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Journal articles on the topic 'Ecogenomics'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Bos, Mark J. W., Roy R. Kloet, Cees M. Koolstra, and Jaap T. J. M. Willems. "Getting adolescents to inform themselves about ecogenomics: a Dutch case study." Journal of Science Communication 08, no. 03 (2009): A02. http://dx.doi.org/10.22323/2.08030202.

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Public opinions toward emergent technologies may be highly dependent on the manner in which people are introduced to these technologies for the very first time. In this light, understanding how such first introductions are related to adolescents’ information seeking behaviors and their developing opinions may be particularly interesting because this target public can be considered to be not only future users of the technology but also future decision makers of its development. The present paper presents a case study of the introduction of ecogenomics among 246 adolescents who were asked to inf

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2

OUBORG, N. J., and W. H. VRIEZEN. "An ecologist's guide to ecogenomics." Journal of Ecology 95, no. 1 (2007): 8–16. http://dx.doi.org/10.1111/j.1365-2745.2006.01197.x.

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3

Haro‐Moreno, Jose M., Francisco Rodriguez‐Valera, Riccardo Rosselli, et al. "Ecogenomics of the SAR11 clade." Environmental Microbiology 22, no. 5 (2019): 1748–63. http://dx.doi.org/10.1111/1462-2920.14896.

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4

Chapman, Robert W. "EcoGenomics—a consilience for comparative immunology?" Developmental & Comparative Immunology 25, no. 7 (2001): 549–51. http://dx.doi.org/10.1016/s0145-305x(01)00045-3.

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5

Dicke, M. "ECOLOGY: Enhanced: Ecogenomics Benefits Community Ecology." Science 305, no. 5684 (2004): 618–19. http://dx.doi.org/10.1126/science.1101788.

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6

Kumar, Manoj, Ajit Varma, and Vivek Kumar. "Ecogenomics Based Microbial Enzyme for Biofuel Industry." Science International 4, no. 1 (2016): 1–11. http://dx.doi.org/10.17311/sciintl.2016.1.11.

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7

Garantziotis, Stavros, and David A. Schwartz. "Ecogenomics of Respiratory Diseases of Public Health Significance." Annual Review of Public Health 31, no. 1 (2010): 37–51. http://dx.doi.org/10.1146/annurev.publhealth.012809.103633.

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8

Chapman, R. W., J. Robalino, and H. F. Trent. "EcoGenomics: analysis of complex systems via fractal geometry." Integrative and Comparative Biology 46, no. 6 (2006): 902–11. http://dx.doi.org/10.1093/icb/icj049.

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9

Walter, Juline M., Felipe H. Coutinho, Luciana Leomil, et al. "Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia." Microbial Ecology 80, no. 2 (2020): 249–65. http://dx.doi.org/10.1007/s00248-019-01480-x.

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10

Béjà, Oded. "To BAC or not to BAC: marine ecogenomics." Current Opinion in Biotechnology 15, no. 3 (2004): 187–90. http://dx.doi.org/10.1016/j.copbio.2004.03.005.

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11

Gobler, C. J., D. L. Berry, S. T. Dyhrman, et al. "Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics." Proceedings of the National Academy of Sciences 108, no. 11 (2011): 4352–57. http://dx.doi.org/10.1073/pnas.1016106108.

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12

ROOSSINCK, MARILYN J., PRASENJIT SAHA, GRAHAM B. WILEY, et al. "Ecogenomics: using massively parallel pyrosequencing to understand virus ecology." Molecular Ecology 19 (March 2010): 81–88. http://dx.doi.org/10.1111/j.1365-294x.2009.04470.x.

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13

Roelofsen, Anneloes, Jacqueline Broerse, Tjard de Cock Buning, and Joske Bunders. "Engaging with future technologies: how potential future users frame ecogenomics." Science and Public Policy 37, no. 3 (2010): 167–79. http://dx.doi.org/10.3152/030234210x497717.

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14

Yang, Jianghua, Xiaowei Zhang, Yuwei Xie, et al. "Ecogenomics of Zooplankton Community Reveals Ecological Threshold of Ammonia Nitrogen." Environmental Science & Technology 51, no. 5 (2017): 3057–64. http://dx.doi.org/10.1021/acs.est.6b05606.

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15

Kloet, Roy, Tjard de Cock Buning, and Joske Bunders. "An introduction to and a reflection on the “ecogenomics promise”." Journal of Integrative Environmental Sciences 8, no. 1 (2011): 23–38. http://dx.doi.org/10.1080/1943815x.2010.542165.

