4751
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Costas J, Casares F, Vieira J. Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 2003; 310:215-20. [PMID: 12801649 DOI: 10.1016/s0378-1119(03)00556-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the importance of cis-regulatory regions in evolution, little is know about their evolutionary dynamics. In this report, we analyze the process of evolution of binding sites for transcription factors using as a model a well characterized system, the Drosophila early developmental enhancers. We compare the sequences of eight enhancer regions for early developmental genes between Drosophila melanogaster and other two species, Drosophila virilis and Drosophila pseudoobscura, searching for the presence/absence of 104 biochemically verified binding sites from D. melanogaster. We also modeled the binding specificity of each binding site by the use of well-defined positional weight matrices (PWMs). The comparisons showed that turnover of binding sites seems to fit a molecular clock, at an approximate rate of 0.94% of gain/loss of binding sites per million years. This intense turnover affects both high and low affinity binding sites at the same extent. Furthermore, the subset of overlapping binding sites is also subjected to this high turnover. Conserved binding sites seem to be constrained to maintain not only location but also the exact sequence at each particular position. Finally, we detected a significant decrease in mean PWM scores for the D. virilis binding sites in the case of Hunchback. Possible explanations for this fact are discussed.
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Affiliation(s)
- Javier Costas
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal.
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4752
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Abstract
This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape.
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Affiliation(s)
- Raimond L Winslow
- The Whitaker Biomedical Engineering Institute and Center for Cardiovascular Bioinformatics and Modeling, The Johns Hopkins University School of Medicine, Baltimore, Md 21218, USA.
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4753
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Thanaraj TA, Clark F, Muilu J. Conservation of human alternative splice events in mouse. Nucleic Acids Res 2003; 31:2544-52. [PMID: 12736303 PMCID: PMC156037 DOI: 10.1093/nar/gkg355] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Human and mouse genomes share similar long-range sequence organization, and have most of their genes being homologous. As alternative splicing is a frequent and important aspect of gene regulation, it is of interest to assess the level of conservation of alternative splicing. We examined mouse transcript data sets (EST and mRNA) for the presence of transcripts that both make spliced-alignment with the draft mouse genome sequence and demonstrate conservation of human transcript-confirmed alternative and constitutive splice junctions. This revealed 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers are patently dependent on the extent of transcript coverage. Transcript coverage of conserved splice patterns is found to correlate well between human and mouse. A model, which extrapolates from observed levels of conservation at increasing levels of transcript support, estimates overall conservation of 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals. Observed numbers of conserved alternative splicing events agreed with those expected on the basis of the model. Thus, it is apparent that many, and probably most, alternative splicing events are conserved between human and mouse. This, combined with the preservation of alternative frame stop codons in conserved frame breaking events, indicates a high level of commonality in patterns of gene expression between these two species.
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Affiliation(s)
- T A Thanaraj
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
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4754
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Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003; 423:241-54. [PMID: 12748633 DOI: 10.1038/nature01644] [Citation(s) in RCA: 1305] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Accepted: 04/01/2003] [Indexed: 11/09/2022]
Abstract
Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.
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Affiliation(s)
- Manolis Kellis
- Whitehead/MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
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4755
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Wainwright MS, Rossi J, Schavocky J, Crawford S, Steinhorn D, Velentza AV, Zasadzki M, Shirinsky V, Jia Y, Haiech J, Van Eldik LJ, Watterson DM. Protein kinase involved in lung injury susceptibility: evidence from enzyme isoform genetic knockout and in vivo inhibitor treatment. Proc Natl Acad Sci U S A 2003; 100:6233-8. [PMID: 12730364 PMCID: PMC156355 DOI: 10.1073/pnas.1031595100] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acute lung injury (ALI) associated with sepsis and iatrogenic ventilator-induced lung injury resulting from mechanical ventilation are major medical problems with an unmet need for small molecule therapeutics. Prevailing hypotheses identify endothelial cell (EC) layer dysfunction as a cardinal event in the pathophysiology, with intracellular protein kinases as critical mediators of normal physiology and possible targets for drug discovery. The 210,000 molecular weight myosin light chain kinase (MLCK210, also called EC MLCK because of its abundance in EC) is hypothesized to be important for EC barrier function and might be a potential therapeutic target. To test these hypotheses directly, we made a selective MLCK210 knockout mouse that retains production of MLCK108 (also called smooth-muscle MLCK) from the same gene. The MLCK210 knockout mice are less susceptible to ALI induced by i.p. injection of the endotoxin lipopolysaccharide and show enhanced survival during subsequent mechanical ventilation. Using a complementary chemical biology approach, we developed a new class of small-molecule MLCK inhibitor based on the pharmacologically privileged aminopyridazine and found that a single i.p. injection of the inhibitor protected WT mice against ALI and death from mechanical ventilation complications. These convergent results from two independent approaches demonstrate a pivotal in vivo role for MLCK in susceptibility to lung injury and validate MLCK as a potential drug discovery target for lung injury.
