Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics

Castrillo, Juan I.; Oliver, Stephen G.

doi:10.5483/bmbrep.2004.37.1.093

Cited by 62 publications

(45 citation statements)

References 160 publications

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“…The integration of data from the different levels of cellular networks (transcriptome, regulome, interactome, and metabolome) is the next obvious step to identify patterns of network interactions in individual species and in multispecies comparisons (32,72,73). This integrative approach has already been fruitful in model organisms such as C. elegans (74) and S. cerevisiae (75).…”

Section: Evolution Of Biological Networkmentioning

confidence: 99%

Genomes, phylogeny, and evolutionary systems biology

Medina

2005

Proc. Natl. Acad. Sci. U.S.A.

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With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.postgenomics ͉ eukaryotic genomics ͉ network evolution Systems biology is in the eye of the beholder.Leroy Hood O nly in the last decade have we had access to nearly complete genomes of a diversity of organisms allowing for large-scale comparative analysis. The access to this immense amount of data is providing profound insight into the tree of life at all levels of divergence ( Fig. 1 A). It is thus not surprising that understanding phylogenetic relationships is a prevalent research goal among not only evolutionary biologists but also all scientists interested in the organization and function of the genome. New genome sequences and analysis methods are helping improve our understanding of phylogeny, and at the same time improved phylogenies and phylogenetic theory are generating a better understanding of genome evolution. Currently however, the level of genome sequencing for different branches of the tree of life is far from equivalent. Prokaryotic genome projects are abundant, mainly due to their small genome sizes, with Ͼ200 genomes already published and at least 500 currently in progress (www. genomesonline.org). In contrast, Ͻ300 eukaryotic genomes are either finished or in progress (www.genomesonline.org). Nevertheless, these data are starting to have a major impact on our understanding of eukaryotic evolution.These new genomic data have informed our understanding of phylogenetic relationships, and the emerging consensus topologies are adding new insight to the small subunit ribosomal RNA phylogenies. For example, the topology of the ribosomal eukaryotic tree has been recently redrawn with the use of genomic signatures that place the root of all eukaryotic life between two newly uncovered major clades, Unikonts and Bikonts (Fig. 1 A). Unikonts, which contain the heterotrophic groups Opisthokonta and the Amebozoa, share a derived three-gene fusion of enzymeencoding genes in the pyrimidine synthesis pathway (1), whereas Bikonts, which contain the remaining eukaryotic clades, share another derived gene fusion between dihydrofolate reductase and thymidine synthase (2). All photosynthetic groups of primary and secondary plastid symbiotic origins are now thought to be within the Bikonts. Although the animal, fungal, and plant lineages are the most widely represented in terms of genome initiatives (Fig. 1 B-D), it is significant that multiple protistan genome projects have also been initiated by th...

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Section: Evolution Of Biological Networkmentioning

confidence: 99%

Genomes, phylogeny, and evolutionary systems biology

Medina

2005

Proc. Natl. Acad. Sci. U.S.A.

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“…In addition to its role in industrial applications, S. cerevisiae is a key model organism in research laboratories to study fundamental biological processes. Being one of the simplest eukaryotes, S. cerevisiae has several features that make it a useful research vehicle [2][3][4]; it grows easily and methods for cultivation under well-controlled conditions are available. Moreover, S. cerevisiae is not pathogenic and, therefore, it can be handled with few precautions.…”

Section: Yeast As a Production Platform And Model Systemmentioning

confidence: 99%

Development and application of proteomics technologies in Saccharomyces cerevisiae

Kolkman

Slijper

Heck

2005

Trends in Biotechnology

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“…Metabolomics research is commonly performed in the context of systems biology [2], which involves integrated study of the genome, transcriptome, proteome, and metabolome. These investigations, typically conducted in plants [3] and individual cells or cell types [4], are often geared toward understanding metabolic regulation (i.e., homeostasis) and fluxes associated with a given genetic, physiological, or developmental state.…”

mentioning

confidence: 99%

Metabolomic applications of electrochemistry/Mass spectrometry

Gamache

Meyer

Granger

et al. 2004

J. Am. Soc. Mass Spectrom.

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Analytical techniques used for multivariate analysis of endogenous metabolites in biological systems (e.g., metabolomics, metabonomics) must be capable of accurately and selectively monitoring many known and unknown molecules that span a diverse chemical spectrum and over extremely large dynamic concentration ranges. Mass spectrometric (MS) and electrochemical array (EC-Array) detection have been widely used for multi-component analysis with applicability to low-level (fmol) metabolites. Described here are practical considerations and results obtained with the combined use of EC-Array and MS for HPLC-based multivariate metabolomic analysis. Data presented include the study of changes in rat urinary metabolite profiles associated with xenobiotic toxin exposure analyzed by HPLC using water:acetonitrile binary gradient conditions and post-column flow splitting between EC-Array and MS detectors. Results show complementary quantitative and qualitative analysis and the ability to differentiate sample groups consistent with xenobiotic-induced histopathological changes. The potential applicability of this hyphenated technique for biomarker elucidation through measurement of redox active compounds that are commonly associated with disease pathology and xenobiotic toxicity is discussed. The use of EC reactor cells in series with MS is also presented as a means of producing likely metabolites to facilitate structural elucidation and confirmation. (J Am Soc Mass Spectrom 2004, 15, 1717-1726

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Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics

Cited by 62 publications

References 160 publications

Genomes, phylogeny, and evolutionary systems biology

Genomes, phylogeny, and evolutionary systems biology

Development and application of proteomics technologies in Saccharomyces cerevisiae

Metabolomic applications of electrochemistry/Mass spectrometry

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