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16

Roux, Simon, Jennifer R. Brum, Bas E. Dutilh, et al. "Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses." Nature 537, no. 7622 (2016): 689–93. http://dx.doi.org/10.1038/nature19366.

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17

Duhaime, Melissa Beth, Antje Wichels, Jost Waldmann, Hanno Teeling, and Frank Oliver Glöckner. "Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1." ISME Journal 5, no. 1 (2010): 107–21. http://dx.doi.org/10.1038/ismej.2010.94.

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18

Maphosa, Farai, Willem M. de Vos, and Hauke Smidt. "Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria." Trends in Biotechnology 28, no. 6 (2010): 308–16. http://dx.doi.org/10.1016/j.tibtech.2010.03.005.

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19

Ralebitso-Senior, T. K., T. J. U. Thompson, and H. E. Carney. "Microbial ecogenomics and forensic archaeology: new methods for investigating clandestine gravesites." Human Remains and Violence: An Interdisciplinary Journal 2, no. 1 (2016): 41–57. http://dx.doi.org/10.7227/hrv.2.1.4.

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In the mid-1990s, the crime scene toolkit was revolutionised by the introduction of DNA-based analyses such as the polymerase chain reaction, low copy number DNA analysis, short-tandem repeat typing, pulse-field gel electrophoresis and variable number tandem repeat. Since then, methodological advances in other disciplines, especially molecular microbial ecology, can now be adapted for cutting-edge applications in forensic contexts. Despite several studies and discussions, there is, however, currently very little evidence of these techniques adoption at the contemporary crime scene. Consequentl

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20

Lawson, Christopher E., Sha Wu, Ananda S. Bhattacharjee, Katherine D. McMahon, Ramesh Goel, and Daniel R. Noguera. "Ecogenomics Reveals Distributed Metabolic Networks In Suspended And Attached Growth Anammox Bioreactors." Proceedings of the Water Environment Federation 2015, no. 10 (2015): 3194–98. http://dx.doi.org/10.2175/193864715819542142.

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21

Nobu, Masaru K., Takashi Narihiro, Christian Rinke, et al. "Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor." ISME Journal 9, no. 8 (2015): 1710–22. http://dx.doi.org/10.1038/ismej.2014.256.

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22

Babenko, V. V., A. Millard, E. E. Kulikov, et al. "The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses." Computational and Structural Biotechnology Journal 18 (2020): 3457–67. http://dx.doi.org/10.1016/j.csbj.2020.10.036.

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23

Cavicchioli, Rick. "Antarctic metagenomics." Microbiology Australia 28, no. 3 (2007): 98. http://dx.doi.org/10.1071/ma07098.

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The DNA sequencing of whole environmental samples (referred to as metagenomics, environmental genomics, ecogenomics or community genomics) captures genome surveys of uncultured microorganisms. By moving away from a species-by-species investigation of the environment, metagenomics enables a greatly expanded view of the diversity and metabolic function of the resident microbial communities. The southern polar region plays a critical role in maintaining microbial processes that are essential for the health of the world?s ecosystems, yet we know less about microorganisms on the vast Antarctic cont

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24

Bos, Mark J. W., Cees M. Koolstra, and Jaap T. J. M. Willems. "Early Exposures to Ecogenomics: Effects of Priming and Web Site Interactivity Among Adolescents." Science Communication 32, no. 2 (2010): 232–55. http://dx.doi.org/10.1177/1075547009358625.

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25

Bonfante, Paola. "From environmental microbiology to ecogenomics: spotting the emerging field of fungal-bacterial interactions." Environmental Microbiology Reports 7, no. 1 (2015): 15–17. http://dx.doi.org/10.1111/1758-2229.12220.

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26

Kant, Merijn R., and Ian T. Baldwin. "The ecogenetics and ecogenomics of plant–herbivore interactions: rapid progress on a slippery road." Current Opinion in Genetics & Development 17, no. 6 (2007): 519–24. http://dx.doi.org/10.1016/j.gde.2007.09.002.

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27

Ozdemir, Vural, Arno G. Motulsky, Eugene Kolker, and Béatrice Godard. "Genome–Environment Interactions and Prospective Technology Assessment: Evolution from Pharmacogenomics to Nutrigenomics and Ecogenomics." OMICS: A Journal of Integrative Biology 13, no. 1 (2009): 1–6. http://dx.doi.org/10.1089/omi.2009.0013.

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28

Li, Hang, Jinyu Hu, Haochen Wei та ін. "Chemical Ecogenomics-Guided Discovery of Phytotoxic α-Pyrones from the Fungal Wheat Pathogen Parastagonospora nodorum". Organic Letters 20, № 19 (2018): 6148–52. http://dx.doi.org/10.1021/acs.orglett.8b02617.