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Affiliation(s)
- Mark S Wainwright
- Departments of Pediatrics, Northwestern University, Chicago, IL 60611, USA
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4756
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Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HHQ, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GAP, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJT, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC. Human chromosome 7: DNA sequence and biology. Science 2003; 300:767-72. [PMID: 12690205 PMCID: PMC2882961 DOI: 10.1126/science.1083423] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.
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Affiliation(s)
- Stephen W Scherer
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8.
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4757
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Affiliation(s)
- Javed Khan
- Oncogenomics Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Advanced Technology Center, Room 134E, 8717 Grovemont Circle, Bethesda, MD 20892-4605, USA.
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4758
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Subramanian S, Kumar S. Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res 2003; 13:838-44. [PMID: 12727904 PMCID: PMC430942 DOI: 10.1101/gr.1152803] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%-60% higher mutation rate in exons than in noncoding DNA. We propose a differential CpG content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. We find that the increased exonic rate is the result of the relative overabundance of synonymous sites involved in CpG dinucleotides, as the evolutionary divergence in non-CpG sites is similar in noncoding DNA and synonymous sites of exons. Expectations and predictions of our hypothesis are confirmed in comparisons involving more distantly related species, including human-orangutan, human-baboon, and human-macaque. Our results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms (SNPs) in the synonymous sites of exons compared to the noncoding regions.
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Affiliation(s)
- Sankar Subramanian
- Center for Evolutionary Functional Genomics, Arizona Biodesign Institute, Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA
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4759
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Abstract
The retroviral capacity for integration into the host genome can give rise to endogenous retroviruses (ERVs): retroviral sequences that are transmitted vertically as part of the host germ line, within which they may continue to replicate and evolve. ERVs represent both a unique archive of ancient viral sequence information and a dynamic component of host genomes. As such they hold great potential as informative markers for studies of both virus evolution and host genome evolution. Numerous novel ERVs have been described in recent years, particularly as genome sequencing projects have advanced. This review discusses the evolution of ERV lineages, considering the processes by which ERV distribution and diversity is generated. The diversity of ERVs isolated so far is summarised in terms of both their distribution across host taxa, and their relationships to recognised retroviral genera. Finally the relevance of ERVs to studies of genome evolution, host disease and viral ecology is considered, and recent findings discussed.
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Affiliation(s)
- Robert Gifford
- Department of Biological Sciences, Imperial College, Silwood Park, Buckhurst Road, Ascot Berkshire, SL5 7PY, UK
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4760
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Refinetti R. Effects of prolonged exposure to darkness on circadian photic responsiveness in the mouse. Chronobiol Int 2003; 20:417-40. [PMID: 12868538 DOI: 10.1081/cbi-120021443] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Circadian rhythms in mammals are generated by an endogenous pacemaker but are modulated by environmental cycles, principally the alternation of light and darkness. Although much is known about nonparametric effects of light on the circadian system, little is known about other effects of photic stimulation. In the present study, which consists of a series of five experiments in mice, various manipulations of photic stimulation were used to dissect the mechanisms responsible for a variation in the magnitude of light-induced phase-shifts that results from prolonged exposure to darkness. The results confirmed previous observations that prolonged exposure to darkness causes an increase in the magnitude of phase shifts (both phase advances and phase delays) evoked by discrete light pulses. The results also indicated that the increase in responsiveness results from the lack of exposure to light per se and not from collateral effects of exposure to constant darkness such as the lack of previous entrainment. The lack of exposure to light causes the circadian system to undergo a process of dark adaptation similar to dark adaptation in the visual system but with a much slower temporal course. The results suggest that circadian dark adaptation may take place at the retinal level, but it is not clear whether it involves a change in the sensitivity or maximal responsiveness of the system.
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Affiliation(s)
- Roberto Refinetti
- Circadian Rhythm Laboratory, University of South Carolina, Walterboro, South Carolina 29488, USA.
