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Beckett LJ, Williams PM, Toh LS, Hessel V, Gerstweiler L, Fisk I, Toronjo-Urquiza L, Chauhan VM. Advancing insights into microgravity induced muscle changes using Caenorhabditis elegans as a model organism. NPJ Microgravity 2024; 10:79. [PMID: 39060303 PMCID: PMC11282318 DOI: 10.1038/s41526-024-00418-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Spaceflight presents significant challenges to the physiological state of living organisms. This can be due to the microgravity environment experienced during long-term space missions, resulting in alterations in muscle structure and function, such as atrophy. However, a comprehensive understanding of the adaptive mechanisms of biological systems is required to devise potential solutions and therapeutic approaches for adapting to spaceflight conditions. This review examines the current understanding of the challenges posed by spaceflight on physiological changes, alterations in metabolism, dysregulation of pathways and the suitability and advantages of using the model organism Caenorhabditis elegans nematodes to study the effects of spaceflight. Research has shown that changes in the gene and protein composition of nematodes significantly occur across various larval stages and rearing environments, including both microgravity and Earth gravity settings, often mirroring changes observed in astronauts. Additionally, the review explores significant insights into the fundamental metabolic changes associated with muscle atrophy and growth, which could lead to the development of diagnostic biomarkers and innovative techniques to prevent and counteract muscle atrophy. These insights not only advance our understanding of microgravity-induced muscle atrophy but also lay the groundwork for the development of targeted interventions to mitigate its effects in the future.
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Affiliation(s)
- Laura J Beckett
- School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | | | - Li Shean Toh
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Volker Hessel
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | - Lukas Gerstweiler
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
| | - Ian Fisk
- International Flavour Research Centre, Division of Food, Nutrition and Dietetics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
- International Flavour Research Centre (Adelaide), School of Agriculture, Food and Wine and Waite Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Luis Toronjo-Urquiza
- School of Chemical Engineering, North Terrace Campus, The University of Adelaide, Adelaide, SA, Australia
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2
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Melouane A, Ghanemi A, Aubé S, Yoshioka M, St-Amand J. Differential gene expression analysis in ageing muscle and drug discovery perspectives. Ageing Res Rev 2018; 41:53-63. [PMID: 29102726 DOI: 10.1016/j.arr.2017.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022]
Abstract
Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery. Herein, we describe the functional genomics strategies, mainly differential gene expression methods microarray, serial analysis of gene expression (SAGE), massively parallel signature sequence (MPSS), RNA sequencing (RNA seq), representational difference analysis (RDA), and suppression subtractive hybridization (SSH). Furthermore, we review these illustrative approaches that have been used to discover new therapeutic targets for some complex diseases along with the application of these tools to study the modulation of the skeletal muscle transcriptome.
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Gasser RB, Schwarz EM, Korhonen PK, Young ND. Understanding Haemonchus contortus Better Through Genomics and Transcriptomics. ADVANCES IN PARASITOLOGY 2016; 93:519-67. [PMID: 27238012 DOI: 10.1016/bs.apar.2016.02.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Parasitic roundworms (nematodes) cause substantial mortality and morbidity in animals globally. The barber's pole worm, Haemonchus contortus, is one of the most economically significant parasitic nematodes of small ruminants worldwide. Although this and related nematodes can be controlled relatively well using anthelmintics, resistance against most drugs in common use has become a major problem. Until recently, almost nothing was known about the molecular biology of H. contortus on a global scale. This chapter gives a brief background on H. contortus and haemonchosis, immune responses, vaccine research, chemotherapeutics and current problems associated with drug resistance. It also describes progress in transcriptomics before the availability of H. contortus genomes and the challenges associated with such work. It then reviews major progress on the two draft genomes and developmental transcriptomes of H. contortus, and summarizes their implications for the molecular biology of this worm in both the free-living and the parasitic stages of its life cycle. The chapter concludes by considering how genomics and transcriptomics can accelerate research on Haemonchus and related parasites, and can enable the development of new interventions against haemonchosis.
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Affiliation(s)
- R B Gasser
- The University of Melbourne, Parkville, VIC, Australia
| | - E M Schwarz
- The University of Melbourne, Parkville, VIC, Australia; Cornell University, Ithaca, NY, United States
| | - P K Korhonen
- The University of Melbourne, Parkville, VIC, Australia
| | - N D Young
- The University of Melbourne, