclude that the 3DSRT, which could be identically set on the anatomically standardised images obtained at baseline and after Acz injection, allowed objective assessment of the pre- and postoperative vascular reserve, which was not easy with conventional ROI settings

  2. Baseline Marine Biological Survey ROI-NAMUR Outfall United States Army Kwajalein Atoll, Republic of the Marshall Islands, 1997(NODC Accession 0000630)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll(USAKA) central command post on...

  3. Baseline marine biological survey at Roi-Namur sewage outfall, United States Army Kwajalein Atoll, Republic of the Marshall Islands, 1997 (NODC Accession 0000630)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll (USAKA) central command post on...

  4. In situ observation data from the grouper roi (Cephalopholis argus) removal project in West Hawaii from 2010-2011 (NODC Accession 0082197)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — In situ observations of the introduced predatory grouper roi (Cephalopholis argus) were taken within the coral reef ecosystem of Puako, northwest side of the Island...

  5. Marine biological survey of ROI-NAMUR outfall at the United States Army Kwajalein Atoll, Republic of the Marshall Islands, May 2000 (NODC Accession 0000653)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Roi-Namur is located at the northernmost tip of Kwajalein Atoll, approximately 64 kilometers north of the U.S. Army Kwajalein Atoll (USAKA) central command post on...

  6. Analysing performance through value creation

    Directory of Open Access Journals (Sweden)

    Adrian TRIFAN

    2015-12-01

    Full Text Available This paper draws a parallel between measuring financial performance in 2 variants: the first one using data offered by accounting, which lays emphasis on maximizing profit, and the second one which aims to create value. The traditional approach to performance is based on some indicators from accounting data: ROI, ROE, EPS. The traditional management, based on analysing the data from accounting, has shown its limits, and a new approach is needed, based on creating value. The evaluation of value based performance tries to avoid the errors due to accounting data, by using other specific indicators: EVA, MVA, TSR, CVA. The main objective is shifted from maximizing the income to maximizing the value created for shareholders. The theoretical part is accompanied by a practical analysis regarding the creation of value and an analysis of the main indicators which evaluate this concept.

  7. The Study on Bone Mineral Density Measurement Error in Accordance with Change in ROI by Utilizing Dual Energy X-ray Absorptiometry

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yun Hong [Dept. of Diagnostic Radiology, Korea University Guro Hospital, Seoul (Korea, Republic of); Lee, In Ja [Dept. of Radiological Technology, Dongnam Health College, Suwon (Korea, Republic of); Yong, Hyung Jin [Dept. of Medicine Physics, The Graduate School of Biomedical Science Korea University, Seoul (Korea, Republic of)

    2012-03-15

    Dual Energy X-ray Absorptiometry(DEXA) is commonly used to diagnose Osteoporosis. The errors of DEXA bone density operation are caused by operator, bone mineral density meter, blood testing, patient. We focus on operator error then study about how much influence operator's region of intest(ROI) in bone testing result. During from March to July in 2011. 50 patients ware selected respectively from 30, 40, 50, 60, and 70 age groups who came to Korea University Medical Center(KUMC) for their Osteoporosis treatment. A-test was performed with usually ROI and B-test was performed with most widely ROI. Then, We compare A-test and B-test for find maximum difference of T-score error which occurred operator ROI controlling. Standard deviation of T-score of B-test showed 0.1 higher then A-test in femur neck. Standard deviation of B-test showed 0.2 higher then A-test in Ward's area which in Greater trocanter and Inter trocanter. Standard deviation of B-test showed 0,1 lower then A-test in L-1. Bone density testing about Two hundred patients results are as follow. When operator ROI was changed wider than normal ROI, bone density of femur was measured more higher but bone density of L-spine was measured more lower then normal bone density. That means, sometime DEXA bone density testing result is dependent by operator ROI controlling. This is relevant with the patient's medicine and health insurance, thus, tester always keep the size of ROI for to prevent any problem in the patient.

  8. Radiologic-pathologic analysis of quantitative 3D tumour enhancement on contrast-enhanced MR imaging: a study of ROI placement

    International Nuclear Information System (INIS)

    Chockalingam, Arun; Duran, Rafael; Sohn, Jae Ho; Schernthaner, Ruediger; Chapiro, Julius; Lee, Howard; Sahu, Sonia; Nguyen, Sonny; Geschwind, Jean-Francois; Lin, MingDe

    2016-01-01

    To investigate the influence of region-of-interest (ROI) placement on 3D tumour enhancement [Quantitative European Association for the Study of the Liver (qEASL)] in hepatocellular carcinoma (HCC) patients treated with transcatheter arterial chemoembolization (TACE). Phase 1: 40 HCC patients had nine ROIs placed by one reader using systematic techniques (3 ipsilateral to the lesion, 3 contralateral to the lesion, and 3 dispersed throughout the liver) and qEASL variance was measured. Intra-class correlations were computed. Phase 2: 15 HCC patients with histosegmentation were selected. Six ROIs were systematically placed by AC (3 ROIs ipsilateral and 3 ROIs contralateral to the lesion). Three ROIs were placed by 2 radiologists. qEASL values were compared to histopathology by Pearson's correlation, linear regression, and median difference. Phase 1: The dispersed method (abandoned in phase 2) had low consistency and high variance. Phase 2: qEASL correlated strongly with pathology in systematic methods [Pearson's correlation coefficient = 0.886 (ipsilateral) and 0.727 (contralateral)] and in clinical methods (0.625 and 0.879). However, ipsilateral placement matched best with pathology (median difference: 5.4 %; correlation: 0.89; regression CI: [0.904, 0.1409]). qEASL is a robust method with comparable values among tested placements. Ipsilateral placement showed high consistency and better pathological correlation. (orig.)

  9. Keeping it real--building an ROI model for an ambulatory EMR initiative that the physician practices espouse.

    Science.gov (United States)

    Mullen, Rńee; Donnelly, John T

    2006-01-01

    The ambulatory electronic medical record initiative at Magic Valley Regional Medical Center (MVRMC) in South Central Idaho underwent a rigorous product evaluation process that resulted in one of the market-leading EMR products being selected for implementation. MVRMC includes four business entities, including a 213-bed regional hospital and a 19-practice management services organization. Early in the process, the organization viewed buy-in from its physicians as a critical success factor. The physicians had been integral to product selection, and it was equally important for them to trust the economic model for its acquisition-especially because it was likely that they would be asked to put "some skin in the game." To make this initiative economically feasible, MVRMC received a grant from Agency for Healthcare Research and Quality based on the potential impact of the endeavor on healthcare delivery in the region. However, because the functional analysis did not result in the selection of the least expensive product, the AHRQ grant would only help defray the startup expenses, but not ongoing support and maintenance expenses after implementation; these costs would be borne by anticipated increases in the practice's revenue or reduction in its operating expenses. The ROI model would need to explain how each practice, from the single physician specialist to an almost 20-physician family practice, could pay for the desirable outcomes discussed during the selection phase of the project. The physicians, who had participated in technology initiatives in the past, were skeptical that cost-justifying an IT system was realistic, even though they recognized the potential benefits it could have on the quality and consistency of the care. Because some process standardization within and between practices would be needed to use electronic charting effectively, it was important that the ROI model did not outweigh the benefits of an as-yet untested operational workflow that

  10. Land-use change and managed aquifer recharge effects on the hydrogeochemistry of two contrasting atoll island aquifers, Roi-Namur Island, Republic of the Marshall Islands

    International Nuclear Information System (INIS)

    Hejazian, Mehrdad; Gurdak, Jason J.; Swarzenski, Peter; Odigie, Kingsley O.; Storlazzi, Curt D.

    2017-01-01

    Freshwater resources on low-lying atoll islands are highly vulnerable to climate change and sea-level rise. In addition to rainwater catchment, groundwater in the freshwater lens is a critically important water resource on many atoll islands, especially during drought. Although many atolls have high annual rainfall rates, dense natural vegetation and high evapotranspiration rates can limit recharge to the freshwater lens. Here we evaluate the effects of land-use/land-cover change and managed aquifer recharge on the hydrogeochemistry and supply of groundwater on Roi-Namur Island, Republic of the Marshall Islands. Roi-Namur is an artificially conjoined island that has similar hydrogeology on the Roi and Namur lobes, but has contrasting land-use/land-cover and managed aquifer recharge only on Roi. Vegetation removal and managed aquifer recharge operations have resulted in an estimated 8.6 × 10"5 m"3 of potable groundwater in the freshwater lens on Roi, compared to only 1.6 × 10"4 m"3 on Namur. We use groundwater samples from a suite of 33 vertically nested monitoring wells, statistical testing, and geochemical modeling using PHREEQC to show that the differences in land-use/land-cover and managed aquifer recharge on Roi and Namur have a statistically significant effect on several groundwater-quality parameters and the controlling geochemical processes. Results also indicate a six-fold reduction in the dissolution of carbonate rock in the freshwater lens and overlying vadose zone of Roi compared to Namur. Mixing of seawater and the freshwater lens is a more dominant hydrogeochemical process on Roi because of the greater recharge and flushing of the aquifer with freshwater as compared to Namur. In contrast, equilibrium processes and dissolution-precipitation non-equilibrium reactions are more dominant on Namur because of the longer residence times relative to the rate of geochemical reactions. Findings from Roi-Namur Island support selective land

  11. Development of intelligent surveillance system (ISS) in region of interest (ROI) using Kalman filter and camshift on Raspberry Pi 2

    Science.gov (United States)

    Park, Junghun; Hong, Kicheon

    2017-06-01

    Due to the improvement of the picture quality of closed-circuit television (CCTV), the demand for CCTV has increased rapidly and its market size has also increased. The current system structure of CCTV transfers compressed images without analysis received from CCTV to a control center. The compressed images are suitable for the evidence required for a criminal arrest, but they cannot prevent crime in real time, which has been considered a limitation. Thus, the present paper proposes a system implementation that can prevent crimes by applying a situation awareness system at the back end of the CCTV cameras for image acquisition to prevent crimes efficiently. In the system implemented in the present paper, the region of interest (ROI) is set virtually within the image data when a barrier, such as fence, cannot be installed in actual sites and unauthorized intruders are tracked constantly through data analysis and recognized in the ROI via the developed algorithm. Additionally, a searchlight or alarm sound is activated to prevent crime in real time and the urgent information is transferred to the control center. The system was implemented in the Raspberry Pi 2 board to be run in real time. The experiment results showed that the recognition success rate was 85% or higher and the track accuracy was 90% or higher. By utilizing the system, crime prevention can be achieved by implementing a social safety network.

  12. Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power

    Directory of Open Access Journals (Sweden)

    Todd C. Pataky

    2016-11-01

    Full Text Available One-dimensional (1D kinematic, force, and EMG trajectories are often analyzed using zero-dimensional (0D metrics like local extrema. Recently whole-trajectory 1D methods have emerged in the literature as alternatives. Since 0D and 1D methods can yield qualitatively different results, the two approaches may appear to be theoretically distinct. The purposes of this paper were (a to clarify that 0D and 1D approaches are actually just special cases of a more general region-of-interest (ROI analysis framework, and (b to demonstrate how ROIs can augment statistical power. We first simulated millions of smooth, random 1D datasets to validate theoretical predictions of the 0D, 1D and ROI approaches and to emphasize how ROIs provide a continuous bridge between 0D and 1D results. We then analyzed a variety of public datasets to demonstrate potential effects of ROIs on biomechanical conclusions. Results showed, first, that a priori ROI particulars can qualitatively affect the biomechanical conclusions that emerge from analyses and, second, that ROIs derived from exploratory/pilot analyses can detect smaller biomechanical effects than are detectable using full 1D methods. We recommend regarding ROIs, like data filtering particulars and Type I error rate, as parameters which can affect hypothesis testing results, and thus as sensitivity analysis tools to ensure arbitrary decisions do not influence scientific interpretations. Last, we describe open-source Python and MATLAB implementations of 1D ROI analysis for arbitrary experimental designs ranging from one-sample t tests to MANOVA.

  13. Can state-of-the-art HVS-based objective image quality criteria be used for image reconstruction techniques based on ROI analysis?

    Science.gov (United States)

    Dostal, P.; Krasula, L.; Klima, M.

    2012-06-01

    Various image processing techniques in multimedia technology are optimized using visual attention feature of the human visual system. Spatial non-uniformity causes that different locations in an image are of different importance in terms of perception of the image. In other words, the perceived image quality depends mainly on the quality of important locations known as regions of interest. The performance of such techniques is measured by subjective evaluation or objective image quality criteria. Many state-of-the-art objective metrics are based on HVS properties; SSIM, MS-SSIM based on image structural information, VIF based on the information that human brain can ideally gain from the reference image or FSIM utilizing the low-level features to assign the different importance to each location in the image. But still none of these objective metrics utilize the analysis of regions of interest. We solve the question if these objective metrics can be used for effective evaluation of images reconstructed by processing techniques based on ROI analysis utilizing high-level features. In this paper authors show that the state-of-the-art objective metrics do not correlate well with subjective evaluation while the demosaicing based on ROI analysis is used for reconstruction. The ROI were computed from "ground truth" visual attention data. The algorithm combining two known demosaicing techniques on the basis of ROI location is proposed to reconstruct the ROI in fine quality while the rest of image is reconstructed with low quality. The color image reconstructed by this ROI approach was compared with selected demosaicing techniques by objective criteria and subjective testing. The qualitative comparison of the objective and subjective results indicates that the state-of-the-art objective metrics are still not suitable for evaluation image processing techniques based on ROI analysis and new criteria is demanded.

  14. Land-use change and managed aquifer recharge effects on the hydrogeochemistry of two contrasting atoll island aquifers, Roi-Namur Island, Republic of the Marshall Islands

    Science.gov (United States)

    Hejazian, Mehrdad; Gurdak, Jason J.; Swarzenski, Peter W.; Odigie, Kingsley; Storlazzi, Curt

    2017-01-01

    Freshwater resources on low-lying atoll islands are highly vulnerable to climate change and sea-level rise. In addition to rainwater catchment, groundwater in the freshwater lens is a critically important water resource on many atoll islands, especially during drought. Although many atolls have high annual rainfall rates, dense natural vegetation and high evapotranspiration rates can limit recharge to the freshwater lens. Here we evaluate the effects of land-use/land-cover change and managed aquifer recharge on the hydrogeochemistry and supply of groundwater on Roi-Namur Island, Republic of the Marshall Islands. Roi-Namur is an artificially conjoined island that has similar hydrogeology on the Roi and Namur lobes, but has contrasting land-use/land-cover and managed aquifer recharge only on Roi. Vegetation removal and managed aquifer recharge operations have resulted in an estimated 8.6 x 105 m3 of potable groundwater in the freshwater lens on Roi, compared to only 1.6 x 104 m3 on Namur. We use groundwater samples from a suite of 33 vertically nested monitoring wells, statistical testing, and geochemical modeling using PHREEQC to show that the differences in land-use/land-cover and managed aquifer recharge on Roi and Namur have a statistically significant effect on several groundwater-quality parameters and the controlling geochemical processes. Results also indicate a seven-fold reduction in the dissolution of carbonate rock in the freshwater lens and overlying vadose zone of Roi compared to Namur. Mixing of seawater and the freshwater lens is a more dominant hydrogeochemical process on Roi because of the greater recharge and flushing of the aquifer with freshwater as compared to Namur. In contrast, equilibrium processes and dissolution-precipitation non-equilibrium reactions are more dominant on Namur because of the longer residence times relative to the rate of geochemical reactions. Findings from Roi-Namur Island support selective land-use/land-cover change and

  15. In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

    Science.gov (United States)

    Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

    2013-01-01

    We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.