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4761
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4762
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Gagnier L, Wilhelm BT, Mager DL. Ly49 genes in non-rodent mammals. Immunogenetics 2003; 55:109-15. [PMID: 12712264 DOI: 10.1007/s00251-003-0558-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2002] [Revised: 02/21/2003] [Indexed: 11/29/2022]
Abstract
The Ly49 family of natural killer (NK) receptors is encoded by a highly polymorphic multigene family in the mouse and is also present in multiple copies in the rat. However, this gene exists as a single copy in primates and is mutated to non-function in humans. We recently showed that the cow also likely has only one Ly49 gene, but it is unclear what the Ly49 gene content is for other mammals. We have now isolated Ly49 cDNAs from the domestic cat, dog and pig and show that the corresponding gene appears to be single copy in these three species. The open reading frame is intact in all the genes and the putative proteins contain an immune tyrosine-based inhibition motif (ITIM), suggesting a role as an inhibitory receptor. In contrast to the other mammals, several Ly49-like genes appear to exist in the horse, indicating that amplification of this locus has occurred in a non-rodent lineage. Finally, phylogenetic analysis suggests that the rodent Ly49 genes have evolved more rapidly than their counterparts in mammals where the gene has remained as a single copy.
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Affiliation(s)
- Liane Gagnier
- Terry Fox Laboratory, B.C. Cancer Research Centre, 601 West 10th Avenue, V5Z1L3, Vancouver, B.C., Canada
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4763
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Barrans JD, Ip J, Lam CW, Hwang IL, Dzau VJ, Liew CC. Chromosomal distribution of the human cardiovascular transcriptome. Genomics 2003; 81:519-24. [PMID: 12706110 DOI: 10.1016/s0888-7543(03)00008-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
On the basis of previous observations in chromosomes 21 and 22, we hypothesize that there is a tissue-specific organization of cardiovascular gene transcripts in the human genome. To examine the distribution of heart-derived transcripts, we assigned a nonredundant set of 4628 fetal and 3574 adult known and uncharacterized cardiovascular expressed-sequence tags (cvESTs) to 5-Mb chromosomal 'windows' on the basis of publicly available sequence mapping data. On a whole-genome level (36,617 genes), chromosome 17 (19.2% in fetal, 16.5% in adult) contained the highest proportion of cvESTs, whereas chromosome Y (2.0% in fetal and adult) contained the lowest. In total, 50 of the 639 windows contained a significantly higher proportion of cvESTs (P < 0.003) compared with the genome-wide cvEST gene density, particularly on gene-dense chromosomes (that is, 17, 19, 22) as opposed to gene-rich chromosomes (for example, 1, 2, 11). This report provides insight into a possible role for complex tissue-specific gene regulation in the human genome.
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Affiliation(s)
- J David Barrans
- The Cardiovascular Genome Unit, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Thorn 1334, Boston, MA 02115, USA
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4764
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Kallos MS, Sen A, Behie LA. Large-scale expansion of mammalian neural stem cells: a review. Med Biol Eng Comput 2003; 41:271-82. [PMID: 12803291 DOI: 10.1007/bf02348431] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A relatively new approach to the treatment of neurodegenerative diseases is the direct use of neural stem cells (NSCs) as therapeutic agents. The expected demand for treatment from the millions of afflicted individuals, coupled with the expected demand from biotechnology companies creating therapies, has fuelled the need to develop large-scale culture methods for these cells. The rapid pace of discovery in this area has been assisted through the use of animal model systems, enabling many experiments to be performed quickly and effectively. This review focuses on recent developments in expanding human and murine NSCs on a large scale, including the development of new serum-free media and bioreactor protocols. In particular, engineering studies that characterise important scale-up parameters are examined, including studies examining the effects of long-term culture of NSCs in suspension bioreactors. In addition, recent advances in the human NSC system are reviewed, including techniques for the evaluation of NSC characteristics.
