What Is Functional Genomics?

Understanding the function of genes and other parts of the genome is known as functional genomics.

Functional genomics is a field of molecular biology that is attempting to make use of the vast wealth of data produced by genome sequencing projects to describe genome function. Functional genomics uses high-throuput techniques like DNA microarrays, proteomics, metabolomics and mutation analysis to describe the function and interactions of genes.

Because of the large quantity of data and the desire to be able to find patterns and predict gene functions and interactions bioinformatics is crucial to this type of analysis. Comparative genomic analyses can also held determine gene function.

Molecular biology is the study of biology at a molecular level. The field overlaps with other areas of biology, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interrelationship of DNA, RNA and protein synthesis and learning how these interactions are regulated.

Genome projects are scientific endeavours that aim to map the genome of a living being or of a species (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus), that is, the complete set of genes caried by this living being or virus. The Human Genome Project was such a project. Some have argued that the era of genomics is one of the more fundamental advances in human history.

Many organisms have genome projects that have either completed or will complete in the 21st century, including: Homo sapiens Humans, Mus musculus Laboratory mouse, Rattus norvegicus Laboratory rat, Chimp, Gallus gallus Chicken, Macropus eugenii Kangaroo, Felis domesticus Cat, Canis lupis Dog, Drosophila melanogaster Fruit fly, Saccharomyces cerevisiae Yeast, Neurospora crassa A type of mold, Arabidopsis thaliana Mustard weed, Oryza sativa Rice, Triticum spp Wheat, Zea mays Maize (or corn), Escherichia coli bacterium E.coli, SARS virus, Arbacia punctulata the purple-spined sea urchin, Caenorhabditis elegans a nematode worm, Brachydanio rerio Zebrafish, Xenopus laevis The African clawed toad, Oryzias latipes A medakafish, Takifugu rubipres A pufferfish.

Genomics is the study of an organism's genome and the use of the genes. It deals with the systematic use of genome information, associated with other data, to provide answers in biology, medicine, and industry.

Genomics has the potential of offering new therapeutic methods for the treatment of some diseases, as well as new diagnostic methods. Other applications are in the food and agriculture sectors. The major tools and methods related to genomics are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function.

Genomics appeared in the 1980s and took off in the 1990s with the initiation of genome projects for several species. The related field of genetics is the study of genes and their role in inheritance.

The first genome to be sequenced in its entirety was that of bacteriophage FX174 (5,368 kb) in 1980. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8Mb) in 1995, and since then genomes are being sequenced at a rapid pace. A rough draft of the human genome was completed by the Human Genome Project in early 2001 amid much fanfare.

Comparison of genomes has resulted in some surprising biological discoveries. If a particular DNA sequence or pattern is present among many members of a clade, that sequence is said to have been conserved among the species. Evolutionary conservation of a DNA sequence may imply that it confers a relative selective advantage to the organisms that possess it. Conservation also suggests that sequence has functional significance. It may be a protein coding sequence or regulatory region. Experimental investigation of some of these sequences has shown that some are transcribed into small RNA molecules, although the functions of these RNAs were not immediately apparent.

There are as many definitions of functional genomics as there are enterprising scientists trying to bend a fashionable term to fit their science! Perhaps a good operating definition is 'any approach which is informed by knowledge of the genome'. The major components of a functional genomics approach are: bioinformatics - the extraction of biological utility from genomic sequence, and the reconciliation of multiple datasets microarrays - the global assessment of how the expression of all genes in the genome varies under changing conditions proteomics - the study of the total protein complement expressed by a particular cell under particular conditions reverse genetics - deducing the function of novel genes by mutating them and studying the mutant phenotype.

The identification of similar sequences (including many genes) in two distantly related organisms, but not in other members of one of the clades, has led to the theory that these sequences were acquired by horizontal gene transfer. This phenomenon is most prominent in thermophilic bacteria, where it seems that genes were transferred from Archaea to Eubacteria. It has also been noticed that bacterial genes exist in eukaryotic nuclear genomes and that these genes generally encode mitochondrial and plastid proteins, giving support to the endosymbiotic theory of the origin of these organelles.

Structural genomics or structural bioinformatics refers to the analysis of macromolecular structure particularly proteins, using computational tools and theoretical frameworks. One of the goals of structural genomics is the extension of idea of genomics, to obtain accurate three-dimensional structural models for all known protein families, protein domains or protein folds. Structural alignment is a tool of structural genomics.

Functional genomics refers to the development and application of global (genome-wide or system-wide) experimental approaches to assess gene function by making use of the information and reagents provided by structural genomics. It is characterized by high-throughput or large-scale experimental methodologies combined with statistical or computational analysis of the results.

In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences.

More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite from the chromosomes of various individuals. In general use, the phrase genetic makeup is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Most biological entities more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and non-coding DNA that have the potential to be present.

In vertebrates such as humans, however, "genome" carries the typical connotation of only chromosomal DNA. So although human mitochondria contain genes, these genes are not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome, often referred to as the "mitochondrial genome".

Note that a genome does not capture the genetic diversity or the genetic polymorphism of a species. For example, the human genome sequence in principle could be determined from just half the DNA of one cell from one individual. To learn what variations in DNA underlie particular traits or diseases requires comparisons across individuals. This point explains the common usage of "genome" (which parallels a common usage of "gene") to refer not to any particular DNA sequence, but to a whole family of sequences that share a biological context.

Although this concept may seem counter intuitive, it is the same concept that says there is no particular shape that is the shape of a cheetah. Cheetahs vary, and so do the sequences of their genomes. Yet both the individual animals and their sequences share commonalities, so one can learn something about cheetahs and "cheetah-ness" from a single example of either.

Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as chromosome number, chromosome size, gene order, codon usage bias, and G-C content to determine what mechanisms could have produced the great variety of genomes that exist today.

Duplications play a major role in shaping the genome. Duplications may range from extension of short tandem repeats, to duplication of a cluster of genes, and all the way to duplications of entire chromosomes or even entire genomes. Such duplications are probably fundamental to the creation of genetic novelty.

Horizontal gene transfer is invoked to explain how there is often extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes. Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes.

Functional genomics as a means of assessing phenotype differs from more classical approaches primarily with respect to the scale and automation of biological investigations. A classical investigation of gene expression might examine how the expression of a single gene varies with the development of an organism in vivo. Modern functional genomics approaches, however, would examine how 1,000 to 10,000 genes are expressed as a function of development.

A DNA microarray (also DNA chip or gene chip in common speech) is a piece of glass or plastic on which pieces of DNA have been affixed in a microscopic array. Scientists use such chips to screen a biological sample for the presence of many genetic sequences at once. The affixed DNA segments are known as probes. Thousands of identical probe molecules are affixed at each point in the array to make the chips effective detectors.

Although the name GeneChip is a trademark of Affymetrix, microarray users generally use this term, or, simply, chip, to refer to any microarray, not just those sold by Affymetrix. While Affymetrix arrays use short oligonucleotide probes of 25 bases or less, many microarrays use PCR products, genomic DNAs, BACs, plasmids, or longer oligos (35 to 70 bases). Microarrays may be made by any number of technologies including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, or ink-jet printers[1] (http://genomebiology.com/2004/5/8/R58). The use of microarrays for expression profiling was first published in 1995 (Science) and the first complete eukaryotic genome (Saccharomyces cerevisiae) on a microarray was published in 1997 (Science).

Typically arrays are used to detect the presence of mRNAs that may have been transcribed from different genes and which encode different proteins. The RNA is extracted from many cells, ideally from a single cell type, then converted to cDNA or cRNA. The copies may be "amplified" in concentration by rtPCR. Fluorescent tags are enzymatically incorporated into the newly synthesized strands or can be chemically attached to the new strands of DNA or RNA. A cDNA or cRNA molecule that contains a sequence complementary to one of the single-stranded probe sequences will hybridize, or stick, via base pairing (more at DNA) to the spot at which the complementary probes are affixed. The spot will then fluoresce (or glow) when examined using a microarray scanner.

Proteomics is the large-scale study of proteins, particularly their structures and functions. This term was coined to make an analogy with genomics, and is often viewed as the "next step", but proteomics is much more complicated than genomics. Most importantly, while the genome is a rather constant entity, the proteome is constantly changing through its biochemical interactions with the genome and the environment. One organism will have radically different protein expression in different parts of its body, in different stages of its life cycle and in different environmental conditions.

The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the proteome of the organism or cell type respectively.

With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins. A surprising finding of the Human Genome Project is that there are far fewer genes that code for proteins in the human genome than there are proteins in the human proteome (~22,000 genes vs ~200,000 proteins). The large increase in protein diversity is thought to be due to alternative splicing and post-translational modification of proteins.

Genes are material entities that parents pass to offspring during reproduction. These entities encode information essential for the construction and regulation of polypeptides, proteins and other molecules that determine the growth and functioning of the organism.

The word "gene" is shared by many disciplines, including classical genetics, molecular genetics, evolutionary biology and population genetics. Because each discipline models the biology of life differently, the material entity that supports the gene in one discipline is not the same as in the other.

Following the discovery that DNA is the genetic material, and with the growth of biotechnology and the project to sequence the human genome, the common usage of the word "gene" has increasingly reflected its meaning in molecular biology. In the molecular-biological sense, genes are the segments of DNA which cells transcribe into RNA and translate, at least in part, into proteins.

In common speech, "gene" is often used to refer to the hereditary cause of a trait, disease or condition�as in "the gene for obesity." Speaking more precisely, a biologist might refer to an allele or a mutation that has been implicated in or is associated with obesity. This is because biologists know that many factors other than genes decide whether a person is obese or not: prenatal environment, upbringing, culture and the availability of food, for example.

Moreover, it is very unlikely that variations within a single gene�or single genetic locus�fully determine one's genetic predisposition for obesity. These aspects of inheritance�the interplay between genes and environment, the influence of many genes�appear to be the norm with regard to many and perhaps most ("complex" or "multifactoral") traits. The term phenotype refers to the characteristics that result from this interplay (see genotype-phenotype distinction).

Plant Physiol . 2005 Jan 14; {Epub ahead of print}
Functional Genomics of Eukaryotic Photosynthesis Using Insertional Mutagenesis of Chlamydomonas reinhardtii; Dent RM et al.; The unicellular green alga Chlamydomonas reinhardtii is a widely used model organism for studies of oxygenic photosynthesis in eukaryotes . Here we describe the development of a resource for functional genomics of photosynthesis using insertional mutagenesis of the Chlamydomonas nuclear genome . Chlamydomonas cells were transformed with either of two plasmids conferring zeocin resistance, and insertional mutants were selected in the dark on acetate-containing medium to recover light-sensitive and nonphotosynthetic mutants . The population of insertional mutants was subjected to a battery of primary and secondary phenotypic screens to identify photosynthesis-related mutants that were pigment deficient, light sensitive, nonphotosynthetic, or hypersensitive to reactive oxygen species . Approximately 9% of the insertional mutants exhibited 1 or more of these phenotypes . Molecular analysis showed that each mutant line contains an average of 1.4 insertions, and genetic analysis indicated that approximately 50% of the mutations are tagged by the transforming DNA . Flanking DNA was isolated from the mutants, and sequence data for the insertion sites in 50 mutants are presented and discussed.

Nucleic Acids Res, 2005 Jan 14, 33(1), 439 - 47 Print 2005.
Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality; Elmen J et al.; Therapeutic application of the recently discovered small interfering RNA (siRNA) gene silencing phenomenon will be dependent on improvements in molecule bio-stability, specificity and delivery . To address these issues, we have systematically modified siRNA with the synthetic RNA-like high affinity nucleotide analogue, Locked Nucleic Acid (LNA) . Here, we show that incorporation of LNA substantially enhances serum half-life of siRNA's, which is a key requirement for therapeutic use . Moreover, we provide evidence that LNA is compatible with the intracellular siRNA machinery and can be used to reduce undesired, sequence-related off-target effects . LNA-modified siRNAs targeting the emerging disease SARS, show improved efficiency over unmodified siRNA on certain RNA motifs . The results from this study emphasize LNA's promise in converting siRNA from a functional genomics technology to a therapeutic platform.

J Chromatogr B Analyt Technol Biomed Life Sci, 2005 Feb 5, 815(1-2), 147 - 55
Proteomic analysis of Korean ginseng (Panax ginseng C.A . Meyer); Nam MH et al.; Although many reports have been published regarding the pharmacological effects of ginseng, little is known about the biochemical pathways operant in ginsenoside biosynthesis, or the genes involved therein . Proteomics analysis is an approach to elucidate the physiological characteristics and biosynthetic pathways of ginsenosides, main components of ginseng . In this review, we introduced the recent progress in proteomics studies of ginseng (Panax ginseng C.A . Meyer) . We briefly reference the genomic analyses of P . ginseng, without which proteomics approaches would have been impossible . Functional genomics studies regarding secondary metabolism in P . ginseng are also introduced here, in order to introduce possible future prospects for further study.

J Chromatogr B Analyt Technol Biomed Life Sci, 2005 Feb 5, 815(1-2), 109 - 23
System, trends and perspectives of proteomics in dicot plants Part I: Technologies in proteome establishment; Agrawal GK et al.; The first 3 years of the 21st century have seen the impact of plant proteomics on functional genomics that has enhanced our understanding, not only on the plant genome(s), but also more importantly, on the functional aspect of proteins . This is mainly due to availability of the complete genome sequence of the Arabidopsis thaliana-a dicotyledoneous (dicot) model plant-and technological advancements in proteomics . Proteomic analyses of a variety of dicot plants, including both Arabidopsis and the model legume species, barrel medic (Medicago truncatula), have greatly helped in an efficient separation, identification and cataloguing of a large number of proteins, and thereby defining their proteomes . Therefore, we have composed an inclusive review on dicot plant materials, as of February 2004, that provides system, trends and perspectives of proteomics in growth and development and the environment . The review is summarized and discussed as three individual, but interlinked, entities: Part I, technologies in proteome establishment (this review), Part II, proteomes of the complex developmental stages {G.K . Agrawal, M . Yonekura, Y . Iwahashi, H . Iwahashi, R . Rakwal, J . Chromatogr . B (2004)}, and Part III, unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships {G.K . Agrawal, M . Yonekura, Y . Iwahashi, H . Iwahashi, R . Rakwal, J . Chromatogr . B (2004)} . This review deals with the diverse proteomic technologies being used in proteome development of different dicot plants.

J Chromatogr B Analyt Technol Biomed Life Sci, 2005 Feb 5, 815(1-2), 97 - 107
Survey of current protein family databases and their application in comparative, structural and functional genomics; Redfern O et al.; The last two decades have witnessed significant expansions in the databases storing information on the sequences and structures of proteins . This has led to the creation of many excellent protein family resources, which classify proteins according to their evolutionary relationship . These have allowed extensive insights into evolution and particularly how protein function mutates and evolves over time . Such analyses have greatly assisted the inheritance of functional annotations between experimentally characterised and uncharacterised genes . Moreover, the development of bioinformatics tools acts as a companion to the new technologies emerging in biology, such as transcriptomics and proteomics . The latter enable researchers to analyse gene expression profiles and interactions on a genome-wide scale, generating vast datasets of proteins, many of which include experimentally uncharacterised proteins . Protein family/function databases can be used to help interpret this data and allow us to benefit more fully from these technologies . This review aims to summarise the most popular sequence- and structure-based protein family databases . We also cover their application to comparative genomics and the functional annotation of the genomes.

J Chromatogr B Analyt Technol Biomed Life Sci, 2005 Feb 5, 815(1-2), 11 - 24
Peptidomics, current status; Soloviev M et al.; Characterisation of the complement of expressed proteins from a single genome is a central focus of the evolving field of proteomics . Traditional proteomics technologies were developed in the 20th century and are based on two-dimensional electrophoresis or multidimensional liquid chromatography . These facilitated functional genomics analysis, but they currently represent a significant bottleneck to progress in this area . We are now witnessing the development of novel alternative technologies for use in expression proteomics research . This review aims to familiarise the reader with the principles underlying the peptidomics approaches to proteomics research and provide examples of their applications.

Int J Mol Med, 2005 Feb, 15(2), 205 - 12
In silico identification of breast cancer genes by combined multiple high throughput analyses; Shen D et al.; Publicly available human genomic sequence data provide an unprecedented opportunity for researchers to decode the functionality of human genome . Such information is extremely valuable in cancer prevention diagnosis and treatment . Cancer Genome Anatomy Project (CGAP) and Gene Expression Omnibus (GEO) are two bioinformatic infrastructures for studying functional genomics . The goal of this study is to explore the feasibility of incorporating the Internet-available bioinformatic databases to discover human breast cancer-related genes . Several tools including the Gene Finder, Virtual Northern (vNorthern) and SAGE digital gene expression displayer (DGED) were used to analyze differential gene expression between benign and malignant breast tissues . A pilot study was performed using both EST and SAGE vNorthern to analyze the expression of a panel of known genes, including high abundance genes beta-actin and G3PDH, low abundance genes BRCA1 and p53, tissue-specific genes CEA and PSA and two breast cancer-related genes Her2/neu and MUC1 . We found a high expression of beta-actin and G3PDH and a low expression of BRCA1 and p53 across different types of tissues as well as a tissue-specific expression of CEA in colon and PSA in prostate . A further analysis of 30 known breast cancer-related genes in breast cancer tissues by vNorthern demonstrated a high expression of oncogenes and low expression of tumor suppressor genes . An open-end analysis of two pools of breast cancer and benign breast tissue libraries by SAGE DGED produced 53 differentially expressed genes according to the screening criteria of a >five-fold difference and p<0.01 . Further analysis by EST vNorthern and virtual microarray analysis reduced the candidate genes to six, with four down-regulated genes, ANXA1, CAV1, KRT5 and MMP7, and two up-regulated genes, ERBB2 and G1P3 in breast cancer . These findings were validated by a real-time RT-PCR analysis in eight paired human breast cancer tissue samples . We conclude that the combined multiple high throughput analyses is an effective data mining strategy in cancer gene identification . This approach may improve the usage of public available genomic data through strategic data mining of high throughput analysis.

