Literature DB >> 23553002

"Eco-omics": a review of the application of genomics, transcriptomics, and proteomics for the study of the ecology of harmful algae.

T I McLean1.   

Abstract

The implementation of molecular techniques has been widely adopted throughout the life sciences except in the marine sciences. The latter trend is quickly being reversed as even more cutting-edge molecular platforms, referred to collectively as 'omics-related technologies, are being used in a number of laboratories that study various aspects of life in the marine environment. This review provides a brief overview of just a few representative studies that have used genomics, transcriptomics, or proteomics approaches to deepen our understanding, specifically, about the underlying molecular biology of harmful algae. The examples of the studies described here are particularly relevant in showing how the information gleaned from these technologies can uncover the genetic capacity of harmful algal bloom-forming species, can generate new hypotheses about mechanistic relationships that bridge gene-environment interactions, and can impinge on our understanding surrounding the ecology of these organisms.

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Year:  2013        PMID: 23553002     DOI: 10.1007/s00248-013-0220-5

Source DB:  PubMed          Journal:  Microb Ecol        ISSN: 0095-3628            Impact factor:   4.552


  65 in total

1.  Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.

Authors:  A Shevchenko; S Sunyaev; A Loboda; A Shevchenko; P Bork; W Ens; K G Standing
Journal:  Anal Chem       Date:  2001-05-01       Impact factor: 6.986

2.  De novo sequencing of peptides using MALDI/TOF-TOF.

Authors:  Alfred L Yergey; Jens R Coorssen; Peter S Backlund; Paul S Blank; Glen A Humphrey; Joshua Zimmerberg; Jennifer M Campbell; Marvin L Vestal
Journal:  J Am Soc Mass Spectrom       Date:  2002-07       Impact factor: 3.109

3.  Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis.

Authors:  Tetyana Nosenko; Kristy L Lidie; Frances M Van Dolah; Erika Lindquist; Jan-Fang Cheng; Debashish Bhattacharya
Journal:  Mol Biol Evol       Date:  2006-07-28       Impact factor: 16.240

4.  Net community production and dark community respiration in a Karenia brevis (Davis) bloom in West Florida coastal waters, USA.

Authors:  Gary L Hitchcock; Gary Kirkpatrick; Peter Minnett; Valeriy Palubok
Journal:  Harmful Algae       Date:  2010-05-01       Impact factor: 4.273

5.  Using the transcriptome to annotate the genome.

Authors:  Saurabh Saha; Andrew B Sparks; Carlo Rago; Viatcheslav Akmaev; Clarence J Wang; Bert Vogelstein; Kenneth W Kinzler; Victor E Velculescu
Journal:  Nat Biotechnol       Date:  2002-05       Impact factor: 54.908

6.  Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics.

Authors:  Christopher J Gobler; Dianna L Berry; Sonya T Dyhrman; Steven W Wilhelm; Asaf Salamov; Alexei V Lobanov; Yan Zhang; Jackie L Collier; Louie L Wurch; Adam B Kustka; Brian D Dill; Manesh Shah; Nathan C VerBerkmoes; Alan Kuo; Astrid Terry; Jasmyn Pangilinan; Erika A Lindquist; Susan Lucas; Ian T Paulsen; Theresa K Hattenrath-Lehmann; Stephanie C Talmage; Elyse A Walker; Florian Koch; Amanda M Burson; Maria Alejandra Marcoval; Ying-Zhong Tang; Gary R Lecleir; Kathryn J Coyne; Gry M Berg; Erin M Bertrand; Mak A Saito; Vadim N Gladyshev; Igor V Grigoriev
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-23       Impact factor: 11.205

7.  Different regulatory mechanisms modulate the expression of a dinoflagellate iron-superoxide dismutase.

Authors:  O K Okamoto; D L Robertson; T F Fagan; J W Hastings; P Colepicolo
Journal:  J Biol Chem       Date:  2001-03-22       Impact factor: 5.157

8.  Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray.

