449 Hits in 4.4 sec

An analysis of the Sargasso Sea resource and the consequences for database composition

Michael L Tress, Domenico Cozzetto, Anna Tramontano, Alfonso Valencia
2006 BMC Bioinformatics  
The environmental sequencing of the Sargasso Sea has introduced a huge new resource of genomic information.  ...  The Sargasso Sea sequences seem to introduce a bias that decreases the potential of current methods to propose structure and function for new proteins.  ...  Acknowledgements The authors wish to thank David Juan, Florencio Pazos, Luis Sanchez-Pulido and the referees for their useful critical input.  ... 
doi:10.1186/1471-2105-7-213 pmid:16623953 pmcid:PMC1513258 fatcat:pbaimezxkfalrmegtidegm3hba

The Marine Viromes of Four Oceanic Regions

Florent E Angly, Ben Felts, Mya Breitbart, Peter Salamon, Robert A Edwards, Craig Carlson, Amy M Chan, Matthew Haynes, Scott Kelley, Hong Liu, Joseph M Mahaffy, Jennifer E Mueller (+7 others)
2006 PLoS Biology  
Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic.  ...  A single sample was collected from the Sargasso Sea (labeled SAR) on 30 June 2005.  ...  Acknowledgments The GOM, BBC, and Arctic samples were collected with the generous help of the crew and scientists aboard the research vessels Longhorn, Mirai, Raddisson, Walton Smith, and Vector.  ... 
doi:10.1371/journal.pbio.0040368 pmid:17090214 pmcid:PMC1634881 fatcat:yokkhah6afhvblh23jhzxakcdq

Estimating the extent of horizontal gene transfer in metagenomic sequences

Javier Tamames, Andrés Moya
2008 BMC Genomics  
The methods are based on phylogenetic and DNA compositional approaches, and have allowed us to assess the extent of possible HGT events in metagenomes for the first time.  ...  Nevertheless, the study of the number of HGT events in metagenomic sequences from different communities shows a consistent trend for both methods: the lower amount is found for the sequences of the Sargasso  ...  Financial support was provided by projects BFU2006-06003 from the Spanish Ministry of Education and Science (MEC) and GV/2007/050 from the Generalitat Valenciana, Spain.  ... 
doi:10.1186/1471-2164-9-136 pmid:18366724 pmcid:PMC2324111 fatcat:viq7b3malngllkvidzjhdikag4

INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

Monzoorul Mohammed, Tarini Ghosh, Rachamalla Reddy, Chennareddy Venkata Siva Kumar Reddy, Nitin Singh, Sharmila S Mande
2011 BMC Genomics  
Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based.  ...  Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources.  ...  Acknowledgements We thank Stephan Schuster and Daniel Huson for allowing us to use MEGAN and MetaSim software for this work. We thank Sudha Chadaram for her help in preparing a web-server for INDUS.  ... 
doi:10.1186/1471-2164-12-s3-s4 pmid:22369237 pmcid:PMC3333187 fatcat:gg6tb3rxy5fppol6x3jlqcpqvm

Comparative Metagenomic Analysis of a Microbial Community Residing at a Depth of 4,000 Meters at Station ALOHA in the North Pacific Subtropical Gyre

K. T. Konstantinidis, J. Braff, D. M. Karl, E. F. DeLong
2009 Applied and Environmental Microbiology  
These adaptations appear to include higher metabolic versatility and genomic plasticity to cope with the sparse and sporadic energy resources available, a preference for hydrophobic and smaller-volume  ...  The deep sea (water depth of >2,000 m) represents the largest biome on Earth.  ...  E.F.D., and sequencing support from the Department of Energy Genomics GTL Program.  ... 
doi:10.1128/aem.00473-09 pmid:19542347 pmcid:PMC2725473 fatcat:ifa77mqw3zgd5gh3nwvmzh43om