  16. Decoding the IT value problem an executive guide for achieving optimal ROI on critical IT investments

    CERN Document Server

    Fell, Gregory J

    2013-01-01

    Gain greater returns from your IT investments Revealing the secrets to proven, effective strategies that enable businesses to leverage the full value of highly expensive IT investments, Decoding the IT Value Problem is a no-nonsense guide for making smart IT investments and cutting through the noise of vendor marketing and media hype. Author Gregory Fell describes in rich detail the actual processes, frameworks, infrastructure and discipline required to develop and execute corporate IT strategies that areprofitable and sustainable.Provides a proven framework for develop

  17. Tombes et cimetières éthiopiens : des rois, des saints, des anonymes1

    OpenAIRE

    Derat, Marie-Laure

    2009-01-01

    L’histoire des tombes et cimetières éthiopiens, dans la longue durée, en est encore à ses balbutiements. Si les tombes des saints et des rois nous sont un peu mieux connus grâce à des textes témoignant à la fois des enjeux entourant les sépultures de ces personnages hors du commun et des soins apportés à leur inhumation, en revanche, les cimetières ordinaires échappent encore largement à l’enquête, en grande partie parce que le commun des mortels est inhumé dans l’anonymat et dans un grand dé...

  18. La Maison du Roi sous Louis XIV, une troupe d’élite. Étude tactique

    OpenAIRE

    Chauviré, Frédéric

    2009-01-01

    La Maison du roi constitue le corps le plus prestigieux de l’armée royale. Mais c’est aussi une troupe d’élite, redoutée sur tous les champs de bataille. Sa supériorité tactique trouve son origine dans la singularité de sa doctrine de combat. Beaucoup plus manœuvrière que les régiments ordinaires, elle s’en distingue également par sa conduite de la charge : choix de l’arme blanche, adoption d’une allure élevée et recherche du choc. Les qualités de cette troupe expliquent que Louis XIV ait vou...

  19. Voxel based statistical analysis method for microPET studies to assess the cerebral glucose metabolism in cat deafness model: comparison to ROI based method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Su; Lee, Jae Sung; Park, Min Hyun; Lee, Jong Jin; Kang, Hye Jin; Lee, Hyo Jeong; Oh, Seung Ha; Kim, Chong Sun; Jung, June Key; Lee, Myung Chul; Lee, Dong Soo [Seoul National University College of Medicine, Seoul (Korea, Republic of); Lim, Sang Moo [KIRAMS, Seoul (Korea, Republic of)

    2005-07-01

    Imaging research on the brain of sensory-deprived cats using small animal PET scanner has gained interest since the abundant information about the sensory system of ths animal is available and close examination of the brain is possible due to larger size of its brain than mouse or rat. In this study, we have established the procedures for 3D voxel-based statistical analysis (SPM) of FDG PET image of cat brain, and confirmed using ROI based-method. FDG PET scans of 4 normal and 4 deaf cats were acquired for 30 minutes using microPET R4 scanner. Only the brain cortices were extracted using a masking and threshold method to facilitate spatial normalization. After spatial normalization and smoothing, 3D voxel-wise and ROI based t-test were performed to identify the regions with significant different FDG uptake between the normal and deaf cats. In ROI analysis, 26 ROIs were drawn on both hemispheres, and regional mean pixel value in each ROI was normalized to the global mean of the brain. Cat brains were spatially normalized well onto the target brain due to the removal of background activity. When cerebral glucose metabolism of deaf cats were compared to the normal controls after removing the effects of the global count, the glucose metabolism in the auditory cortex, head of caudate nucleus, and thalamus in both hemispheres of the deaf cats was significantly lower than that of the controls (P<0.01). No area showed a significantly increased metabolism in the deaf cats even in higher significance level (P<0.05). ROI analysis also showed significant reduction of glucose metabolism in the same region. This study established and confirmed a method for voxel-based analysis of animal PET data of cat brain, which showed high localization accuracy and specificity and was useful for examining the cerebral glucose metabolism in a cat cortical deafness model.

  20. Voxel based statistical analysis method for microPET studies to assess the cerebral glucose metabolism in cat deafness model: comparison to ROI based method

    International Nuclear Information System (INIS)

    Kim, Jin Su; Lee, Jae Sung; Park, Min Hyun; Lee, Jong Jin; Kang, Hye Jin; Lee, Hyo Jeong; Oh, Seung Ha; Kim, Chong Sun; Jung, June Key; Lee, Myung Chul; Lee, Dong Soo; Lim, Sang Moo

    2005-01-01

    Imaging research on the brain of sensory-deprived cats using small animal PET scanner has gained interest since the abundant information about the sensory system of ths animal is available and close examination of the brain is possible due to larger size of its brain than mouse or rat. In this study, we have established the procedures for 3D voxel-based statistical analysis (SPM) of FDG PET image of cat brain, and confirmed using ROI based-method. FDG PET scans of 4 normal and 4 deaf cats were acquired for 30 minutes using microPET R4 scanner. Only the brain cortices were extracted using a masking and threshold method to facilitate spatial normalization. After spatial normalization and smoothing, 3D voxel-wise and ROI based t-test were performed to identify the regions with significant different FDG uptake between the normal and deaf cats. In ROI analysis, 26 ROIs were drawn on both hemispheres, and regional mean pixel value in each ROI was normalized to the global mean of the brain. Cat brains were spatially normalized well onto the target brain due to the removal of background activity. When cerebral glucose metabolism of deaf cats were compared to the normal controls after removing the effects of the global count, the glucose metabolism in the auditory cortex, head of caudate nucleus, and thalamus in both hemispheres of the deaf cats was significantly lower than that of the controls (P<0.01). No area showed a significantly increased metabolism in the deaf cats even in higher significance level (P<0.05). ROI analysis also showed significant reduction of glucose metabolism in the same region. This study established and confirmed a method for voxel-based analysis of animal PET data of cat brain, which showed high localization accuracy and specificity and was useful for examining the cerebral glucose metabolism in a cat cortical deafness model

  1. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    2016-11-01

    Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

  2. Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses.

    Science.gov (United States)

    Wan, Jingjing; Jing, Yuhang; Rao, Yue; Zhang, Shicheng; Luo, Gang

    2018-03-15

    dynamics of bacterial pathogens in the process, which is important for the utilization and safe application of WAS. The study also made an attempt to combine metagenomic and qPCR analyses to reveal the dynamics of bacterial pathogens in anaerobic processes, which could overcome the limitations of each method and provide new insights regarding bacterial pathogens in environmental samples. Copyright © 2018 American Society for Microbiology.

  3. Le roi et la parole dans quelques recueils d’exempla castillans des XIIIe et XIVe siècles

    Directory of Open Access Journals (Sweden)

    Olivier Biaggini

    2007-05-01

    Full Text Available Aquí se examina el hablar del rey tal como lo ponen en escena los relatos ejemplares de Calila e Dimna, Sendebar, Castigos de Sancho IV y El conde Lucanor de don Juan Manuel. Un recorrido previo por el discurso alfonsí (Espéculo y Segunda partida permite precisar los planteamientos de la cuestión mostrando que la palabra regia vale menos por su enunciado que por su enunciación, sometida a unas reglas estrictas. Ahora bien, regular la palabra sirve para definir las condiciones de su poder. De modo muy diverso, las colecciones de exempla representan el hablar del rey en situaciones que subrayan su prestigio o que indican a la inversa la necesidad de controlar sus efectos nefastos. En todo caso, contribuye directamente a la construcción de modelos políticos que, si bien se aplican ante todo a la realeza (Calila, Sendebar, Castigos, pueden en cierta medida ajustarse también a la nobleza (Conde Lucanor.On examine ici la parole du roi telle que la mettent en scène les récits exemplaires du Calila e Dimna, du Sendebar, des Castigos de Sanche IV et du Conde Lucanor de Don Juan Manuel. Un détour par le discours juridique alphonsin (Espéculo et Segunda partida permet de préciser les enjeux de cette question en montrant que la parole royale vaut moins par son énoncé que par son énonciation, soumise à des contraintes strictes. Or, réguler la parole sert à définir les conditions de son pouvoir. De façon très variée, les recueils d’exempla représentent la parole du roi dans des situations qui soulignent son prestige ou, inversement, pointent la nécessité d’en contrôler les effets néfastes. Dans tous les cas, elle contribue directement à la construction de modèles politiques qui, s’ils s’appliquent avant tout à la royauté (Calila, Sendebar, Castigos, sont aussi en partie transposables à la noblesse (Conde Lucanor.

  4. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L. Exposed to Water Deficit

    Directory of Open Access Journals (Sweden)

    Stefania Savoi

    2017-07-01

    Full Text Available Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  5. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit.

    Science.gov (United States)

    Savoi, Stefania; Wong, Darren C J; Degu, Asfaw; Herrera, Jose C; Bucchetti, Barbara; Peterlunger, Enrico; Fait, Aaron; Mattivi, Fulvio; Castellarin, Simone D

    2017-01-01

    Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis -regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.

  6. Selection of optimum ROI for dual radionuclide analysis of 55Fe-63Ni and 63Ni-60Co

    International Nuclear Information System (INIS)

    Priya, S.; Prabhath Ravi, K.; Yadav, R.K.B.; Rao, D.D.; Gopalakrishnan, R.K.

    2016-01-01

    Dual label counting in liquid scintillation counting (LSC) enables simultaneous activity determination of two radionuclides. Dual counting procedure for 3 H and 14 C has been well established. There are several other nuclides like 63 Ni (E β- =67keV), 55 Fe (6 keV X-ray and auger electron) which are often chemically separated using detailed procedures with high decontamination factors (DF) and quantified using LSC. Despite the laborious separations, traces of these nuclides in the chemically separated fractions can mutually make their quantification difficult due to overlap of counts from both radionuclides in the spectrum, which gets further complicated in presence of traces of 60 Co. For dual label counting technique, it is essential to establish the discriminator setting at which there will be spillover of counts from both radionuclides in the two counting regions required for the inclusion method. The objective of the current work is to establish two counting ROI's for dual counting of (i) 63 Ni- 55 Fe and (ii) 63 Ni- 60 Co in a TDCR based LSC system

  7. Hydrogeology and geochemistry of the freshwater lens on Roi Namur atoll, the Republic of the Marshall Islands

    Science.gov (United States)

    Swarzenski, P. W.

    2015-12-01

    More than 90% of the world's ~400 larger atoll islands are located in the Pacific and Indian Oceans and are inhabited by ~ 3/4 million people. As ground elevations of these atolls rarely exceed a few meters above mean sea level, atoll communities must rely precariously on finite resources, including fresh water and land. When demand for water exceeds precipitation rates, fresh groundwater may provide an additional, albeit also limited resource. The shape and size of this freshwater lens is controlled by precipitation, infiltration, discharge, and groundwater pumping, as well as hydrogeologic characteristics of the aquifer, and climate. Small atoll islands like Roi Namur on Kwajalein perhaps best illustrate the strong interdependence of the islet's depositional history and geochemical transformations that occur within the shallow aquifer and its host rock. This study utilized electrical resistivity tomography (ERT) to define the position of the freshwater lens above underlying seawater and to examine scales of freshwater /saltwater mixing. Time series Rn-222 measurements were used to evaluate groundwater discharge rates to the coastal waters, and a suite of groundwater geochemical tracers, including select nutrients, trace elements, and water isotopes, were used to develop a better understanding of how the fresh water lens will likely to respond to external perturbations, such as managed recharge, and the inevitability of future marine over wash events that will be become more frequent and severe under expected sea level rise.

  8. A method to estimate the fractional fat volume within a ROI of a breast biopsy for WAXS applications: Animal tissue evaluation

    International Nuclear Information System (INIS)

    Tang, Robert Y.; McDonald, Nancy; Laamanen, Curtis; LeClair, Robert J.

    2014-01-01

    Purpose: To develop a method to estimate the mean fractional volume of fat (ν ¯ fat ) within a region of interest (ROI) of a tissue sample for wide-angle x-ray scatter (WAXS) applications. A scatter signal from the ROI was obtained and use of ν ¯ fat in a WAXS fat subtraction model provided a way to estimate the differential linear scattering coefficient μ s of the remaining fatless tissue. Methods: The efficacy of the method was tested using animal tissue from a local butcher shop. Formalin fixed samples, 5 mm in diameter 4 mm thick, were prepared. The two main tissue types were fat and meat (fibrous). Pure as well as composite samples consisting of a mixture of the two tissue types were analyzed. For the latter samples, ν fat for the tissue columns of interest were extracted from corresponding pixels in CCD digital x-ray images using a calibration curve. The means ν ¯ fat were then calculated for use in a WAXS fat subtraction model. For the WAXS measurements, the samples were interrogated with a 2.7 mm diameter 50 kV beam and the 6° scattered photons were detected with a CdTe detector subtending a solid angle of 7.75 × 10 −5 sr. Using the scatter spectrum, an estimate of the incident spectrum, and a scatter model, μ s was determined for the tissue in the ROI. For the composite samples, a WAXS fat subtraction model was used to estimate the μ s of the fibrous tissue in the ROI. This signal was compared to μ s of fibrous tissue obtained using a pure fibrous sample. Results: For chicken and beef composites, ν ¯ fat =0.33±0.05 and 0.32 ± 0.05, respectively. The subtractions of these fat components from the WAXS composite signals provided estimates of μ s for chicken and beef fibrous tissue. The differences between the estimates and μ s of fibrous obtained with a pure sample were calculated as a function of the momentum transfer x. A t-test showed that the mean of the differences did not vary from zero in a statistically significant way thereby

  9. Dynamic PET reconstruction using temporal patch-based low rank penalty for ROI-based brain kinetic analysis

    International Nuclear Information System (INIS)

    Kim, Kyungsang; Ye, Jong Chul; Son, Young Don; Cho, Zang Hee; Bresler, Yoram; Ra, Jong Beom

    2015-01-01

    Dynamic positron emission tomography (PET) is widely used to measure changes in the bio-distribution of radiopharmaceuticals within particular organs of interest over time. However, to retain sufficient temporal resolution, the number of photon counts in each time frame must be limited. Therefore, conventional reconstruction algorithms such as the ordered subset expectation maximization (OSEM) produce noisy reconstruction images, thus degrading the quality of the extracted time activity curves (TACs). To address this issue, many advanced reconstruction algorithms have been developed using various spatio-temporal regularizations. In this paper, we extend earlier results and develop a novel temporal regularization, which exploits the self-similarity of patches that are collected in dynamic images. The main contribution of this paper is to demonstrate that the correlation of patches can be exploited using a low-rank constraint that is insensitive to global intensity variations. The resulting optimization framework is, however, non-Lipschitz and non-convex due to the Poisson log-likelihood and low-rank penalty terms. Direct application of the conventional Poisson image deconvolution by an augmented Lagrangian (PIDAL) algorithm is, however, problematic due to its large memory requirements, which prevents its parallelization. Thus, we propose a novel optimization framework using the concave-convex procedure (CCCP) by exploiting the Legendre–Fenchel transform, which is computationally efficient and parallelizable. In computer simulation and a real in vivo experiment using a high-resolution research tomograph (HRRT) scanner, we confirm that the proposed algorithm can improve image quality while also extracting more accurate region of interests (ROI) based kinetic parameters. Furthermore, we show that the total reconstruction time for HRRT PET is significantly accelerated using our GPU implementation, which makes the algorithm very practical in clinical environments

  10. Du bon maniement de l’argent du roi en Espagne au XVIIIe siècle. Les enseignements d’un procès pour fraude

    Directory of Open Access Journals (Sweden)

    Anne Dubet

    2010-07-01

    Full Text Available Pour nombre d’historiens – dont je fais partie – les réformes financières entreprises par les premiers Bourbons d’Espagne au XVIIIe siècle n’affectent pas tant l’organisation fiscale de leurs territoires que leur administration. Avant que de modifier la répartition sociale des contributions, il s’agit de rendre au roi et à ses ministres de confiance la décision en matière de dépenses et de s’assurer de son exécution. Ce projet de contrôle accru du roi sur ses propres deniers se traduit certes...