Methods Enzymol, 2005, 392, 242 - 77
High-Throughput RNA Interference Strategies for Target Discovery and Validation by Using Synthetic Short Interfering RNAs: Functional Genomics Investigations of Biological Pathways; Sachse C et al.; During the past five years, RNA interference (RNAi) has emerged as arguably the best functional genomics tool available to date, providing direct, causal links between individual genes and loss-of-function phenotypes through robust, broadly applicable, and readily upscalable methodologies . Originally applied experimentally in C . elegans and Drosophila, RNAi is now widely used in mammalian cell systems also . The development of commercially available libraries of short interfering RNAs (siRNAs) and other RNAi silencing reagents targeting entire classes of human genes provide the opportunity to carry out genome-scale screens to discover and characterize gene functions directly in human cells . A key challenge of these studies, also faced by earlier genomics or proteomics approaches, resides in reaching an optimal balance between the necessarily high throughput and the desire to achieve the same level of detailed analysis that is routine in conventional small-scale studies . This chapter discusses technical aspects of how to perform such screens, what parameters to monitor, and which readouts to apply . Examples of homogenous assays and multiplexed high-content microscopy-based screens are demonstrated.

Methods Enzymol, 2005, 392, 73 - 96
Mechanistic insights aid computational short interfering RNA design; Boese Q et al.; RNA interference is widely recognized for its utility as a functional genomics tool . In the absence of reliable target site selection tools, however, the impact of RNA interference (RNAi) may be diminished . The primary determinants of silencing are influenced by highly coordinated RNA-protein interactions that occur throughout the RNAi process, including short interfering RNA (siRNA) binding and unwinding followed by target recognition, cleavage, and subsequent product release . Recently developed strategies for identification of functional siRNAs reveal that thermodynamic and siRNA sequence-specific properties are crucial to predict functional duplexes (Khvorova et al., 2003; Reynolds et al., 2004; Schwarz et al., 2003) . Additional assessments of siRNA specificity reveal that more sophisticated sequence comparison tools are also required to minimize potential off-target effects (Jackson et al., 2003; Semizarov et al., 2003) . This chapter reviews the biological basis for current computational design tools and how best to utilize and assess their predictive capabilities for selecting functional and specific siRNAs.

Methods Enzymol, 2005, 392, 36 - 55
RNA Interference in Caenorhabditis elegans; Wang J et al.; RNA interference (RNAi) was first discovered in the nematode Caenorhabditis elegans (Fire et al., 1998; Guo and Kemphues, 1995) . The completion of the C . elegans genome in 1998 coupled with the advent of RNAi techniques to knock down gene function ushered in a new age in the field of functional genomics . There are four methods for double-stranded RNA (dsRNA) delivery in C . elegans: (1) injection of dsRNA into any region of the animal (Fire et al., 1998), (2) feeding with bacteria producing dsRNA (Timmons et al., 2001), (3) soaking in dsRNA (Tabara et al., 1998), and (4) in vivo production of dsRNA from transgenic promoters (Tavernarakis et al., 2000) . In this chapter, we discuss the molecular genetic mechanisms, techniques, and applications of RNAi in C . elegans.

Methods Enzymol, 2005, 392, 1 - 24
Transgene-induced RNA interference as a tool for plant functional genomics; McGinnis K et al.; RNA interference (RNAi) is a powerful tool for functional genomics in a number of species . The logistics and procedures for doing high-throughput RNAi to investigate the functions of large numbers of genes in Arabidopsis thaliana and in Zea mays are described . Publicly available plasmid vectors that facilitate the stable chromosomal integration of inverted repeat transgenes that trigger RNAi have been used to generate more than 50 independent transgenic lines each in Arabidopsis and maize . Analysis of mRNA abundance of the targeted genes in independent lines transformed with distinct constructs indicates that the success of RNAi-induced silencing is gene dependent . mRNA levels were not detectably reduced for some genes, but were dramatically reduced for a number of genes targeted . A common pattern was that multiple independent lines transgenic for the same construct showed the same extent of silencing . This chapter describes the procedures used to generate and test transgenic lines mediating RNAi in Arabidopsis and maize.

Brief Funct Genomic Proteomic, 2004 Nov, 3(3), 257 - 66
Fruits and flies: A genomics perspective of an invertebrate model organism; Burdett H et al.; The increasing number of species for which a full genome sequence is available offers rich pickings for geneticists, but comparative analysis and assembly of information gathered across species does not always lead to answers about the function of a particular gene . This paper aims to place the invertebrate model system - the fly Drosophila melanogaster - into this playing field and to discuss how the organism arrived at its position in functional genetic analysis . Indeed, despite the wealth of knowledge on how a fly lives, breathes and flies, this organism is likely to remain a player in the analysis of biological, disease and pharmaceutical processes . The fast genetics Drosophila offers, combined with a well-annotated genome and a wealth of techniques facilitating gene function discovery, will ensure its place in functional genomics for some time to come . Although the fly cannot speak, it certainly can tell a tale.

Yi Chuan, 2004 Nov, 26(6), 953 - 6
{A Novel Gene in APOA1/C3/A4/A5 cluster : Apolipoprotein A5.}; Liu HK et al.; Using methods of comparative and functional genomics, a new gene coding for apolipoprotein A5 was identified in the vicinity of APOA1/C3/A4 cluster on human chromosome 11q23 by Pennaccio team and Vliet team . The open reading frame of human APOA5 encoded a 366-amino acid protein with high sequence homology to mouse Apoa5 and human APOA4 . Mice expressing a human APOA5 transgene showed a decrease in plasma triglyceride concentrations to one-third of those in control mice; conversely, knockout mice lacking Apoa5 had four times as much plasma triglycerides as controls . Single nucleotide polymorphisms (SNPs) in APOA5 (S19W, -1131T>C) and APOA5 haplotype (APOA5*3) were independently associated with high plasma triglyceride levels . These findings indicate that APOA5 is an important determinant of plasma triglyceride levels, a major risk factor for coronary artery disease.

Yi Chuan, 2004 Jul, 26(4), 560 - 6
{The Moss Physcomitrella patens, a New Model System for Functional Genomics.}; Dong W et al.; The potential of moss as a model system to study plant biological process is associated with their relatively simple developmental pattern and the dominance of the haploid gametophyte in the life cycle . The moss Physcomitrella patens exhibits a very high rate of homologous recombination in its nuclear DNA, making gene targeting approaches in this plant as convenient as in yeast or in ES cells of mice . Sharing many biological features with higher plants and having many other advantages, the moss Physcomitrella patens will be an attractive model system for plant biology and functional genome analysis.

Yi Chuan, 2003 Nov, 25(6), 735 - 9
{Application of single nucleotide polymorphism in crop genetics and improvement.}; Du CF et al.; Single nucleotide polymorphism(SNP) is the most common type of sequence difference between alleles,which can be used as a kind of high-throughput genetic marker.Several different routes have been developed to discover and identify SNP.These include the direct sequencing of PCR amplicons,electronic SNP(eSNP) and so on.SNP assays have been made in many crop species such as maize and soybean.The elite germplasm of some crops have been narrowed in genetic diversity,increasing the amount of linkage disequilibrium(LD) present and facilitating the association of SNP haplotypes at candidate gene loci with phenotypes.SNP analysis has been broadly used in the field of plant gene mapping,integration of genetic and physical maps,DNA marker-assisted breeding and functional genomics.

Yi Chuan, 2003 Sep, 25(5), 628 - 32
{The Red Recombination System and Its Application to Gene Knock-out in Microorganism.}; Hu K et al.; Since many DNA-sequencing projects of varied microorganisms have been completed,studies on their functional genomics become more important.Inactivation of an interesting gene is a direct method to characterize its function.Though the Esherichia coli RecA recombination system can be used to produce gene mutants,it needs a complex manipulation process.Furthermore,its efficiency is very low.Recently a Red recombination system was developed.This recombination system consists of three proteins:alpha protein (gamma exonuclease),beta protein and Gam protein.In this system,the linear targeting DNA which contains a selectable marker flanked with a homologous region as short as only 35~60 bp can be directly targeted for gene knock-out with a higher efficiency.

Yi Chuan, 2003 Jul, 25(4), 489 - 94
{RNA-based Transgene Silencing:Mechanism and Applications.}; Chen W et al.; RNA-based transgene silencing is a phenomenon that endogenous and exogenous mRNAs are degraded specifically directed by double-stranded RNA.Here we review the recent advances on its mechanism and summarize related proteins and expatiate their functions.Furthermore,we introduce the enormous potential of dsRNA as a tool in functional genomics research and practical biotechnology.

FEBS J, 2005 Jan, 272(1), 2 - 15
Towards discovery-driven translational research in breast cancer; Celis JE et al.; Discovery-driven translational research in breast cancer is moving steadily from the study of cell lines to the analysis of clinically relevant samples that, together with the ever increasing number of novel and powerful technologies available within genomics, proteomics and functional genomics, promise to have a major impact on the way breast cancer will be diagnosed, treated and monitored in the future . Here we present a brief report on long-term ongoing strategies at the Danish Centre for Translational Breast Cancer Research to search for markers for early detection and targets for therapeutic intervention, to identify signalling pathways affected in individual tumours, as well as to integrate multiplatform 'omic' data sets collected from tissue samples obtained from individual patients . The ultimate goal of this initiative is to coalesce knowledge-based complementary procedures into a systems biology approach to fight breast cancer.

Plant Mol Biol, 2004 Nov, 56(4), 613 - 24
A geminivirus-induced gene silencing system for gene function validation in cassava; Fofana IB et al.; We have constructed an African cassava mosaic virus (ACMV) based gene-silencing vector as a reverse genetics tool for gene function analysis in cassava . The vector carrying a fragment from the Nicotiana tabacumsulfur gene (su), encoding one unit of the chloroplast enzyme magnesium chelatase, was used to induce the silencing of the cassava orthologous gene resulting in yellow-white spots characteristic of the inhibition of su expression . This result suggests that well developed sequence databases from model plants like Arabidopsis thaliana, Nicotiana benthamiana, N . tabacum, Lycopersicon esculentum and others could be used as a major source of information and sequences for functional genomics in cassava . Furthermore, a fragment of the cassava CYP79D2endogenous gene, sharing 89% homology with CYP79D1endogenous gene was inserted into the ACMV vector . The resultant vector was inducing the down regulation of the expression of these two genes which catalyze the first-dedicated step in the synthesis of linamarin, the major cyanogenic glycoside in cassava . At 21 days post-inoculation (dpi), a 76% reduction of linamarin content was observed in silenced leaves . Using transgenic plants expressing antisense RNA of CYP79D1and CYP79D2, Siritunga and Sayre (2003) obtained several lines with a reduction level varying from 60% to 94% . This result provides the first example of direct comparison of the efficiency of a virus-induced gene silencing (VIGS) system and the transgenic approach for suppression of a biosynthetic pathway . The ACMV VIGS system will certainly be a complement and in some cases an alternative to the transgenic approach, for gene discovery and gene function analysis in cassava.

Trends Biotechnol, 2005 Jan, 23(1), 11 - 6
Towards replacing closed with open target selection strategies; van der Werf MJ; Increasingly, microbial production processes are being improved by targeted approaches . In directed strain improvement, the selection of the relevant targets is the limiting step in metabolic engineering . Currently, the identification of leads is still a random process relying largely on expert knowledge . Recently, this approach has been complemented by metabolic flux and control analysis approaches . However, both are closed approaches, and biological processes or interactions that are not currently known to exist, or to be important for bioproduct formation, are not taken into account . By contrast, the recently introduced functional genomics technologies enable an open approach towards target selection . In the near future, we might see that metabolomics, and its integration with transcriptomics and/or proteomics into a systems biology approach, in combination with multivariate data analysis tools, will become of increasing importance for the unbiased selection and ranking of targets, not only for strain improvement but also for bioprocess improvement.

Mol Cell, 2005 Jan 7, 17(1), 1 - 10
Defining and Assaying RNAi in Mammalian Cells; Huppi K et al.; The investigation of protein function through the inhibition of activity has been critical to our understanding of many normal and abnormal biological processes . Until recently, functional inhibition in biological systems has been induced using a variety of approaches including small molecule antagonists, antibodies, aptamers, ribozymes, antisense oligonucleotides or transcripts, morpholinos, dominant-negative mutants, and knockout transgenic animals . Although all of these approaches have made substantial advances in our understanding of the function of many proteins, a lack of specificity or restricted applicability has limited their utility . Recently, exploitation of the naturally occurring posttranscriptional gene silencing mechanism triggered by double-stranded RNA (dsRNA), termed RNA interference (RNAi), has gained much favor as an alternative means for analyzing gene function . Aspects of the basic biology of RNAi, its application as a functional genomics tool, and its potential as a therapeutic approach have been extensively reviewed ; however, there has been only limited discussion as to how to design and validate an individual RNAi effector molecule and how to interpret RNAi data overall, particularly with reference to experimentation in mammalian cells . This perspective will aim to consider some of the issues encountered when conducting and interpreting RNAi experiments in mammalian cells.

Genomics Proteomics Bioinformatics, 2003 Nov, 1(4), 263 - 78
Functional genomics of wood quality and properties; Tang W et al.; Genomics promises to enrich the investigations of biology and biochemistry . Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication . Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly . Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide . In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus . The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. , , . Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense . Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.

Biochemistry (Mosc), 2004 Nov, 69(11), 1283 - 98
Proteomic studies of human and other vertebrate muscle proteins; Shishkin SS et al.; This review summarizes results of some systemic studies of muscle proteins of humans and some other vertebrates . The studies, started after introduction of two-dimensional gel electrophoresis of O'Farrell, were significantly extended during development of proteomics, a special branch of functional genomics . Special attention is paid to analysis of characteristic features of strategy for practical realization of the systemic approach during three main stages of these studies: pre-genomic, genomic (with organizational registration of proteomics), and post-genomic characterized by active use of structural genomics data . Proteomic technologies play an important role in detection of changes in isoforms of various muscle proteins (myosins, troponins, etc.) . These changes possibly reflecting tissue specificity of gene expression may underline functional state of muscle tissues under normal and pathological conditions, and such proteomic analysis is now used in various fields of medicine.

Theriogenology, 2005 Jan 15, 63(2), 283 - 99
Perspectives for artificial insemination and genomics to improve global swine populations; Gerrits RJ et al.; Civilizations throughout the world continue to depend on pig meat as an important food source . Approximately 40% of the red meat consumed annually worldwide (94 million metric tons) is pig meat . Pig numbers (940 million) and consumption have increased consistent with the increasing world population (FAO 2002) . In the past 50 years, research guided genetic selection and nutrition programs have had a major impact on improving carcass composition and efficiency of production in swine . The use of artificial insemination (AI) in Europe has also had a major impact on pig improvement in the past 35 years and more recently in the USA . Several scientific advances in gamete physiology and/or manipulation have been successfully utilized while others are just beginning to be applied at the production level . Semen extenders that permit the use of fresh semen for more than 5 days post-collection are largely responsible for the success of AI in pigs worldwide . Transfer of the best genetics has been enabled by use of AI with fresh semen, and to some extent, by use of AI with frozen semen over the past 25 years . Sexed semen, now a reality, has the potential for increasing the rate of genetic progress in AI programs when used in conjunction with newly developed low sperm number insemination technology . Embryo cryopreservation provides opportunities for international transport of maternal germplasm worldwide; non-surgical transfer of viable embryos in practice is nearing reality . While production of transgenic animals has been successful, the low level of efficiency in producing these animals and lack of information on multigene interactions limit the use of the technology in applied production systems . Technologies based on research in functional genomics, proteomics and cloning have significant potential, but considerable research effort will be required before they can be utilized for AI in pig production . In the past 15 years, there has been a coordinated worldwide scientific effort to develop the genetic linkage map of the pig with the goal of identifying pigs with genetic alleles that result in improved growth rate, carcass quality, and reproductive performance . Molecular genetic tests have been developed to select pigs with improved traits such as removal of the porcine stress (RYR1) syndrome, and selection for specific estrogen receptor (ESR) alleles . Less progress has been made in developing routine tests related to diseases . Major research in genomics is being pursued to improve the efficiency of selection for healthier pigs with disease resistance properties . The sequencing of the genome of the pig to identify new genes and unique regulatory elements holds great promise to provide new information that can be used in pig production . AI, in vitro embryo production and embryo transfer will be the preferred means of implementing these new technologies to enhance efficiency of pig production in the future.

Nucleic Acids Res . 2004 Dec 29;32(22):e189.
Expression of the sorghum 10-member kafirin gene cluster in maize endosperm; Song R et al.; Functional analysis of chromosomal segments containing linked genes requires the insertion of contiguous genomic sequences from bacterial artificial chromosomes (BACs) into the genome . Therefore, we introduced a 90-kb large BAC clone carrying a 10-copy tandem array of kafirin storage protein genes from sorghum linkage group J, mixed with a selectable marker gene, directly into maize cells using the particle bombardment method . Transgenic plants were regenerated and seeds from eight different transgenic lines were produced . One such transgenic plant was selected that had the entire kafirin gene cluster on a single continuous DNA fragment spanning more than 45 kb integrated into its genome . When alcohol-soluble proteins from individual T2 and T3 seeds of this event were analyzed, significant levels of kafirin were found in addition to the endogenous zein storage proteins, demonstrating that the large exogenous DNA segment is stably integrated into the maize genome and expressed at high levels in subsequent generations . Therefore, we could provide a new utility of plant transformation by the particle bombardment method for functional genomics of multigene families and the modification of the nutritive quality of cereal grains . Despite a tandem array of highly homologous sequences at the transgenic locus, no gene silencing was observed, probably owing to the effects of co-transformed flanking sequences . The expression studies of the transgenic locus also revealed new features of storage protein gene promoters that differed from previous transient gene expression studies, thereby illustrating the significance of the concentration and configuration of DNA-protein interactions in the regulation of gene expression.

Ann Surg, 2005 Jan, 241(1), 16 - 26
DNA array-based gene profiling: from surgical specimen to the molecular portrait of cancer; Mocellin S et al.; Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors . Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes . The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously . Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology . Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents . Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated . In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology.

Plant Physiol, 2005 Jan, 137(1), 176 - 89 Epub 2004 Dec 23.
Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells; Xie Z et al.; The WRKY proteins are a superfamily of regulators that control diverse developmental and physiological processes . This family was believed to be plant specific until the recent identification of WRKY genes in nonphotosynthetic eukaryotes . We have undertaken a comprehensive computational analysis of the rice (Oryza sativa) genomic sequences and predicted the structures of 81 OsWRKY genes, 48 of which are supported by full-length cDNA sequences . Eleven OsWRKY proteins contain two conserved WRKY domains, while the rest have only one . Phylogenetic analyses of the WRKY domain sequences provide support for the hypothesis that gene duplication of single- and two-domain WRKY genes, and loss of the WRKY domain, occurred in the evolutionary history of this gene family in rice . The phylogeny deduced from the WRKY domain peptide sequences is further supported by the position and phase of the intron in the regions encoding the WRKY domains . Analyses for chromosomal distributions reveal that 26% of the predicted OsWRKY genes are located on chromosome 1 . Among the dozen genes tested, OsWRKY24, -51, -71, and -72 are induced by abscisic acid (ABA) in aleurone cells . Using a transient expression system, we have demonstrated that OsWRKY24 and -45 repress ABA induction of the HVA22 promoter-beta-glucuronidase construct, while OsWRKY72 and -77 synergistically interact with ABA to activate this reporter construct. , , . This study provides a solid base for functional genomics studies of this important superfamily of regulatory genes in monocotyledonous plants and reveals a novel function for WRKY genes, i.e . mediating plant responses to ABA.

J Exp Bot, 2005 Jan, 56(410), 273 - 86 Epub 2004 Dec 23.
Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics; Smedsgaard J et al.; Filamentous fungi and yeast from the genera Saccharomyces, Penicillium, Aspergillus, and Fusarium are well known for their impact on our life as pathogens, involved in food spoilage by degradation or toxin contamination, and also for their wide use in biotechnology for the production of beverages, chemicals, pharmaceuticals, and enzymes . The genomes of these eukaryotic micro-organisms range from about 6000 genes in yeasts (S . cerevisiae) to more than 10 000 genes in filamentous fungi (Aspergillus sp.) . Yeast and filamentous fungi are expected to share much of their primary metabolism; therefore much understanding of the central metabolism and regulation in less-studied filamentous fungi can be learned from comparative metabolite profiling and metabolomics of yeast and filamentous fungi . Filamentous fungi also have a very active and diverse secondary metabolism in which many of the additional genes present in fungi, compared with yeast, are likely to be involved . Although the 'blueprint' of a given organism is represented by the genome, its behaviour is expressed as its phenotype, i.e . growth characteristics, cell differentiation, response to the environment, the production of secondary metabolites and enzymes . Therefore the profile of (secondary) metabolites-fungal chemodiversity-is important for functional genomics and in the search for new compounds that may serve as biotechnology products . Fungal chemodiversity is, however, equally efficient for identification and classification of fungi, and hence a powerful tool in fungal taxonomy . In this paper, the use of metabolite profiling is discussed for the identification and classification of yeasts and filamentous fungi, functional analysis or discovery by integration of high performance analytical methodology, efficient data handling techniques and core concepts of species, and intelligent screening . One very efficient approach is direct infusion Mass Spectrometry (diMS) integrated with automated data handling, but a full metabolic picture requires the combination of several different analytical techniques.

J Synchrotron Radiat, 2005 Jan 1, 12(Pt 1), 19 - 22 Epub 2004 Dec 23.
Bottlenecks and roadblocks in high-throughput XAS for structural genomics; Scott RA; Structural and functional characterization of the entire protein complement (the proteome) of an organism can provide an infrastructure upon which questions about biological pathways and systems biology can be framed . The technology necessary to perform this proteome-level structural and functional characterization is under development in numerous structural genomics and functional genomics initiatives . Given the ubiquity of metal active sites in a proteome, it seems appropriate to ask whether comprehensive local structural characterization of metal sites within a proteome (metalloproteomics) is either a valid or obtainable goal . With a proteome-wide knowledge of the active-site structures of all metalloproteins, one could start to ask how metal insertion, cluster assembly and metalloprotein expression are affected by growth conditions or developmental status etc . High-throughput X-ray absorption spectroscopy (HTXAS) is being developed as a technology for investigating the metalloproteome . In creating a pipeline from genome to metalloproteome, several bottlenecks to high-throughput determination of metal-site structures must be overcome . For example, automation of arraying small samples for XAS examination must be invented, automation of rapid data collection of multiple low-volume low-concentration samples must be developed, automation of data reduction and analysis must be perfected . Discussed here are the promises and the pitfalls of HTXAS development, including the results of initial feasibility experiments.

Genet Mol Res, 2004 Sep 30, 3(3), 323 - 41
The potential of virus-induced gene silencing for speeding up functional characterization of plant genes; Benedito VA et al.; Virus-induced gene silencing (VIGS) has been shown to be of great potential in plant reverse genetics . Advantages of VIGS over other approaches, such as T-DNA or transposon tagging, include the circumvention of plant transformation, methodological simplicity and robustness, and speedy results . These features make VIGS an attractive alternative instrument in functional genomics, even in a high throughput fashion . The system is already well established in Nicotiana benthamiana; however, efforts are being made to improve VIGS in other species, including monocots . Current research is focussed on unravelling the mechanisms of post-transcriptional gene silencing and VIGS, as well as on finding novel viral vectors in order to broaden the host species spectrum . We examined how VIGS has been used to assess gene functions in plants, including molecular mechanisms involved in the process, available methodological elements, such as vectors and inoculation procedures, and we looked for examples in which the system has been applied successfully to characterize gene function in plants.

Appl Microbiol Biotechnol . 2004 Dec 22; {Epub ahead of print}
Examination of fungal stress response genes using Saccharomyces cerevisiae as a model system: targeting genes affecting aflatoxin biosynthesis by Aspergillus flavus Link; Kim JH et al.; Saccharomyces cerevisiae served as a model fungal system to examine functional genomics of oxidative stress responses and reactions to test antioxidant compounds . Twenty-two strains of S . cerevisiae, including a broad spectrum of singular gene deletion mutants, were exposed to hydrogen peroxide (H(2)O(2)) to examine phenotypic response to oxidative stress . Responses of particular mutants treated with gallic, tannic or caffeic acids, or methyl gallate, during H(2)O(2) exposure, indicated that these compounds alleviated oxidative stress . These compounds are also potent inhibitors of aflatoxin biosynthesis in Aspergillus flavus . To gain further insights into a potential link between oxidative stress and aflatoxin biosynthesis, 43 orthologs of S . cerevisiae genes involved in gene regulation, signal transduction (e.g., SHO1, HOG1, etc.) and antioxidation (e.g., CTT1, CTA1, etc.) were identified in an A . flavus expressed sequence tag library . A successful exemplary functional complementation of an antioxidative stress gene from A . flavus, mitochondrial superoxide dismutase (sodA), in a sod2Delta yeast mutant further supported the potential of S . cerevisiae deletion mutants to serve as a model system to study A . flavus . Use of this system to further examine functional genomics of oxidative stress in aflatoxigenesis and reduction of aflatoxin biosynthesis by antioxidants is discussed.

J Vet Sci, 2004 Dec, 5(4), 279 - 88
Application of biotechnological tools for coccidia vaccine development; Min W et al.; Coccidiosis is a ubiquitous intestinal protozoan infection of poultry seriously impairing the growth and feed utilization of infected animals . Conventional disease control strategies have relied on prophylactic medication . Due to the continual emergence of drug resistant parasites in the field and increasing incidence of broiler condemnations due to coccidia, novel approaches are urgently needed to reduce economic losses . Understanding the basic biology of host-parasite interactions and protective intestinal immune mechanisms, as well as characterization of host and parasite genes and proteins involved in eliciting protective host responses are crucial for the development of new control strategy . This review will highlight recent developments in coccidiosis research with special emphasis on the utilization of cutting edge techniques in molecular/cell biology, immunology, and functional genomics in coccidia vaccine development . The information will enhance our understanding of host-parasite biology, mucosal immunology, and host and parasite genomics in the development of a practical and effective control strategy against Eimeria and design of nutritional interventions to maximize growth under the stress caused by vaccination or infection . Furthermore, successful identification of quantitative economic traits associated with disease resistance to coccidiosis will provide poultry breeders with a novel selection strategy for development of genetically stable, coccidiosis-resistant chickens, thereby increasing the production efficiency.

Bioinformatics . 2004 Dec 21; {Epub ahead of print}
GMD@CSB.DB: the Golm metabolome database; Kopka J et al.; SUMMARY: Metabolomics, in particular gas chromatography - mass spectrometry (GC-MS) based metabolite profiling of biological extracts, is rapidly becoming one of the cornerstones of functional genomics and systems biology . Metabolite profiling has profound applications in discovering the mode of action of drugs or herbicides and in unravelling the effect of altered gene expression on metabolism and organism performance in biotechnological applications . As such the technology needs to be available to many laboratories . For this, an open exchange of information is required, like that already achieved for transcript and protein data . One of the key-steps in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations from biological samples . Collections of mass spectra, which comprise frequently observed metabolites of either known or unknown exact chemical structure, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world . Here we present GMD - The Golm Metabolome Database, an open access metabolome database, which should enable these processes . GMD provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g . regarding to methods, spectral information or compounds . The main goal will be the representation of an exchange platform for experimental research activities and bioinformatics to develop and improve metabolomics by multidisciplinary cooperation . AVAILABILITY: http://csbdb.mpimp-golm.mpg.de/gmd.html.

Mech Ageing Dev, 2005 Jan, 126(1), 153 - 9
Genomic technologies and the interrogation of the transcriptome; Liu ET; Functional genomics refers to the study of whole genomes and the function of its constituent parts to explain biological processes . Though these investigations may involve whole proteome analysis, the primary focus is on the transcriptome and how it is regulated . Recent advances in technologies that can interrogate cellular transcripts on a genome-wide scale seek the complete disclosure of the transcriptome over time-intervals and across many different cellular states . This massively complex data when viewed as a whole can provide surprisingly precise assessment of cellular conditions . Moreover, these data can define hierarchies of importance and have shown us new transcriptional elements . Herein, we describe the technologies and the experimental strategies to study the transcriptome that would be pertinent to cancer and ageing research.

Mech Ageing Dev, 2005 Jan, 126(1), 87 - 97
Genetic regulation of thymic involution; Hsu HC et al.; In this review, we have summarized our work using combined complex statistical genetics, bioinformatics, and functional genomics to determine the genetic basis of the age-related thymic involution in C57BL/6J X DBA/2J recombinant inbred mice and the parental B6 and D2 mice . We have shown that these mice provided a valuable genetic model that can permit resampling of thymuses from different aged but genetically identical animals and determination of the relative significance of age-associated changes in the thymus . Our results suggest that the quantitative trait loci (QTL) regulating the Con A-induced thymocyte proliferative response were mapped to mouse chromosome Chr 11 (D11Mit51 at 18cM), a region that harbors the IL-12b gene . The importance of IL-12b in maintaining thymic integrity and function during the aging process was confirmed by a more rapid involution of the thymus in IL-12b knockout (IL-12b(-/-)) mice compared to wild-type (WT) mice . Functionally, IL-12 provided a strong synergistic effect to augment the IL-7 or IL-2 induced thymocyte proliferative response, especially in both aged WT and IL-12b(-/-) mice, but not in normal young mice . In contract to the proliferative response, the age-related decline in the total number of thymocytes was determined at different age, and mapped to loci on Chr 9, 62cM and Chr 10, 32cM . Using matrix-assisted laser desorption/ionisation-time of flight-mass spectrometry (MALDI-TOF-MS), increased expression of peroxiredoxin was found to be correlated with thymic involution. , , . Our results suggest the possibility to identify the complex molecular network that can be associated with the regulation of thymic involution in aged mice using a high-dimensional functional genomics approach.

Mech Ageing Dev, 2005 Jan, 126(1), 43 - 9
Diverse aging rates in metazoans: targets for functional genomics; Austad SN; Aging, or senescence, has typically been measured by demographic analysis, which has its merits but is blind to key aspects of functional development and deterioration . If one uses demographic analyses, however, the approach providing most insight is the analysis of age-specific mortality . The continuing increase in DNA sequencing power combined with emerging computational techniques will allow in the near future detailed investigation of mechanisms of aging in diverse species beyond the typical laboratory bestiary . A comparative approach of this sort needs to consider, in addition to simple longevity, the effects of phylogeny and body size on the species in question . Insight may be gained from the study of species exhibiting accelerated aging relative to more "typical" species . These naturally short-lived species, such as several small shrews and marsupials, avoid the worry inherent in "accelerated aging" genotypes of common models, which is that they are only short-lived because of some idiosyncratic pathology unrelated to general aging . A case of special interest that has yet to be seriously investigated is the domestic dog, in which selective breeding has produced phenotypes within the same species that age at two-fold different rates . Exceptionally long-lived species offer exceptional opportunities to discover whether there are few or many ways to create long-lived organisms . Slow-aging species with the most to offer include bats and naked mole-rats . Perhaps no fundamental question in biology is more intriguing that why and how nature has produced such a dazzling array of aging rates . The development of functional genetics over the next several decades promises to lead us toward an answer.

BMC Genomics . 2004 Dec 20;5(1):96 {Epub ahead of print}
FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression; Paschall JE et al.; BACKGROUND: While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research . Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species . This type of systems-level analysis is critical to the understanding of patterns of gene expression that underlie biological processes . RESULTS: We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus . Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses . Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly . An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized . In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism . CONCLUSION: The methods described have application for functional genomics studies, particularly among non-model organisms . The web interface for FunnyBase can be accessed at Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.

Plant J, 2005 Jan, 41(1), 56 - 67
Functional genomics uncovers three glucosyltransferases involved in the synthesis of the major sweet glucosides of Stevia rebaudiana; Richman A et al.; Summary Stevia rebaudiana leaves accumulate a mixture of at least eight different steviol glycosides . The pattern of glycosylation heavily influences the taste perception of these intensely sweet compounds . The majority of the glycosides are formed by four glucosylation reactions that start with steviol and end with rebaudioside A . The steps involve the addition of glucose to the C-13 hydroxyl of steviol, the transfer of glucose to the C-2' and C-3' of the 13-O-glucose and the addition of glucose to the hydroxyl of the C-4 carboxyl group . We used our collection of ESTs, an UDP-glucosyltransferase (UGT)-specific electronic probe and key word searches to identify candidate genes resident in our collection . Fifty-four expressed sequence tags (ESTs) belonging to 17 clusters were found using this procedure . We isolated full length cDNAs for 12 of the UGTs, cloned them into an expression vector, and produced recombinant enzymes in Escherichia coli . An in vitro glucosyltransferase activity enzyme assay was conducted using quercetin, kaempferol, steviol, steviolmonoside, steviolbioside, and stevioside as sugar acceptors, and (14)C-UDP-glucose as the donor . Thin layer chromatography was used to separate the products and three of the recombinant enzymes produced labelled products that co-migrated with known standards . HPLC and LC-ES/MS were then used to further define those reaction products . We determined that steviol UGTs behave in a regioselective manner and propose a modified pathway for the synthesis of rebaudioside A from steviol.

Nucleic Acids Res, 2005 Jan 1, 33 Database Issue, D59 - 66
HOPPSIGEN: a database of human and mouse processed pseudogenes; Adel K et al.; Processed pseudogenes result from reverse transcribed mRNAs . In general, because processed pseudogenes lack promoters, they are no longer functional from the moment they are inserted into the genome . Subsequently, they freely accumulate substitutions, insertions and deletions . Moreover, the ancestral structure of processed pseudogenes could be easily inferred using the sequence of their functional homologous genes . Owing to these characteristics, processed pseudogenes represent good neutral markers for studying genome evolution . Recently, there is an increasing interest for these markers, particularly to help gene prediction in the field of genome annotation, functional genomics and genome evolution analysis (patterns of substitution) . For these reasons, we have developed a method to annotate processed pseudogenes in complete genomes . To make them useful to different fields of research, we stored them in a nucleic acid database after having annotated them . In this work, we screened both mouse and human complete genomes from ENSEMBL to find processed pseudogenes generated from functional genes with introns . We used a conservative method to detect processed pseudogenes in order to minimize the rate of false positive sequences . Within processed pseudogenes, some are still having a conserved open reading frame and some have overlapping gene locations . We designated as retroelements all reverse transcribed sequences and more strictly, we designated as processed pseudogenes, all retroelements not falling in the two former categories (having a conserved open reading or overlapping gene locations) . We annotated 5823 retroelements (5206 processed pseudogenes) in the human genome and 3934 (3428 processed pseudogenes) in the mouse genome . Compared to previous estimations, the total number of processed pseudogenes was underestimated but the aim of this procedure was to generate a high-quality dataset . To facilitate the use of processed pseudogenes in studying genome structure and evolution, DNA sequences from processed pseudogenes, and their functional reverse transcribed homologs, are now stored in a nucleic acid database, HOPPSIGEN . HOPPSIGEN can be browsed on the PBIL (Pole Bioinformatique Lyonnais) World Wide Web server or fully downloaded for local installation.