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29

Bos, Mark J. W., Cees M. Koolstra, and Jaap T. J. M. Willems. "Adolescent responses toward a new technology: first associations, information seeking and affective responses to ecogenomics." Public Understanding of Science 18, no. 2 (2008): 243–53. http://dx.doi.org/10.1177/0963662507087306.

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30

Morya, V. K., Yachna Singh, Birendra K. Singh, and G. Thomas. "Ecogenomics of Geminivirus from India and Neighbor Countries: An In Silico Analysis of Recombination Phenomenon." Interdisciplinary Sciences: Computational Life Sciences 7, no. 2 (2015): 168–76. http://dx.doi.org/10.1007/s12539-015-0020-3.

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31

Saxena, Gourvendu, Ezequiel M. Marzinelli, Nyi N. Naing, et al. "Ecogenomics Reveals Metals and Land-Use Pressures on Microbial Communities in the Waterways of a Megacity." Environmental Science & Technology 49, no. 3 (2015): 1462–71. http://dx.doi.org/10.1021/es504531s.

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32

Benites, L. Felipe, Nicole Poulton, Karine Labadie, Michael E. Sieracki, Nigel Grimsley, and Gwenael Piganeau. "Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1786 (2019): 20190089. http://dx.doi.org/10.1098/rstb.2019.0089.

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Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13–22 Mb genomes from three genera, Ostreococcus , Bathycoccus and Micromonas , are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain bio

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33

Podder, Aditi, Debra Reinhart, and Ramesh Goel. "Nitrogen management in landfill leachate using single-stage anammox process-illustrating key nitrogen pathways under an ecogenomics framework." Bioresource Technology 312 (September 2020): 123578. http://dx.doi.org/10.1016/j.biortech.2020.123578.

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34

Morinaga, Shin-Ichi, Atsushi J. Nagano, Saori Miyazaki, et al. "Ecogenomics of cleistogamous and chasmogamous flowering: genome-wide gene expression patterns from cross-species microarray analysis in Cardamine kokaiensis (Brassicaceae)." Journal of Ecology 96, no. 5 (2008): 1086–97. http://dx.doi.org/10.1111/j.1365-2745.2008.01392.x.

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35

Patreze, C. M., D. B. Felix, F. R. Scarano, and M. Alves-Ferreira. "Isolating of a putative glyceraldehyde-3 phosphate dehydrogenase (GAPDH) from Calophyllum brasiliense, an important tropical forest tree." Silvae Genetica 61, no. 1-6 (2012): 44–51. http://dx.doi.org/10.1515/sg-2012-0006.

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Abstract Calophyllum brasiliense Cambess. has characteristics that made it an excellent candidate model for ecogenomics in rain forest trees such as widespread natural occurrence and geographical patterns of adaptive genetic variation. Besides, it is also becoming a popular species for reforestation efforts in Brazil. Although, very little is known about its genetic diversity and the molecular mechanisms involved genetic adaptation traits. The first difficulty in launching genetic studies in a wild wood species is the lack of an optimized protocol for RNA and DNA isolation. In this work we bui

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36

Scholin, C. A. "What are "ecogenomic sensors?" – a review and thoughts for the future." Ocean Science Discussions 6, no. 1 (2009): 191–213. http://dx.doi.org/10.5194/osd-6-191-2009.

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Abstract. The OceanSensors08 workshop held 31 March–4 April 2008 in Warnemünde, Germany, brought together an international group of marine scientists, sensor developers and technologists with a common interest in shaping the future of ocean sensing. In preparation for that meeting a series of review papers were commissioned, one of which was meant to cover Sensors for Ocean-omics. The "ocean-omics" topic was cast very broadly. The notion was to review use of genetic techniques for assessing presence and diversity of organisms, their genomic capacity and gene expression, and to provide a prospe

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37

Scholin, C. A. "What are "ecogenomic sensors?" A review and thoughts for the future." Ocean Science 6, no. 1 (2010): 51–60. http://dx.doi.org/10.5194/os-6-51-2010.

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Abstract. The OceanSensors08 workshop held 31 March–4 April 2008 in Warnemünde, Germany, brought together an international group of marine scientists, sensor developers and technologists with a common interest in shaping the future of ocean sensing. In preparation for that meeting a series of review papers was commissioned, one of which was meant to cover Sensors for Ocean-omics. The "ocean-omics" topic was cast very broadly. The notion was to review use of genetic techniques for assessing presence and diversity of organisms, their genomic capacity and gene expression, and to provide a prospec

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38

Ottesen, Elizabeth A. "Probing the living ocean with ecogenomic sensors." Current Opinion in Microbiology 31 (June 2016): 132–39. http://dx.doi.org/10.1016/j.mib.2016.03.012.