  11. Efficient ConvNet Feature Extraction with Multiple RoI Pooling for Landmark-Based Visual Localization of Autonomous Vehicles

    Directory of Open Access Journals (Sweden)

    Yi Hou

    2017-01-01

    Full Text Available Efficient and robust visual localization is important for autonomous vehicles. By achieving impressive localization accuracy under conditions of significant changes, ConvNet landmark-based approach has attracted the attention of people in several research communities including autonomous vehicles. Such an approach relies heavily on the outstanding discrimination power of ConvNet features to match detected landmarks between images. However, a major challenge of this approach is how to extract discriminative ConvNet features efficiently. To address this challenging, inspired by the high efficiency of the region of interest (RoI pooling layer, we propose a Multiple RoI (MRoI pooling technique, an enhancement of RoI, and a simple yet efficient ConvNet feature extraction method. Our idea is to leverage MRoI pooling to exploit multilevel and multiresolution information from multiple convolutional layers and then fuse them to improve the discrimination capacity of the final ConvNet features. The main advantages of our method are (a high computational efficiency for real-time applications; (b GPU memory efficiency for mobile applications; and (c use of pretrained model without fine-tuning or retraining for easy implementation. Experimental results on four datasets have demonstrated not only the above advantages but also the high discriminating power of the extracted ConvNet features with state-of-the-art localization accuracy.

  12. SU-F-J-29: Dosimetric Effect of Image Registration ROI Size and Focus in Automated CBCT Registration for Spine SBRT

    Energy Technology Data Exchange (ETDEWEB)

    Magnelli, A; Smith, A; Chao, S; Suh, J; Xia, P [The Cleveland Clinic Foundation, Cleveland, OH (United States)

    2016-06-15

    Purpose: Spinal stereotactic body radiotherapy (SBRT) involves highly conformal dose distributions and steep dose gradients due to the proximity of the spinal cord to the treatment volume. To achieve the planning goals while limiting the spinal cord dose, patients are setup using kV cone-beam CT (kV-CBCT) with 6 degree corrections. The kV-CBCT registration with the reference CT is dependent on a user selected region of interest (ROI). The objective of this work is to determine the dosimetric impact of ROI selection. Methods: Twenty patients were selected for this study. For each patient, the kV-CBCT was registered to the reference CT using three ROIs including: 1) the external body, 2) a large anatomic region, and 3) a small region focused in the target volume. Following each registration, the aligned CBCTs and contours were input to the treatment planning system for dose evaluation. The minimum dose, dose to 99% and 90% of the tumor volume (D99%, D90%), dose to 0.03cc and the dose to 10% of the spinal cord subvolume (V10Gy) were compared to the planned values. Results: The average deviations in the tumor minimum dose were 2.68%±1.7%, 4.6%±4.0%, 14.82%±9.9% for small, large and the external ROIs, respectively. The average deviations in tumor D99% were 1.15%±0.7%, 3.18%±1.7%, 10.0%±6.6%, respectively. The average deviations in tumor D90% were 1.00%±0.96%, 1.14%±1.05%, 3.19%±4.77% respectively. The average deviations in the maximum dose to the spinal cord were 2.80%±2.56%, 7.58%±8.28%, 13.35%±13.14%, respectively. The average deviation in V10Gy to the spinal cord were 1.69%±0.88%, 1.98%±2.79%, 2.71%±5.63%. Conclusion: When using automated registration algorithms for CBCT-Reference alignment, a small target-focused ROI results in the least dosimetric deviation from the plan. It is recommended to focus narrowly on the target volume to keep the spinal cord dose below tolerance.

  13. Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

    Directory of Open Access Journals (Sweden)

    Diogo M O Ogawa

    Full Text Available We propose the technique of biogeochemical typing (BGC typing as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES; and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR spectroscopy and proton nuclear magnetic resonance (1H-NMR all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that

  14. Global regulatory roles of the cAMP/PKA pathway revealed by phenotypic, transcriptomic and phosphoproteomic analyses in a null mutant of the PKA catalytic subunit in Candida albicans.

    Science.gov (United States)

    Cao, Chengjun; Wu, Mei; Bing, Jian; Tao, Li; Ding, Xuefen; Liu, Xiaoyun; Huang, Guanghua

    2017-07-01

    The conserved cAMP-dependent protein kinase (PKA) plays critical roles in the regulation of morphological transitions and virulence in the human fungal pathogen Candida albicans. It has long been thought that the PKA catalytic subunit is essential for cell viability in this fungus. Paradoxically, the single adenylyl cyclase-encoding gene, CYR1, which is required for the production of cAMP in C. albicans, is not essential for cell growth. Here, a double mutant of TPK1 and TPK2 (tpk2/tpk2 tpk1/tpk1, t2t1), which encode two isoforms of the PKA catalytic subunit was successfully generated, suggesting that this subunit is not essential for cell viability. Inactivation of the PKA catalytic subunit blocked filamentation and dramatically attenuated white-to-opaque switching, but promoted sexual mating. Comparative transcriptomic analyses demonstrated that the t2t1 and cyr1/cyr1 mutants exhibited similar global gene expression profiles. Compared with the WT strain, the general transcriptional activity and metabolism were significantly decreased in both the t2t1 and cyr1/cyr1 mutants. Using combined phosphoproteomic and bioinformatic analyses, we identified 181 potential PKA phosphorylation targets, which represent 148 unique proteins involved in a wide spectrum of biological processes. The study sheds new insights into the global regulatory features of the cAMP/PKA pathway in C. albicans. © 2017 John Wiley & Sons Ltd.

  15. A method to estimate the fractional fat volume within a ROI of a breast biopsy for WAXS applications: Animal tissue evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Robert Y., E-mail: rx-tang@laurentian.ca [Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada); McDonald, Nancy, E-mail: mcdnancye@gmail.com; Laamanen, Curtis, E-mail: cx-laamanen@laurentian.ca [Department of Physics, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada); LeClair, Robert J., E-mail: rleclair@laurentian.ca [Department of Physics, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada and Biomolecular Sciences Program, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario P3E 2C6 (Canada)

    2014-11-01

    Purpose: To develop a method to estimate the mean fractional volume of fat (ν{sup ¯}{sub fat}) within a region of interest (ROI) of a tissue sample for wide-angle x-ray scatter (WAXS) applications. A scatter signal from the ROI was obtained and use of ν{sup ¯}{sub fat} in a WAXS fat subtraction model provided a way to estimate the differential linear scattering coefficient μ{sub s} of the remaining fatless tissue. Methods: The efficacy of the method was tested using animal tissue from a local butcher shop. Formalin fixed samples, 5 mm in diameter 4 mm thick, were prepared. The two main tissue types were fat and meat (fibrous). Pure as well as composite samples consisting of a mixture of the two tissue types were analyzed. For the latter samples, ν{sub fat} for the tissue columns of interest were extracted from corresponding pixels in CCD digital x-ray images using a calibration curve. The means ν{sup ¯}{sub fat} were then calculated for use in a WAXS fat subtraction model. For the WAXS measurements, the samples were interrogated with a 2.7 mm diameter 50 kV beam and the 6° scattered photons were detected with a CdTe detector subtending a solid angle of 7.75 × 10{sup −5} sr. Using the scatter spectrum, an estimate of the incident spectrum, and a scatter model, μ{sub s} was determined for the tissue in the ROI. For the composite samples, a WAXS fat subtraction model was used to estimate the μ{sub s} of the fibrous tissue in the ROI. This signal was compared to μ{sub s} of fibrous tissue obtained using a pure fibrous sample. Results: For chicken and beef composites, ν{sup ¯}{sub fat}=0.33±0.05 and 0.32 ± 0.05, respectively. The subtractions of these fat components from the WAXS composite signals provided estimates of μ{sub s} for chicken and beef fibrous tissue. The differences between the estimates and μ{sub s} of fibrous obtained with a pure sample were calculated as a function of the momentum transfer x. A t-test showed that the mean of the

  16. Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development.

    Science.gov (United States)

    Agarwal, Aakrati; Mudgil, Yashwanti; Pandey, Saurabh; Fartyal, Dhirendra; Reddy, Malireddy K

    2016-01-01

    Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants.

  17. The Development of Rally Activities to Environmental Conservationfor Social Education Teachers of Mathayom Suksa Education Area Office 27 Roi-Et Province

    Directory of Open Access Journals (Sweden)

    Phiphop Sinthuphong

    2016-09-01

    Full Text Available The purposes of this research on the development of rally activities to environmental conservation for social education teachers of Mathayom suksa education area office 27 Roi-et province were ; 1 to study and analyze the place organized rally to environmental conservation, 2 to develop activities rally to environmental conservation for social education teachers 3 and compare knowledge and attitude toward environmental conservation, before and after the activity 4 to study participation in activities rally to environmental conservation after the activities. The samples used in the study and analysis of the event was social Education Teachers of Mathayom Suksa Education Area Office 27 Roi-Et Province were 77 and sample used in the event of 50 people. Social education teachers under the office of the secondary area 27 province. The tools used in this study were manual and brochures of Green activities Car Rally to environmental conservation, knowledge test, attitudes test and participating questionnaire manuals. The statistical analysis of data were percentage, mean, standard deviation and Paired t-test The results showed that there were proper place in activity all 9 points include 1. Wat Burapharam, 2. Pralanchai Swamp, 3.Roi-Et aquarium, 4. Ku Ka Sing ancient park, 5. Ku Phra Kona ancient park, 6. Jasmine rice learning source (land development station , 7. Chi river, 8.Don Swamp and 9. Rai Dakdea and dodo scouts camp. The tool in rally activities environmental conservation had suitability at more level. After participation of rally activities environmental conservation, social education teachers had mean score of knowledge and attitude to environmental conservation at more than before the participation at statistical significant level .05. And the score of knowledge and attitude toward environmental conservation, before and after the organized activities, it was found that, according to the hypothesis .05 and They had participation in

  18. 包装彩盒检测中定位核提取算法%Extraction algorithm of ROI for detecting colored box

    Institute of Scientific and Technical Information of China (English)

    陈功明; 李锋

    2016-01-01

    To reduce the complexity of the existing method for automatically extracting region of interest (ROI)and improve the detection efficiency in package printing detection process,an algorithm for automatic extraction of ROI was proposed on account of multi-feature.Based on the input selected rectangular region,by comparing the output parameters like contrast ratio,duty cycle,XY direction confidence interval and the symmetry of the fitting curve of the matching coefficient,the ROI was j udged to be good or not.The feasibility of the scheme was verified using the method of automatically calculative center coordinate error. Simulation analysis demonstrates that the algorithm succeeds in extracting automatic ROI for less than 100 ms,and success rate reaches 99.78% or more,the complexity of the proposed algorithm is much lower than that of the existing ones.The proposed verification method is simple and reliable.%为降低现有包装印刷品检测过程中感兴趣区域(简称定位核)提取方法的复杂度,提高检测效率,提出一种基于多特征的定位核自动提取方案。通过输入选中的矩形区域,输出参数对比度、占空比、XY 方向置信区间的取值范围及匹配系数拟合曲线的对称性,综合判断提取定位核的好坏。提出自动求取中心点坐标误差法对该方案的有效性进行验证。仿真分析结果表明,该方案可在100 ms内自动提取定位核,成功率达到99.78%以上,明显优于已有方案,所提验证方法简单可靠。

  19. Revealing the functional structure of a new PLA2 K49 from Bothriopsis taeniata snake venom employing automatic "de novo" sequencing using CID/HCD/ETD MS/MS analyses.

    Science.gov (United States)

    Carregari, Victor Corasolla; Dai, Jie; Verano-Braga, Thiago; Rocha, Thalita; Ponce-Soto, Luis Alberto; Marangoni, Sergio; Roepstorff, Peter

    2016-01-10

    Snake venoms are composed of approximately 90% of proteins with several pharmacological activities having high potential in research as biological tools. One of the most abundant compounds is phospholipases A2 (PLA2), which are the most studied venom protein due to their wide pharmacological activity. Using a combination of chromatographic steps, a new PLA2 K49 was isolated and purified from the whole venom of the Bothriopsis taeniata and submitted to analyses mass spectrometry. An automatic “de novo” sequencing of this new PLA2 K49 denominated Btt-TX was performed using Peaks Studio 6 for analysis of the spectra. Additionally, a triplex approach CID/HCD/ETD has been performed, to generate higher coverage of the sequence of the protein. Structural studies correlating biological activities were made associating specific Btt-TX regions and myotoxic activity. Lysine acetylation was performed to better understand the mechanism of membrane interaction, identifying the extreme importance of the highly hydrophobic amino acids L, P and F for disruption of the membrane. Our myotoxical studies show a possible membrane disruption mechanism by Creatine Kinase release without a noticeable muscle damage, that probably occurred without phospholipid hydrolyses, but with a probable penetration of the hydrophobic amino acids present in the C-terminal region of the protein.

  20. Species-delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis, including a new species from Brazil.

    Science.gov (United States)

    de Jesus, Priscila Barreto; Nauer, Fabio; Lyra, Goia de Mattos; Cassano, Valéria; Oliveira, Mariana Cabral; Nunes, José Marcos de Castro; Schnadelbach, Alessandra Selbach

    2016-10-01

    Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI-5P and rbcL) and performed several DNA-based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods. © 2016 Phycological Society of America.

  1. Image-Guided Analyses Reveal that Non-CD4 Splenocytes Contribute to CD4+ T Cell–Mediated Inflammation Leading to Islet Destruction by Altering Their Local Function and Not Systemic Trafficking Patterns

    Directory of Open Access Journals (Sweden)

    Mi-Heon Lee

    2007-11-01

    Full Text Available Recruitment of CD4+ T cells into islets is a critical component of islet inflammation (insulitis leading to type 1 diabetes; therefore, determining if conditions used to treat diabetes change their trafficking patterns is relevant to the outcome. Cotransfer of CD4+BDC2.5 (BDC cells with non-CD4 splenocytes obtained from newly diabetic NOD mice, but not when they are transferred alone, induces accelerated diabetes. It is unclear whether these splenocytes affect diabetes development by altering the systemic and/or local trafficking and proliferation patterns of BDC cells in target and nontarget tissues. To address these questions, we developed an animal model to visualize BDC cell trafficking and proliferation using whole-body in vivo bioluminescence imaging and used the images to direct tissue sampling for further analyses of the cell distribution within tissues. The whole-body, or macroscopic, trafficking patterns were not dramatically altered in both groups of recipient mice. However, the local patterns of cell distribution were distinct, which led to invasive insulitis only in cotransferred mice with an increased number of islet-infiltrating CD11b+ and CD11c+ cells. Taken together, the non-CD4 splenocytes act locally by promoting invasive insulitis without altering the systemic trafficking patterns or proliferation of BDC cells and thus contributing to diabetes by altering the localization within the tissue.