Nucleic Acids Res, 2005 Jan 1, 33 Database Issue, D108 - 11
HuSiDa--the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells; Truss M et al.; Small interfering RNAs (siRNAs) have become a standard tool in functional genomics . Once incorporated into the RNA-induced silencing complex (RISC), siRNAs mediate the specific recognition of corresponding target mRNAs and their cleavage . However, only a small fraction of randomly chosen siRNA sequences is able to induce efficient gene silencing . In common laboratory practice, successful RNA interference experiments typically require both, the labour and cost-intensive identification of an active siRNA sequence and the optimization of target cell line-specific procedures for optimal siRNA delivery . To optimize the design and performance of siRNA experiments, we have established the human siRNA database (HuSiDa) . The database provides sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments, including the mode of siRNA generation, recipient cell lines, transfection reagents and procedures and direct links to published references (PubMed) . The database can be accessed at We used the siRNA sequence information stored in the database for scrutinizing published sequence selection parameters for efficient gene silencing.

Plant Mol Biol, 2004 Oct, 56(3), 465 - 80
Comparative map and trait viewer (CMTV): an integrated bioinformatic tool to construct consensus maps and compare QTL and functional genomics data across genomes and experiments; Sawkins MC et al.; In the past few decades, a wealth of genomic data has been produced in a wide variety of species using a diverse array of functional and molecular marker approaches . In order to unlock the full potential of the information contained in these independent experiments, researchers need efficient and intuitive means to identify common genomic regions and genes involved in the expression of target phenotypic traits across diverse conditions . To address this need, we have developed a Comparative Map and Trait Viewer (CMTV) tool that can be used to construct dynamic aggregations of a variety of types of genomic datasets . By algorithmically determining correspondences between sets of objects on multiple genomic maps, the CMTV can display syntenic regions across taxa, combine maps from separate experiments into a consensus map, or project data from different maps into a common coordinate framework using dynamic coordinate translations between source and target maps . We present a case study that illustrates the utility of the tool for managing large and varied datasets by integrating data collected by CIMMYT in maize drought tolerance research with data from public sources . This example will focus on one of the visualization features for Quantitative Trait Locus (QTL) data, using likelihood ratio (LR) files produced by generic QTL analysis software and displaying the data in a unique visual manner across different combinations of traits, environments and crosses. , , , . Once a genomic region of interest has been identified, the CMTV can search and display additional QTLs meeting a particular threshold for that region, or other functional data such as sets of differentially expressed genes located in the region; it thus provides an easily used means for organizing and manipulating data sets that have been dynamically integrated under the focus of the researcher's specific hypothesis.

Plant Mol Biol, 2004 Sep, 56(2), 255 - 70
MYB transcription factors are differentially expressed and regulated during secondary vascular tissue development in hybrid aspen; Karpinska B et al.; More than 120,000 poplar ESTs have been sequenced from 20 different cDNA libraries by the Swedish Centre for Tree Functional Genomics . We screened this EST collection for MYB transcription factors involved in secondary vascular tissue formation, and genes assigned as PttMYB3Ra, PttMYB4a and PttMYB21a were selected for further characterisation . Three MYB genes showed different expression patterns in various organs, tissues and stem sub-sections representing different developmental stages of vascular tissue formation . Furthermore, the analysis showed that PttMYB21a expression was much higher in secondary cell wall formation zone of xylem and phloem fibers than in other developmental zones . Transgenic hybrid aspen plants, expressing the 3'-part of the PttMYB21a gene in antisense orientation were generated to assess the function of PttMYB21a gene in vascular tissue formation and lignification . All transgenic lines showed reduced growth and had fewer internodes compared to the wild-type . The analysis of selected lines showed that acid soluble lignin present in the bark was higher in transgenic lines as compared to wild-type plants . Moreover a higher transcript level of caffeoyl-CoA 3-O-methyltransferase {CCoAOMT}; EC 2.1.1.104) was found in the phloem of the transgenic plants, suggesting that PttMYB21a might function as a transcriptional repressor.

Plant Mol Biol, 2004 May, 55(2), 263 - 80
Identification of genes preferentially expressed during wood formation in Eucalyptus; Paux E et al.; Wood is the most abundant biological resource on earth and it is also an important raw material for a major global industry with rapidly increasing demand . The genus Eucalyptus includes the most widely used tree species for industrial plantation, mainly for making pulp and paper . With the aim of identifying major genes involved in wood formation in Eucalyptus , we have developed a targeted approach of functional genomics based on the isolation of xylem preferentially expressed genes by subtractive PCR . Transcript profiling using cDNA arrays and analysis of variance (ANOVA) were used to identify differentially expressed ESTs between secondary xylem and leaves . Real-time RT-PCR was performed to confirm the differential expression of representative EST . Of 224 independent EST sequences obtained, 81% were preferentially expressed in xylem . One-third of the ESTs exhibiting homologies with proteins of known function fell into two main classes highlighting the importance of the auxin signalling through ubiquitin-dependent proteolysis on one hand, and of the enzymes involved in cell wall biosynthesis and remodelling, on the other . The functions of the genes represented by the remaining 61% of ESTs should be of great interest for future research . This systematic analysis of genes involved in wood formation in Eucalyptus provides valuable insights into the molecular mechanisms involved in secondary xylem differentiation as well as new candidate-genes for wood quality improvement.

Plant Mol Biol, 2004 Apr, 54(6), 911 - 29
Functional genomics of cell elongation in developing cotton fibers; Arpat AB et al.; Cotton fibers are single-celled seed trichomes of major economic importance . Factors that regulate the rate and duration of cell expansion control fiber morphology and important agronomic traits . For genetic characterization of rapid cell elongation in cotton fibers, approximately 14,000 unique genes were assembled from 46,603 expressed sequence tags (ESTs) from developmentally staged fiber cDNAs of a cultivated diploid species ( Gossypium arboreum L.) . Conservatively, the fiber transcriptome represents 35-40% of the genes in the cotton genome . In silico expression analysis revealed that rapidly elongating fiber cells exhibit significant metabolic activity, with the bulk of gene transcripts, represented by three major functional groups - cell wall structure and biogenesis, the cytoskeleton and energy/carbohydrate metabolism . Oligonucleotide microarrays revealed dynamic changes in gene expression between primary and secondary cell wall biogenesis showing that fiber genes in the dbEST are highly stage-specific for cell expansion - a conclusion supported by the absence of known secondary cell wall-specific genes from our fiber dbEST . During the developmental switch from primary to secondary cell wall syntheses, 2553 "expansion-associated" fiber genes are significantly down regulated . Genes (81) significantly up-regulated during secondary cell wall synthesis are involved in cell wall biogenesis and energy/carbohydrate metabolism, which is consistent with the stage of cellulose synthesis during secondary cell wall modification in developing fibers . This work provides the first in-depth view of the genetic complexity of the transcriptome of an expanding cell, and lays the groundwork for studying fundamental biological processes in plant biology with applications in agricultural biotechnology.

Curr Opin Drug Discov Devel, 2004 Mar, 7(2), 179 - 87
Antisense and RNA interference approaches to target validation in pain research; Kurreck J; In recent years numerous potential new targets for the development of novel drugs to treat chronic pain have been identified . Antisense strategies provide a straightforward approach to validate and further analyze their function . Furthermore, they offer the possibility of investigating a single member of a closely related family of proteins that cannot be easily targeted using small-molecule pharmacological tools . The recent discovery that short double-stranded RNA molecules can be employed to induce RNA interference in mammalian systems has opened exciting new roads for functional genomics . Gene silencing by small interfering RNAs has been demonstrated in neurons, and several targets involved in pain perception have been addressed . Furthermore, promising in vivo results have recently been obtained with small interfering RNAs.

Alcohol Clin Exp Res, 2004 Oct, 28(10), 1437 - 48
On the integration of alcohol-related quantitative trait loci and gene expression analyses; Hitzemann R et al.; BACKGROUND: Quantitative trait loci (QTLs) have been detected for a wide variety of ethanol-related phenotypes, including acute and chronic ethanol withdrawal, acute locomotor activation, and ethanol preference . This study was undertaken to determine whether the process of moving from QTL to quantitative trait gene (QTG) could be accelerated by the integration of functional genomics (gene expression) into the analysis strategy . METHODS: Six ethanol-related QTLs, all detected in C57BL/6J and DBA/2J intercrosses were entered into the analysis . Each of the QTLs had been confirmed in independent genetic models at least once; the cumulative probabilities for QTL existence ranged from 10 to 10 . Brain gene expression data for the C57BL/6 and DBA/2 strains (n = 6 per strain) and an F2 intercross sample (n = 56) derived from these strains were obtained by using the Affymetrix U74Av2 and 430A arrays; additional data with the U74Av2 array were available for the extended amygdala, dorsomedial striatum, and hippocampus . Low-level analysis was performed by using multiple methods to determine the likelihood that a transcript was truly differentially expressed . For the 430A array data, the F2 sample was used to determine which of the differentially expressed transcripts within the QTL intervals were cis-regulated and, thus, strong candidates for QTGs . RESULTS: Within the 6 QTL intervals, 39 transcripts (430A array) were identified as being highly likely to be differentially expressed between the C57BL/6 and DBA/2 strains at a false discovery rate of 0.01 or better . Twenty-eight of these transcripts showed significant (logarithm of odds > or =3.6) to highly significant (logarithm of odds >7) cis-regulation . The process correctly detected Mpdz (chromosome 4) as a candidate QTG for acute withdrawal . CONCLUSIONS: Although improvements are needed in the expression databases, the integration of QTL and gene expression analyses seems to have potential as a high-throughput strategy for moving from QTL to QTG.

J Exp Bot, 2005 Jan, 56(410), 287 - 96 Epub 2004 Dec 13.
Application of metabolite profiling to the identification of traits in a population of tomato introgression lines; Overy SA et al.; Naturally occurring variation in wild species can be used to increase the genetic diversity of cultivated crops and improve agronomic value . Populations of introgression lines carrying wild species alleles afford an opportunity to identify traits associated with the introgressed regions, and facilitate characterization of the biochemistry and genetics underlying these phenotypes . Understanding plant metabolic pathways and the interactions between genes, phenotype, and environment is fundamental to functional genomics . Successful analysis of the complex network of plant metabolism requires analytical methods able to record information on as many metabolites as possible . Metabolite profiling is used to provide a snapshot of the metabolome in samples which differ in a known factor such as genetic background . Differences between the metabolite profiles can identify those metabolites/metabolic pathways affected by the introgression and allow genetic maps for metabolic alterations to be established . A Time-of-Flight Mass Spectrometry method is presented, with associated data reduction, used for profiling aqueous metabolites fom tomato . Analysis of ripe fruits of two tomato species, Lycopersicon esculentum and L . pennellii, showed differences in the amounts of many metabolites, including organic acids and sugars . Six introgression lines, L . pennellii introgressions within L . esculentum, were also examined and showed that Principal Component Analysis can reveal subtle differences in metabolism of the introgressed lines when compared to their parents.

Alzheimer Dis Assoc Disord, 2004 Oct, 18(4), 264 - 269
Expression Profiling and Pharmacotherapeutic Development in the Central Nervous System; Galvin JE et al.; Expression profiling data is available for many diverse tissues throughout the body, allowing for exciting hypothesis testing of critical concepts such as cellular development, differentiation, normative function, and disease pathogenesis . The central nervous system is an ideal structure to evaluate relationships between functional genomics and expression data . Recent developments in gene array technologies, specifically cDNA microarray platforms, have made it easier to try to understand the multiplicity of gene alterations that occur within the brains of animal models and postmortem human tissues . However, unlike structures have one principal cell type, the brain contains diverse populations of phenotypically distinct cell types . A goal of modern molecular and cellular neuroscience is to assay gene expression from homogeneous populations of cells within a defined region without potential contamination by expression profiles of adjacent neuronal subtypes and non-neuronal cells . This is a difficult task that demands a multidisciplinary approach that is highlighted in this review within the context of neurodegenerative pathology.

Bioinformatics . 2004 Dec 10; {Epub ahead of print}
Highly specific and accurate selection of siRNAs for high-throughput functional assays; Santoyo J et al.; MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes . The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of software capable of the high-throughput design of highly specific siRNA . The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity . Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs . RESULT: Here we present a program that for the first time completely automates the search for siRNAs . In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method . After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, that can cause cross-hybridisation, are checked in databases containing a unique entry for each gene . These truly non-redundant databases are constructed from the genome annotations (Ensembl) . Also intron/exon boundaries, presence of polymorphisms (SNPs), specificity for either gene or transcript, and other features can selected to be considered in the design of siRNAs . AVAILABILITY: The program is available as a web server in: The program was written under the GPL license.

Curr Biol, 2004 Dec 14, 14(23), R1014 - 27
How cells coordinate growth and division; Jorgensen P et al.; Size is a fundamental attribute impacting cellular design, fitness, and function . Size homeostasis requires a doubling of cell mass with each division . In yeast, division is delayed until a critical size has been achieved . In metazoans, cell cycles can be actively coupled to growth, but in certain cell types extracellular signals may independently induce growth and division . Despite a long history of study, the fascinating mechanisms that control cell size have resisted molecular genetic insight . Recently, genetic screens in Drosophila and functional genomics approaches in yeast have macheted into the thicket of cell size control.

J Biol . 2004;3(5):21 . Epub 2004 Dec 06.
The functional landscape of mouse gene expression; Zhang W et al.; BACKGROUND: Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast . Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function . RESULTS: We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays . We show that quantitative transcriptional co-expression is a powerful predictor of gene function . Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin . In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories . As an example, the highly conserved mouse gene PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis. , , , . CONCLUSIONS: We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated . Our data and analyses provide a public resource for mammalian functional genomics.

C R Biol, 2004 Sep-Oct, 327(9-10), 889 - 901
Lignification and tension wood; Pilate G et al.; Hardwood trees are able to reorient their axes owing to tension wood differentiation . Tension wood is characterised by important ultrastructural modifications, such as the occurrence in a number of species, of an extra secondary wall layer, named gelatinous layer or G-layer, mainly constituted of cellulose microfibrils oriented nearly parallel to the fibre axis . This G-layer appears directly involved in the definition of tension wood mechanical properties . This review gathers the data available in the literature about lignification during tension wood formation . Potential roles for lignin in tension wood formation are inferred from biochemical, anatomical and mechanical studies, from the hypotheses proposed to describe tension wood function and from data coming from new research areas such as functional genomics.

Pac Symp Biocomput . 2000;:443-54.
In silico analysis of gene expression patterns during early development of Xenopus laevis; Pollet N et al.; The information as to where and when a mRNA is present in a given cell is essential to bridge the gap between the DNA sequence of a gene and its physiological function . Therefore, a major component of functional genomics is to characterize the levels and the spatio-temporal domains of gene expression . Currently, there is just a few specialised public databases available storing the data on gene expression while they are needed as a resource for the field . Moreover, there is a need to develop and assess computational tools to compare and analyse expression profiles in a suitable way for biological interpretation . Here we describe our recent work on developing a database on gene expression for the frog Xenopus laevis, and on setting up and using new tools for the analysis and comparison of gene expression patterns . We used histogram clustering to compare expression profiles at both gene and tissue levels using a set of data coming from the characterization of the expression of genes during early development of Xenopus . This enabled us to draw a tree of tissue relatedness and to identify coexpressed genes by in silico analysis.

Yeast, 2000 Jun 30, 17(2), 159 - 66
Current awareness; Drysdale R et al.; In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics . Each bibliography is divided into 16 sections . 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics . Within each section, articles are listed in alphabetical order with respect to author . If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted

Proc Natl Acad Sci U S A, 2000 Jul 18, 97(15), 8566 - 71
Identification of eIF2Bgamma and eIF2gamma as cofactors of hepatitis C virus internal ribosome entry site-mediated translation using a functional genomics approach; Kruger M et al.; The 5'-untranslated region of hepatitis C virus (HCV) is highly conserved, folds into a complex secondary structure, and functions as an internal ribosome entry site (IRES) to initiate translation of HCV proteins . We have developed a selection system based on a randomized hairpin ribozyme gene library to identify cellular factors involved in HCV IRES function . A retroviral vector ribozyme library with randomized target recognition sequences was introduced into HeLa cells, stably expressing a bicistronic construct encoding the hygromycin B phosphotransferase gene and the herpes simplex virus thymidine kinase gene (HSV-tk) . Translation of the HSV-tk gene was mediated by the HCV IRES . Cells expressing ribozymes that inhibit HCV IRES-mediated translation of HSV-tk were selected via their resistance to both ganciclovir and hygromycin B . Two ribozymes reproducibly conferred the ganciclovir-resistant phenotype and were shown to inhibit IRES-mediated translation of HCV core protein but did not inhibit cap-dependent protein translation or cell growth . The functional targets of these ribozymes were identified as the gamma subunits of human eukaryotic initiation factors 2B (eIF2Bgamma) and 2 (eIF2gamma), respectively . The involvement of eIF2Bgamma and eIF2gamma in HCV IRES-mediated translation was further validated by ribozymes directed against additional sites within the mRNAs of these genes . In addition to leading to the identification of cellular IRES cofactors, ribozymes obtained from this cellular selection system could be directly used to specifically inhibit HCV viral translation, thereby facilitating the development of new antiviral strategies for HCV infection.