Sargassum Watch Warns of Incoming Seaweed

Chuanmin Hu, Brock Murch, Brian Barnes, Mengqiu Wang, Jean-Philippe Maréchal, James Franks, Donald Johnson, Brian Lapointe, Deborah Goodwin, Jeffrey Schell, Amy Siuda
2016 EOS  
The Sargassum Watch System processes satellite data and feeds results to a Web portal, giving decision makers timely information on seaweed location and warnings for potential beaching events.  ...  The Sargasso Sea Alliance thanks the National Oceanography Centre, UK for providing library facilities and overall support for this work.  ...  However, the provision of the data does not, in and of itself, indicate U.S. government (or any department or agency thereof) support for any specific proposal contained in this report or that the Sargasso  ... 
doi:10.1029/2016eo058355 fatcat:agwsy3u6argpdekwgr2uoad6ei

A bibliometric analysis of scientific trends in phytoplankton research

Chao Wang, Yang Liu, Xinhui Li, Zini Lai, Michèle Tackx, Sovan Lek
2015 Annales de Limnologie  
We summarize the scientific trends in phytoplankton studies between 1991 and 2013 based on bibliometric analysis.  ...  Under the context of fast scientific research development, the yearly numbers of dependent publications (in terms of multi-aquatic ecosystems and international collaborations) indicate a linear increasing  ...  We acknowledge the editors and the anonymous reviewers for insightful suggestions on this work! This work was supported by National Natural Science Foundation of China (grant No. 41403071).  ... 
doi:10.1051/limn/2015019 fatcat:drlqk6a4yrgq5mg7ptzzqki5hu

Going Deeper: Metagenome of a Hadopelagic Microbial Community

Emiley A. Eloe, Douglas W. Fadrosh, Mark Novotny, Lisa Zeigler Allen, Maria Kim, Mary-Jane Lombardo, Joyclyn Yee-Greenbaum, Shibu Yooseph, Eric E. Allen, Roger Lasken, Shannon J. Williamson, Douglas H. Bartlett (+1 others)
2011 PLoS ONE  
A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea.  ...  In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT).  ...  Acknowledgments We would like to thank the BIOS scientific crew and R/V Atlantic Explorer crew for allowing us to join their BV42 cruise and Christine Shulse for help in sample collection.  ... 
doi:10.1371/journal.pone.0020388 pmid:21629664 pmcid:PMC3101246 fatcat:xitlttmxibhj3op7dr5ipxfn3a

A century of research on the larval distributions of the Atlantic eels: a re-examination of the data

Michael J. Miller, Sylvain Bonhommeau, Peter Munk, Martin Castonguay, Reinhold Hanel, James D. McCleave
2014 Biological Reviews  
adult eels spawn and how they find their spawning areas. 2) Analysis of the new database shows there is an east-west divergence of the two overlapping spawning areas and that there are differences in  ...  ANALYSIS OF THE DATABASE The new database provides the first chance to analyse comprehensively the catches of anguillid larvae from the last 100 years.  ... 
doi:10.1111/brv.12144 pmid:25291986 fatcat:nuaeogvl45cl5ghufz4b2xgquy

Challenges for genetic research in European eel management

G. E. Maes, F. A. M. Volckaert
2007 ICES Journal of Marine Science  
from pre-decline historical collections for critical long-term monitoring and modelling of its genetic composition; (ii) the analysis of adaptive genetic polymorphism (genes under selection) to detect  ...  The catadromous European eel (Anguilla anguilla) is no exception. Its spawning habitat in the Sargasso Sea and long migration across the North Atlantic qualify it as marine.  ...  Acknowledgements We thank the following for the lively and inspiring discus-  ... 
doi:10.1093/icesjms/fsm108 fatcat:vim2q3zozbcgdh5xpbsi6bibxy

Pteropods are excellent recorders of surface temperature and carbonate ion concentration

N. Keul, K. T. C. A. Peijnenburg, N. Andersen, V. Kitidis, E. Goetze, R. R. Schneider
2017 Scientific Reports  
Pteropods are excellent recorders of surface temperature and carbonate ion concentration Keul, N.; Peijnenburg, K.T.C.A.; Andersen, N.; Kitidis, V.; Goetze, E.; Schneider, R.R.  ...  Thomas and scientists from the AMT programme, as well as the crew of the RRS James Cook, for supporting zooplankton and oceanographic data collections on AMT22.  ...  behalf of the German federal and state governments.  ... 
doi:10.1038/s41598-017-11708-w pmid:28974691 pmcid:PMC5626693 fatcat:rne7pi7cknc7hprd4jyvcaybti

Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre

Domenico D'Alelio, Salvatore Rampone, Luigi Maria Cusano, Valerio Morfino, Luca Russo, Nadia Sanseverino, James E. Cloern, Michael W. Lomas
2020 Scientific Reports  
consequent weakening of vertical mixing in the upper ocean, induced a negative feedback on phytoplankton productivity by reducing the availability of essential resources, nitrogen and light.  ...  In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso Sea (North Atlantic gyre) provides a unique opportunity to explore effects of warming on phytoplankton production across the  ...  The study presented herein is part of the internship of Luca Russo, under the supervision of Domenico D' Alelio, at Stazione Zoologica Anton Dohrn (Naples, Italy), and of the Master Thesis of Luigi Maria  ... 
doi:10.1038/s41598-020-59989-y pmid:32098970 fatcat:tz7dfrnoprch3od4bl6pv5qgmi

Contribution of zooplankton fecal pellets to deep ocean particle flux in the Sargasso Sea assessed using quantitative image analysis

O. Shatova, D. Koweek, M. H. Conte, J. C. Weber
2012 Journal of Plankton Research  
pellet mass and the carbon flux of 0.5-1.7 mg m 22 day 21 and 0.07-0.25 mg C m 22 day 21 , respectively.  ...  During the study, three mesoscale eddies passed through: a cyclonic eddy in bloom stage (February through mid-April), a decaying post-bloom mode-water eddy (late April through May), and an anticyclonic  ...  We thank Tommy Dickey for access to unpublished data and the many BATS technicians and principal investigators for their contribution to the BATS data resources.  ... 
doi:10.1093/plankt/fbs053 fatcat:4a5ozj7jy5dydoeyhymfi3siyu

DMS dynamics in the most oligotrophic subtropical zones of the global ocean

Sauveur Belviso, Italo Masotti, Alessandro Tagliabue, Laurent Bopp, P. Brockmann, Cédric Fichot, Guy Caniaux, Louis Prieur, Joséphine Ras, Julia Uitz, Hubert Loisel, David Dessailly (+3 others)
2011 Biogeochemistry  
As metrics for the dynamics of DMS and the so-called 'summer DMS paradox' of elevated summer concentrations when surface chlorophyll a (Chl) and particulate organic carbon (POC) levels are lowest, we used  ...  Our 'model based' experiments suggest that it is the limitation of phytoplankton/bacterial production and bacterial consumption of DMS by pervasive phosphorus limitation that is responsible for the 'summer  ...  Johnson (JISAO, University of Washington) and T.S. Bates (PMEL, NOAA) for the maintenance and personal involvement in the Global Surface Seawater DMS Database.  ... 
doi:10.1007/s10533-011-9648-1 fatcat:j3nhnpolpzcdfgznnpiwx3arey

Is the Atlantic surface temperature a good proxy for forecasting the recruitment of European eel in the Guadalquivir estuary?

Juan Carlos Gutiérrez-Estrada, Inmaculada Pulido-Calvo
2015 Progress in Oceanography  
from an unofficial database on commercial catches provided by one of the main local marketer-buyers) were standardised to obtain a single time series on a monthly scale.  ...  This study analysed the possibility of using the sea surface temperature (SST) of the Atlantic Ocean to predict the recruitment of European eels in one of the most important estuaries of the south of Europe  ...  José Hernando Casal for providing data on the daily purchases of glass eel in the Guadalquivir estuary from November 14 of 1983 to May 27 of 1998 data base. We also thank Dr. Dudley B.  ... 
doi:10.1016/j.pocean.2014.10.007 fatcat:fi6mcheixvhhbmc5nveqkjuvwe
« Previous Showing results 1 — 15 out of 449 results