  2. Sequence analyses reveal that a TPR-DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR-DP domains and prokaryotic GerD proteins.

    Science.gov (United States)

    Hernández Torres, Jorge; Papandreou, Nikolaos; Chomilier, Jacques

    2009-05-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR-DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR-DP domains.

  3. Sequence analyses reveal that a TPR–DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR–DP domains and prokaryotic GerD proteins

    Science.gov (United States)

    Papandreou, Nikolaos; Chomilier, Jacques

    2008-01-01

    The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR–DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR–DP domains. Electronic supplementary material The online version of this article (doi:10.1007/s12192-008-0083-8) contains supplementary material, which is available to authorized users. PMID:18987995

  4. Integrative Analyses of miRNA-mRNA Interactions Reveal let-7b, miR-128 and MAPK Pathway Involvement in Muscle Mass Loss in Sex-Linked Dwarf Chickens

    Science.gov (United States)

    Luo, Wen; Lin, Shumao; Li, Guihuan; Nie, Qinghua; Zhang, Xiquan

    2016-01-01

    The sex-linked dwarf (SLD) chicken is an ideal model system for understanding growth hormone (GH)-action and growth hormone receptor (GHR) function because of its recessive mutation in the GHR gene. Skeletal muscle mass is reduced in the SLD chicken with a smaller muscle fiber diameter. Our previous study has presented the mRNA and miRNA expression profiles of the SLD chicken and normal chicken between embryo day 14 and seven weeks of age. However, the molecular mechanism of GHR-deficient induced muscle mass loss is still unclear, and the key molecules and pathways underlying the GHR-deficient induced muscle mass loss also remain to be illustrated. Here, by functional network analysis of the differentially expressed miRNAs and mRNAs between the SLD and normal chickens, we revealed that let-7b, miR-128 and the MAPK pathway might play key roles in the GHR-deficient induced muscle mass loss, and that the reduced cell division and growth are potential cellular processes during the SLD chicken skeletal muscle development. Additionally, we also found some genes and miRNAs involved in chicken skeletal muscle development, through the MAPK, PI3K-Akt, Wnt and Insulin signaling pathways. This study provides new insights into the molecular mechanism underlying muscle mass loss in the SLD chickens, and some regulatory networks that are crucial for chicken skeletal muscle development. PMID:26927061

  5. Seasonal diversity of planktonic protists in Southwestern Alberta rivers over a 1-year period as revealed by terminal restriction fragment length polymorphism and 18S rRNA gene library analyses.

    Science.gov (United States)

    Thomas, Matthew C; Selinger, L Brent; Inglis, G Douglas

    2012-08-01

    The temporal dynamics of planktonic protists in river water have received limited attention despite their ecological significance and recent studies linking phagotrophic protists to the persistence of human-pathogenic bacteria. Using molecular-based techniques targeting the 18S rRNA gene, we studied the seasonal diversity of planktonic protists in Southwestern Alberta rivers (Oldman River Basin) over a 1-year period. Nonmetric multidimensional scaling analysis of terminal restriction fragment length polymorphism (T-RFLP) data revealed distinct shifts in protistan community profiles that corresponded to season rather than geographical location. Community structures were examined by using clone library analysis; HaeIII restriction profiles of 18S rRNA gene amplicons were used to remove prevalent solanaceous plant clones prior to sequencing. Sanger sequencing of the V1-to-V3 region of the 18S rRNA gene libraries from spring, summer, fall, and winter supported the T-RFLP results and showed marked seasonal differences in the protistan community structure. The spring library was dominated by Chloroplastidae (29.8%), Centrohelida (28.1%), and Alveolata (25.5%), while the summer and fall libraries contained primarily fungal clones (83.0% and 88.0%, respectively). Alveolata (35.6%), Euglenozoa (24.4%), Chloroplastida (15.6%), and Fungi (15.6%) dominated the winter library. These data demonstrate that planktonic protists, including protozoa, are abundant in river water in Southwestern Alberta and that conspicuous seasonal shifts occur in the community structure.

  6. Profilin-1 overexpression in MDA-MB-231 breast cancer cells is associated with alterations in proteomics biomarkers of cell proliferation, survival, and motility as revealed by global proteomics analyses.

    Science.gov (United States)

    Coumans, Joëlle V F; Gau, David; Poljak, Anne; Wasinger, Valerie; Roy, Partha; Moens, Pierre D J

    2014-12-01

    Despite early screening programs and new therapeutic strategies, metastatic breast cancer is still the leading cause of cancer death in women in industrialized countries and regions. There is a need for novel biomarkers of susceptibility, progression, and therapeutic response. Global analyses or systems science approaches with omics technologies offer concrete ways forward in biomarker discovery for breast cancer. Previous studies have shown that expression of profilin-1 (PFN1), a ubiquitously expressed actin-binding protein, is downregulated in invasive and metastatic breast cancer. It has also been reported that PFN1 overexpression can suppress tumorigenic ability and motility/invasiveness of breast cancer cells. To obtain insights into the underlying molecular mechanisms of how elevating PFN1 level induces these phenotypic changes in breast cancer cells, we investigated the alteration in global protein expression profiles of breast cancer cells upon stable overexpression of PFN1 by a combination of three different proteome analysis methods (2-DE, iTRAQ, label-free). Using MDA-MB-231 as a model breast cancer cell line, we provide evidence that PFN1 overexpression is associated with alterations in the expression of proteins that have been functionally linked to cell proliferation (FKPB1A, HDGF, MIF, PRDX1, TXNRD1, LGALS1, STMN1, LASP1, S100A11, S100A6), survival (HSPE1, HSPB1, HSPD1, HSPA5 and PPIA, YWHAZ, CFL1, NME1) and motility (CFL1, CORO1B, PFN2, PLS3, FLNA, FLNB, NME2, ARHGDIB). In view of the pleotropic effects of PFN1 overexpression in breast cancer cells as suggested by these new findings, we propose that PFN1-induced phenotypic changes in cancer cells involve multiple mechanisms. Our data reported here might also offer innovative strategies for identification and validation of novel therapeutic targets and companion diagnostics for persons with, or susceptibility to, breast cancer.

  7. Total Mini-Mental State Examination score and regional cerebral blood flow using Z score imaging and automated ROI analysis software in subjects with memory impairment

    International Nuclear Information System (INIS)

    Ikeda, Eiji; Shiozaki, Kazumasa; Takahashi, Nobukazu; Togo, Takashi; Odawara, Toshinari; Oka, Takashi; Inoue, Tomio; Hirayasu, Yoshio

    2008-01-01

    The Mini-Mental State Examination (MMSE) is considered a useful supplementary method to diagnose dementia and evaluate the severity of cognitive disturbance. However, the region of the cerebrum that correlates with the MMSE score is not clear. Recently, a new method was developed to analyze regional cerebral blood flow (rCBF) using a Z score imaging system (eZIS). This system shows changes of rCBF when compared with a normal database. In addition, a three-dimensional stereotaxic region of interest (ROI) template (3DSRT), fully automated ROI analysis software was developed. The objective of this study was to investigate the correlation between rCBF changes and total MMSE score using these new methods. The association between total MMSE score and rCBF changes was investigated in 24 patients (mean age±standard deviation (SD) 71.5±9.2 years; 6 men and 18 women) with memory impairment using eZIS and 3DSRT. Step-wise multiple regression analysis was used for multivariate analysis, with the total MMSE score as the dependent variable and rCBF change in 24 areas as the independent variable. Total MMSE score was significantly correlated only with the reduction of left hippocampal perfusion but not with right (P<0.01). Total MMSE score is an important indicator of left hippocampal function. (author)

  8. Semi-automatic ROI placement system for analysis of brain PET images based on elastic model. Application to diagnosis of Alzheimer's disease

    International Nuclear Information System (INIS)

    Ohyama, Masashi; Mishina, Masahiro; Kitamura, Shin; Katayama, Yasuo; Senda, Michio; Tanizaki, Naoki; Ishii, Kenji

    2000-01-01

    PET with 18F-fluorodeoxyglucose (FDG) is a useful technique to image cerebral glucose metabolism and to detect patients with Alzheimer's disease in the early stage, in which characteristic temporoparietal hypometabolism is visualized. We have developed a new system, in which the standard brain ROI atlas made of networks of segments is elastically transformed to match the subject brain images, so that standard ROIs defined on the segments are placed on the individual brain images and are used to measure radioactivity over each brain region. We applied this methods to Alzheimer's disease. This method was applied to the images of 10 normal subjects (ages 55 +/- 12) and 21 patients clinically diagnosed as Alzheimer's disease (age 61 +/- 10). The FDG uptake reflecting glucose metabolism was evaluated with SUV, i.e. decay corrected radioactivity divided by injected dose per body weight in (Bq/ml)/(Bq/g). The system worked all right in every subject including those with extensive hypometabolism. Alzheimer patients showed markedly lower in the parietal cortex (4.0-4.1). When the threshold value of FDG uptake in the parietal lobe was set as 5 (Bq/ml)/(Bq/g), we could discriminate the patients with Alzheimer's disease from the normal subjects. The sensitivity was 86% and the specificity was 90%. This system can assist diagnosis of FDG images and may be useful for treating data of a large number of subjects; e.g. when PET is applied to health screening. (author)

  9. Investigating the Impact uf E-Learning as an Alternative for Business Education in Pharmaceutical Industry in Romania by Roi Methodology

    Directory of Open Access Journals (Sweden)

    Petruţa Blaga

    2014-08-01

    Full Text Available The capability of organizations to accumulate and apply new knowledge is a key factor in order to achieve the new competitive standards. A continuous changing diversity, to which the need of adaptation to the changes of external environment is added, speeds up the rate of development and business education. The new information and communication technologies speed up the rate of change and increase the need of education that is subject to a higher information flow. The achievements of information technology, along with changes within society, determine the creation of new paradigms for business education and training. Under these circumstances, e-learning has become one of the main educational forms of human resources in business. This research aims to measure the impact of some initiatives within human resources on an organization, market leader within pharmaceutical field, namely measuring the efficiency of business education programs concerning human resources through e-learning. Under these circumstances, the carried-out research aims to put into practice the theoretical frame of ROI (Return on Investment methodology of evaluating the business education programs concerning human resources in five stages, suggested by J. J. Phillips. The research validates theoretical data of the surveyed model and it is based on the analysis of the data gathering process within the ROI Methodology. This work shows only aspects related to the measuring of the participants` reaction towards the e-learning business education program, respectively

  10. A persistent Holocene wetting trend in arid central Asia, with wettest conditions in the late Holocene, revealed by multi-proxy analyses of loess-paleosol sequences in Xinjiang, China

    Science.gov (United States)

    Chen, Fahu; Jia, Jia; Chen, Jianhui; Li, Guoqiang; Zhang, Xiaojian; Xie, Haichao; Xia, Dunsheng; Huang, Wei; An, Chengbang

    2016-08-01

    There are significant differences in the interpretation of the moisture (precipitation) history of arid central Asia (ACA) during the Holocene, as inferred on one hand from speleothem oxygen isotope records, and on the other from lake sediments. Here we present the results of measurements of climatically-sensitive magnetic properties and soil color from four well-dated loess-paleosol sequences from the northern slopes of the Tienshan Mountains and the Yili River valley, Xinjiang, China, in the core area of ACA. Our results demonstrate that the characteristic Holocene paleosol, indicating relatively moist conditions, generally formed after ∼6 ka (1 ka = 1000 cal yr BP) in the study region, and that the accumulation of unweathered loess prevailed during the early Holocene, indicating a dry climate at that time. The magnetic proxies further reveal a trend of generally increasing moisture since the Last Glacial Maximum, with the wettest climate occurring during the late Holocene. This trend of increasing moisture during the Holocene is representative of the Xinjiang region and possibly of the whole of the core area of ACA, and is in marked contrast both to the mid-Holocene moisture maximum observed in the East Asian summer monsoon region and to the general decrease in the strength of the Indian summer monsoon since the early Holocene. Our findings are supported by the results of a climate simulation which indicate a trend of increasing summer and winter precipitation during the Holocene in the core area of ACA, caused mainly by an increase in the strength of the westerlies effected by an increasing latitudinal insolation gradient and by a negative trend of the Arctic Oscillation (AO) or North Atlantic Oscillation (NAO).

  11. Detailed molecular analyses of the hexon loop-1 and fibers of fowl aviadenoviruses reveal new insights into the antigenic relationship and confirm that specific genotypes are involved in field outbreaks of inclusion body hepatitis.

    Science.gov (United States)

    Schachner, Anna; Marek, Ana; Grafl, Beatrice; Hess, Michael

    2016-04-15

    Forty-eight fowl aviadenoviruses (FAdVs) isolated from recent IBH outbreaks across Europe were investigated, by utilizing for the first time the two major adenoviral antigenic domains, hexon loop-1 and fiber, for compound molecular characterization of IBH-associated FAdVs. Successful target gene amplification, following virus isolation in cell culture or from FTA-card samples, demonstrated presence of FAdVs in all cases indicative for IBH. Based on hexon loop-1 analysis, 31 European field isolates exhibited highest nucleotide identity (>97.2%) to reference strains FAdV-2 or -11 representing FAdV-D, while 16 and one European isolates shared >96.0% nucleotide identity with FAdV-8a and -8b, or FAdV-7, the prototype strains representing FAdV-E. These results extend recognition of specific FAdV-D and FAdV-E affiliate genotypes as causative agents of IBH to the European continent. In all isolates, species specificity determined by fiber gene analysis correlated with hexon-based typing. A threshold of 72.0% intraspecies nucleotide identity between fibers from investigated prototype and field strains corresponded with demarcation criteria proposed for hexon, suggesting fiber-based analysis as a complementary tool for molecular FAdV typing. A limited number of strains exhibited inconsistencies between hexon and fiber subclustering, indicating potential constraints for single-gene based typing of those FAdVs. Within FAdV-D, field isolate fibers shared a high degree of nucleotide (>96.7%) and aa (>95.8%) identity, while FAdV-E field isolate fibers displayed greater nucleotide divergence of up to 22.6%, resulting in lower aa identities of >81.7%. Furthermore, comparison with FAdVs from IBH outbreaks outside Europe revealed close genetic relationship in the fiber, independent of the strains' geographic origin. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Virus-induced Gene Silencing-based Functional Analyses Revealed the Involvement of Several Putative Trehalose-6-Phosphate Synthase/Phosphatase Genes in Disease Resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato

    Directory of Open Access Journals (Sweden)

    Huijuan Zhang

    2016-08-01

    Full Text Available Trehalose and its metabolism have been demonstrated to play important roles in control of plant growth, development and stress responses. However, direct genetic evidence supporting the functions of trehalose and its metabolism in defense response against pathogens is lacking. In the present study, genome-wide characterization of putative trehalose-related genes identified 11 SlTPSs for trehalose-6-phosphate synthase, 8 SlTPPs for trehalose-6-phosphate phosphatase and one SlTRE1 for trehalase in tomato genome. Nine SlTPSs, 4 SlTPPs and SlTRE1 were selected for functional analyses to explore their involvement in tomato disease resistance. Some selected SlTPSs, SlTPPs and SlTRE1 responded with distinct expression induction patterns to Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst DC3000 as well as to defense signaling hormones (e.g. salicylic acid, jasmonic acid and a precursor of ethylene. Virus-induced gene silencing-mediated silencing of SlTPS3, SlTPS4 or SlTPS7 led to deregulation of ROS accumulation and attenuated the expression of defense-related genes upon pathogen infection and thus deteriorated the resistance against B. cinerea or Pst DC3000. By contrast, silencing of SlTPS5 or SlTPP2 led to an increased expression of the defense-related genes upon pathogen infection and conferred an increased resistance against Pst DC3000. Silencing of SlTPS3, SlTPS4, SlTPS5, SlTPS7 or SlTPP2 affected trehalose level in tomato plants with or without infection of B. cinerea or Pst DC3000. These results demonstrate that SlTPS3, SlTPS4, SlTPS5, SlTPS7 and SlTPP2 play roles in resistance against B. cinerea and Pst DC3000, implying the importance of trehalose and tis metabolism in regulation of defense response against pathogens in tomato.