Electrophoresis, 2000 Jun, 21(11), 2099 - 104
Proteomics: applications and opportunities in preclinical drug development; Steiner S et al.; Advances in DNA sequencing and the near-term availability of whole genome sequences for several pharmaceutically relevant organisms promise to dramatically alter the breadth and scale of high-throughput proteomic studies . The substantial amount of literature is available in the public domain, demonstrate the potential of proteomics in the preclinical phases of pharmaceutical development . Over the next few years, it is anticipated that functional genomics and proteomics will have major impacts on the clinical phases of drug development . Expected benefits are earlier proof-of-concept studies in man and increased efficiency of clinical trials through the availability of biologically relevant markers for drug efficacy and safety.

Bioseparation, 2000, 9(2), 59 - 67
Short cut of protein purification by integration of cell-disrupture and affinity extraction; Schuster M et al.; Screening strategies based on functional genomics require the isolation of gene products of several hundred cDNA clones in a fast and versatile manner . Conventional purification strategies will fail to accomplish this goal within a reasonable time frame . In order to short-cut these procedures, we have developed a combination of cell disintegration and affinity technique for rapid isolation and purification . For our purpose, tagged proteins have been produced in yeast by fusing the FLAG-sequence adjacent to the 5' end of cDNAs coding for the respective protein . The example of an over-expressed FLAG-tagged fusion protein, human serum albumin (HSA), was released into the cytoplasm . Detection and purification of the FLAG-fusion protein were carried out by using a mouse monoclonal antibody directed against the FLAG-peptide . For purification purposes, the antibody was immobilized on PROSEP magnetic glass beads . These magnetic glass beads with 500 microns diameter have been investigated for disintegration of yeast and simultaneous capturing of the target protein . After 60 s, 90% of the maximal disintegration level was achieved when a ratio of 20 microliters yeast cell suspension and 100 microliters glass are vortexed . After a wash step, the FLAG-fusion proteins have been eluted with chelating agents such as EDTA . The short-cut procedure has been compared to a conventional purification strategy using an affinity chromatography process . Due to the highly favorable binding characteristics of the applied immunoaffinity sorbent the yield observed in batch operation was 90% and purity in the range of 70-80%.

Plant J, 2000 Jun, 22(6), 561 - 70
T-DNA insertional mutagenesis for functional genomics in rice; Jeon JS et al.; We have produced 22 090 primary transgenic rice plants that carry a T-DNA insertion, which has resulted in 18 358 fertile lines . Genomic DNA gel-blot and PCR analyses have shown that approximately 65% of the population contains more than one copy of the inserted T-DNA . Hygromycin resistance tests revealed that transgenic plants contain an average of 1.4 loci of T-DNA inserts . Therefore, it can be estimated that approximately 25 700 taggings have been generated . The binary vector used in the insertion contained the promoterless beta-glucuronidase (GUS) reporter gene with an intron and multiple splicing donors and acceptors immediately next to the right border . Therefore, this gene trap vector is able to detect a gene fusion between GUS and an endogenous gene, which is tagged by T-DNA . Histochemical GUS assays were carried out in the leaves and roots from 5353 lines, mature flowers from 7026 lines, and developing seeds from 1948 lines . The data revealed that 1.6-2.1% of tested organs were GUS-positive in the tested organs, and that their GUS expression patterns were organ- or tissue-specific or ubiquitous in all parts of the plant . The large population of T-DNA-tagged lines will be useful for identifying insertional mutants in various genes and for discovering new genes in rice.

Scand J Work Environ Health, 1999 Dec, 25(6), 537 - 40
Progress and potential of genetic susceptibility to environmental toxicants; Haugen A; Gene-environment interactions are thought to be critical for such multifactorial diseases as cancer, diabetes, heart disease, asthma, and some neurological disorders . The genetic constitution of an individual (genotype) may influence the risk of disease of a person exposed to environmental or occupational insults . Major advances will occur in the coming years with respect to the identification of the genetic and molecular causes of susceptibility to common diseases . In these studies microarrays and chip technology are rapidly becoming central in the detection of mutations and polymorphisms and in functional genomics . These rapid advances in genetics present new and complex ethical issues for both the individual and society.

Biotechnol Annu Rev, 2000, 5, 45 - 86
Functional genomics with protein-protein interactions; Rudert F et al.; Knowing the sequence of a gene does not mean knowing its function . Although, information stored at the DNA level can be used to predict biological processes, proteins are the final executors of the various response programs of a cell . Transient information, like posttranslational modifications or interactions among proteins, cannot be deduced from DNA sequences . The rapid accumulation of large amounts of DNA sequence data in genomics projects has led to an increasing demand for powerful tools to analyze proteins and their behaviour at a large scale . This review aims to compare different technologies used for identification of interacting proteins and discusses recent developments in the field of high-throughput protein-protein interaction mapping.

Parasitology, 2000, 120 Suppl, S43 - 61
Development of vaccines against gastrointestinal nematodes; Knox DP; Vaccination against complex metazoan parasites has become a reality with the development and registration of recombinant protein-based vaccines against the cattle tick Boophilus microplus and the sheep cestode Taenia ovis . Progress towards the development of similar vaccines against gastrointestinal nematodes, primarily of ruminants, is outlined within a framework of defining the practical requirements for successful vaccination, antigen selection, recombinant protein production and antigen delivery, be it mucosal delivery or DNA vaccination . Antigen selection strategies include the fractionation of complex, but protective, parasite extracts, the use of antibody probes, evaluation of excretory-secretory components and gut-expressed hidden antigens as well as antigens targeted on the basis of function such as enzyme activity . The difficulties being encountered in recombinant protein production and their solution are discussed as are the requirements for successful antigen delivery . Recent technological developments such as the use of functional genomics to identify new vaccine candidates and DNA vaccination to present the selected antigen to the host immune system are discussed and are anticipated to have a profound effect on vaccine development in the future.

Nucleic Acids Res, 2000 Jul 1, 28(13), 2605 - 12
A novel functional genomics approach identifies mTERT as a suppressor of fibroblast transformation; Li QX et al.; As a tool for functional genomics, a hairpin ribozyme gene library with randomized target recognition sequences was constructed in a retroviral vector . This library has the potential to target and cleave any possible RNA substrate . Mouse fibroblasts transduced with this ribozyme gene vector library were selected in a focus formation assay to isolate in vivo functional ribozymes that promote cell transformation in tissue culture . After two successive rounds of selection by focus formation assay, a transforming ribozyme (Rz007) was identified . The sequence of this ribozyme was used to identify the putative target genes responsible for the transformation . A candidate gene target for Rz007 encodes telomerase reverse transcriptase (mTERT) . Both mRNA level and enzymatic activity of mTERT were down-regulated in Rz007-transformed cells . Furthermore, newly designed ribozymes, recognizing other potential ribozyme cleavage sites unique to the mTERT mRNA, also cause cell transformation, thus validating the role of mTERT in suppressing the transformation phenotype . These surprising results suggest that the commonly accepted role of telomerase in maintaining cellular immortalization is more complicated than previously thought. , , , , . These studies also demonstrate the utility of this novel 'reverse' functional genomics approach, enabling the targeted discovery of genes, whether previously known or not, that are involved in any selectable phenotype.

Res Microbiol, 2000 Mar, 151(2), 121 - 8
Functional genomics of Escherichia coli in Japan; Mori H et al.; Completion of the genome sequence of the model bacterium Escherichia coli has produced nearly 2000 open reading frames (ORFs) that remain to be functionally characterized . To accomplish this goal, we have organized a working project team in Japan and have begun construction of clones containing each of the putative ORFs . The procedure has been conceived such that we shall be able to perform systematic analysis of the shut-off as well as forced expression in vivo of each ORF and purification of its protein product for further biochemical studies . In addition, we have started a collection of various genetic and biochemical data of E . coli published in the past, and analyses of the data from a bio-informatics point of view . Thus, we aim at reaching complete understanding of this model organism in the near future.

Res Microbiol, 2000 Mar, 151(2), 97 - 106
Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics; Benner SA et al.; If bioinformatics tools are constructed to reproduce the natural, evolutionary history of the biosphere, they offer powerful approaches to some of the most difficult tasks in genomics, including the organization and retrieval of sequence data, the updating of massive genomic databases, the detection of database error, the assignment of introns, the prediction of protein conformation from protein sequences, the detection of distant homologs, the assignment of function to open reading frames, the identification of biochemical pathways from genomic data, and the construction of a comprehensive model correlating the history of biomolecules with the history of planet Earth.

Prog Drug Res, 2000, 54, 213 - 56
Applications of developmental biology to medicine and animal agriculture; Smith RC et al.; With the complete sequence of the human genome expected by winter 2001, genomic-based drug discovery efforts of the pharmaceutical industry are focusing on finding the relatively few therapeutically useful genes from among the total gene set . Methods to rapidly elucidate gene function will have increasing value in these investigations . The use of model organisms in functional genomics has begun to be recognized and exploited and is one example of the emerging use of the tools of developmental biology in recent drug discovery efforts . The use of protein products expressed during embryo-genesis and the use of certain pluripotent cell populations (stem cells) as candidate therapeutics are other applications of developmental biology to the treatment of human diseases . These agents may be used to repair damaged or diseased tissues by inducing or directing developmental programs that recapitulate embryonic processes to replace specialized cells . The activation or silencing of embryonic genes in the disease state, particularly those encoding transcription factors, is another avenue of exploitation . Finally, the direct drug-induced manipulation of embryonic development is a unique application of developmental biology in animal agriculture.

Curr Opin Microbiol, 2000 Jun, 3(3), 309 - 15
Genome-wide mutant collections: toolboxes for functional genomics; Coelho PS et al.; The sequencing of entire genomes has led to the identification of many genes . A future challenge will be to determine the function of all of the genes of an organism . One of the best ways to ascertain function is to disrupt genes and determine the phenotype of the resulting organism . Novel large-scale approaches for generating gene disruptions and analyzing the resulting phenotype are underway in the budding yeast Saccharomyces cerevisiae and other organisms including flies, Mycoplasma, worms, plants and mice . These approaches and mutant collections will be extremely valuable to the scientific community and will dramatically alter the manner in which science is performed in the future.

Curr Opin Microbiol, 2000 Jun, 3(3), 298 - 302
Protein arrays for gene expression and molecular interaction screening; Walter G et al.; The array format has revolutionised biomedical experimentation and diagnostics, enabling ordered high-throughput analysis . During the past decade, classic solid phase substrates, such as microtitre plates, membrane filters and microscopic slides, were turned into high-density, chip-like structures . The concept of the arrayed library was central to this development which now extends from DNA to protein . The new and versatile protein array technology allows high-throughput screening for gene expression and molecular interactions . As a major platform for functional genomics, it is already on its way into medical diagnostics.

Curr Opin Microbiol, 2000 Jun, 3(3), 285 - 91
Monitoring gene expression using DNA microarrays; Harrington CA et al.; The concurrent development of high-density array technologies and the complete sequencing of a number of microbial genomes is providing the opportunity to comprehensively and efficiently survey the transcription profile of microorganisms under different conditions and well-defined genotypes . Microarray-based studies are uncovering broad patterns of genetic activity, providing new understanding of gene functions and, in some cases, generating unexpected insight into transcriptional processes and biological mechanisms . One topic that has come to the forefront is how best to effectively manage and interpret the large data sets being generated . Although progress has been made, this remains a challenging opportunity for functional genomics research.

Annu Rev Pharmacol Toxicol, 2000, 40, 177 - 91
Drug discovery in the next millennium; Ohlstein EH et al.; Selection and validation of novel molecular targets have become of paramount importance in light of the plethora of new potential therapeutic drug targets that have emerged from human gene sequencing . In response to this revolution within the pharmaceutical industry, the development of high-throughput methods in both biology and chemistry has been necessitated . This review addresses these technological advances as well as several new areas that have been created by necessity to deal with this new paradigm, such as bioinformatics, cheminformatics, and functional genomics . With many of these key components of future drug discovery now in place, it is possible to map out a critical path for this process that will be used into the new millennium.

Nat Biotechnol, 2000 Jun, 18(6), 609 - 13
Who's your neighbor? New computational approaches for functional genomics; Galperin MY et al.; Several recently developed computational approaches in comparative genomics go beyond sequence comparison . By analyzing phylogenetic profiles of protein families, domain fusions, gene adjacency in genomes, and expression patterns, these methods predict many functional interactions between proteins and help deduce specific functions for numerous proteins . Although some of the resultant predictions may not be highly specific, these developments herald a new era in genomics in which the benefits of comparative analysis of the rapidly growing collection of complete genomes will become increasingly obvious.

Am J Med Genet, 2000 Spring, 97(1), 12 - 7
Twin studies of schizophrenia: from bow-and-arrow concordances to star wars Mx and functional genomics; Cardno AG et al.; Twin studies have been vital for establishing an important genetic contribution to the etiology of schizophrenia . The five newest studies since 1995 from Europe and Japan have confirmed earlier findings . They yielded probandwise concordance rates of 41-65% in monozygotic (MZ) pairs and 0-28% in dizygotic (DZ) pairs, and heritability estimates of approximately 80-85% . Twin studies are also valuable for investigating the etiological relationships between schizophrenia and other disorders, and the genetic basis of clinical heterogeneity within schizophrenia . Studies of discordant MZ pairs provide further insights into non-inherited factors that contribute to the multifactorial etiology of this disorder . More recently, twin studies have begun to be used to directly investigate molecular genetic and epigenetic processes underlying schizophrenia .

Yeast, 2000 Apr, 17(1), 71 - 8
Current awareness on comparative and functional genomics {bibliography}; PROfusion: genetically tagged proteins for functional proteomics and beyond; Phylos, Inc., 128 Spring Street, Lexington, MA 02421, USAAs a new enabling technology in functional genomics, Phylos, Inc . has pioneered PROfusiontrade mark technology, whereby proteins are covalently tagged with their own genetic information (mRNA) . Using this technology, both synthetic and natural libraries (representing the repertoire of proteins naturally expressed in a given cell type or tissue source) have been constructed . Due to the in vitro nature of library construction, Phylos libraries are the largest described to date, up to 10(14) in size . From a library of such molecules, one can select for a protein function of choice with the benefit that the genetic material is linked to the protein for subsequent PCR amplification, enrichment, and, ultimately, identification .

Curr Pharm Des, 2000 Mar, 6(4), 379 - 92
Cell cycle molecular targets in novel anticancer drug discovery; Buolamwini JK; A number of potential molecular targets for novel anticancer drug discovery have been identified in cell cycle control mechanisms . Prominent among these are the regulatory proteins, cyclins and their effector counterparts the cyclin dependent kinases (CDKs) . Aberrant expression of these proteins, particularly cyclins involved in the G1 phase of the cell cycle, namely the D and E cyclins, has been associated with a variety of human cancers, including breast and colorectal cancer, B-lymphoma, prostate and non-small cell lung cancer . Inhibition of CDK kinase activity has turned out to be the most productive strategy for the discovery and design novel anticancer agents specifically targeting the cell cycle . Other potentially useful cell cycle areas for exploration include cyclin-CDK interactions, Cdc25 activation of cyclin-CDK complexes, ubiquitin-mediated proteolysis of cyclins, cell cycle check point kinases like Chk1, and recently identified oncogenic cell cycle-related aurora and polo-like kinases . Potent specific inhibitors have been identified that bind to the ATP site of CDKs, mainly cyclin B-CDK1, cyclin A-CDK2, and cyclin D-CDK4 complexes, and inhibit kinase activity . X-ray crystallographic data of CDKs, and their complexes with inhibitors have played a major role in the success of drug discovery efforts . Combinatorial chemistry, highthroughput screening, functional genomics and informatics have also contributed . CDK inhibitors currently under investigation include flavopiridol, olomoucine, roscovitine, puvalanol B, the dihydroindolo{3,2-d}{1}benzazepinone kenpaullone, indirubin-3 -monoxime and novel diaminothiazoles such as AG12275 . The anticancer therapeutic potential of CDK inhibitors has been demonstrated in preclinical studies, and Phases I and II clinical trials in cancer patients are currently underway.

Electrophoresis, 2000 Apr, 21(6), 1164 - 77
Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry; Merchant M et al.; The overall history and recent advances in surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) technology is reviewed herein . Fundamentals of SELDI-TOF analysis are presented while drawing comparisons with other laser-based mass spectrometry techniques . The application of SELDI-TOF-MS to functional genomics and biomarker discovery is discussed and exemplified by elucidating a biomarker candidate for prostatic carcinoma . Finally, a short discussion regarding future SELDI requirements and developments is supplied.

