The Experts below are selected from a list of 12951 Experts worldwide ranked by ideXlab platform
Ivan Couée - One of the best experts on this subject based on the ideXlab platform.
-
Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics
Frontiers in Microbiology, 2015Co-Authors: Francoise Bringel, Ivan CouéeAbstract:The phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. Phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. Recent –omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional, and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyze recent advances, especially those resulting from Environmental Genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights• The phyllosphere is one of the most prevalent microbial habitats on earth. • Phyllosphere microbiota colonize extreme, stressful, and changing environments.• Plants, phyllosphere microbiota and the atmosphere present a dynamic continuum. • Phyllosphere microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gasses.
-
pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics
Frontiers in Microbiology, 2015Co-Authors: Francoise Bringel, Ivan CouéeAbstract:The phyllosphere, which lato sensu consists in the aerial parts of plants, and therefore primarily, in the set of photosynthetic leaves, is one of the most prevalent microbial habitats on Earth. Phyllospheric microbiota are related to original and specific processes that govern the interface between plants, microorganisms and the atmosphere. Recent –omics studies have opened fascinating opportunities for characterising the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyse recent advances, especially those resulting from Environmental Genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights • The phyllosphere is one of the most prevalent microbial habitats on Earth • Phyllospheric microbiota colonize extreme, stressful and changing environments • Plants, phyllospheric microbiota and the atmosphere present a dynamic continuum • Phyllospheric microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gases
-
Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of Environmental Genomics and post-Genomics
Ecology Letters, 2010Co-Authors: Philippe Vandenkoornhuyse, Achim Quaiser, Alexis Dufresne, Gwenola Gouesbet, Françoise Binet, Andre-jean Francez, Stéphane Mahé, Myriam Bormans, Yvan Lagadeuc, Ivan CouéeAbstract:Environmental Genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from Environmental samples, at organismal, population or community levels. To date, Environmental Genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, Environmental Genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, Environmental Genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, Environmental Genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate highthroughput molecular biology techniques into ecology. In this review, the validity of Environmental Genomics and post-Genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.
Jae-seong Lee - One of the best experts on this subject based on the ideXlab platform.
-
sequence analysis of genomic dna 680 mb by gs flx titanium sequencer in the monogonont rotifer brachionus ibericus
Hydrobiologia, 2011Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Chang Joo Lee, Yongdal Yoon, Jongsung LimAbstract:The monogonont rotifer, Brachionus ibericus (S type), is considered to be a promising model species for developmental biology, evolution, and Environmental Genomics. In an attempt to accelerate the molecular understanding of B. ibericus, we sequenced 680.5 Mb of genomic DNA using the genome sequencer GS-FLX-Titanium. We obtained 2,062,621 reads (average read length 329.9 bp) and 145,418 contigs (total contigs length 125.7 Mb) after excluding small reads (less than 200 bp) from the assembly, and finally obtained 10,133 unigenes (E value ≤ 9.00E−04) after non-redundant (NR) BLAST search. In this article, we summarize the genomic DNA sequences of B. ibericus and discuss their potential use in the study of reproductive biology, endocrinology, Environmental Genomics, and ecotoxicological studies, and for providing insight into the genetic basis of mechanisms such as egg formation, antioxidant stress defense, and xenobiotic metabolism.
-
The copepod Tigriopus japonicus genomic DNA information (574 Mb) and molecular anatomy
Marine Environmental Research, 2010Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value > 0.1; length > 200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.
-
The copepod Tigriopus japonicus genomic DNA information (574Mb) and molecular anatomy.
Marine environmental research, 2009Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value>0.1; length>200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.
-
the copepod tigriopus a promising marine model organism for ecotoxicology and Environmental Genomics
Aquatic Toxicology, 2007Co-Authors: Sheikh Raisuddin, Kenneth M.y. Leung, Kevin W H Kwok, Daniel Schlenk, Jae-seong LeeAbstract:There is an increasing body of evidence to support the significant role of invertebrates in assessing impacts of Environmental contaminants on marine ecosystems. Therefore, in recent years massive efforts have been directed to identify viable and ecologically relevant invertebrate toxicity testing models. Tigriopus, a harpacticoid copepod has a number of promising characteristics which make it a candidate worth consideration in such efforts. Tigriopus and other copepods are widely distributed and ecologically important organisms. Their position in marine food chains is very prominent, especially with regard to the transfer of energy. Copepods also play an important role in the transportation of aquatic pollutants across the food chains. In recent years there has been a phenomenal increase in the knowledge base of Tigriopus spp., particularly in the areas of their ecology, geophylogeny, Genomics and their behavioural, biochemical and molecular responses following exposure to Environmental stressors and chemicals. Sequences of a number of important marker genes have been studied in various Tigriopus spp., notably T. californicus and T. japonicus. These genes belong to normal biophysiological functions (e.g. electron transport system enzymes) as well as stress and toxic chemical exposure responses (heat shock protein 20, glutathione reductase, glutathione S-transferase). Recently, 40,740 expressed sequenced tags (ESTs) from T. japonicus, have been sequenced and of them, 5,673 ESTs showed significant hits (E-value, >1.0E-05) to the red flour beetle Tribolium genome database. Metals and organic pollutants such as antifouling agents, pesticides, polycyclic aromatic hydrocarbons (PAH) and polychrlorinated biphenyls (PCB) have shown reproducible biological responses when tested in Tigriopus spp. Promising results have been obtained when Tigriopus was used for assessment of risk associated with exposure to endocrine-disrupting chemicals (EDCs). Application of Environmental gene expression techniques has allowed evaluation of transcriptional changes in T. japonicus with the ultimate aim of understanding the mechanisms of action of Environmental stressors. Through a better understanding of toxicological mechanisms, ecotoxicologists may use this ecologically relevant species in risk assessment studies in marine systems. The combination of uses as a whole-animal bioassay and gene expression studies indicate that Tigriopus may serve as an excellent tool to evaluate the impacts of marine pollution throughout the coastal region. The purpose of this review is to illustrate the potential of using Tigriopus to fulfill the niche as an important invertebrate marine model organism for ecotoxicology and Environmental Genomics. In addition, the knowledge gaps and areas for further studies have also been discussed.