  13. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human.

    Science.gov (United States)

    Linguiti, Giovanna; Antonacci, Rachele; Tasco, Gianluca; Grande, Francesco; Casadio, Rita; Massari, Serafina; Castelli, Vito; Consiglio, Arianna; Lefranc, Marie-Paule; Ciccarese, Salvatrice

    2016-08-15

    those of the so far examined artiodactyls, genomic results highlight in dolphin an unusually simple TRG locus. The cDNA analysis reveal productive TRA/TRD transcripts and unusual ratios of productive/unproductive TRG transcripts. Comparing multiple different individuals, evidence is found for a "public" gamma delta TCR repertoire thus suggesting that in dolphins as in human the gamma delta TCR repertoire is accompanied by selection for public gamma chain.

  14. Using Soil Conservation Strategies in the Development of Learning Activities for the Students of Roi - Et College of Agriculture and Technology

    Directory of Open Access Journals (Sweden)

    Jariya Kanchanwong

    2017-06-01

    Full Text Available The purposes of this research were 1 to study nutrient content in soil samples taken from Roi - Et College of Agriculture and Technology Campus, 2 to study the social factors, economic factors and technological factors the effect on soil conservation of Roi - Et College of Agriculture and Technology students, 3 the development of soil conservation activities Learning package efficiency of 80/80, 4 to Study and to compare the knowledge, attitudes and skills regarding soil conservation of students of Roi - Et College of Agriculture and Technology. The student activities package of learning soil conservation was enrolled by 40 people in its club. These people were selected by purposive sampling. The instruments were used in this research as follows; 1 scientific analysis, 2 social questionnaire on economic and technological factors affecting soil conservation, 3 test of knowledge about soil conservation, 4 test of attitudes about soil conservation, 5 test of skill about soil conservation. The experimental research was designed to use students as key informants. The statistics analysis was used in the research as follows: frequency, percentage, average, standard deviation, test results, assumptions which included a dependent t-test statistical at the significance level of 0.05. The results of the study were as follows: 1 The study found that the amount of soil nutrient content (N: P: K around cultivated plants in an area of converted agriculture land have the significance: Soil checks collected in plots from soil containing morning glory, chrysanthemums, marigolds, corn and cassava, and had neutral pH. 2 The results of the analysis determing the factors that affected the conservation of soil found economic factors were at a high level Social factors and technology factors were moderate thus leading the approach that has come to create of learning activities package in soil conservation. 3 The results showed that the efficiency of the manual was 83

  15. MRI Texture Analysis Reveals Deep Gray Nuclei Damage in Amyotrophic Lateral Sclerosis.

    Science.gov (United States)

    de Albuquerque, Milena; Anjos, Lara G V; Maia Tavares de Andrade, Helen; de Oliveira, Márcia S; Castellano, Gabriela; Junqueira Ribeiro de Rezende, Thiago; Nucci, Anamarli; França Junior, Marcondes Cavalcante

    2016-01-01

    Amyotrophic Lateral Sclerosis (ALS) is characterized by extensive corticospinal damage, but extrapyramidal involvement is suggested in pathological studies. Texture analysis (TA) is an image processing technique that evaluates the distribution of gray levels between pixels in a given region of interest (ROI). It provides quantitative data and has been employed in several neurodegenerative disorders. Here, we used TA to investigate possible deep gray nuclei (DGN) abnormalities in a cohort of ALS patients. Thirty-two ALS patients and 32 healthy controls underwent MRI in a 3T scanner. The T1 volumetric sequence was used for DGN segmentation and extraction of 11 texture parameters using the MaZda software. Statistical analyses were performed using the Mann-Whitney non-parametric test, with a significance level set at α = 0.025 (FDR-corrected) for TA. Patients had significantly higher values for the parameter correlation (CO) in both thalami and in the right caudate nucleus compared to healthy controls. Also, the parameter Inverse Difference Moment or Homogeneity (IDM) presented significantly smaller values in the ALS group in both thalami. TA of T1 weighted images revealed DGN alterations in patients with ALS, namely in the thalami and caudate nuclei. Copyright © 2015 by the American Society of Neuroimaging.

  16. Development of Guidelines for Mentoring Internal Supervision for the Schools under Roi-Et Office of Primary Education Service Area 2

    Directory of Open Access Journals (Sweden)

    Natchana Sahunil

    2017-06-01

    Full Text Available The research aimed to 1 study the factors and indicators of mentoring internal supervision for schools, 2 study the current state and the desirable state of mentoring internal supervision for schools, and 3 study the guidelines on the operation of mentoring internal supervision for the schools under Roi-Et Office of Primary Education Service Area 2. The research was divided into 3 phases. In phase 1 the informants comprised 5 certified experts. In phase 2 the sample comprised 488 government teachers under Roi-Et Office of Primary Education Service Area 2, btained through multi-stage random sampling. In phase 3 the informants comprised school directors, school deputy directors and supervisor teachers under Roi-Et Office of Primary Education Service Area 2, totally 9 persons. The research instruments onsisted of 1 a questionnaire having the discrimination from 0.34 to 0.79 and the total reliability of 0.87, 2 a structured interview form, and 3 a suitability and feasibility assessment form for the guidelines on the operation of mentoring internal supervision. The analysis of data employed percentage, the mean and standard deviation. The results are as follows: 1. There are 4 factors of the guidelines on mentoring internal supervision for schools. They are: preparation of mentoring supervision, with 12 indicators ; management of mentoring supervision, with 12 indicators ; operation of mentoring supervision, with 14 indicators ; and evaluation of mentoring supervision, with 10 indicators, all of which had been evaluated by the experts as, on the whole, very suitable. 2. The current state of the mentoring internal supervision for schools, on the whole and factor by factor, was in the moderate level in every factor. Meanwhile, the desirable state of mentoring internal supervision for schools, on the whole, was in the high level. When considered factor by factor, the factor with the highest mean is management of mentoring supervision. The factor with

  17. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    When prosecuting crimes, the main question to answer is often who had a motive and the possibility to commit the crime. When investigating cyber crimes, the question of possibility is often hard to answer, as in a networked system almost any location can be accessed from almost anywhere. The most...... common tool to answer this question, analysis of log files, faces the problem that the amount of logged data may be overwhelming. This problems gets even worse in the case of insider attacks, where the attacker’s actions usually will be logged as permissible, standard actions—if they are logged at all....... Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  18. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  19. Monitoring health spending increases: incremental budget analyses reveal challenging tradeoffs.

    Science.gov (United States)

    Hartman, Micah; Smith, Cynthia; Heffler, Stephen; Freeland, Mark

    2006-01-01

    With each passing decade, health care has consumed a larger share of gross domestic product (GDP) and Federal budgets. By the 2000-2004 period, society was willing to devote over 20 percent of the cumulative increase in GDP and the cumulative increase in Federal outlays towards health care. The financing challenges are expected to become more acute for private payers as well as Federal, State, and local budgets. With the implementation of Part D in 2006, the U.S. Office of Management and Budget projects that Federal budget pressures will heighten, bringing increased attention to Medicare's long-term fiscal outlook.

  20. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    2015-03-12

    Mar 12, 2015 ... 1National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. ... 2Institute of Post Graduate Medical Education and Research, J. C. Bose Road, ...... Torres D. M. and Harrison S. A 2008 Diagnosis and therapy of.

  1. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    0.85. 0.8. 0.95. 0.93. 0.81 rs1227756. 0.5. 0.56. 0.75. 0.55. 0.7. 0.71. 0.58. 0.81. 0.25. 0.5. 0.53. 0.48. 0.64. 0.58. 0.58. 0.8. 0.68. 0.78. 0.48. 0.65. NA. NA. NA. NA rs1501299. 0.64. 0.78. 0.75. 0.83. 0.83. 0.89. 0.83. 0.72. 0.63. 0.73. 0.78. 0.75. 0.84. 0.79. 0.61. 0.78. 0.78. 0.7. 0.73. 0.73. NA. NA. NA. NA rs16944. 0.64. 0.72. 0.68.

  2. Observation de terrain et télédétection (Baie du Roi, Spitsberg nord-occidental

    Directory of Open Access Journals (Sweden)

    Dominique Laffly

    1999-06-01

    Full Text Available Les observations de terrain sont fondamentales en télédétection. Selon la finalité de l’étude, la description des paysages observés sera plus ou moins détaillée. Une simple reconnaissance des principaux postes d’occupation du sol demande peu d’indicateurs et ne nécessite pas une localisation à la tachèle près. En revanche, l’analyse du contenu des pixels en vue d’une modélisation statistique s’appuie sur une description thématique détaillée de points localisés très précisément. Dans ce cas les images utilisées doivent être correctement géoréférencées et la localisation sur le terrain se fait à l’aide d’un GPS différentiel. Restent les problèmes du choix des points à analyser ainsi que celui de l’observation elle-même de leur "contenu". Nous présentons dans cet article une méthode qui vise à répondre à ces deux questions. Notre approche est fondée sur la technique du sondage systématique non-aligné. Cette dernière permet de tenir compte à la fois de la valeur des points observés et de leur localisation pour définir le plan d’échantillonnage. Les exemples présentés sont issus d’une étude réalisée sur les sandurs de la presqu’île de Br¯gger au Spitsberg nord-occidental (images SPOT XSP.

  3. IntroductionLa parole des rois à la fin du Moyen Âge : les voies d’une enquête

    Directory of Open Access Journals (Sweden)

    Stéphane PÉQUIGNOT

    2007-10-01

    Full Text Available El artículo sugiere algunas propuestas para una investigación general sobre el hablar de los reyes a finales de la Edad Media. Basándose en un estado de la cuestión para el caso de la Corona de Aragón, se indaga la inscripción del hablar de los reyes en distintas temporalidades imbricadas entre sí. La transcripción de las palabras resulta de un proceso complejo, la « fábrica de la palabra », cuyos mecanismos y huellas son objeto de estudio. Por otra parte, las representaciones del hablar de los reyes hacen a menudo referencia a unos modelos traídos del pasado, a veces se dirigen a un público futuro, mientras testimonian también su necesaria adaptación a las circunstancias de cada momento. Estos « actas reales de palabra », así como los « estilos expresivos » que contribuyen a forjar, se examinan en la secunda parte del artículo. Finalmente, el tiempo dedicado o dejado a las palabras reales participa de las evoluciones a largo plazo de las relaciones a lo escrito, de los regímenes políticos y de su forma de legitimación ; constituye un modo de comunicación político importante, un recurso y, también, una toma de riesgo para el poder y la autoridad monarquica.L’article invite à une enquête générale sur la parole des rois à la fin du Moyen Âge et en esquisse plusieurs voies possibles. À l’aide d’un état de la question sur la couronne d’Aragon, c’est l’inscription de la parole des rois dans différentes temporalités imbriquées qui est visée. Sa transcription même résulte d’un processus complexe, la « fabrique de la parole », dont mécanismes et traces sont examinés. D’autre part, les représentations de la parole des rois renvoient souvent à des modèles du passé, visent parfois un public futur tout en témoignant aussi d’une nécessaire adaptation aux circonstances présentes. Ces « actes royaux de parole » et les « styles expressifs » qu’ils contribuent à consolider

  4. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  5. Evaluation of bone involvement in patients with Gaucher disease: a semi-quantitative magnetic resonance imaging method (using ROI estimation of bone lesion) as an alternative method to semi-quantitative methods used so far.

    Science.gov (United States)

    Komninaka, Veroniki; Kolomodi, Dionysia; Christoulas, Dimitrios; Marinakis, Theodoros; Papatheodorou, Athanasios; Repa, Konstantina; Voskaridou, Ersi; Revenas, Konstantinos; Terpos, Evangelos

    2015-10-01

    The aim of this study was to evaluate bone involvement in patients with Gaucher disease (GD) and to propose a novel semi-quantitative magnetic resonance imaging (MRI) staging. MRI of the lumbar spine, femur, and tibia was performed in 24 patients with GD and 24 healthy controls. We also measured circulating levels of C-C motif ligand-3 (CCL-3) chemokine, C-telopeptide of collagen type-1 (CTX), and tartrate-resistant acid phosphatase isoform type-b (TRACP-5b). We used the following staging based on MRI data: stage I: region of interest (ROI) 1/2 of normal values and bone infiltration up to 30%; stage II: ROI 1/3 of normal values and bone infiltration from 30 to 60%; stage III: ROI 1/4 of normal values and bone infiltration from 60% to 80%; and stage IV: detection of epiphyseal infiltration, osteonecrosis and deformity regardless of the ROI's values. All but two patients had abnormal MRI findings: 9 (37.5%), 6 (25%), 3 (12.5%), and 4 (16.7%) had stages I-IV, respectively. Patients with GD had elevated chitotriosidase, serum TRACP-5b, and CCL-3 levels (P < 0.001). We propose an easily reproducible semi-quantitative scoring system and confirm that patients with GD have abnormal MRI bone findings and enhanced osteoclast activity possibly due to elevated CCL-3. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Comparison of a zero-profile anchored spacer (ROI-C) and the polyetheretherketone (PEEK) cages with an anterior plate in anterior cervical discectomy and fusion for multilevel cervical spondylotic myelopathy.

    Science.gov (United States)

    Liu, Yijie; Wang, Heng; Li, Xuefeng; Chen, Jie; Sun, Han; Wang, Genlin; Yang, Huilin; Jiang, Weimin

    2016-06-01

    We aimed to analyze the clinical and radiographic efficacy of a new zero-profile anchored spacer called the ROI-C in anterior discectomy and fusion (ACDF) for multilevel cervical spondylotic myelopathy (MCSM). We retrospectively reviewed the clinical, radiological outcomes and complications of multilevel ACDF with the ROI-C or with the polyetheretherketone (PEEK) cages with an anterior plate. From April 2011 to April 2014, 60 patients with MCSM were operated on using ACDF, with the ROI-C in 28 patients and PEEK cages with an anterior plate in 32 patients. The operative time, intraoperative blood loss, and clinical and radiological results were compared between the ROI-C group and the cage-plate group. The mean follow-up time was 23.8 ± 6.6 months, ranging from 12 to 36 months. At the first month and the last follow-up, the neck disability index (NDI) scores were decreased, and the Japanese Orthopedic Association (JOA) scores were significantly increased, compared with the presurgical measurements in both groups. There were no significant differences in NDI scores or JOA scores between the two groups (P > 0.05), but there were significant differences in the operation time, blood loss and the presence of dysphagia (P PEEK cage with an anterior plate.

  7. « Les rois de Ségou » : De l'épopée à la série télévisée | Tamari ...

    African Journals Online (AJOL)

    Les Rois de Ségou (“The Kings of Segu”) is a television series from Mali directed by ... Together with another film released at about the same time, Samanyana Basi (“Basi from ... dialogues are laden with adages, thus approximating the characteristics of bardic speech. ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  8. Maintenance of water uptake and reduced water loss contribute to water stress tolerance of Spiraea alba Du Roi and Spiraea tomentosa L.

