Large-scale Genomic Research Research Articles

Agrobacterium‐mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T‐DNA insertional mutagenesis

Brachypodium distachyon is a promising model system for the structural and functional genomics of temperate grasses because of its physical, genetic and genome attributes. The sequencing of the inbred line Bd21 (http://www.brachypodium.org) started in 2007. However, a transformation method remains to be developed for the community standard line Bd21. In this article, a facile, efficient and rapid transformation system for Bd21 is described using Agrobacterium-mediated transformation of compact embryogenic calli (CEC) derived from immature embryos. Key features of this system include: (i) the use of the green fluorescent protein (GFP) associated with hygromycin selection for rapid identification of transgenic calli and plants; (ii) the desiccation of CEC after inoculation with Agrobacterium; (iii) the utilization of Bd21 plants regenerated from tissue culture as a source of immature embryos; (iv) the control of the duration of the selection process; and (v) the supplementation of culture media with CuSO4 prior to and during the regeneration of transgenic plants. Approximately 17% of CEC produced transgenic plants, enabling the generation of hundreds of T-DNA insertion lines per experiment. GFP expression was observed in primary transformed Bd21 plants (T0) and their progeny (T1). The Mendelian inheritance of the transgenes was confirmed. An adaptor-anchor strategy was developed for efficient retrieval of flanking sequence tags (FSTs) of T-DNA inserts, and the resulting sequences are available in public databases. The production of T-DNA insertion lines and the retrieval of associated FSTs reported here for the reference inbred line Bd21 will facilitate large-scale functional genomics research in this model system.

Proteomics and genomics of microgravity

Many serious adverse physiological changes occur during spaceflight. In the search for underlying mechanisms and possible new countermeasures, many experimental tools and methods have been developed to study microgravity caused physiological changes, ranging from in vitro bioreactor studies to spaceflight investigations. Recently, genomic and proteomic approaches have gained a lot of attention; after major scientific breakthroughs in the fields of genomics and proteomics, they are now widely accepted and used to understand biological processes. Understanding gene and/or protein expression is the key to unfolding the mechanisms behind microgravity-induced problems and, ultimately, finding effective countermeasures to spaceflight-induced alterations. Significant progress has been made in identifying the genes/proteins responsible for these changes. Although many of these genes and/or proteins were observed to be either upregulated or downregulated, however, no large-scale genomics and proteomics studies have been published so far. This review aims at summarizing the current status of microgravity-related genomics and proteomics studies and stimulating large-scale proteomics and genomics research activities.

Co-Funding in Canada: Another View

The letter “Problems with co-funding in Canada” by M. Tyers et al. (24 June, p. [1867][1]) gives a misleading and inaccurate picture of recent increases in federal research funding. The Letter leaves the distinct impression that Canadian scientific excellence is being compromised by an overemphasis on short-term industrial and commercial interests. Statements such as “[m]uch of this renewed commitment to research… is in the form of “co-funded” programs…” and “co-funding is often biased against fundamental research…” not only belie the facts but do a tremendous disservice to a range of innovative Canadian programs that have changed the face of the research environment in Canadian universities over the last 7 years and have reaped a “brain gain” of exceptional young and established stars from other countries. Federal allocations to university RD the creation of the 2000 Canada Research Chairs; Millennium and Canada Graduate Scholarships; permanent funding for the Networks of Centres of Excellence; and the funding of indirect costs of research. Although co-funding programs represent a relatively small portion of the total federal investment, they are an important element in a range of funding vehicles designed to foster a world-class research enterprise in Canada. The largest programs with co-funding requirements are the Canada Foundation for Innovation (CFI) and Genome Canada (GC). To date, CFI, through its 60% matching requirement, has generated $4.3 billion in co-funding for university infrastructure from $2.7 billion in federal investments. For the much smaller GC program (which enables Canada to compete internationally in large-scale genomics research projects), co-funding has leveraged an additional $470 million for genomics researchers from a $375 million federal investment. Genomics programs in the Netherlands and Spain have been modeled after GC. Similar programs in Sweden, UK, and the United States use a co-funding model. For both the CFI and GC programs, provincial governments and not industry have provided most of the co-funding, a fact not mentioned by the Letter writers. Co-funding is an important component of funding in many countries, particularly for very large projects, to harness resources that would not otherwise be accessible to researchers. Another major point made in the Letter is that “[by] eschewing scientific excellence as the primary consideration, co-funded programs imperil scientific credibility…,” implying that co-funded proposals fail to meet the highest standards of excellence set by international peer review. This is demonstrably not the case: For both CFI and GC competitions, review panels have been made up of individuals with impeccable scientific credentials. Publicly funded research in Canada is subject to rigorous peer review, and scientific excellence is not compromised. However, scientific merit is not necessarily the sole determinant of success. For projects involving multimillion dollar investments of public money, funders have a responsibility to ensure that grantees are accountable for the use of funds through sound financial and management practices. In conclusion, I believe the facts show that Canada and Canadian researchers have benefited enormously not only from the massive federal investments, but also from the additional $5 billion that has been leveraged via co-funding mostly from provincial governments over the past 7 years and from the broader engagement of the R&D community. However, a portion of publicly funded research is subject to a double test of peer-reviewed excellence and the ability to attract co-funding partners from the public and private sectors. The result is more support for science and a stronger underpinning for the science and technology enterprise in Canada. [1]: /lookup/doi/10.1126/science.308.5730.1867b

Genome-wide promoter extraction and analysis in human, mouse, and rat

An investigation of how to improve mammalian promoter prediction by incorporating both transcript and conservation information leads to the creation of CSHLmpd, a mammalian promoter database.

Extraction of Organism Groups from Whole Genome Comparisons

The availability of a growing number of fully sequenced genomes makes it possible for us to conduct a large-scale comparative genomic research. In recent years, functional prediction and genome tree construction methods based on phylogenetic proles have been developed. The phylogenetic prole is dened as a bit pattern that encodes the presence or absence of orthologous genes in a set of organisms with fully sequenced genomes, so the phylogenetic prole can be regarded as the evolutionary pattern of gene acquisition and gene loss across organisms. The genome tree methods based on phylogenetic proles stem from the assumption that evolutionarily correlated organisms have similar gene inheritance patterns. The purpose of this paper is to conduct a whole genome scale phylogenetic analysis in order to extract major organism groups from the comparison of fully sequenced genomes using the independent component analysis, at the same, to identify genes that are characteristic to a certain organism group. In the experiment, we show that 24 major organism groups are extracted from phylogenetic proles composed of orthologous gene clusters, and our genome tree corresponds to the simplied classication of KEGG organism groups and suggests that two prokaryotic kingdoms, Archaea and Bacteria, are closer to each other than to Eukaryotes on the whole genome level. We also show a possibility for predicting biological functions of hypothetical genes by examining the correspondence between the extent of their aliation and specic properties of certain organism groups.

Options available--from start to finish--for obtaining data from DNA microarrays II.

Microarray technology has undergone a rapid evolution. With widespread interest in large-scale genomic research, an abundance of equipment and reagents have now become available and affordable to a large cross section of the scientific community. As protocols become more refined, careful investigators are able to obtain good quality microarray data quickly. In most recent times, however, perhaps one of the biggest obstacles researchers face is not the manufacture and use of microarrays at the bench, but storage and analysis of the array data. This review discusses the most recent equipment, reagents and protocols available to the researcher, as well as describing data analysis and storage options available from the evolving field of microarray informatics.