Genome Res, 2000 Apr, 10(4), 431 - 45
Systematic management and analysis of yeast gene expression data; Aach J et al.; We report steps toward the systematic management, standardization, and analysis of functional genomics data . We developed the ExpressDB database for yeast RNA expression data and loaded it with approximately 17.5 million pieces of data reported by 11 studies with three different kinds of high-throughput RNA assays . A web-based tool supports queries across the data from these studies . We examined comparability of data by converting data from 9 studies (217 conditions) into mRNA relative abundance estimates (ERAs) and by clustering of conditions by ERAs . We report on generation of ERAs and condition clustering for non-microarray data (5 studies, 63 conditions) and describe initial attempts to generate microarray-based ERAs (4 studies, 154 conditions), which exhibit increased error, on our web site edu/ExpressDB . We recommend standards for data reporting, suggest research into improving comparability of microarray data through quantifying and standardizing control condition RNA populations, and also suggest research into the calibration of different RNA assays . We introduce a model for a database that integrates different kinds of functional genomics data, Biomolecule Interaction, Growth and Expression Database (BIGED).

Transgenic Res, 1999, 8(6), 451 - 8
Gene trap insertional mutagenesis in mice: new vectors and germ line mutations in two novel genes; Neilan EG et al.; Insertional mutagenesis based on gene trap vectors that capture endogenous splice sites is a promising tool for functional genomics . Several groups have proposed large-scale gene trap screens, but questions remain as to the type of vectors and their design . We report a set of plasmid-encoded gene trap vectors and the disruption of two novel genes . Our results include a comparison of the relative gene trapping efficiencies of two different splice acceptor sequences in ES cells and an analysis of the structure of several gene trap insertions.

Nature, 2000 Apr 6, 404(6778), 644 - 51
Genetics of body-weight regulation; Barsh GS et al.; The role of genetics in obesity is twofold . Studying rare mutations in humans and model organisms provides fundamental insight into a complex physiological process, and complements population-based studies that seek to reveal primary causes . Remarkable progress has been made on both fronts, and the pace of advance is likely to accelerate as functional genomics and the human genome project expand and mature . Approaches based on mendelian and quantitative genetics may well converge, and lead ultimately to more rational and selective therapies.

J Biotechnol, 2000 Mar 31, 78(3), 281 - 92
Progress in Arabidopsis genome sequencing and functional genomics; Wambutt R et al.; Arabidopsis thaliana has a relatively small genome of approximately 130 Mb containing about 10% repetitive DNA . Genome sequencing studies reveal a gene-rich genome, predicted to contain approximately 25000 genes spaced on average every 4.5 kb . Between 10 to 20% of the predicted genes occur as clusters of related genes, indicating that local sequence duplication and subsequent divergence generates a significant proportion of gene families . In addition to gene families, repetitive sequences comprise individual and small clusters of two to three retroelements and other classes of smaller repeats . The clustering of highly repetitive elements is a striking feature of the A . thaliana genome emerging from sequence and other analyses.

Biosystems, 2000 Feb, 55(1-3), 5 - 14
The application of shannon entropy in the identification of putative drug targets; Fuhrman S et al.; A major challenge in the field of functional genomics is the development of computational techniques for organizing and interpreting large amounts of gene expression data . These methods will be critical for the discovery of new therapeutic drug targets . Here, we present a simple method for determining the most likely drug target candidates from temporal gene expression patterns assayed with reverse-transcription polymerase chain reaction (RT-PCR) and DNA microarrays.

Nat Genet, 2000 Apr, 24(4), 355 - 61
Robustness against mutations in genetic networks of yeast; Wagner A; There are two principal mechanisms that are responsible for the ability of an organism's physiological and developmental processes to compensate for mutations . In the first, genes have overlapping functions, and loss-of-function mutations in one gene will have little phenotypic effect if there are one or more additional genes with similar functions . The second mechanism has its origin in interactions between genes with unrelated functions, and has been documented in metabolic and regulatory gene networks . Here I analyse, on a genome-wide scale, which of these mechanisms of robustness against mutations is more prevalent . I used functional genomics data from the yeast Saccharomyces cerevisiae to test hypotheses related to the following: if gene duplications are mostly responsible for robustness, then a correlation is expected between the similarity of two duplicated genes and the effect of mutations in one of these genes. , , , . My results demonstrate that interactions among unrelated genes are the major cause of robustness against mutations . This type of robustness is probably an evolved response of genetic networks to stabilizing selection.

Theriogenology, 1998 Jan 1, 49(1), 129 - 38
Cloning: new breakthroughs leading to commercial opportunities; Stice SL et al.; Research on cloning animals, again, came to the forefront of public attention in 1997 . Most scientists involved in biomedical and agricultural research have emphasized the benefits, of which there are many, of cloning to the public . Basic studies on nuclear transfer have and will continue to contribute to our understanding of how genomic activation and cell cycle synchrony affect nuclear reprogramming and cloning efficiencies, specifically . Also, more basic information on actual mechanisms and specific factors in the oocyte causing nuclear reprogramming is forthcoming . As new molecular approaches in functional genomics are combined with nuclear transfer experiments, new genes involved in nuclear reprogramming will be found . The commercial potentials of products stemming from discoveries in cloning are vast . Cloning will be a more efficient, faster and more useful way of making transgenic fetuses for cell therapies, adult animals for protein production and organs for xenotransplantation . Clearly there are new opportunities in animal cloning technology that will produce many benefits to society.

Folia Biol (Praha), 2000, 46(1), 31 - 41
PWD/Ph and PWK/Ph inbred mouse strains of Mus m . musculus subspecies--a valuable resource of phenotypic variations and genomic polymorphisms; Gregorova S et al.; PWD/Ph and PWK/Ph (abbreviated PW*) are highly inbred mouse strains (F66 and F70) derived from wild mice of Mus musculus musculus subspecies . When compared with laboratory inbred strains, they display a plethora of differences in many complex phenotypes such as body weight, fat distribution pattern, blood levels of intermediary metabolites, sensitivity to type-1 diabetes or behaviour patterns . The PWD/Ph genes can rescue the lethal effect of lack of the Igf2 receptor . The male-limited hybrid sterility of (PWD/Ph x laboratory strain)F1 hybrids is a specific phenotype controlled by three or four unlinked loci . These complex phenotypic traits can be genetically dissected by QTL analysis using microsatellite markers of known genetic location . The PW strains are particularly useful for such genome-wide scans since 70-80% of randomly chosen microsatellite markers are polymorphic in (PW x laboratory strain) crosses compared to 35-45% in crosses between two laboratory strains . The list of polymorphic microsatellite loci is included in this report . The high degree of sequence polymorphism allows easier distinction between paternal and maternal mRNA transcripts in PW hybrids, which makes the PW* strains a useful tool also in molecular studies of genomic imprinting . The high frequency of phenotypic differences together with the high degree of sequence polymorphism and the relatively easy breeding of PW strains make them a valuable mammalian model organism for the functional genomics of the traits of biomedical importance.

Genome Res, 2000 Mar, 10(3), 277 - 92
A phenotype map of the mouse X chromosome: models for human X-linked disease; Boyd Y et al.; The identification of many of the transcribed genes in man and mouse is being achieved by large scale sequencing of expressed sequence tags (ESTs) . Attention is now being turned to elucidating gene function and many laboratories are looking to the mouse as a model system for this phase of the genome project . Mouse mutants have long been used as a means of investigating gene function and disease pathogenesis, and recently, several large mutagenesis programs have been initiated to fulfill the burgeoning demand of functional genomics research . Nevertheless, there is a substantial existing mouse mutant resource that can be used immediately . This review summarizes the available information about the loci encoding X-linked phenotypic mutants and variants, including 40 classical mutants and 40 that have arisen from gene targeting.

Proc Natl Acad Sci U S A, 2000 Mar 14, 97(6), 2934 - 9
Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes; Lange BM et al.; Functional genomics approaches, which use combined computational and expression-based analyses of large amounts of sequence information, are emerging as powerful tools to accelerate the comprehensive understanding of cellular metabolism in specialized tissues and whole organisms . As part of an ongoing effort to identify genes of essential oil (monoterpene) biosynthesis, we have obtained sequence information from 1,316 randomly selected cDNA clones, or expressed sequence tags (ESTs), from a peppermint (Mentha x piperita) oil gland secretory cell cDNA library . After bioinformatic selection, candidate genes putatively involved in essential oil biosynthesis and secretion have been subcloned into suitable expression vectors for functional evaluation in Escherichia coli . On the basis of published and preliminary data on the functional properties of these clones, it is estimated that the ESTs involved in essential oil metabolism represent about 25% of the described sequences . An additional 7% of the recognized genes code for proteins involved in transport processes, and a subset of these is likely involved in the secretion of essential oil terpenes from the site of synthesis to the storage cavity of the oil glands . The integrated approaches reported here represent an essential step toward the development of a metabolic map of oil glands and provide a valuable resource for defining molecular targets for the genetic engineering of essential oil formation.

Proc Natl Acad Sci U S A, 2000 Mar 28, 97(7), 3324 - 9
Male-male competition magnifies inbreeding depression in wild house mice; Meagher S et al.; The detrimental effects of inbreeding on vertebrates are well documented for early stages of the life cycle in the laboratory . However, the consequences of inbreeding on long-term survival and reproductive success (Darwinian fitness) are uncertain for vertebrates in the wild . Here, we report direct experimental evidence for vertebrates that competition increases the harmful effects of inbreeding on offspring survival and reproduction . We compared the fitness of inbred (from full-sib matings) and outbred wild house mice (Mus domesticus) in large, seminatural enclosures . Inbred males sired only one-fifth as many surviving offspring as outbred males because of their poor competitive ability and survivorship . In laboratory conditions, inbreeding had relatively minor effects on male reproductive success and no effect on survivorship . Seminatural conditions did not increase inbreeding depression for females, probably because females were not competing for any critical resources . The overall reduction in fitness from inbreeding was 57%, which is 4.5 times as great as previous estimates from the laboratory . These results have important implications for medicine, conservation, evolutionary biology, and functional genomics.

Curr Opin Plant Biol, 2000 Apr, 3(2), 117 - 24
Genomic approaches to plant stress tolerance; Cushman JC et al.; Past efforts to improve plant tolerance to drought, high salinity and low-temperature through breeding and genetic engineering have had limited success owing to the genetic complexity of stress responses . Progress is now anticipated through comparative genomics studies of an evolutionarily diverse set of model organisms, and through the use of techniques such as high-throughput analysis of expressed sequence tags, large-scale parallel analysis of gene expression, targeted or random mutagenesis, and gain-of-function or mutant complementation . The discovery of novel genes, determination of their expression patterns in response to abiotic stress, and an improved understanding of their roles in stress adaptation (obtained by the use of functional genomics) will provide the basis of effective engineering strategies leading to greater stress tolerance.

Curr Opin Plant Biol, 2000 Apr, 3(2), 108 - 16
Chasing the dream: plant EST microarrays; Richmond T et al.; DNA microarray technology is poised to make an important contribution to the field of plant biology . Stimulated by recent funding programs, expressed sequence tag sequencing and microarray production either has begun or is being contemplated for most economically important plant species . Although the DNA microarray technology is still being refined, the basic methods are well established . The real challenges lie in data analysis and data management . To fully realize the value of this technology, centralized databases that are capable of storing microarray expression data and managing information from a variety of sources will be needed . These information resources are under development and will help usher in a new era in plant functional genomics.

Mol Microbiol, 2000 Mar, 35(5), 1156 - 67
Functional genomics of Helicobacter pylori: identification of a beta-1,4 galactosyltransferase and generation of mutants with altered lipopolysaccharide; Logan SM et al.; A previously annotated open reading frame (ORF) (HP0826) from Helicobacter pylori was cloned and expressed in Escherichia coli cells and determined to be a beta-1,4-galactosyltransferase that used GlcNAc as an acceptor . Mutational analysis in H . pylori strains demonstrated that this enzyme plays a key role in the biosynthesis of the type 2 N-acetyl-lactosamine (LacNAc) polysaccharide O-chain backbone, by catalysing the addition of Gal to GlcNAc . To examine the potential role of this O-chain structure in bacterial colonization of the host stomach, the mutation was introduced into H . pylori strain SS1 which is known to be capable of colonizing the gastric mucosa of mice . Compared with the parental strain, mutated SS1 was less efficient at colonizing the murine stomach.

Genetica, 1999, 106(1-2), 159 - 70
Functional genomics and enzyme evolution . Homologous and analogous enzymes encoded in microbial genomes; Galperin MY et al.; Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses--the area of research often referred to as 'functional genomics'--aims at deciphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function . This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution . Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed . A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism . Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size-parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives . Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function . An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle.

Curr Opin Lipidol, 1999 Dec, 10(6), 515 - 9
Functional genomics and DNA array techniques in atherosclerosis research; Hiltunen MO et al.; DNA arrays are revolutionizing the analysis of gene expression and single nucleotide polymorphisms of genomic DNA . Currently, the expression of 10-15% of human genes can be analysed simultaneously in a single experiment using cDNA or oligonucleotide-based format of DNA array . Alternatively, smaller DNA arrays with a limited number of selected genes, such as cytokines, growth factors or transcription factors, can be used . In concordance with Human Genome Project, after a few years, the DNA arrays will allow the analysis of expression of the whole human genome and will have a great impact on basic research, drug development and diagnostics . It is important to characterise mechanisms of atherosclerosis-related diseases at the level of gene expression so that new therapeutic strategies can be identified . With the aid of DNA array it is possible to identify multiple, simultaneous, transcriptional events that ameliorate or contribute to atherogenesis . The results are non-physical maps of the function, hierarchy and interactions of genetic programs . In this review we focus on DNA array technology and its applications in atherosclerosis research.

Curr Opin Chem Biol, 2000 Feb, 4(1), 34 - 9
Design of novel sequence-specific DNA-binding proteins; Segal DJ et al.; The design and selection of DNA-binding proteins or individual domains capable of novel sequence recognition continues to make great strides . Recent studies have also highlighted the role of the non-DNA-contacting portions of the protein and the optimal assembly of the domains . For the first time, it appears that it is possible to produce proteins capable of targeting any gene with an 18 base pair recognition domain . A variety of applications are being explored, such as targeted transcriptional regulation, recombination and viral integration . These proteins will probably find diverse applications in gene therapy, functional genomics, and agriculture.

Trends Biotechnol, 2000 Mar, 18(3), 93 - 8
On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning; Kell DB et al.; At present, the assignment of function to novel genes uncovered by the systematic genome-sequencing programmes is a problem . Many studies anticipate that this can be achieved by analysing patterns of gene expression via the transcriptome, proteome and metabolome . Thus, functional genomics is, in part, an exercise in pattern classification . Because many genes have known functional classes, the problem of predicting their functional class is a supervised learning problem . However, most pattern classification methods that have been applied to the problem have been unsupervised clustering methods . Consequently, the best classification tools have not always been used . Furthermore, the present functional classes are suboptimal and new unsupervised clustering methods are needed to improve them . Better-structured functional classes will facilitate the prediction of biochemically testable functions.

J Mol Biol, 2000 Feb 18, 296(2), 497 - 508
Bacteriophage lambda display of complex cDNA libraries: a new approach to functional genomics; Santi E et al.; We describe the construction and characterization of two lambda surface displayed cDNA expression libraries derived from human brain and mouse embryo . cDNA inserts were obtained by tagged random-priming elongation of commercially available cDNA libraries and cloned into a novel lambda vector at the 3' end of the D capsid protein gene, which produced highly complex repertoires (1x10(8) and 2x10(7) phage) . These libraries were affinity selected with a monoclonal antibody against the neural specific factor GAP-43 and with polyclonal antibodies that recognize the EMX1 and EMX2 homeoproteins . In both cases rapid identification of specific clones was achieved, which demonstrates the great potential of the lambda display system for generating affinity selectable cDNA libraries from complex genomes .

Biotechnol Prog, 2000 Jan-Feb, 16(1), 2 - 16
Recent progress in biomolecular engineering; Ryu DD et al.; During the next decade or so, there will be significant and impressive advances in biomolecular engineering, especially in our understanding of the biological roles of various biomolecules inside the cell . The advances in high throughput screening technology for discovery of target molecules and the accumulation of functional genomics and proteomics data at accelerating rates will enable us to design and discover novel biomolecules and proteins on a rational basis in diverse areas of pharmaceutical, agricultural, industrial, and environmental applications . As an applied molecular evolution technology, DNA shuffling will play a key role in biomolecular engineering . In contrast to the point mutation techniques, DNA shuffling exchanges large functional domains of sequences to search for the best candidate molecule, thus mimicking and accelerating the process of sexual recombination in the evolution of life . The phage-display system of combinatorial peptide libraries will be extensively exploited to design and create many novel proteins, as a result of the relative ease of screening and identifying desirable proteins . Even though this system has so far been employed mainly in screening the combinatorial antibody libraries, its application will be extended further into the science of protein-receptor or protein-ligand interactions . The bioinformatics for genome and proteome analyses will contribute substantially toward ever more accelerated advances in the pharmaceutical industry . Biomolecular engineering will no doubt become one of the most important scientific disciplines, because it will enable systematic and comprehensive analyses of gene expression patterns in both normal and diseased cells, as well as the discovery of many new high-value molecules . When the functional genomics database, EST and SAGE techniques, microarray technique, and proteome analysis by 2-dimensional gel electrophoresis or capillary electrophoresis in combination with mass spectrometer are all put to good use, biomolecular engineering research will yield new drug discoveries, improved therapies, and significantly improved or new bioprocess technology . With the advances in biomolecular engineering, the rate of finding new high-value peptides or proteins, including antibodies, vaccines, enzymes, and therapeutic peptides, will continue to accelerate . The targets for the rational design of biomolecules will be broad, diverse, and complex, but many application goals can be achieved through the expansion of knowledge based on biomolecules and their roles and functions in cells and tissues . Some engineered biomolecules, including humanized Mab's, have already entered the clinical trials for therapeutic uses . Early results of the trials and their efficacy are positive and encouraging. , , , , . Among them, Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA . Soon, new therapeutic drugs and high-value biomolecules will be designed and produced by biomolecular engineering for the treatment or prevention of not-so-easily cured diseases such as cancers, genetic diseases, age-related diseases, and other metabolic diseases . Many more industrial enzymes, which will be engineered to confer desirable properties for the process improvement and manufacturing of high-value biomolecular products at a lower production cost, are also anticipated . New metabolites, including novel antibiotics that are active against resistant strains, will also be produced soon by recombinant organisms having de novo engineered biosynthetic pathway enzyme systems . The biomolecular engineering era is here, and many of benefits will be derived from this field of scientific research for years to come if we are willing to put it to good use.