    Science.gov (United States)

    Stanton, Kelly M; Mickelbart, Michael V

    2014-01-01

    Two primarily eastern US native shrubs, Spiraea alba Du Roi and Spiraea tomentosa L., are typically found growing in wet areas, often with standing water. Both species have potential for use in the landscape, but little is known of their environmental requirements, including their adaptation to water stress. Two geographic accessions of each species were evaluated for their response to water stress under greenhouse conditions. Above-ground biomass, water relations and gas exchange were measured in well-watered and water stress treatments. In both species, water stress resulted in reduced growth, transpiration and pre-dawn water potential. However, both species also exhibited the ability to osmotically adjust to lower soil water content, resulting in maintained midday leaf turgor potential in all accessions. Net CO2 assimilation was reduced only in one accession of S. alba, primarily due to large reductions in stomatal conductance. S. tomentosa lost a larger proportion of leaves than S. alba in response to water stress. The primary water stress tolerance strategies of S. alba and S. tomentosa appear to be the maintenance of water uptake and reduced water loss.

  9. Groundwater movement on a Low-lying Carbonate Atoll Island and its Response to Climatic and Sea-level Fluctuations: Roi Namur, Republic of the Marshall Islands

    Science.gov (United States)

    Oberle, F. J.; Swarzenski, P. W.; Storlazzi, C. D.

    2017-12-01

    Atoll islands, most of which only average 1-2 meters above today's sea level, provide a tremendous natural laboratory in which to study and better understand the intensifying impacts of high rates of sea-level rise on tropical reef-lined islands. These islands are unique and on the frontline of negative societal impacts due to their geologic structure and limited water supply. Groundwater resources on atolls are typically minimal due to the low elevation and small surface area of the islands and are also subject to recurring droughts, and more frequent, storm-driven seawater overwash events. Although groundwater is the principal means of freshwater storage on atoll islands and is a major factor in determining the overall sustainability of island settlements, hydrological data on how an aquifer will response to changes in sea-level rise or storm-driven overwash remain limited. Here we present high-resolution time series hydrogeological and geochemical data from a 16 month study to determine the role of an atoll's carbonate geology, land use, and atmospheric and oceanographic forcing in driving coastal groundwater exchange including submarine groundwater discharge on the island of Roi-Namur on Kwajalein Atoll in the Republic of the Marshall Islands. This information can provide new estimates on the recovery and resilience of coastal groundwater resources on similar islands that are expected to experience climate change-driven perturbations.

  10. Un inventaire phytosociologique des dunes à la côte méditerranéenne française entre carnon et le grau du roi (département de l’hérault)

    NARCIS (Netherlands)

    Hekking, W.H.A.

    1959-01-01

    Dans la région des dunes et des bas-fonds située à une distance de 3.6 à 5.3 kilomètres de Carnon au Grau du Roi, entre l’Etang de Mauguio et la Mer méditerranéenne et dans le département de l’Hérault on peut constater deux suites progressives des associations phytosociologiques : A) LA VÉGÉ TATION

  11. Laser Beam Focus Analyser

    DEFF Research Database (Denmark)

    Nielsen, Peter Carøe; Hansen, Hans Nørgaard; Olsen, Flemming Ove

    2007-01-01

    the obtainable features in direct laser machining as well as heat affected zones in welding processes. This paper describes the development of a measuring unit capable of analysing beam shape and diameter of lasers to be used in manufacturing processes. The analyser is based on the principle of a rotating......The quantitative and qualitative description of laser beam characteristics is important for process implementation and optimisation. In particular, a need for quantitative characterisation of beam diameter was identified when using fibre lasers for micro manufacturing. Here the beam diameter limits...... mechanical wire being swept through the laser beam at varying Z-heights. The reflected signal is analysed and the resulting beam profile determined. The development comprised the design of a flexible fixture capable of providing both rotation and Z-axis movement, control software including data capture...

  12. Contesting Citizenship: Comparative Analyses

    DEFF Research Database (Denmark)

    Siim, Birte; Squires, Judith

    2007-01-01

    importance of particularized experiences and multiple ineequality agendas). These developments shape the way citizenship is both practiced and analysed. Mapping neat citizenship modles onto distinct nation-states and evaluating these in relation to formal equality is no longer an adequate approach....... Comparative citizenship analyses need to be considered in relation to multipleinequalities and their intersections and to multiple governance and trans-national organisinf. This, in turn, suggests that comparative citizenship analysis needs to consider new spaces in which struggles for equal citizenship occur...

  13. Procès inquisitorial contra el castellà d'Amposta Fra Pedro Roiç de Moros a la cúria pontificia del papa Benet XIII (I414-1418

    Directory of Open Access Journals (Sweden)

    Alanyà i Roig, Josep

    2002-06-01

    Full Text Available The Arxiu de la Corona d'Aragó in Barcelona houses the original commital proceedings instituted by a court of cardinals set up by pope Benedict XIII in the year 1414 and teh trial itself of the lord of Amposta, Fra Pedro Roiç de Moros, knight of the Order of St. John of Jerusalem, who had been charged with indictable offences—concubinage, robbery, housing apostates, oath breaking and counterfeiting money, mismanagement of the Castlery's assets, excesses against his vassals, wasteful use of assets, dereliction and property abandonment— of which he was found guilty, and thereafter sentenced to losing the dignity of his lordship. Roiç de Moros appealed to the Council of Constance as well as to pope Martin V. It would be to no avail. Roiç de Moros paid a very high price for choosing to support count Jaume d'Urgell and deciding to oppose Ferran dAntequera and the policies of pope Benedict XIII. The follow up and analysis of the court´s records are very interesting for their human variety and interesting informations about fortresses, houses, barns, treaures and services there were in different locations of the Castlery of Amposta, such as Batea, Gandesa, Miravet, Ulldecona, Ascó and other towns and villages along the Ribera d´Ebre. The whole criminal prosecution bears a very peculiar historic interest mainly because the protagonists, the court procedures, and their causes are the link between the Interregnum in the Aragonese Crown and the fìnal days of the Western Schism.

    A l'Arxiu de la Corona d'Aragó de Barcelona es conserva el procés original instruït per un tribunal de cardenals creat pel papa Benet XIII l'any 1414 per jutjar el Castella d'Amposta, l'hospitaler Fra Pedro Roiç de Moros, acusat de crims greus —concubinat, bandositats, recepció d’apòstates, perjuri i fabricació de moneda falsa, mala administració dels bens de la Castellania, comissió d'excessos contra els seus vassalls, dilapidado de bens i abando

  14. Risico-analyse brandstofpontons

    NARCIS (Netherlands)

    Uijt de Haag P; Post J; LSO

    2001-01-01

    Voor het bepalen van de risico's van brandstofpontons in een jachthaven is een generieke risico-analyse uitgevoerd. Er is een referentiesysteem gedefinieerd, bestaande uit een betonnen brandstofponton met een relatief grote inhoud en doorzet. Aangenomen is dat de ponton gelegen is in een

  15. Fast multichannel analyser

    Energy Technology Data Exchange (ETDEWEB)

    Berry, A; Przybylski, M M; Sumner, I [Science Research Council, Daresbury (UK). Daresbury Lab.

    1982-10-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10/sup 7/ s/sup -1/ has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format.

  16. A fast multichannel analyser

    International Nuclear Information System (INIS)

    Berry, A.; Przybylski, M.M.; Sumner, I.

    1982-01-01

    A fast multichannel analyser (MCA) capable of sampling at a rate of 10 7 s -1 has been developed. The instrument is based on an 8 bit parallel encoding analogue to digital converter (ADC) reading into a fast histogramming random access memory (RAM) system, giving 256 channels of 64 k count capacity. The prototype unit is in CAMAC format. (orig.)

  17. Effects of Land-Use Change and Managed Aquifer Recharge on Geochemical Reactions with Implications for Groundwater Quantity and Quality in Atoll Island Aquifers, Roi-Namur, Republic of the Marshall Islands

    Science.gov (United States)

    Hejazian, M.; Swarzenski, P. W.; Gurdak, J. J.; Odigie, K. O.; Storlazzi, C. D.

    2015-12-01

    This study compares the hydrogeochemistry of two contrasting atoll groundwater systems in Roi-Namur, Republic of the Marshall Islands. Roi-Namur houses a U.S. Department of Defense military installation and presents an ideal study location where a human impacted aquifer is co-located next to a natural aquifer as part of two artificially conjoined atoll islands. The hydrogeology and geochemistry of carbonate atoll aquifers has been well studied, particularly because of its small, well-defined hydrologic system that allows for relatively precise modeling. However, it is unknown how changes in land-use/land cover and managed aquifer recharge (MAR) alters natural geochemical processes in atoll aquifers. A better understanding of this has implications on groundwater quantity and quality, carbonate dissolution, and best aquifer management practices in the context of rising sea level and saltwater intrusion. Roi has been heavily modified to house military and civilian operations; here, lack of vegetation and managed recharge has increased the volume of potable groundwater and affected the geochemical processes in the freshwater lens and saltwater transition zone. Namur is heavily vegetated and the hydrogeology is indicative of a natural atoll island. A suite of monitoring wells were sampled across both island settings for major ions, nutrients, trace elements, DOC/DIC, δ13C and δ18O/2H isotopes. By modeling geochemical reactions using a conservative mixing approach, we measure deviations from expected reactions and compare the two contrasting settings using derived geochemical profiles through a wide salinity spectrum. Results indicate that groundwater on Namur is more heavily depleted in δ13C and has greater dissolved inorganic carbon, suggesting higher microbial oxidation and greater dissolution within the carbonate aquifer. This suggests MAR and reduction of vegetation makes the groundwater supply on atoll islands more resilient to sea level rise.

  18. Possible future HERA analyses

    International Nuclear Information System (INIS)

    Geiser, Achim

    2015-12-01

    A variety of possible future analyses of HERA data in the context of the HERA data preservation programme is collected, motivated, and commented. The focus is placed on possible future analyses of the existing ep collider data and their physics scope. Comparisons to the original scope of the HERA pro- gramme are made, and cross references to topics also covered by other participants of the workshop are given. This includes topics on QCD, proton structure, diffraction, jets, hadronic final states, heavy flavours, electroweak physics, and the application of related theory and phenomenology topics like NNLO QCD calculations, low-x related models, nonperturbative QCD aspects, and electroweak radiative corrections. Synergies with other collider programmes are also addressed. In summary, the range of physics topics which can still be uniquely covered using the existing data is very broad and of considerable physics interest, often matching the interest of results from colliders currently in operation. Due to well-established data and MC sets, calibrations, and analysis procedures the manpower and expertise needed for a particular analysis is often very much smaller than that needed for an ongoing experiment. Since centrally funded manpower to carry out such analyses is not available any longer, this contribution not only targets experienced self-funded experimentalists, but also theorists and master-level students who might wish to carry out such an analysis.

  19. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  20. AMS analyses at ANSTO

    Energy Technology Data Exchange (ETDEWEB)

    Lawson, E.M. [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia). Physics Division

    1998-03-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with {sup 14}C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for {sup 14}C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent`s indigenous Aboriginal peoples. (author)

  1. AMS analyses at ANSTO

    International Nuclear Information System (INIS)

    Lawson, E.M.

    1998-01-01

    The major use of ANTARES is Accelerator Mass Spectrometry (AMS) with 14 C being the most commonly analysed radioisotope - presently about 35 % of the available beam time on ANTARES is used for 14 C measurements. The accelerator measurements are supported by, and dependent on, a strong sample preparation section. The ANTARES AMS facility supports a wide range of investigations into fields such as global climate change, ice cores, oceanography, dendrochronology, anthropology, and classical and Australian archaeology. Described here are some examples of the ways in which AMS has been applied to support research into the archaeology, prehistory and culture of this continent's indigenous Aboriginal peoples. (author)

  2. Analyses of MHD instabilities

    International Nuclear Information System (INIS)

    Takeda, Tatsuoki

    1985-01-01

    In this article analyses of the MHD stabilities which govern the global behavior of a fusion plasma are described from the viewpoint of the numerical computation. First, we describe the high accuracy calculation of the MHD equilibrium and then the analysis of the linear MHD instability. The former is the basis of the stability analysis and the latter is closely related to the limiting beta value which is a very important theoretical issue of the tokamak research. To attain a stable tokamak plasma with good confinement property it is necessary to control or suppress disruptive instabilities. We, next, describe the nonlinear MHD instabilities which relate with the disruption phenomena. Lastly, we describe vectorization of the MHD codes. The above MHD codes for fusion plasma analyses are relatively simple though very time-consuming and parts of the codes which need a lot of CPU time concentrate on a small portion of the codes, moreover, the codes are usually used by the developers of the codes themselves, which make it comparatively easy to attain a high performance ratio on the vector processor. (author)

  3. Uncertainty Analyses and Strategy

    International Nuclear Information System (INIS)

    Kevin Coppersmith

    2001-01-01

    The DOE identified a variety of uncertainties, arising from different sources, during its assessment of the performance of a potential geologic repository at the Yucca Mountain site. In general, the number and detail of process models developed for the Yucca Mountain site, and the complex coupling among those models, make the direct incorporation of all uncertainties difficult. The DOE has addressed these issues in a number of ways using an approach to uncertainties that is focused on producing a defensible evaluation of the performance of a potential repository. The treatment of uncertainties oriented toward defensible assessments has led to analyses and models with so-called ''conservative'' assumptions and parameter bounds, where conservative implies lower performance than might be demonstrated with a more realistic representation. The varying maturity of the analyses and models, and uneven level of data availability, result in total system level analyses with a mix of realistic and conservative estimates (for both probabilistic representations and single values). That is, some inputs have realistically represented uncertainties, and others are conservatively estimated or bounded. However, this approach is consistent with the ''reasonable assurance'' approach to compliance demonstration, which was called for in the U.S. Nuclear Regulatory Commission's (NRC) proposed 10 CFR Part 63 regulation (64 FR 8640 [DIRS 101680]). A risk analysis that includes conservatism in the inputs will result in conservative risk estimates. Therefore, the approach taken for the Total System Performance Assessment for the Site Recommendation (TSPA-SR) provides a reasonable representation of processes and conservatism for purposes of site recommendation. However, mixing unknown degrees of conservatism in models and parameter representations reduces the transparency of the analysis and makes the development of coherent and consistent probability statements about projected repository

  4. A simple beam analyser

    International Nuclear Information System (INIS)

    Lemarchand, G.

    1977-01-01

    (ee'p) experiments allow to measure the missing energy distribution as well as the momentum distribution of the extracted proton in the nucleus versus the missing energy. Such experiments are presently conducted on SACLAY's A.L.S. 300 Linac. Electrons and protons are respectively analysed by two spectrometers and detected in their focal planes. Counting rates are usually low and include time coincidences and accidentals. Signal-to-noise ratio is dependent on the physics of the experiment and the resolution of the coincidence, therefore it is mandatory to get a beam current distribution as flat as possible. Using new technologies has allowed to monitor in real time the behavior of the beam pulse and determine when the duty cycle can be considered as being good with respect to a numerical basis

  5. EEG analyses with SOBI.

    Energy Technology Data Exchange (ETDEWEB)

    Glickman, Matthew R.; Tang, Akaysha (University of New Mexico, Albuquerque, NM)

    2009-02-01

    The motivating vision behind Sandia's MENTOR/PAL LDRD project has been that of systems which use real-time psychophysiological data to support and enhance human performance, both individually and of groups. Relevant and significant psychophysiological data being a necessary prerequisite to such systems, this LDRD has focused on identifying and refining such signals. The project has focused in particular on EEG (electroencephalogram) data as a promising candidate signal because it (potentially) provides a broad window on brain activity with relatively low cost and logistical constraints. We report here on two analyses performed on EEG data collected in this project using the SOBI (Second Order Blind Identification) algorithm to identify two independent sources of brain activity: one in the frontal lobe and one in the occipital. The first study looks at directional influences between the two components, while the second study looks at inferring gender based upon the frontal component.