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Affiliation(s)
- M S Kallos
- Pharmaceutical Production Research Facility, Faculty of Engineering, University of Calgary, Calgary, Alberta, Canada
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4765
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Reed DR, Li X, McDaniel AH, Lu K, Li S, Tordoff MG, Price RA, Bachmanov AA. Loci on chromosomes 2, 4, 9, and 16 for body weight, body length, and adiposity identified in a genome scan of an F2 intercross between the 129P3/J and C57BL/6ByJ mouse strains. Mamm Genome 2003; 14:302-13. [PMID: 12856282 PMCID: PMC1435867 DOI: 10.1007/s00335-002-2170-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mice have proved to be a powerful model organism for understanding obesity in humans. Single gene mutants and genetically modified mice have been used to identify obesity genes, and the discovery of loci for polygenic forms of obesity in the mouse is an important next step. To pursue this goal, the inbred mouse strains 129P3/J (129) and C57BL/6ByJ (B6), which differ in body weight, body length, and adiposity, were used in an F2 cross to identify loci affecting these phenotypes. Linkages were determined in a two-phase process. In the first phase, 169 randomly selected F2 mice were genotyped for 134 markers that covered all autosomes and the X Chromosome (Chr). Significant linkages were found for body weight and body length on Chr 2. In addition, we detected several suggestive linkages on Chr 2 (adiposity), 9 (body weight, body length, and adiposity), and 16 (adiposity), as well as two suggestive sex-dependent linkages for body length on Chrs 4 and 9. In the second phase, 288 additional F2 mice were genotyped for markers near these regions of linkage. In the combined set of 457 F2 mice, six significant linkages were found: Chr 2 (Bwq5, body weight and Bdln3, body length), Chr 4 (Bdln6, body length, males only), Chr 9 (Bwq6, body weight and Adip5, adiposity), and Chr 16 (Adip9, adiposity), as well as several suggestive linkages (Adip2, adiposity on Chr 2, Bdln4 and Bdln5, body length on Chr 9). In addition, there was a suggestive linkage to body length in males on Chr 9 (Bdln4). For adiposity, there was evidence for epistatic interactions between loci on Chr 9 (Adip5) and 16 (Adip9). These results reinforce the concept that obesity is a complex trait. Genetic loci and their interactions, in conjunction with sex, age, and diet, determine body size and adiposity in mice.
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Affiliation(s)
- Danielle R Reed
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, Pennsylvania 19104, USA.
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4766
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Hellmann I, Zollner S, Enard W, Ebersberger I, Nickel B, Paabo S. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res 2003; 13:831-7. [PMID: 12727903 PMCID: PMC430916 DOI: 10.1101/gr.944903] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection. Further, when the divergence between human and chimpanzee is compared with the extent of nucleotide polymorphisms among humans in the same sequences, there is significantly higher divergence in the 5' untranslated regions (UTRs) but not in other parts of the transcript. This indicates that positive selection may have had a considerable influence on 5'UTRs. The dinucleotide CG (CpG) also exhibits a different substitution pattern within 5'UTRs as compared with other parts of the genome.
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Affiliation(s)
- Ines Hellmann
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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4767
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Response to Petri: Can a proteomics strategy be used to identify the anti-malarial activity of chloroquine? Trends Pharmacol Sci 2003. [DOI: 10.1016/s0165-6147(03)00072-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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4768
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Abstract
Understanding the genetic basis of the physical and behavioural traits that distinguish humans from other primates presents one of the great new challenges in biology. Of the millions of base-pair differences between humans and chimpanzees, which particular changes contributed to the evolution of human features after the separation of the Pan and Homo lineages 5-7 million years ago? How can we identify the 'smoking guns' of human genetic evolution from neutral ticks of the molecular evolutionary clock? The magnitude and rate of morphological evolution in hominids suggests that many independent and incremental developmental changes have occurred that, on the basis of recent findings in model animals, are expected to be polygenic and regulatory in nature. Comparative genomics, population genetics, gene-expression analyses and medical genetics have begun to make complementary inroads into the complex genetic architecture of human evolution.
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Affiliation(s)
- Sean B Carroll
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, Wisconsin 53706, USA.
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4769
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Collins FS, Green ED, Guttmacher AE, Guyer MS. A vision for the future of genomics research. Nature 2003; 422:835-47. [PMID: 12695777 DOI: 10.1038/nature01626] [Citation(s) in RCA: 1004] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2003] [Accepted: 03/25/2003] [Indexed: 01/04/2023]
Affiliation(s)
- Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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4770
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Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest 2003. [DOI: 10.1172/jci200317842] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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4771
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Pennacchio LA, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest 2003; 111:1099-106. [PMID: 12697725 PMCID: PMC152942 DOI: 10.1172/jci17842] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Len A Pennacchio
- Genome Sciences Department, MS 84-171, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
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4772
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Gordon JI, Stappenbeck TS, Hooper LV. Response from Jeffrey I. Gordon et al.: Commensal bacteria make a difference. Trends Microbiol 2003; 11:150-1. [PMID: 12706987 DOI: 10.1016/s0966-842x(03)00044-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The importance of the gut microbiota has been recognized since the days of Pasteur. What makes today different from yesterday, and tomorrow so exciting, is that we now have the tools to identify the molecular mechanisms that regulate assembly of the microbiota and determine how its components affect postnatal mammalian development and adult physiology.