Young-mi Lee - One of the best experts on this subject based on the ideXlab platform.
-
The copepod Tigriopus japonicus genomic DNA information (574 Mb) and molecular anatomy
Marine Environmental Research, 2010Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value > 0.1; length > 200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.
-
The copepod Tigriopus japonicus genomic DNA information (574Mb) and molecular anatomy.
Marine environmental research, 2009Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value>0.1; length>200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.
Jochen J. Brocks - One of the best experts on this subject based on the ideXlab platform.
-
Unravelling ancient microbial history with community proteoGenomics and lipid geochemistry
Nature Reviews Microbiology, 2009Co-Authors: Jochen J. Brocks, Jillian BanfieldAbstract:Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how Environmental Genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth. Information about ancient microbial ecosystems can be obtained by using fossil lipids found in ancient sedimentary rocks as biomarkers. In this Opinion article, Jochen Brocks and Jillian Banfield describe how Environmental genomic approaches are set to revolutionize the study of these microbial ecosystems and improve our understanding of the evolution of ancient communities of microorganisms.
-
Unravelling ancient microbial history with community proteoGenomics and lipid geochemistry
Nature reviews. Microbiology, 2009Co-Authors: Jochen J. Brocks, Jillian F. BanfieldAbstract:Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how Environmental Genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth.
Beom-soon Choi - One of the best experts on this subject based on the ideXlab platform.
-
sequence analysis of genomic dna 680 mb by gs flx titanium sequencer in the monogonont rotifer brachionus ibericus
Hydrobiologia, 2011Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Chang Joo Lee, Yongdal Yoon, Jongsung LimAbstract:The monogonont rotifer, Brachionus ibericus (S type), is considered to be a promising model species for developmental biology, evolution, and Environmental Genomics. In an attempt to accelerate the molecular understanding of B. ibericus, we sequenced 680.5 Mb of genomic DNA using the genome sequencer GS-FLX-Titanium. We obtained 2,062,621 reads (average read length 329.9 bp) and 145,418 contigs (total contigs length 125.7 Mb) after excluding small reads (less than 200 bp) from the assembly, and finally obtained 10,133 unigenes (E value ≤ 9.00E−04) after non-redundant (NR) BLAST search. In this article, we summarize the genomic DNA sequences of B. ibericus and discuss their potential use in the study of reproductive biology, endocrinology, Environmental Genomics, and ecotoxicological studies, and for providing insight into the genetic basis of mechanisms such as egg formation, antioxidant stress defense, and xenobiotic metabolism.
-
The copepod Tigriopus japonicus genomic DNA information (574 Mb) and molecular anatomy
Marine Environmental Research, 2010Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value > 0.1; length > 200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.
-
The copepod Tigriopus japonicus genomic DNA information (574Mb) and molecular anatomy.
Marine environmental research, 2009Co-Authors: Jae-seong Lee, Jae-sung Rhee, Ryeo-ok Kim, Dae-sik Hwang, Jeonghoon Han, Beom-soon Choi, Gyung Soo Park, Il-chan Kim, Heum Gi Park, Young-mi LeeAbstract:The intertidal copepod, Tigriopus japonicus, has been recognized as a promising model species for marine Environmental Genomics. To obtain extensive genomic DNA sequences from this species, we sequenced genomic DNA from adult copepods using genomic sequencers GS-FLX and GS-FLX-Titanium and attained 1,914,995 reads (average read length 299.8 bp) including 574.2 Mb of genomic DNA information. After subjecting them to assembly, we acquired 193,642 contigs (total contigs length 129.7 Mb), and finally were able to obtain 10,894 unigenes (E-value>0.1; length>200 bp) containing 33,081,455 bp after a nonredundant (NR) blast search. In this paper, we summarize the genomic DNA sequences of T. japonicus and discuss its potential use in Environmental Genomics and ecotoxicological studies for uncovering mechanisms of Environmental stresses and chemical toxicities to marine crustaceans.