  6. Pathway-based analyses.

    Science.gov (United States)

    Kent, Jack W

    2016-02-03

    New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

  7. Network class superposition analyses.

    Directory of Open Access Journals (Sweden)

    Carl A B Pearson

    Full Text Available Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30 for the yeast cell cycle process, considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  8. Seismic fragility analyses

    International Nuclear Information System (INIS)

    Kostov, Marin

    2000-01-01

    In the last two decades there is increasing number of probabilistic seismic risk assessments performed. The basic ideas of the procedure for performing a Probabilistic Safety Analysis (PSA) of critical structures (NUREG/CR-2300, 1983) could be used also for normal industrial and residential buildings, dams or other structures. The general formulation of the risk assessment procedure applied in this investigation is presented in Franzini, et al., 1984. The probability of failure of a structure for an expected lifetime (for example 50 years) can be obtained from the annual frequency of failure, β E determined by the relation: β E ∫[d[β(x)]/dx]P(flx)dx. β(x) is the annual frequency of exceedance of load level x (for example, the variable x may be peak ground acceleration), P(fI x) is the conditional probability of structure failure at a given seismic load level x. The problem leads to the assessment of the seismic hazard β(x) and the fragility P(fl x). The seismic hazard curves are obtained by the probabilistic seismic hazard analysis. The fragility curves are obtained after the response of the structure is defined as probabilistic and its capacity and the associated uncertainties are assessed. Finally the fragility curves are combined with the seismic loading to estimate the frequency of failure for each critical scenario. The frequency of failure due to seismic event is presented by the scenario with the highest frequency. The tools usually applied for probabilistic safety analyses of critical structures could relatively easily be adopted to ordinary structures. The key problems are the seismic hazard definitions and the fragility analyses. The fragility could be derived either based on scaling procedures or on the base of generation. Both approaches have been presented in the paper. After the seismic risk (in terms of failure probability) is assessed there are several approaches for risk reduction. Generally the methods could be classified in two groups. The

  9. Website-analyse

    DEFF Research Database (Denmark)

    Thorlacius, Lisbeth

    2009-01-01

    eller blindgyder, når han/hun besøger sitet. Studier i design og analyse af de visuelle og æstetiske aspekter i planlægning og brug af websites har imidlertid kun i et begrænset omfang været under reflektorisk behandling. Det er baggrunden for dette kapitel, som indleder med en gennemgang af æstetikkens......Websitet er i stigende grad det foretrukne medie inden for informationssøgning,virksomhedspræsentation, e-handel, underholdning, undervisning og social kontakt. I takt med denne voksende mangfoldighed af kommunikationsaktiviteter på nettet, er der kommet mere fokus på at optimere design og...... planlægning af de funktionelle og indholdsmæssige aspekter ved websites. Der findes en stor mængde teori- og metodebøger, som har specialiseret sig i de tekniske problemstillinger i forbindelse med interaktion og navigation, samt det sproglige indhold på websites. Den danske HCI (Human Computer Interaction...

  10. A channel profile analyser

    International Nuclear Information System (INIS)

    Gobbur, S.G.

    1983-01-01

    It is well understood that due to the wide band noise present in a nuclear analog-to-digital converter, events at the boundaries of adjacent channels are shared. It is a difficult and laborious process to exactly find out the shape of the channels at the boundaries. A simple scheme has been developed for the direct display of channel shape of any type of ADC on a cathode ray oscilliscope display. This has been accomplished by sequentially incrementing the reference voltage of a precision pulse generator by a fraction of a channel and storing ADC data in alternative memory locations of a multichannel pulse height analyser. Alternative channels are needed due to the sharing at the boundaries of channels. In the flat region of the profile alternate memory locations are channels with zero counts and channels with the full scale counts. At the boundaries all memory locations will have counts. The shape of this is a direct display of the channel boundaries. (orig.)

  11. The 'revealed preferences' theory: Assumptions and conjectures

    International Nuclear Information System (INIS)

    Green, C.H.

    1983-01-01

    Being kind of intuitive psychology the 'Revealed-Preferences'- theory based approaches towards determining the acceptable risks are a useful method for the generation of hypotheses. In view of the fact that reliability engineering develops faster than methods for the determination of reliability aims the Revealed-Preferences approach is a necessary preliminary help. Some of the assumptions on which the 'Revealed-Preferences' theory is based will be identified and analysed and afterwards compared with experimentally obtained results. (orig./DG) [de

  12. Micromechanical Analyses of Sturzstroms

    Science.gov (United States)

    Imre, Bernd; Laue, Jan; Springman, Sarah M.

    2010-05-01

    Sturzstroms are very fast landslides of very large initial volume. As type features they display extreme run out, pared with intensive fragmentation of the involved blocks of rock within a collisional flow. The inherent danger to the growing communities in alpine valleys below future potential sites of sturzstroms must be examined and results of predictions of endangered zones allow to impact upon the planning processes in these areas. This calls for the ability to make Type A predictions, according to Lambe (1973), which are done before an event. But Type A predictions are only possible if sufficient understanding of the mechanisms involved in a process is available. The motivation of the doctoral thesis research project presented is therefore to reveal the mechanics of sturzstroms in more detail in order to contribute to the development of a Type A run out prediction model. It is obvious that a sturzstrom represents a highly dynamic collisional granular regime. Thus particles do not only collide but will eventually crush each other. Erismann and Abele (2001) describe this process as dynamic disintegration, where kinetic energy is the main driver for fragmenting the rock mass. In this case an approach combining the type features long run out and fragmentation within a single hypothesis is represented by the dynamic fragmentation-spreading model (Davies and McSaveney, 2009; McSaveney and Davies, 2009). Unfortunately, sturzstroms, and fragmentation within sturzstroms, can not be observed directly in a real event because of their long "reoccurrence time" and the obvious difficulties in placing measuring devices within such a rock flow. Therefore, rigorous modelling is required in particular of the transition from static to dynamic behaviour to achieve better knowledge of the mechanics of sturzstroms, and to provide empirical evidence to confirm the dynamic fragmentation-spreading model. Within this study fragmentation and their effects on the mobility of sturzstroms

  13. NOAA's National Snow Analyses

    Science.gov (United States)

    Carroll, T. R.; Cline, D. W.; Olheiser, C. M.; Rost, A. A.; Nilsson, A. O.; Fall, G. M.; Li, L.; Bovitz, C. T.

    2005-12-01

    NOAA's National Operational Hydrologic Remote Sensing Center (NOHRSC) routinely ingests all of the electronically available, real-time, ground-based, snow data; airborne snow water equivalent data; satellite areal extent of snow cover information; and numerical weather prediction (NWP) model forcings for the coterminous U.S. The NWP model forcings are physically downscaled from their native 13 km2 spatial resolution to a 1 km2 resolution for the CONUS. The downscaled NWP forcings drive an energy-and-mass-balance snow accumulation and ablation model at a 1 km2 spatial resolution and at a 1 hour temporal resolution for the country. The ground-based, airborne, and satellite snow observations are assimilated into the snow model's simulated state variables using a Newtonian nudging technique. The principle advantages of the assimilation technique are: (1) approximate balance is maintained in the snow model, (2) physical processes are easily accommodated in the model, and (3) asynoptic data are incorporated at the appropriate times. The snow model is reinitialized with the assimilated snow observations to generate a variety of snow products that combine to form NOAA's NOHRSC National Snow Analyses (NSA). The NOHRSC NSA incorporate all of the available information necessary and available to produce a "best estimate" of real-time snow cover conditions at 1 km2 spatial resolution and 1 hour temporal resolution for the country. The NOHRSC NSA consist of a variety of daily, operational, products that characterize real-time snowpack conditions including: snow water equivalent, snow depth, surface and internal snowpack temperatures, surface and blowing snow sublimation, and snowmelt for the CONUS. The products are generated and distributed in a variety of formats including: interactive maps, time-series, alphanumeric products (e.g., mean areal snow water equivalent on a hydrologic basin-by-basin basis), text and map discussions, map animations, and quantitative gridded products

  14. Maximizing your Process Improvement ROI through Harmonization

    Science.gov (United States)

    2008-03-01

    ISO 12207 ) provide comprehensive guidance on what system and software engineering processes are needed. The frameworks of Six Sigma provide specific...reductions. Their veloci-Q Enterprise integrated system, includes ISO 9001, CMM, P-CMM, TL9000, British Standard 7799, and Six Sigma. They estimate a 30...at their discretion. And, they chose to blend process maturity models and ISO standards to support their objective regarding the establishment of

  15. Academic ROI: What Does the Most Good?

    Science.gov (United States)

    Levenson, Nathan

    2012-01-01

    The author, who has served as a school board member and district superintendent, advocates that school districts use an academic return on investment approach to evaluate and make decisions about spending, specifically in special education. This approach requires that schools formally evaluate all programs, efforts, and strategies by multiple…

  16. Kaks intervjuud Sophie Roisiga / Sophie Rois

    Index Scriptorium Estoniae

    Rois, Sophie, 1961-

    2010-01-01

    Saksa Volksbühne truppi näitleja Sophie Roisi mõtteid teatrist ja näitlejatööst. Intervjuu on pärit ajalehtedest Frankfurter Allgemeine Zeitung 2010 aasta jaanuari numbrist ja Planet Interview 2004 aasta juuli numbrist

  17. Pawnee Nation Energy Option Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Matlock, M.; Kersey, K.; Riding In, C.

    2009-07-21

    Pawnee Nation of Oklahoma Energy Option Analyses In 2003, the Pawnee Nation leadership identified the need for the tribe to comprehensively address its energy issues. During a strategic energy planning workshop a general framework was laid out and the Pawnee Nation Energy Task Force was created to work toward further development of the tribe’s energy vision. The overarching goals of the “first steps” project were to identify the most appropriate focus for its strategic energy initiatives going forward, and to provide information necessary to take the next steps in pursuit of the “best fit” energy options. Description of Activities Performed The research team reviewed existing data pertaining to the availability of biomass (focusing on woody biomass, agricultural biomass/bio-energy crops, and methane capture), solar, wind and hydropower resources on the Pawnee-owned lands. Using these data, combined with assumptions about costs and revenue streams, the research team performed preliminary feasibility assessments for each resource category. The research team also reviewed available funding resources and made recommendations to Pawnee Nation highlighting those resources with the greatest potential for financially-viable development, both in the near-term and over a longer time horizon. Findings and Recommendations Due to a lack of financial incentives for renewable energy, particularly at the state level, combined mediocre renewable energy resources, renewable energy development opportunities are limited for Pawnee Nation. However, near-term potential exists for development of solar hot water at the gym, and an exterior wood-fired boiler system at the tribe’s main administrative building. Pawnee Nation should also explore options for developing LFGTE resources in collaboration with the City of Pawnee. Significant potential may also exist for development of bio-energy resources within the next decade. Pawnee Nation representatives should closely monitor

  18. Sample preparation in foodomic analyses.

    Science.gov (United States)

    Martinović, Tamara; Šrajer Gajdošik, Martina; Josić, Djuro

    2018-04-16

    Representative sampling and adequate sample preparation are key factors for successful performance of further steps in foodomic analyses, as well as for correct data interpretation. Incorrect sampling and improper sample preparation can be sources of severe bias in foodomic analyses. It is well known that both wrong sampling and sample treatment cannot be corrected anymore. These, in the past frequently neglected facts, are now taken into consideration, and the progress in sampling and sample preparation in foodomics is reviewed here. We report the use of highly sophisticated instruments for both high-performance and high-throughput analyses, as well as miniaturization and the use of laboratory robotics in metabolomics, proteomics, peptidomics and genomics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  19. ATHENA/INTRA analyses for ITER, NSSR-2

    International Nuclear Information System (INIS)

    Shen, Kecheng; Eriksson, John; Sjoeberg, A.

    1999-02-01

    The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes

  20. ATHENA/INTRA analyses for ITER, NSSR-2

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Kecheng; Eriksson, John; Sjoeberg, A

    1999-02-01

    The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes 8 refs, 14 figs, 15 tabs

  1. Revealing the programming process

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Caspersen, Michael Edelgaard

    2005-01-01

    One of the most important goals of an introductory programming course is that the students learn a systematic approach to the development of computer programs. Revealing the programming process is an important part of this; however, textbooks do not address the issue -- probably because...... the textbook medium is static and therefore ill-suited to expose the process of programming. We have found that process recordings in the form of captured narrated programming sessions are a simple, cheap, and efficient way of providing the revelation.We identify seven different elements of the programming...

  2. TypeScript revealed

    CERN Document Server

    Maharry, Dan

    2013-01-01

    TypeScript Revealed is a quick 100-page guide to Anders Hejlsberg's new take on JavaScript. With this brief, fast-paced introduction to TypeScript, .NET, Web and Windows 8 application developers who are already familiar with JavaScript will easily get up to speed with TypeScript and decide whether or not to start incorporating it into their own development. TypeScript is 'JavaScript for Application-scale development'; a superset of JavaScript that brings to it an additional object-oriented-like syntax familiar to .NET programmers that compiles down into simple, clean JavaScript that any browse

  3. Descriptive Analyses of Mechanical Systems

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Hansen, Claus Thorp

    2003-01-01

    Forord Produktanalyse og teknologianalyse kan gennmføres med et bredt socio-teknisk sigte med henblik på at forstå kulturelle, sociologiske, designmæssige, forretningsmæssige og mange andre forhold. Et delområde heri er systemisk analyse og beskrivelse af produkter og systemer. Nærværende kompend...

  4. Analysing and Comparing Encodability Criteria

    Directory of Open Access Journals (Sweden)

    Kirstin Peters

    2015-08-01

    Full Text Available Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of different criteria and different variants of criteria in order to reason in different settings. This leads to incomparable results. Moreover it is not always clear whether the criteria used to obtain a result in a particular setting do indeed fit to this setting. We show how to formally reason about and compare encodability criteria by mapping them on requirements on a relation between source and target terms that is induced by the encoding function. In particular we analyse the common criteria full abstraction, operational correspondence, divergence reflection, success sensitiveness, and respect of barbs; e.g. we analyse the exact nature of the simulation relation (coupled simulation versus bisimulation that is induced by different variants of operational correspondence. This way we reduce the problem of analysing or comparing encodability criteria to the better understood problem of comparing relations on processes.

  5. Analysing Children's Drawings: Applied Imagination

    Science.gov (United States)

    Bland, Derek

    2012-01-01

    This article centres on a research project in which freehand drawings provided a richly creative and colourful data source of children's imagined, ideal learning environments. Issues concerning the analysis of the visual data are discussed, in particular, how imaginative content was analysed and how the analytical process was dependent on an…

  6. Impact analyses after pipe rupture

    International Nuclear Information System (INIS)

    Chun, R.C.; Chuang, T.Y.

    1983-01-01

    Two of the French pipe whip experiments are reproduced with the computer code WIPS. The WIPS results are in good agreement with the experimental data and the French computer code TEDEL. This justifies the use of its pipe element in conjunction with its U-bar element in a simplified method of impact analyses

  7. Millifluidic droplet analyser for microbiology

    NARCIS (Netherlands)

    Baraban, L.; Bertholle, F.; Salverda, M.L.M.; Bremond, N.; Panizza, P.; Baudry, J.; Visser, de J.A.G.M.; Bibette, J.