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Affiliation(s)
- Jeffrey I Gordon
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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4773
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Moore JB, Blanchard RK, Cousins RJ. Dietary zinc modulates gene expression in murine thymus: results from a comprehensive differential display screening. Proc Natl Acad Sci U S A 2003; 100:3883-8. [PMID: 12646709 PMCID: PMC153017 DOI: 10.1073/pnas.0330670100] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Differential mRNA display was used to comprehensively screen the murine thymic transcriptome for genes modulated in vivo by dietary zinc. A moderate feeding protocol rendered young adult, outbred mice zinc-deficient and zinc-supplemented without alterations in feeding behavior or growth. However, these levels of deficiency and supplementation altered specific mRNA abundances in a manner detectable by differential display. In total, 240 primer-pair combinations were used to generate >48,000 interpretable cDNA bands derived from thymic total RNA, of which only 265 or 0.55% were identified as zinc-modulated under these moderate dietary conditions. The most strongly zinc-modulated cDNAs identified by display were reamplified and sequenced. No cDNAs encoding zinc-metalloenzymes or zinc-finger transcription factors were identified as zinc-modulated in this global screening. Those zinc-regulated genes independently confirmed by quantitative PCR included: heat shock proteins 40 and 60; heat shock cognate 70; histocompatibility 2, class II antigen A, alpha; and the T cell cytokine receptor. In addition, a variety of transcription- and translation-related factors (such as ribosomal proteins L3, L5, and L28; nuclear matrix protein 84; matrin cyclophilin; the H3 histone family 3A protein; beta(2) microglobulin; and a cleavage and polyadenylation factor) were identified as zinc-modulated. These profiling data show that differential expression of genes in the thymus in response to the dietary zinc supply precedes many of the phenotypic effects on thymic function associated with severe zinc restriction or supplementation. Several genes involved in T cell development were identified as regulated by zinc and will be targets to evaluate the effects of zinc on immune function.
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Affiliation(s)
- J Bernadette Moore
- Nutritional Genomics Laboratory, Food Science and Human Nutrition Department and Center for Nutritional Sciences, University of Florida, Gainesville, FL 32611-0370, USA
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4774
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Abstract
The construction of evolutionary trees is now a standard part of exploratory sequence analysis. Bayesian methods for estimating trees have recently been proposed as a faster method of incorporating the power of complex statistical models into the process. Researchers who rely on comparative analyses need to understand the theoretical and practical motivations that underlie these new techniques, and how they differ from previous methods. The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.
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Affiliation(s)
- Mark Holder
- Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, Connecticut 06269-3043, USA.
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4775
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Abstract
Evolution is of interest not only to developmental biology but also to genetics and genomics. We are witnessing a new era in which evolution, development, genetics and genomics are merging to form a new discipline, a good example of which is the study of the origin and evolution of the chordates. Recent studies on the formation of the notochord and the dorsal neural tube in the increasingly famous Ciona intestinalis tadpole larva, and the availability of its draft genome, show how the combination of comparative molecular development and evolutionary genomics might help us to better understand our chordate ancestor.
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Affiliation(s)
- Nori Satoh
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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4776
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Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 2003; 4:251-62. [PMID: 12671656 DOI: 10.1038/nrg1043] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The increasing number of complete and nearly complete metazoan genome sequences provides a significant amount of material for large-scale comparative genomic analysis. Finding new effective methods to analyse such enormous datasets has been the object of intense research. Three main areas in comparative genomics have recently shown important developments: whole-genome alignment, gene prediction and regulatory-region prediction. Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them.
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Affiliation(s)
- Abel Ureta-Vidal
- EnsEMBL Project, Room A2-06, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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4777
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Paigen K. One hundred years of mouse genetics: an intellectual history. II. The molecular revolution (1981-2002). Genetics 2003; 163:1227-35. [PMID: 12702670 PMCID: PMC1462511 DOI: 10.1093/genetics/163.4.1227] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kenneth Paigen
- The Jackson Laboratory, Bar Harbor, Maine 04609-1517, USA
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4778
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Dow JAT. THE MOUSE GENOME: A FUTURE FOR COMPARATIVE PHYSIOLOGY? J Exp Biol 2003. [DOI: 10.1242/jeb.00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4779
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Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a database for genomic sequence alignments and annotations. Genome Res 2003; 13:732-41. [PMID: 12671007 PMCID: PMC430176 DOI: 10.1101/gr.603103] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2002] [Accepted: 01/24/2003] [Indexed: 01/26/2023]
Abstract
We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.