Lipids, 1999 Dec, 34(12), 1339 - 46
Nondestructive NMR determination of oil composition in transformed canola seeds; Hutton WC et al.; Magic-angle spinning (MAS) 13C nuclear magnetic resonance (NMR) spectroscopy is a convenient method for nondestructive, quantitative characterization of seed oil composition . We describe results for intact hybrid and transformed canola seeds . The MAS 13C NMR technique complements and agrees with gas chromatography results . The spectral resolution approaches that of neat, liquid oils . MAS 13C NMR data allow quantitative analysis of major oil components, including saturates and oleic, linoleic, and linolenic acyl chains . 13C NMR directly and quantitatively elucidates, triglyceride regiochemistry and acyl chain cis-trans isomers that cannot be quickly detected by other methods . MAS 13C NMR can serve as the primary method for development of near-infrared seed oil calibrations . These NMR methods are nondestructive and attractive for plant-breeding programs or other studies (e.g., functional genomics) where loss of seed viability is inconvenient.

J Immunol Methods, 1999 Dec 10, 231(1-2), 39 - 51
Phage display of cDNA repertoires: the pVI display system and its applications for the selection of immunogenic ligands; Hufton SE et al.; The selection of phage displayed cDNA repertoires on an immobilised target has been reported to be an efficient way to rapidly identify interacting partners . To date, however, only a few successful applications have been reported . Here, we present a review of the current status of the display and selection of cDNA libraries using phage . As an example, we report the construction of a set of phage display vectors suitable for cDNA display based on fusion to the minor bacteriophage coat protein 6 (pVI) of filamentous phage . We have evaluated these vectors through the display of the C(H)3 domain of human IgG and of the Escherichia coli alkaline phosphatase (PhoA) gene . Both the C(H)3 domain of IgG and PhoA are shown to be displayed on pVI, and PhoA is also shown to be enzymatically active . We have constructed primary colorectal tumor cDNA repertoires in these vectors and performed selections on both a monoclonal antibody to beta2 microglobulin (beta2M) and polyclonal antibody sera to human IgG . In both cases, relevant ligands were recovered from the phage displayed cDNA repertoire . These vectors may be used for selection of phage displayed cDNA libraries with polyclonal sera from patients . This will allow the identifying antigenic cDNA products in such diseases as cancer, viral/bacterial infections or autoimmune disease . Furthermore, by selections with other specific biomolecules, this display system may aid the identification of interacting partners in functional genomics.

Cell Mol Biol (Noisy-le-grand), 1999 Dec, 45(8), 1131 - 7
Genomic organization and expression of the ubiquitin-proteasome complex-associated protein Rbx1/ROC1/Hrt1; Perin J-P et al.; Rbx1/ROC1/Hrt1 (Rbx1) has been recently shown to be involved in the regulation of protein turn-over . Here, we report the organization of the human Rbx1 gene, established by both a cloning and a functional genomics approach . The human gene, composed of five exons, encompasses 22.3 kb on chromosome 22q 13 . The expression of Rbx1 transcripts (0.5 kb) appears developmentally regulated during mouse embryonic development and is prevalent in the adult mouse genital tract . A Genbank database search for Rbx1 related sequences in various species, from plants to mammals, is indicative of a high degree of evolutionary conservation in mouse rat and zebra fish and also, for the main functional part of the molecule, in other living species, although their gene structures can be significantly altered.

J Appl Physiol, 2000 Jan, 88(1), 332 - 6
Research in the exercise sciences: where do we go from here?
Baldwin KM.
The goal of this article is to provide a perspective on how research involving the acute and chronic effects of exercise (referred to as "exercise sciences") on the structure and function of organs systems will evolve in the next century . Within the last 30 years, exercise-related research has rapidly transitioned from an organ to a subcellular/molecular focus . Thus future research will continue to be heavily influenced by molecular biology tools, fueled by both emerging technologies (e.g., "gene-chip microarrays") designed to dissect gene function on a macro scale as well as by the completion of the human genome project in which the approximately 80,000 genes comprising humans will be completely sequenced . These successes will drive the emerging fields of functional genomics (the dissecting of a gene's identity and function) and proteomics (the study of the properties of proteins) . Funding levels at the National Institutes of Health will likely increase in order to expand these emerging fields as well as provide avenues for translating fundamental knowledge into solving the complexities of a number of degenerative diseases influenced heavily by activity/inactivity factors such as cardiopulmonary disease, diabetes, obesity, and the debilitating disorders associated with aging . Thus there are many challenges facing future exercise scientists who must harness the new technologies and take an aggressive stance in bringing this important field to the forefront.

Drug Discov Today, 2000 Jan, 5(1), 10 - 16
Adenovirus technology for gene manipulation and functional studies; Wang I I et al.; Recombinant adenoviral vectors are highly efficient at gene transfer in a broad spectrum of cell types and species, and have been used, both in vitro and in vivo, to achieve gain or loss of function in functional studies . In recent years, there have been several significant advances in adenovirus technologies, including new generations of vectors, improved production systems and sophisticated methods of delivery . In this review, recent progress and innovative applications are discussed to demonstrate the potential of the recombinant adenoviral vector as an effective tool in functional genomics.

Nucleic Acids Res, 2001 Jan 1, 29(1), 114 - 7
The Medicago Genome Initiative: a model legume database; Bell CJ et al.; The Medicago Genome Initiative (MGI) is a database of EST sequences of the model legume MEDICAGO: truncatula . The database is available to the public and has resulted from a collaborative research effort between the Samuel Roberts Noble Foundation and the National Center for Genome Resources to investigate the genome of M.truncatula . MGI is part of the greater integrated MEDICAGO: functional genomics program at the Noble Foundation , which is taking a global approach in studying the genetic and biochemical events associated with the growth, development and environmental interactions of this model legume . Our approach will include: large-scale EST sequencing, gene expression profiling, the generation of M.truncatula activation-tagged and promoter trap insertion mutants, high-throughput metabolic profiling, and proteome studies . These multidisciplinary information pools will be interfaced with one another to provide scientists with an integrated, holistic set of tools to address fundamental questions pertaining to legume biology . The public interface to the MGI database can be accessed at http://www.ncgr.org/research/mgi.

Nucleic Acids Res, 2001 Jan 1, 29(1), 111 - 3
PlantsP: a functional genomics database for plant phosphorylation; Gribskov M et al.; The PlantsP database is a curated database that combines information derived from sequences with experimental functional genomics information . PlantsP focuses on plant protein kinases and protein phosphatases . The database will specifically provide a resource for information on a collection of T-DNA insertion mutants (knockouts) in each protein kinase and phosphatase in Arabidopsis thaliana . PlantsP also provides a curated view of each protein that includes a comprehensive annotation of functionally related sequence motifs, sequence family definitions, alignments and phylogenetic trees, and descriptive information drawn directly from the literature . PlantsP is available at http://PlantsP.sdsc.edu.

Neth J Med, 1999 Dec, 55(6), 271 - 5
Endocrinology in the 21st century: unmasking the mysteries of biology; Romijn JA; The traditional concept of endocrinology has provided a model, that enabled to understand and treat endocrine diseases . Molecular and (patho)physiological differentiations of this concept will further improve the treatment of complex endocrine and metabolic diseases . Nature has lifted a tip of her veil, reveiling a number of orphan receptors, which may reflect presently unknown physiological pathways and may be important targets for drug development . Although the integrative function of hormones and receptors can be further elucidated by approaches like reverse endocrinology and functional genomics, the structural interaction between bench (basic science) and bedside (clinical endocrinology) will remain instrumental for the progress of endocrinology.

Nat Genet, 1999 Nov, 23(3), 348 - 53
Leukaemia disease genes: large-scale cloning and pathway predictions; Li J et al.; Retroviral insertional mutagenesis in BXH2 and AKXD recombinant inbred mice induces a high incidence of myeloid or B- and T-cell leukaemia and the proviral integration sites in the leukaemias provide powerful genetic tags for disease gene identification . Some of the disease genes identified by proviral tagging are also associated with human disease, validating this approach for human disease gene identification . Although many leukaemia disease genes have been identified over the years, many more remain to be cloned . Here we describe an inverse PCR (IPCR) method for proviral tagging that makes use of automated DNA sequencing and the genetic tools provided by the Mouse Genome Project, which increases the throughput for disease gene identification . We also use this IPCR method to clone and analyse more than 400 proviral integration sites from AKXD and BXH2 leukaemias and, in the process, identify more than 90 candidate disease genes . Some of these genes function in pathways already implicated in leukaemia, whereas others are likely to define new disease pathways . Our studies underscore the power of the mouse as a tool for gene discovery and functional genomics.

Neuropediatrics, 2003 Feb, 34(1), 14 - 22
Human mitochondrial complex I deficiency: investigating transcriptional responses by microarray; van der Westhuizen FH et al.; NADH:ubiquinone oxidoreductase (complex I) deficiency is one of the most frequently encountered defects of the mitochondrial energy generating system . A deficiency of this enzyme complex leads to a wide variety in clinical disease expression . The cell biological consequences of such mutations, however, are poorly understood . We investigated transcriptional responses in fibroblast cell lines harboring mutations in the five different nuclear DNA encoded subunits using a mitochondria-targeting microarray . Expression profiles of cell lines cultured under conditions that favor glycolytic metabolism were compared to profiles when cultured under conditions favoring oxidative metabolism . Approximately 60 genes displayed differential expression under these conditions in either all mutated cell lines or selected cell lines only . A marked induction of metallothioneins as well as ATP1G1 transcripts was detected in all patient cell lines . Transcriptional responses such as the induction of heat shock protein transcripts, decreased PDK1,BNIP3 and mitochondrial genome encoding gene transcripts occurred in selected patient cell lines . The observed transcript profile points to a common, putative defensive, response relating to oxidative stress . Although further investigations of other human OXPHOS system diseases is warranted, these results clearly underline that functional genomics holds for the study of inherited metabolic disease.

Eukaryot Cell, 2003 Apr, 2(2), 247 - 55
Identification of essential genes in the human fungal pathogen Aspergillus fumigatus by transposon mutagenesis; Firon A et al.; The opportunistic pathogen Aspergillus fumigatus is the most frequent cause of deadly airborne fungal infections in developed countries . In order to identify novel antifungal-drug targets, we investigated the genome of A . fumigatus for genes that are necessary for efficient fungal growth . An artificial A . fumigatus diploid strain with one copy of an engineered impala160 transposon from Fusarium oxysporum integrated into its genome was used to generate a library of diploid strains by random in vivo transposon mutagenesis . Among 2,386 heterozygous diploid strains screened by parasexual genetics, 1.2% had a copy of the transposable element integrated into a locus essential for A . fumigatus growth . Comparison of genomic sequences flanking impala160 in these mutants with that of the genome of A . fumigatus allowed the characterization of 20 previously uncharacterized A . fumigatus genes . Among these, homologues of genes essential for Saccharomyces cerevisiae growth have been identified, as well as genes that do not have homologues in other fungal species . These results confirm that heterologous transposition using the transposable element impala is a powerful tool for functional genomics in ascomycota, and they pave the way for defining the complete set of essential genes in A . fumigatus, the first step toward target-based development of new antifungal drugs.

Vet Clin North Am Food Anim Pract, 2003 Mar, 19(1), 1 - 45, v
Immunity and mastitis . Some new ideas for an old disease; Burton JL et al.; The biggest challenge for host immune defense against mastitis-causing bacteria in dairy cows is to quickly recruit large enough numbers of opsonizing molecules and mature neutrophils into milk such that intramammary pathogens are cleared before they multiply significantly and the inflammatory response gets out of control . Currently, this challenge is best facilitated when established mastitis control procedures are practiced on the farm, including proper hygiene, milking procedures, and regular administration of approved mastitis vaccines . However, mastitis is still a significant problem . New animal functional genomics research is beginning to allow scientists to solve the puzzle of mastitis susceptibility . Results of this type of research offer the hope of giant leaps toward a clear identification of molecular genetic variation and potential gene targets for therapies and immune manipulations that could significantly reduce the risk of clinical mastitis in traditionally susceptible cows.

Trends Biotechnol, 2003 Apr, 21(4), 146 - 7; discussion 147-8
One step further towards real high-throughput functional genomics; Oude Elferink R; In a recent paper by Michiels et al . an important step was made towards genuine high throughput functional genomics . The authors produced an arrayed adenoviral library containing >120000 cDNAs isolated from human placenta . This library can be used for arrayed transduction of cell lines in phenotypic assays and to screen for genes involved in the induction of any phenotype for which a robust high-throughput assay can be designed.

Physiol Res, 2003, 52(2), 141 - 6
New apolipoprotein A-V: comparative genomics meets metabolism; Seda O et al.; The availability of the human genome sequence and the recently completed draft sequences of two major mammalian model species, the mouse (Mus musculus) and the rat (Rattus norvegicus), allow researchers to apply novel approaches for gene identification and characterization, using methods of comparative and functional genomics . Recently, a new gene coding for apolipoprotein A-V was identified in the vicinity of APOA-I/C-III/A-IV cluster on human chromosome 11q23 by comparative sequencing method . In a relatively short time, compelling evidence accumulated for the substantial role of APOA-V in lipid metabolism . Studies in knock-out and transgenic mice revealed that its expression pattern correlates negatively with triglyceride levels . This observation was verified in human population studies in variety of ethnic and age groups . Several single nucleotide polymorphisms were described and particular SNP alleles and haplotypes in the APO A-V gene region were shown to be associated with dyslipidemia . The discovery and characterization of the APO A-V demonstrates current possibilities of the integrative approaches in biology, boosted by the available bioinformatic tools.

Am Nat, 2003 Feb, 161(2), 171 - 80
The naturalist in a world of genomics; Stearns SC et al.; Functional genomics provides new opportunities to address issues of fundamental interest in evolutionary biology and suggests many new research directions that are ripe for evolutionary investigation . New types of data, and the ability to study biological processes from a whole genome perspective, are likely to have a profound impact on evolutionary biology and ecology . To illustrate, we discuss how genomewide gene expression studies can be used to reformulate questions about trade-offs and pleiotropy . We then touch on some of the new research opportunities that the application of functional genomics affords to evolutionary biologists . We end with some brief notes about how evolutionary biology and comparative approaches will probably have an impact on functional genomics.

Genome, 2003 Feb, 46(1), 28 - 47
A molecular marker map in 'Kanota' x 'Ogle' hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework; Wight CP et al.; Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C . Koch cv . Kanota x Avena sativa L . cv . Ogle . In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs . 71) than previously reported . A robust, updated framework map was developed to resolve linkage associations among 286 markers . The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests . This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations . The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.

Science, 2003 Mar 28, 299(5615), 2039 - 45
Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells; Lum L et al.; Classical genetic screens can be limited by the selectivity of mutational targeting, the complexities of anatomically based phenotypic analysis, or difficulties in subsequent gene identification . Focusing on signaling response to the secreted morphogen Hedgehog (Hh), we used RNA interference (RNAi) and a quantitative cultured cell assay to systematically screen functional roles of all kinases and phosphatases, and subsequently 43% of predicted Drosophila genes . Two gene products reported to function in Wingless (Wg) signaling were identified as Hh pathway components: a cell surface protein (Dally-like protein) required for Hh signal reception, and casein kinase 1alpha, a candidate tumor suppressor that regulates basal activities of both Hh and Wg pathways. , , , . This type of cultured cell-based functional genomics approach may be useful in the systematic analysis of other biological processes.

Am J Physiol Heart Circ Physiol, 2003 Aug, 285(2), H907 - 14 Epub 2003 Mar 27.
24-h Langendorff-perfused neonatal rat heart used to study the impact of adenoviral gene transfer; Wiechert S et al.; The human genome project has increased the demand for simple experimental systems that allow the impact of gene manipulations to be studied under controlled ex vivo conditions . We hypothesized that, in contrast to adult hearts, neonatal hearts allow long-term perfusion and efficient gene transfer ex vivo . A Langendorff perfusion system was modified to allow perfusion for >24 h with particular emphasis on uncompromised contractile activity, sterility, online measurement of force of contraction, inotropic response to beta-adrenergic stimulation, and efficient gene transfer . The hearts were perfused with serum-free medium (DMEM + medium 199, 4 + 1) supplemented with hydrocortisone, triiodothyronine, ascorbic acid, insulin, pyruvate, l-carnitine, creatine, taurine, l-glutamine, mannitol, and antibiotics recirculating (500 ml/2 hearts) at 1 ml/min . Hearts from 2 day-old rats beat constantly at 135-155 beats/min and developed active force of 1-2 mN . During 24 h of perfusion, twitch tension increased to approximately 165% of initial values (P < 0.05), whereas the inotropic response to isoprenaline remained constant . A decrease in total protein content of 10% and histological examination indicated moderate edema, but actin and calsequestrin concentration remained unchanged and perfusion pressure remained constant at 7-11 mmHg . Perfusion with a LacZ-encoding adenovirus at 3 x 108 active virus particles yielded homogeneous transfection of approximately 80% throughout the heart and did not affect heart rate, force of contraction, or response to isoprenaline compared with uninfected controls (n = 7 each) . Taken together, the 24-h Langendorff-perfused neonatal rat heart is a relatively simple, inexpensive, and robust new heart model that appears feasible as a test bed for functional genomics.