    2011-01-01

    We present a novel millifluidic droplet analyser (MDA) for precisely monitoring the dynamics of microbial populations over multiple generations in numerous (=103) aqueous emulsion droplets (100 nL). As a first application, we measure the growth rate of a bacterial strain and determine the minimal

  8. Analyser of sweeping electron beam

    International Nuclear Information System (INIS)

    Strasser, A.

    1993-01-01

    The electron beam analyser has an array of conductors that can be positioned in the field of the sweeping beam, an electronic signal treatment system for the analysis of the signals generated in the conductors by the incident electrons and a display for the different characteristics of the electron beam

  9. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

    NARCIS (Netherlands)

    E.K. Speliotes (Elizabeth); C.J. Willer (Cristen); S.I. Berndt (Sonja); K.L. Monda (Keri); G. Thorleifsson (Gudmar); A.U. Jackson (Anne); H.L. Allen; C.M. Lindgren (Cecilia); J. Luan; R. Mägi (Reedik); J.C. Randall (Joshua); S. Vedantam (Sailaja); T.W. Winkler (Thomas); L. Qi (Lu); T. Workalemahu (Tsegaselassie); I.M. Heid (Iris); V. Steinthorsdottir (Valgerdur); H.M. Stringham (Heather); E. Wheeler (Eleanor); A.R. Wood (Andrew); T. Ferreira (Teresa); R.J. Weyant (Robert); A.V. Segrè (Ayellet); K. Eestrada (Karol); L. Liang (Liming); J. Nemesh (James); J.H. Park; S. Gustafsson (Stefan); T.O. Kilpeläinen (Tuomas); J. Yang (Joanna); N. Bouatia-Naji (Nabila); T. Eesko (Tõnu); M.F. Feitosa (Mary Furlan); Z. Kutalik (Zoltán); M. Mangino (Massimo); S. Raychaudhuri (Soumya); A. Scherag (Andre); A.V. Smith (Albert Vernon); R.P. Welch (Ryan); J.H. Zhao (Jing Hua); K.K.H. Aben (Katja); D. Absher (Devin); N. Amin (Najaf); A.L. Dixon (Anna); E. Fisher (Eeva); N.L. Glazer (Nicole); M.E. Goddard (Michael); N.L. Heard-Costa (Nancy); V. Hoesel (Volker); J.J. Hottenga (Jouke Jan); A. Johansson (Åsa); T. Johnson (Toby); S. Ketkar (Shamika); C. Lamina (Claudia); S. Li (Shengxu); M.F. Moffatt (Miriam); R.H. Myers (Richard); N. Narisu (Narisu); J.R.B. Perry (John); M.J. Peters (Marjolein); M. Preuss (Michael); S. Ripatti (Samuli); F. Rivadeneira Ramirez (Fernando); C. Sandholt (Camilla); L.J. Scott (Laura); N.J. Timpson (Nicholas); J.P. Tyrer (Jonathan); S. van Wingerden (Sophie); C.C. White (Charles); F. Wiklund (Fredrik); C. Barlassina (Christina); D.I. Chasman (Daniel); M.N. Cooper (Matthew); J.O. Jansson; R.W. Lawrence (Robert); N. Pellikka (Niina); I. Prokopenko (Inga); J. Shi (Jianxin); E. Thiering (Eelisabeth); H. Alavere (Helene); M.T.S. Alibrandi (Maria); P. Almgren (Peter); A.M. Arnold (Alice); T. Aspelund (Thor); L.D. Atwood (Larry); B. Balkau (Beverley); A.J. Balmforth (Anthony); A.J. Bennett (Amanda); Y. Ben-Shlomo; R.N. Bergman (Richard); S.M. Bergmann (Sven); H. Biebermann (Heike); A.I.F. Blakemore (Alexandra); T. Boes (Tanja); L.L. Bonnycastle (Lori); S.R. Bornstein (Stefan); M.J. Brown (Morris); T.A. Buchanan (Thomas); F. Busonero; H. Campbell (Harry); F.P. Cappuccio (Francesco); C. Cavalcanti-Proença (Christine); Y.D.I. Chen (Yii-Der Ida); C.-M. Chen (Chih-Mei); P.S. Chines (Peter); R. Clarke; L. Coin (Lachlan); J. Connell (John); I.N.M. Day (Ian); M. den Heijer (Martin); J. Duan (Jubao); S. Eebrahim (Shah); P. Eelliott (Paul); R. Eelosua (Roberto); G. Eeiriksdottir (Gudny); M.R. Eerdos (Micheal); J.G. Eeriksson (Johan); M.F. Facheris (Maurizio); S.B. Felix (Stephan); P. Fischer-Posovszky (Pamela); A.R. Folsom (Aaron); N. Friedrich (Nele); N.B. Freimer (Nelson); M. Fu (Mao); S. Gaget (Stefan); P.V. Gejman (Pablo); E.J.C. de Geus (Eco); C. Gieger (Christian); A.P. Gjesing (Anette); A. Goel (Anuj); P. Goyette (Philippe); H. Grallert (Harald); J. Gräßler (Jürgen); D. Greenawalt (Danielle); C.J. Groves (Christopher); V. Gudnason (Vilmundur); C. Guiducci (Candace); A.L. Hartikainen; N. Hassanali (Neelam); A.S. Hall (Alistair); A.S. Havulinna (Aki); C. Hayward (Caroline); A.C. Heath (Andrew); C. Hengstenberg (Christian); A.A. Hicks (Andrew); A. Hinney (Anke); A. Hofman (Albert); G. Homuth (Georg); J. Hui (Jennie); W. Igl (Wilmar); C. Iribarren (Carlos); B. Isomaa (Bo); K.B. Jacobs (Kevin); I. Jarick (Ivonne); E. Jewell (Eelizabeth); U. John (Ulrich); T. Jørgensen (Torben); P. Jousilahti (Pekka); A. Jula (Antti); M. Kaakinen (Marika); E. Kajantie (Eero); R.C. Kaplan (Robert); S. Kathiresan (Sekar); J. Kettunen (Johannes); L. Kinnunen (Leena); J.W. Knowles (Joshua); I. Kolcic (Ivana); I.R. König (Inke); S. Koskinen (Seppo); P. Kovacs (Peter); J. Kusisto (Johanna); P. Kraft (Peter); K. Kvaløy (Kirsti); J. Laitinen (Jaana); O. Lantieri (Olivier); C. Lanzani (Chiara); L.J. Launer (Lenore); C. Lecoeur (Cécile); T. Lehtimäki (Terho); G. Lettre (Guillaume); J. Liu (Jianjun); M.L. Lokki; M. Lorentzon (Mattias); R.N. Luben (Robert); B. Ludwig (Barbara); P. Manunta (Paolo); D. Marek (Diana); M. Marre (Michel); N.G. Martin (Nicholas); W.L. McArdle (Wendy); M.I. McCarthy (Mark); B. McKnight (Barbara); T. Meitinger (Thomas); O. Melander (Olle); D. Meyre (David); K. Midthjell (Kristian); G.W. Montgomery (Grant); M.A. Morken (Mario); A.D. Morris (Andrew); R. Mulic (Rosanda); J.S. Ngwa; M. Nelis (Mari); M.J. Neville (Matthew); D.R. Nyholt (Dale); C.J. O'Ddonnell (Christopher); S. O'Rahilly (Stephen); K. Ong (Ken); B.A. Oostra (Ben); G. Paré (Guillaume); A.N. Parker (Alex); M. Perola (Markus); I. Pichler (Irene); K.H. Pietilainen (Kirsi Hannele); C.P. Platou (Carl); O. Polasek (Ozren); A. Pouta (Anneli); S. Rafelt (Suzanne); O. Raitakari (Olli); N.W. Rayner (Nigel William); M. Ridderstråle (Martin); W. Rief (Winfried); A. Ruokonen (Aimo); N.R. Robertson (Neil); P. Rzehak (Peter); V. Salomaa (Veikko); A.R. Sanders (Alan); M.S. Sandhu (Manjinder); S. Sanna (Serena); J. Saramies (Jouko); M.J. Savolainen (Markku); S. Schipf (Sabine); S. Schreiber (Stefan); H. Schunkert (Heribert); K. Silander (Kaisa); J. Sinisalo (Juha); D.S. Siscovick (David); J.H. Smit (Jan); N. Soranzo (Nicole); U. Sovio (Ulla); J. Stephens (Jonathan); I. Surakka (Ida); A.J. Swift (Amy); M.L. Tammesoo; J.-C. Tardif (Jean-Claude); M. Teder-Laving (Maris); T.M. Teslovich (Tanya); J.R. Thompson (John); B. Thomson (Brian); A. Tönjes (Anke); T. Tuomi (Tiinamaija); J.B.J. van Meurs (Joyce); G.J. van OMen; V. Vatin (Vincent); J. Viikari (Jorma); S. Visvikis-Siest (Sophie); V. Vitart (Veronique); C.I. Vogel (Carla); B.F. Voight (Benjamin); L. Waite (Lindsay); H. Wallaschofski (Henri); G.B. Walters (Bragi); E. Widen (Elisabeth); S. Wiegand (Susanna); S.H. Wild (Sarah); G.A.H.M. Willemsen (Gonneke); D.R. Witte (Deniel); J.C.M. Witteman (Jacqueline); J. Xu (Jianfeng); Q. Zhang (Qunyuan); L. Zgaga (Lina); A. Ziegler (Andreas); P. Zitting (Paavo); J.P. Beilby (John); I.S. FarOqi (Ssadaf); J. Hebebrand (Johannes); H.V. Huikuri (Heikki); A. James (Alan); M. Kähönen (Mika); D.F. Levinson (Douglas); F. MacCiardi (Fabio); M.S. Nieminen (Markku); C. Ohlsson (Claes); C. Palmer (Cameron); P.M. Ridker (Paul); M. Stumvoll (Michael); J.S. Beckmann (Jacques); H. Boeing (Heiner); E.A. Boerwinkle (Eric); D.I. Boomsma (Dorret); M. Caulfield (Mark); S.J. Chanock (Stephen); F.S. Collins (Francis); L.A. Cupples (Adrienne); J. Eerdmann (Jeanette); P. Frogue (Philippe); H. Grönberg (Henrik); U. Gyllensten (Ulf); T. Hansen (Torben); T.B. Harris (Tamara); A.T. Hattersley (Andrew); R.B. Hayes (Richard); J. Heinrich (Joachim); F.B. Hu (Frank); K. Hveem (Kristian); T. Illig (Thomas); M.R. Järvelin; J. Kaprio (Jaakko); F. Karpe (Fredrik); K-T. Khaw (Kay-Tee); L.A.L.M. Kiemeney (Bart); H. Krude; M. Laakso (Markku); D.A. Lawlor (Debbie); A. Metspalu (Andres); P. Munroe (Patricia); W.H. Ouwehand (Willem); O. Pedersen (Oluf); B.W.J.H. Penninx (Brenda); P.P. Pramstaller (Peter Paul); T. Quertermous (Thomas); T. Reinehr (Thomas); A. Rissanen (Aila); I. Rudan (Igor); N.J. Samani (Nilesh); P.E.H. Schwarz (Peter); A.R. Shuldiner (Alan); T.D. Spector (Timothy); J. Tuomilehto (Jaakko); M. Uda (Manuela); A.G. Uitterlinden (André); T.T. Valle (Timo); M. Wabitsch (Martin); G. Waeber (Gérard); N.J. Wareham (Nick); H. Watkins (Hugh); J.F. Wilson (James); A.F. Wright (Alan); M.C. Zillikens (Carola); N. ChatterjE (Nilanjan); S.A. McCarroll (Steve); S. Purcell (Shaun); E.E. Schadt (Eric); P.M. Visscher (Peter); T.L. Assimes (Themistocles); I.B. Borecki (Ingrid); P. Deloukas (Panagiotis); C.S. Fox (Caroline); L. Groop (Leif); T. Haritunians (Talin); D.J. Hunter (David); K.L. Mohlke (Karen); J.R. O'ConneL (Jeffrey); L. Peltonen (Leena Johanna); D. SchleSinger (David); D.P. Strachan (David); R.M. Watanabe (Richard); C.M. van Duijn (Cornelia); H.E. Wichmann (Heinz Erich); T.M. Frayling (Timothy); U. Thorsteinsdottir (Unnur); G.R. Abecasis (Gonçalo); M. Boehnke (Michael); K. StefanSon (Kari); K.E. North (Kari); M.I. McArthy (Mark); J.N. Hirschhorn (Joel); E. IngelSon (Erik); R.J.F. Loos (Ruth); M.N. Weedon (Michael)

    2010-01-01

    textabstractObesity is globaLy prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined aSociations betwEn body maS index and ĝ̂1/42.8 miLion SNPs in up to 123,865 individuals with targeted foLow up of

  10. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer.

    Science.gov (United States)

    Du, Zhou; Sun, Tong; Hacisuleyman, Ezgi; Fei, Teng; Wang, Xiaodong; Brown, Myles; Rinn, John L; Lee, Mary Gwo-Shu; Chen, Yiwen; Kantoff, Philip W; Liu, X Shirley

    2016-03-15

    Mounting evidence suggests that long noncoding RNAs (lncRNAs) can function as microRNA sponges and compete for microRNA binding to protein-coding transcripts. However, the prevalence, functional significance and targets of lncRNA-mediated sponge regulation of cancer are mostly unknown. Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours. We confirm the tumour-suppressive function of two lncRNAs (TUG1 and CTB-89H12.4) and their regulation of PTEN expression in prostate cancer. Surprisingly, one of the two lncRNAs, TUG1, was previously known for its function in polycomb repressive complex 2 (PRC2)-mediated transcriptional regulation, suggesting its sub-cellular localization-dependent function. Our findings not only suggest an important role of lncRNA-mediated sponge regulation in cancer, but also underscore the critical influence of cytoplasmic localization on the efficacy of a sponge lncRNA.

  11. Classification tree analyses reveal limited potential for early targeted prevention against childhood overweight.

    Science.gov (United States)

    Beyerlein, Andreas; Kusian, Dennis; Ziegler, Anette-Gabriele; Schaffrath-Rosario, Angelika; von Kries, Rüdiger

    2014-02-01

    Whether specific combinations of risk factors in very early life might allow identification of high-risk target groups for overweight prevention programs was examined. Data of n = 8981 children from the German KiGGS study were analyzed. Using a classification tree approach, predictive risk factor combinations were assessed for overweight in 3-6, 7-10, and 11-17-year-old children. In preschool children, the subgroup with the highest overweight risk were migrant children with at least one obese parent, with a prevalence of 36.6 (95% confidence interval or CI: 22.9, 50.4)%, compared to an overall prevalence of 10.0 (8.9, 11.2)%. The prevalence of overweight increased from 18.3 (16.8, 19.8)% to 57.9 (46.6, 69.3)% in 7-10-year-old children, if at least one parent was obese and the child had been born large-for-gestational-age. In 11-17-year-olds, the overweight risk increased from 20.1 (18.9, 21.3)% to 63.0 (46.4, 79.7)% in the highest risk group. However, high prevalence ratios were found only in small subgroups, containing <10% of all overweight cases in the respective age group. Our results indicate only a limited potential for early targeted preventions against overweight in children and adolescents. Copyright © 2013 The Obesity Society.