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Affiliation(s)
- Belinda Giardine
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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4780
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Abstract
Nutrigenomics is the application of high-throughput genomics tools in nutrition research. Applied wisely, it will promote an increased understanding of how nutrition influences metabolic pathways and homeostatic control, how this regulation is disturbed in the early phase of a diet-related disease and to what extent individual sensitizing genotypes contribute to such diseases. Ultimately, nutrigenomics will allow effective dietary-intervention strategies to recover normal homeostasis and to prevent diet-related diseases.
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Affiliation(s)
- Michael Müller
- Division of Human Nutrition, Wageningen University, Bomenweg 2, 6703 HD Wageningen, The Netherlands.
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4781
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Abstract
The accelerating pace of the discovery of genes has far surpassed our capabilities to understand their biological function--in other words, the phenotypes they engender. We need efficient and comprehensive large-scale phenotyping technologies. This presents a difficult challenge because phenotypes are numerous and diverse, and they can be observed and annotated at the molecular, cellular and organismal level. New technologies and approaches will therefore be required. Here, I describe recent efforts to develop new and efficient technologies for assessing cellular phenotypes.
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Affiliation(s)
- Barry R Bochner
- Biolog, Inc., 3938 Trust Way, Hayward, California 94545, USA.
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4782
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Abstract
For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a 'supergene') and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.
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Affiliation(s)
- S Blair Hedges
- NASA Astrobiology Institute and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802-5301, USA.
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4783
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Bowers JE, Chapman BA, Rong J, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003; 422:433-8. [PMID: 12660784 DOI: 10.1038/nature01521] [Citation(s) in RCA: 1024] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 02/05/2003] [Indexed: 11/09/2022]
Abstract
Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ancestry approximately 170-235 million years ago yield conflicting results. This difference may be largely due to the propensity of angiosperms to undergo chromosomal duplication ('polyploidization') and subsequent gene loss ('diploidization'); these evolutionary mechanisms have profound consequences for comparative biology. Here we integrate a phylogenetic approach (relating chromosomal duplications to the tree of life) with a genomic approach (mitigating information lost to diploidization) to show that a genome-wide duplication post-dates the divergence of Arabidopsis from most dicots. We also show that an inferred ancestral gene order for Arabidopsis reveals more synteny with other dicots (exemplified by cotton), and that additional, more ancient duplication events affect more distant taxonomic comparisons. By using partial sequence data for many diverse taxa to better relate the evolutionary history of completely sequenced genomes to the tree of life, we foster comparative approaches to the study of genome organization, consequences of polyploidy, and the molecular basis of quantitative traits.
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Affiliation(s)
- John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
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4784
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Abstract
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.
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Affiliation(s)
- Maureen M Barr
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.
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4785
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Waterston RH, Lander ES, Sulston JE. More on the sequencing of the human genome. Proc Natl Acad Sci U S A 2003; 100:3022-4; author reply 3025-6. [PMID: 12631699 PMCID: PMC152236 DOI: 10.1073/pnas.0634129100] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Robert H Waterston
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA.
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4786
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Adams MD, Sutton GG, Smith HO, Myers EW, Venter JC. The independence of our genome assemblies. Proc Natl Acad Sci U S A 2003; 100:3025-6. [PMID: 16576752 PMCID: PMC152237 DOI: 10.1073/pnas.0637478100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mark D Adams
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850; Institute for Biological Energy Alternatives, 1901 Research Boulevard, Suite 600, Rockville, MD 20850; Department of Electrical Engineering and Computer Sciences, 231 Cory Hall, University of California, Berkeley, CA 94720; and Center for the Advancement of Genomics, 1901 Research Boulevard, Suite 600, Rockville, MD 20850
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4787
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Baum C, Düllmann J, Li Z, Fehse B, Meyer J, Williams DA, von Kalle C. Side effects of retroviral gene transfer into hematopoietic stem cells. Blood 2003; 101:2099-114. [PMID: 12511419 DOI: 10.1182/blood-2002-07-2314] [Citation(s) in RCA: 288] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent conceptual and technical improvements have resulted in clinically meaningful levels of gene transfer into repopulating hematopoietic stem cells. At the same time, evidence is accumulating that gene therapy may induce several kinds of unexpected side effects, based on preclinical and clinical data. To assess the therapeutic potential of genetic interventions in hematopoietic cells, it will be important to derive a classification of side effects, to obtain insights into their underlying mechanisms, and to use rigorous statistical approaches in comparing data. We here review side effects related to target cell manipulation; vector production; transgene insertion and expression; selection procedures for transgenic cells; and immune surveillance. We also address some inherent differences between hematopoiesis in the most commonly used animal model, the laboratory mouse, and in humans. It is our intention to emphasize the need for a critical and hypothesis-driven analysis of "transgene toxicology," in order to improve safety, efficiency, and prognosis for the yet small but expanding group of patients that could benefit from gene therapy.