Biochem Soc Trans, 2003 Apr, 31(2), 437 - 43
A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets; Schadt EE et al.; Application of statistical genetics approaches to variations in mRNA transcript abundances in segregating populations can be used to identify genes and pathways associated with common human diseases . The combination of this genetic information with gene expression and clinical trait data can also be used to identify subtypes of a disease and the genetic loci specific to each subtype . Here we highlight results from some of our recent work in this area and further explore the many possibilities that exist in employing a more comprehensive genetics and functional genomics approach to the functional annotation of genomes, and in applying such methods to the validation of targets for complex traits in the drug discovery process.

Electrophoresis, 2003 Jan, 24(1-2), 96 - 100
Transcription factor binding study by capillary zone electrophoretic mobility shift assay; Ronai Z et al.; Regulation of gene expression through interaction of proteins with specific DNA sequences is a central issue in functional genomics . Capillary electrophoretic mobility shift assay is an efficient novel method for the investigation of sequence specific protein-DNA interactions, allowing rapid and sensitive quantification of the complex formation . In this paper, we present a pilot study on capillary zone electrophoretic mobility shift assay (CZEMSA) to investigate the interaction between the transcription factors of HeLa nuclear extract and Sp1-specific fluorescein-labeled oligonucleotide, using the unlabeled probe as competitor . The mobility shift assay was accomplished by CZE in coated capillaries without polymeric buffer additives . Specificity of the DNA protein complex formation was verified by competition experiments, as well as by supershift assay with an anti-Sp1 antibody . The applied electric field strength did not affect the stability of DNA-protein complex during the electrophoretic analysis, allowing rapid identification and quantification of the protein DNA interaction . A practical application to study the interaction between Oryza sativa MADS-box transcription factor 4 (OsMADS4) and its consensus sequence is also reported.

FEBS Lett, 2003 Mar 27, 539(1-3), 111 - 4
Gene silencing by adenovirus-delivered siRNA; Shen C et al.; RNA interference is the process that double-stranded RNA induces the homology-dependent degradation of cognate mRNA mediated by 21-23 nucleotide short interfering RNA (siRNA) . Here, we describe a simple virus vector for efficient delivery of siRNA into mammalian cells utilizing the well-defined H1-RNA promoter and conventional adenovirus . In this pilot study, p53 was targeted by this vector . Our results demonstrate efficient and specific knock-down of p53 in breast cancer MCF-7 and lung carcinoma A549 cells and indicate a prospective application of this siRNA expressing recombinant adenovirus system in functional genomics, cancer gene therapy and virus inhibition.

J Soc Biol, 2002, 196(4), 303 - 7
{Transcriptomes for serial analysis of gene expression}; Marti J et al.; The availability of the sequences for whole genomes is changing our understanding of cell biology . Functional genomics refers to the comprehensive analysis, at the protein level (proteome) and at the mRNA level (transcriptome) of all events associated with the expression of whole sets of genes . New methods have been developed for transcriptome analysis . Serial Analysis of Gene Expression (SAGE) is based on the massive sequential analysis of short cDNA sequence tags . Each tag is derived from a defined position within a transcript . Its size (14 bp) is sufficient to identify the corresponding gene and the number of times each tag is observed provides an accurate measurement of its expression level . Since tag populations can be widely amplified without altering their relative proportions, SAGE may be performed with minute amounts of biological extract . Dealing with the mass of data generated by SAGE necessitates computer analysis . A software is required to automatically detect and count tags from sequence files . Criterias allowing to assess the quality of experimental data can be included at this stage . To identify the corresponding genes, a database is created registering all virtual tags susceptible to be observed, based on the present status of the genome knowledge . By using currently available database functions, it is easy to match experimental and virtual tags, thus generating a new database registering identified tags, together with their expression levels . As an open system, SAGE is able to reveal new, yet unknown, transcripts . Their identification will become increasingly easier with the progress of genome annotation . However, their direct characterization can be attempted, since tag information may be sufficient to design primers allowing to extend unknown sequences . A major advantage of SAGE is that, by measuring expression levels without reference to an arbitrary standard, data are definitively acquired and cumulative . All publicly available data can thus be stored in a unique database, facilitating whole-genome analysis of differential expression between cell types, normal and diseased samples, or samples with and without drug treatment . SAGE data are readily amenable to statistical comparisons, allowing to determine the level of confidence of the observed variations . A major limitation of SAGE is that, because each analysis is obligatory performed on the whole set of expressed genes, it can hardly be performed on multiple samples, for example in kinetics studies or to compare the effects of large numbers of drugs . To overcome this limitation, high-throughput detection of a subset of mRNAs is more rapidly performed by parallel hybridization of mRNAs on arrays of nucleic acids immobilized on solid supports . From this point of view, a SAGE platform is a powerful instrument for selecting the most informative subset of genes, assembling them to design microarrays dedicated to a specific problem and calibrating measurement by comparison with a standard cell model for which SAGE data are available . This approach is an attractive alternative to strategies based exclusively on pangenomic arrays . A very large amount of SAGE data are already available and the problem is now to extract their biological meaning . Knowledge on metabolic pathways is already organized so that its successful integration in a SAGE platform can be undertaken . For other cell components and pathways, the problem lies on the lack of controlled vocabulary to describe gene activities, starting form a clear definition of the concept of biological function itself . Progress in gene and cell ontology is expected to facilitate computer-based extraction of biological knowledge from existing and forthcoming SAGE data.

Physiol Genomics, 2003 Mar 18, 13(1), 15 - 24
Super models; Barr MM; Model organisms have been used over a century to understand basic, conserved biological processes . The study of these experimental systems began with genetics and development, moved into molecular and cellular biology, and most recently propelled into functional genomics and proteomics . The goal of this review is simple: to discuss the place of model organisms in "The Age of the Ome": the genome, the transcriptome, and the proteome . This review will address the following questions . What exactly is a model organism? What characteristics make an excellent model system? Using the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans as examples, this review will discuss these issues with the aim of demonstrating how model organisms remain indispensable scientific tools for understanding complex biological pathways and human disease.

Acc Chem Res, 2003 Mar, 36(3), 183 - 9
Structural proteomics: toward high-throughput structural biology as a tool in functional genomics; Yee A et al.; Structural proteomics is the determination of atomic resolution three-dimensional protein structures on a genome-wide scale in order to better understand the relationship between protein sequence, structure, and function . Here we describe our ongoing structural proteomics project on the nonmembrane proteins of the archeaon, Methanobacterium thermoautotrophicum . This article provides a snapshot of an ongoing pilot project in an emerging area of multidisciplinary research that involves bioinformatics, molecular biology, biochemistry, and instrumental methods such as NMR spectroscopy and X-ray crystallography . An assessment of the technical challenges in this type of large-scale project along with a comparison of the efficiency of sample production for both X-ray crystallography and NMR spectroscopy will be discussed . Examples of new insights into protein function and the relationship between structure and sequence will also be presented.

Crit Rev Eukaryot Gene Expr, 2002, 12(4), 297 - 316
Functional genomics in rat models of hypertension: using differential expression and congenic strains to identify and evaluate candidate genes; Lee SJ et al.; Hypertension is a leading contributor to cardiovascular diseases such as heart attack and stroke . Genetic and environmental factors contribute to the development of hypertension . Animal models have been developed to study the genetic contributions to blood pressure (BP) regulation and to identify chromosomal regions harboring candidate genes causative of differences in BP regulation (i.e., BP quantitative trait loci {QTL}) . Advances in both mammalian genome projects and global gene expression analysis present opportunities to study functional genomics in these animal models . In this article, novel approaches for designing experiments and interpreting global gene expression data using the Dahl salt-sensitive hypertension rat model are presented . We describe two-step screening protocols that can be used to identify BP QTL candidate genes . Genetically determined expression differences are identified in the target organs of inbred strains of contrasting phenotype in the first screen . Expression patterns in a panel of congenic strains or expression differences stemming from gene x environment interactions are examined in the second screen . Chromosomal locations of these genes can then be examined to determine whether they map to BP QTL-containing regions . Another approach is to study the expression of genes identified from public databases to be located within BP QTL-containing congenic regions . Several candidate genes have been identified using these strategies.

Kokuritsu Iyakuhin Shokuhin Eisei Kenkyusho Hokoku, 2002, (120), 39 - 52
{Toxicogenomics--a new paradigm of toxicology and birth of reverse toxicology}; Hirabayashi Y et al.; Toxicogenomics is, similar to other genome science fields, based on DNA microarray and/or DNA chip technologies, which has enabled a large number of gene expressions, thus, have been applied to such functional genomics as pharmacogenomics, oncogenomics, proteomics, metabonomics, etc . Toxicogenomics has advantages such as deducing the number of test animals and the test period, and adopts simpler techniques using new biomarkers . What toxicogenomics can offer to conventional toxicology is given herein.

Arch Microbiol, 2003 Apr, 179(4), 301 - 4 Epub 2003 Mar 12.
Application of crossover-PCR-mediated deletion-insertion mutagenesis to analysis of the bdhA-xdhA2-xdhB2 mixed-function operon of Sinorhizobium meliloti; Sukdeo N et al.; The bdhA-xdhA2-xdhB2 mixed-function operon was used to demonstrate the application of crossover PCR to the construction of in-frame, non-polar deletion-insertion mutations in Sinorhizobium meliloti . Replacement of a 474-bp internal portion of the 774-bp coding sequence of bdhA with a 21-bp in-frame synthetic sequence resulted in loss of the bdhA-encoded d-3-hydroxybutyrate dehydrogenase activity . Such mutants retained the xanthine oxidase activity encoded by xdhA2-xdhB2, thus illustrating the non-polar nature of the mutation . This method of constructing unmarked, in-frame deletions should be generally applicable to functional genomics studies in S . meliloti and other alpha-Proteobacteria.

Plant J, 2003 Mar, 33(6), 1001 - 11
Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags; Ogihara Y et al.; Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents . To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat . Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis . Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5' and 3' ends . Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology . By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified . Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns . Genes with similar functions were grouped with one another by clustering gene expression profiles . This technique might enable estimation of the functions of anonymous genes . Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.

Microbiol Mol Biol Rev, 2003 Mar, 67(1), 86 - 156, table of contents
Bacteriophage T4 genome; Miller ES et al.; Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry . Its complete genome sequence of 168,903 bp encodes about 300 gene products . T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics . Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods . The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition . Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level . The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments . Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection . Despite these advances, nearly 130 potential T4 genes remain uncharacterized . Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli . T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.

Genetics, 2003 Feb, 163(2), 647 - 61
piggyBac-based insertional mutagenesis and enhancer detection as a tool for functional insect genomics; Horn C et al.; Transposon mutagenesis provides a fundamental tool for functional genomics . Here we present a non-species-specific, combined enhancer detection and binary expression system based on the transposable element piggyBac: For the different components of this insertional mutagenesis system, we used widely applicable transposons and distinguishable broad-range transformation markers, which should enable this system to be operational in nonmodel arthropods . In a pilot screen in Drosophila melanogaster, piggyBac mutator elements on the X chromosome were mobilized in males by a Hermes-based jumpstarter element providing piggyBac transposase activity under control of the alpha1-tubulin promoter . As primary reporters in the piggyBac mutator elements, we employed the heterologous transactivators GAL4delta or tTA . To identify larval and adult enhancer detectors, strains carrying UASp-EYFP or TRE-EYFP as secondary reporter elements were used . Tissue-specific enhancer activities were readily observed in the GAL4delta/UASp-based systems, but only rarely in the tTA/TRE system . Novel autosomal insertions were recovered with an average jumping rate of 80% . Of these novel insertions, 3.8% showed homozygous lethality, which was reversible by piggyBac excision . Insertions were found in both coding and noncoding regions of characterized genes and also in noncharacterized and non-P-targeted CG-number genes . This indicates that piggyBac will greatly facilitate the intended saturation mutagenesis in Drosophila.

Mech Ageing Dev, 2003 Jan, 124(1), 133 - 8
Microarray workshop on aging; Nair PN et al.; The advent of microarrays in studying gene expression in aging has created tremendous excitement due to its potential for uncovering molecular mechanisms of aging and age-related disease . However, the appropriate implementation of this technology in the science of aging requires serious attention to methodological detail and statistical rigor . This report highlights discussions from the microarray workshop on aging held at the First Conference on Functional Genomics of Aging in Seville, Spain . The topics discussed by the participants included technical issues relating to the printing of arrays, RNA isolation, cDNA labeling and hybridization, optimal design of microarray experiments, and statistical analysis of these data . Microarray analysis of complex tissues through the use of laser capture microdissection was also discussed.

Mech Ageing Dev, 2003 Jan, 124(1), 85 - 92
Somatic mutations and ageing in silico; Kirkwood TB et al.; Considerable evidence points to an accumulation of somatic mutations in older cells and organisms but the causal role of mutations in the ageing process is still unclear . In addition to demonstrating that mutations accumulate, it is important to address the question of whether they do so at a sufficient rate and with a dynamic profile that is consistent with them playing a causative role . We describe the development of in silico models that can be used to explore the role of somatic mutations in ageing and which form a part of a growing effort to build predictive mathematical and computer models that can help unravel the complexity of the functional genomics of ageing . Our models address, in particular, how mutations affect populations of dividing cells like human fibroblasts, in which the challenge to the somatic mutation theory is greatest, since selection at the cellular level will tend to suppress the accumulation of mutations.

Mech Ageing Dev, 2003 Jan, 124(1), 3 - 8
Functional genomics of ageing; Vijg J et al.; Ageing is the most complex phenotype currently known, since it becomes manifest in all organs and tissues, affects an organism's entire physiology, impacts function at all levels and increases susceptibility to all major chronic diseases . Insight into the molecular and cellular targets of the ageing process would offer the unprecedented opportunity to postpone and prevent some, if not all, of its deteriorative aspects by preventive and therapeutic means . Thus far, our understanding of the causes of ageing is limited . To an important extent this is due to our inability, in the past, to study ageing systems . Instead, ample information has been gathered about individual cellular components at various ages, but this has not allowed a clear understanding of the integrated genomic circuits that control mechanisms of ageing, survival and stress responses . With the emergence of functional genomics, we finally have the opportunity to study ageing in a comprehensive manner, as a function of the dynamic network of genes that determines the physiology of an individual organism over time.

Diabetes Technol Ther, 2002, 4(6), 867 - 71
Using CAVE technology for functional genomics studies; Sensen CW; We have established the first Java 3D-enabled CAVE (CAVE automated virtual environment) . The Java application programming interface allows the complete separation of the program development from the program execution, opening new application domains for the CAVE technology . Programs can be developed on any Java-enabled computer platform, including Windows, Macintosh, and Linux workstations, and executed in the CAVE without modification . The introduction of Java, one of the major programming environments for bioinformatics, into the CAVE environment allows the rapid development applications for genome research, especially for the analysis of the spatial and temporal data that are being produced by functional genomics experiments . The CAVE technology will play a major role in the modeling of biological systems that is necessary to understand how these systems are organized and how they function.

Curr Opin Drug Discov Devel, 2003 Jan, 6(1), 110 - 6
New understanding in cardiotoxicity; Kang YJ; Interest in cardiotoxicity has dramatically increased during the past two years, leading to exciting progress in our understanding of the field . Both clinical and experimental animal studies have emphasized the role of cardiotoxicity in myocardial pathogenesis . Exploration of the cardiotoxicity of air pollution and highly active antiretroviral therapy (HAART) through experimental animal studies have led to mechanistic insights . Novel therapeutic approaches are also under development . Continued efforts to investigate the mechanisms of cardiotoxicity induced by well-known drugs and chemicals, such as Adriamycin, have also generated critical insights into cardiac response to toxicants . Recognition of the significance of cardiotoxicity in myocardial pathogenesis has resulted in the identification of many other drugs or chemicals, such as arsenic trioxide, whose cardiotoxicity is of major concern in clinical applications . Mitochondrial cardiomyopathy, along with control of myocardial cell death, has also become an extensively studied subject . Ionic transport across the inner membrane of mitochondria, especially the function of mitochondrial ATP-sensitive K+ channels and the Ca(2+)-activated K+ channels in myocardial protection against oxidative injury, has attracted a great deal of attention . Novel approaches, such as functional genomics, proteomics and metabonomics, should significantly improve our understanding of cardiotoxicity.

Functional Genomics is a relatively new technology that uses high throughputmethods to analyse large numbers of genes at the one time. It studies thefunction of individual or groups of genes.Functional genomics allows researchers to gain an understanding of the controlof genes during normal growth and development, and in response toenvironmental stresses. The researchers can further investigate the complexinteractions that occur in genetic and cellular networks and ideally, thetechnology will allow the entire genetic make-up of an organism to be studied.

Comparative genomics attempts to extract information by comparing the genomes of different species. The recent explosion in the number of sequenced genomes has created a rich set of data for which to apply the techniques of comparative genomics . Conserved features can be used to improve the accuracy of computational gene prediction.

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