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39

Golyshina, Olga V., Rafael Bargiela, and Peter N. Golyshin. "Cuniculiplasmataceae, their ecogenomic and metabolic patterns, and interactions with ‘ARMAN’." Extremophiles 23, no. 1 (2018): 1–7. http://dx.doi.org/10.1007/s00792-018-1071-2.

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40

Mathur, Vartika, Tom O. G. Tytgat, Cornelis A. Hordijk, et al. "An ecogenomic analysis of herbivore-induced plant volatiles inBrassica juncea." Molecular Ecology 22, no. 24 (2013): 6179–96. http://dx.doi.org/10.1111/mec.12555.

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41

Rossberg, Axel G., Tim Rogers, and Alan J. McKane. "Current noise-removal methods can create false signals in ecogenomic data." Proceedings of the Royal Society B: Biological Sciences 281, no. 1783 (2014): 20140191. http://dx.doi.org/10.1098/rspb.2014.0191.

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42

Miner, Brooks E., Luc De Meester, Michael E. Pfrender, Winfried Lampert, and Nelson G. Hairston. "Linking genes to communities and ecosystems: Daphnia as an ecogenomic model." Proceedings of the Royal Society B: Biological Sciences 279, no. 1735 (2012): 1873–82. http://dx.doi.org/10.1098/rspb.2011.2404.

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How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse cont

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43

Buttigieg, Pier Luigi, Wolfgang Hankeln, Ivaylo Kostadinov, et al. "Ecogenomic Perspectives on Domains of Unknown Function: Correlation-Based Exploration of Marine Metagenomes." PLoS ONE 8, no. 3 (2013): e50869. http://dx.doi.org/10.1371/journal.pone.0050869.

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44

SNOEREN, TJEERD A. L., PETER W. DE JONG, and MARCEL DICKE. "Ecogenomic approach to the role of herbivore-induced plant volatiles in community ecology." Journal of Ecology 95, no. 1 (2007): 17–26. http://dx.doi.org/10.1111/j.1365-2745.2006.01183.x.

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45

Robidart, Julie C., Matthew J. Church, John P. Ryan, et al. "Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean." ISME Journal 8, no. 6 (2014): 1175–85. http://dx.doi.org/10.1038/ismej.2013.244.

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46

Ogilvie, Lesley A., Jonathan Nzakizwanayo, Fergus M. Guppy, et al. "Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking." ISME Journal 12, no. 4 (2017): 942–58. http://dx.doi.org/10.1038/s41396-017-0015-7.

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47

Bornancini, Verónica A., José M. Irazoqui, Ceferino R. Flores, Carlos G. Vaghi Medina, Ariel F. Amadio, and Paola M. López Lambertini. "Reconstruction and Characterization of Full-Length Begomovirus and Alphasatellite Genomes Infecting Pepper through Metagenomics." Viruses 12, no. 2 (2020): 202. http://dx.doi.org/10.3390/v12020202.

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In northwestern Argentina (NWA), pepper crops are threatened by the emergence of begomoviruses due to the spread of its vector, Bemisia tabaci (Gennadius). The genus Begomovirus includes pathogens that can have a monopartite or bipartite genome and are occasionally associated with sub-viral particles called satellites. This study characterized the diversity of begomovirus and alphasatellite species infecting pepper in NWA using a metagenomic approach. Using RCA-NGS (rolling circle amplification-next generation sequencing), 19 full-length begomovirus genomes (DNA-A and DNA-B) and one alphasatel

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48

Morgan, M. J., D. Bass, H. Bik, et al. "A critique of Rossberg et al. : noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets." Proceedings of the Royal Society B: Biological Sciences 281, no. 1783 (2014): 20133076. http://dx.doi.org/10.1098/rspb.2013.3076.

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49

Tanaka, Mami, Daiki Kumakura, Sayaka Mino, et al. "Genomic characterization of closely related species in the Rumoiensis clade infers ecogenomic signatures to non‐marine environments." Environmental Microbiology 22, no. 8 (2020): 3205–17. http://dx.doi.org/10.1111/1462-2920.15062.

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50

Pawlowski, Jan, Mary Kelly-Quinn, Florian Altermatt, et al. "The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems." Science of The Total Environment 637-638 (October 2018): 1295–310. http://dx.doi.org/10.1016/j.scitotenv.2018.05.002.

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