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Affiliation(s)
- Christopher Baum
- Department of Hematology and Oncology, Hannover Medical School, Hannover, Germany.
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4788
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Venter JC, Levy S, Stockwell T, Remington K, Halpern A. Massive parallelism, randomness and genomic advances. Nat Genet 2003; 33 Suppl:219-27. [PMID: 12610531 DOI: 10.1038/ng1114] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In reviewing the past decade, it is clear that genomics was, and still is, driven by innovative technologies, perhaps more so than any other scientific area in recent memory. From the outset, computing, mathematics and new automated laboratory techniques have been key components in allowing the field to move forward rapidly. We highlight some key innovations that have come together to nurture the explosive growth that makes a new era of genomics a reality. We also document how these new approaches have fueled further innovations and discoveries.
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Affiliation(s)
- J Craig Venter
- The Center for the Advancement of Genomics, 1901 Research Blvd., Rockville, Maryland 20850, USA.
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4789
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Abstract
We urgently need animal models to study infectious disease. Mice are susceptible to a similar range of microbial infections as humans. Marked differences between inbred strains of mice in their response to pathogen infection can be exploited to analyse the genetic basis of infections. In addition, the genetic tools that are available in the laboratory mouse, and new techniques to monitor the expression of bacterial genes in vivo, make it the principal experimental animal model for studying mechanisms of infection and immunity.
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Affiliation(s)
- Jan Buer
- German Research Centre for Biotechnology (GBF), Mascheroder Weg 1, D-38124 Braunschweig, Germany
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4790
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Abstract
Autoimmune diseases are, in general, under complex genetic control and subject to strong interactions between genetics and the environment. Greater knowledge of the underlying genetics will provide immunologists with a framework for study of the immune dysregulation that occurs in such diseases. Ascertaining the number of genes that are involved and their characterization have, however, proven to be difficult. Improved methods of genetic analysis and the availability of a draft sequence of the complete mouse genome have markedly improved the outlook for such research, and they have emphasized the advantages of mice as a model system. In this review, we provide an overview of the genetic analysis of autoimmune diseases and of the crucial role of congenic and consomic mouse strains in such research.
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Affiliation(s)
- Ute C Rogner
- Institut Pasteur, Unité Génétique Moléculaire Murine, 25 rue du Docteur Roux, 75015 Paris, France
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4791
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Affiliation(s)
- Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
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4792
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Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003; 299:1391-4. [PMID: 12610304 DOI: 10.1126/science.1081331] [Citation(s) in RCA: 364] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.
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Affiliation(s)
- Dario Boffelli
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
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4793
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Saada N, Dai B, Echetebu C, Sarna SK, Palade P. Smooth muscle uses another promoter to express primarily a form of human Cav1.2 L-type calcium channel different from the principal heart form. Biochem Biophys Res Commun 2003; 302:23-8. [PMID: 12593842 DOI: 10.1016/s0006-291x(03)00097-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Several different first exons and amino termini have been reported for the cardiac Ca channel known as alpha(1C) or Ca(V)1.2. The aim of this study was to investigate whether the expression of this channel is regulated by different promoters in smooth muscle cells and in heart in humans. Ribonuclease protection assay (RPA) indicates that the longer first exon 1a is found in certain human smooth muscle-containing tissues, notably bladder and fetal aorta, but that it is not expressed to any significant degree in lung or intestine. On the other hand, all four smooth muscle-containing tissues examined strongly express transcripts containing exon 1b, first reported cloned from human fibroblast cells. In addition, primary cultures of human colonic myocytes and coronary artery smooth muscle cells express predominantly transcripts containing exon 1b. The promoter immediately upstream of exon 1b was cloned, and it displays functional promoter activity when luciferase-expressing constructs were transfected into three different cultured smooth muscle cells: primary human coronary artery smooth muscles cells, primary human colonocytes, and the fetal rat aorta-derived A7r5 cell line. These results indicate that expression in smooth muscle is primarily driven by a promoter different from that which drives expression in cardiac myocytes.