Authors:  Kristy B Lidie; James C Ryan; Michele Barbier; Frances M Van Dolah
Journal:  Mar Biotechnol (NY)       Date:  2005 Sep-Oct       Impact factor: 3.619

9.  Identification and optimization of classifier genes from multi-class earthworm microarray dataset.

Authors:  Ying Li; Nan Wang; Edward J Perkins; Chaoyang Zhang; Ping Gong
Journal:  PLoS One       Date:  2010-10-28       Impact factor: 3.240

10.  A computational investigation of kinetoplastid trans-splicing.

Authors:  Shuba Gopal; Saria Awadalla; Terry Gaasterland; George A M Cross
Journal:  Genome Biol       Date:  2005-10-17       Impact factor: 13.583

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  10 in total

Review 1.  Probing the evolution, ecology and physiology of marine protists using transcriptomics.

Authors:  David A Caron; Harriet Alexander; Andrew E Allen; John M Archibald; E Virginia Armbrust; Charles Bachy; Callum J Bell; Arvind Bharti; Sonya T Dyhrman; Stephanie M Guida; Karla B Heidelberg; Jonathan Z Kaye; Julia Metzner; Sarah R Smith; Alexandra Z Worden
Journal:  Nat Rev Microbiol       Date:  2016-11-21       Impact factor: 60.633

2.  Arthrospira platensis Mutagenesis for Protein and C-Phycocyanin Improvement and Proteomics Approaches.

Authors:  Wanida Pan-Utai; Siriluck Iamtham; Sittiruk Roytrakul; Sarn Settachaimongkon; Ladda Sangduean Wattanasiritham; Sumitra Boonbumrung; Juta Mookdasanit; Sayamon Sithtisarn
Journal:  Life (Basel)       Date:  2022-06-17

3.  Functional Differences in the Blooming Phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense Revealed by Comparative Metaproteomics.

Authors:  Hao Zhang; Yan-Bin He; Peng-Fei Wu; Shu-Feng Zhang; Zhang-Xian Xie; Dong-Xu Li; Lin Lin; Feng Chen; Da-Zhi Wang
Journal:  Appl Environ Microbiol       Date:  2019-09-17       Impact factor: 4.792

4.  Molecular mechanism of arachidonic acid biosynthesis in Porphyridium purpureum promoted by nitrogen limitation.

Authors:  Kailin Jiao; Wupeng Xiao; Xingguo Shi; Shih-Hsin Ho; Jo-Shu Chang; I-Son Ng; Xing Tang; Yong Sun; Xianhai Zeng; Lu Lin
Journal:  Bioprocess Biosyst Eng       Date:  2021-03-12       Impact factor: 3.210

5.  Metabolic changes in Medaka fish induced by cyanobacterial exposures in mesocosms: an integrative approach combining proteomic and metabolomic analyses.

Authors:  Benoît Sotton; Alain Paris; Séverine Le Manach; Alain Blond; Gérard Lacroix; Alexis Millot; Charlotte Duval; Hélène Huet; Qin Qiao; Sophie Labrut; Giovanni Chiappetta; Joelle Vinh; Arnaud Catherine; Benjamin Marie
Journal:  Sci Rep       Date:  2017-06-22       Impact factor: 4.379

6.  Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics.

Authors:  Bryan John J Subong; Arturo O Lluisma; Rhodora V Azanza; Lilibeth A Salvador-Reyes
Journal:  Toxins (Basel)       Date:  2020-12-23       Impact factor: 4.546

7.  From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?

Authors:  Solène Geffroy; Marc-Marie Lechat; Mickael Le Gac; Georges-Augustin Rovillon; Dominique Marie; Estelle Bigeard; Florent Malo; Zouher Amzil; Laure Guillou; Amandine M N Caruana
Journal:  Front Microbiol       Date:  2021-02-24       Impact factor: 5.640

Review 8.  Algal glycobiotechnology: omics approaches for strain improvement.

Authors:  Ranjna Sirohi; Jaemin Joun; Hong Ii Choi; Vivek Kumar Gaur; Sang Jun Sim
Journal:  Microb Cell Fact       Date:  2021-08-21       Impact factor: 5.328

Review 9.  The Mechanism of Diarrhetic Shellfish Poisoning Toxin Production in Prorocentrum spp.: Physiological and Molecular Perspectives.

Authors:  Thomas Chun-Hung Lee; Fiona Long-Yan Fong; Kin-Chung Ho; Fred Wang-Fat Lee
Journal:  Toxins (Basel)       Date:  2016-09-22       Impact factor: 4.546

10.  Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina.

Authors:  Brittany N Sprecher; Huan Zhang; Senjie Lin
Journal:  Microorganisms       Date:  2020-01-16
  10 in total

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