Frontiers in Polar Biology in the Genomic Era (2003) / Chapter Skim
Currently Skimming:
3. The Polar Genome Science Initiative
3. The Polar Genome Science Initiative
Pages 82-104
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 82... ...
Clearly, the sequencing of genomes should no longer be constrained to "model" organisms or limited by resource considerations, and the Polar Genome Science Initiative need not focus on technology development. Nevertheless, the selection of organisms or consortia must be guided by appropriate criteria.
|
From page 83... ...
The knowledge gained from these organisms will provide an invaluable framework for identifying other organisms for future sequencing projects. Whether some or all of the organisms listed below or other polar organisms are selected for genome analysis will depend on the availability of funding and on changes in research .
|
From page 84... ...
that might play a role in adaptation to the cold. In addition, the sequence information would serve as the basis for conducting functional genomic studies (transcriptome, proteome, and metabalome analysis)
|
From page 85... ...
The occurrence of a shared rare 11-nt insertion in concert with phylogenetic relationships implies that psychrotolerant strains from both Arctic and Antarctic isolates originated from temperate species, whereas psychrophilic strains appear to have arisen independently. A complete genome sequence of a psychrophilic cyanobacterium will allow scientists to establish a database for examining issues of biodiversity, biogeography, and community structure in these important polar mat-forming organisms.
|
From page 86... ...
, C subcaudata exhibits unique physiological responses to low temperature when compared to temperate algae or psychrotolerant cyanobacteria isolated from the poles.
|
From page 87... ...
One distinctive characteristic of Phaeocystis is the formation of globular cell colonies, sometimes containing thousands of cells and attaining millimeter size.
|
From page 88... ...
Among polar organisms, the phylogenetic history of the Antarctic notothenioid fishes is, without doubt, the most complete (Chen et al., 1998; Eastman, 2000; Eastman and McCune, 2000; Ritchie et al., 1996~. Living at constant extreme cold for ectothermic bony fishes required adaptive changes in their biochemical and physiological functions; thus, the notothenioids are a "swimming library" of cold-adapted genes and proteins.
|
From page 89... ...
A comparative approach to analyzing the genomes and the differences in gene expression patterns in ground squirrels and bears during hibernation will facilitate our understanding of the underlying molecular mechanisms that provide tolerance by molecules, cells, and organs to these extreme changes and will provide great potential for beneficial biomedical applications for humans. For example, understanding the molecular mechanisms of bone mass maintenance in bears may lead to therapeutic modalities that prevent osteoporosis in chronically hospitalized patients (Becker et al., 2002~.
|
From page 90... ...
Another potential use of data obtained in the study of hibernators could be in the development of emergency field medical protocols for inducing a state of hypometabolism in gravely injured humans, for example, soldiers wounded on the battlefield who cannot be transported rapidly to a medical center. By inducing reductions in metabolic rate and enhancing tolerance of reduced blood flow, mechanisms may be developed for sustaining life until sophisticated medical attention can be given to a patient.
|
From page 91... ...
. Hence, it will be necessary to develop a framework for prioritization of polar organisms for full genome sequence characterization versus functional genomic profiling.
|
From page 92... ...
A Polar Genome Science Initiative, by its very nature, will require a strong comparative genomic component; and suggestions for appropriate species comparison are given in previous sections. Finally, as the initially exploratory phase of these genomic projects proceed, we anticipate that each will transition to directed, hypothesis-driven research based on the discoveries made in the first phase.
|
From page 93... ...
. Given the long generation times of many polar organisms (especially metazoans)
|
From page 94... ...
Whereas microbial genomes are generally sequenced to completion, the "finished" genomes of eukaryotes will normally contain gaps. A major consideration for any genome project, such as the Polar Genome Science Initiative contemplated here, is the cost of the sequencing itself as well as the computational power required to assemble the genome.
|
From page 95... ...
Population Analysis with Single-Nucleotide Polymorphisms Generating a genome sequence based on one, or at most a few, individuals of a species represents merely a beginning for population biologists. Natural variation among genomes in a population is the "stuff" of phenotypic variation and evolutionary speciation.
|
From page 96... ...
Indeed, the ability to compare genomes will speed our understanding of genome evolution and the phylogenetic relationships of all organisms, whether polar or temperate. A comprehensive Polar Genome Science Initiative must make provision for creation, curation, validation, and management of these databases and for the bioinformatics tools necessary for insightful genome analyses.
|
From page 97... ...
The applicability of proteomic methodologies to the study of polar organisms, for which large amounts of DNA and protein sequence data are not available, appears promising for several reasons. First and foremost, the conservation found in the sequences of orthologous proteins facilitates identification of proteins from genetically uncharacterized species.
|
From page 98... ...
Ecogenome Analysis Ecogenomics, the use of genome science to study ecology, has great potential to advance our understanding of microbial ecology (Stahl and Tiedje, 2002; Torsvik and Ovreas, 2002~. One promising approach is metagenome analysis (Rondon et al., 2000~.
|
From page 99... ...
Thus, microarrays developed for examining community structure and function must include probes from both culturable and unculturable species. Although metagenome analysis is still in the development and testing stage, it holds great promise for providing a new, integrated view of the phylogenetic composition of microbial communities and of their functional capabilities.
|
From page 100... ...
Ecogenomics has great potential for addressing some of the research questions in polar biology outlined in the previous chapter. Impediments to the Study of the Transcriptomes, Proteomes, and Metabolomes of Polar Species Implementation of the study of transcriptomes, proteomes, and metabolomes of polar organisms faces a number of challenges, most of which are common to all three types of "-omic" analysis.
|
From page 101... ...
Large amounts of DNA sequencing accompany transcriptome analysis, and facilities for this purpose must be available to investigators. For DNA microarrays spotted with uncharacterized cDNAs, the spots that exhibit interesting patterns of up- or down-regulation must be sequenced to identify the genes undergoing shifts in expression.
|
From page 102... ...
The polar research community should become actively involved in the ongoing database discussions that are taking place. CREATION OF A POLAR GENOME SCIENCE INITIATIVE Given the great potential of genomic science to address important new research questions in polar regions, some special effort to facilitate and guide these activities is justified.
|
From page 103... ...
Using this approach to implement a comprehensive, coordinated Polar Genome Science Initiative would generate synergies of effort that would maximize scientific output while minimizing the resources required. Under this approach, the Scientific Steering Committee would establish priorities and coordinate large-scale efforts for genome-enabled polar science (for example, genome sequencing, transcriptome analysis, coordinated bioinformatics databases)
|
From page 104... ...
. However, the suggested Polar Genome Science Initiative is a large-scale research effort that aims to facilitate the application of genome research in the polar regions, coordinate the sequencing efforts of polar organisms, and encourage collaboration between polar and nonpolar scientists.
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.