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Affiliation(s)
- Nehad Saada
- Department of Physiology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0641, USA
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4794
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Saito R, Suzuki H, Hayashizaki Y. Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality. Biochem Biophys Res Commun 2003; 301:633-40. [PMID: 12565826 DOI: 10.1016/s0006-291x(03)00013-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We performed an integrated computational analysis of data derived from a comprehensive set of protein-protein interactions (interactome) and a phenotype dataset on lethality in Saccharomyces cerevisiae. For the analysis, we selected reliable interactome data using our previous 'interaction generality,' a computational approach to assess reliability of interactions. Those efforts gave clear evidence that proteins with lethal phenotypes in knockout studies (lethal proteins) may interact with each other to form functional protein complexes to perform their cellular roles. However, our analysis indicates that interactions between lethal proteins are rather restricted to the same cellular pathway or function, and it is quite unlikely that they interact with other lethal proteins functioning in different cellular roles. Furthermore, our results allowed us predictions on the functions of thus far uncharacterized lethal proteins with an estimated 93% accuracy. Thus, the analysis described in here can provide global insights into the biological features of the protein complexes.
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Affiliation(s)
- Rintaro Saito
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama, Japan
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4795
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Guigo R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, Reymond A, Abril JF, Keibler E, Lyle R, Ucla C, Antonarakis SE, Brent MR. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A 2003; 100:1140-5. [PMID: 12552088 PMCID: PMC298740 DOI: 10.1073/pnas.0337561100] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2002] [Accepted: 12/11/2002] [Indexed: 11/18/2022] Open
Abstract
A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this goal proved challenging because of the large proportion of the mouse and human genomes that is apparently conserved but apparently does not code for protein. We developed a two-stage procedure that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods. RT-PCR amplification and direct sequencing applied to an initial sample of mouse predictions that do not overlap previously known genes verified the regions flanking one intron in 139 predictions, with verification rates reaching 76%. On average, the confirmed predictions show more restricted expression patterns than the mouse orthologs of known human genes, and two-thirds lack homologs in fish genomes, demonstrating the sensitivity of this dual-genome approach to hard-to-find genes. We verified 112 previously unknown homologs of known proteins, including two homeobox proteins relevant to developmental biology, an aquaporin, and a homolog of dystrophin. We estimate that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes. This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes.
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Affiliation(s)
- Roderic Guigo
- Research Group in Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra/Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain
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4796
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Abstract
Retroviral integrations have been used for many years to identify genes involved in cancer. The recently published mouse genome sequence has allowed large-scale identification of potential human cancer genes and their classification into distinct signaling pathways.
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Affiliation(s)
- Jaquelin P Dudley
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX 78705, USA.
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4797
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Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics 2003; 2:96-106. [PMID: 12644571 DOI: 10.1074/mcp.m200074-mcp200] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have developed a systematic analytical approach, termed PRISM (Proteomic Investigation Strategy for Mammals), that permits routine, large scale protein expression profiling of mammalian cells and tissues. PRISM combines subcellular fractionation, multidimensional liquid chromatography-tandem mass spectrometry-based protein shotgun sequencing, and two newly developed computer algorithms, STATQUEST and GOClust, as a means to rapidly identify, annotate, and categorize thousands of expressed mammalian proteins. The application of PRISM to adult mouse lung and liver resulted in the high confidence identification of over 2,100 unique proteins including more than 100 integral membrane proteins, 400 nuclear proteins, and 500 uncharacterized proteins, the largest proteome study carried out to date on this important model organism. Automated clustering of the identified proteins into Gene Ontology annotation groups allowed for streamlined analysis of the large data set, revealing interesting and physiologically relevant patterns of tissue and organelle specificity. PRISM therefore offers an effective platform for in-depth investigation of complex mammalian proteomes.
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Affiliation(s)
- Thomas Kislinger
- Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
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4798
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Mao JH, Balmain A. Genomic approaches to identification of tumour-susceptibility genes using mouse models. Curr Opin Genet Dev 2003; 13:14-9. [PMID: 12573430 DOI: 10.1016/s0959-437x(03)00005-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Individual susceptibility to cancer in humans is determined by complex interactions between germline genetic variation and levels of exposure to environmental carcinogens or tumour promoters. Only a small fraction of cancer susceptibility is inherited in a Mendelian manner (high-penetrance familial cancer), and most tumours result from the combined effects of many gene-gene and gene-environment interactions. The sequencing of the mouse genome provides new approaches to one of the most challenging tasks of cancer genetics today.
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Affiliation(s)
- Jian-Hua Mao
- University of California, San Francisco Comprehensive Cancer Center, San Francisco, California 94143, USA.
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4799
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4800
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Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W. Global predictions and tests of erythroid regulatory regions. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 68:335-44. [PMID: 15338635 DOI: 10.1101/sqb.2003.68.335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- R C Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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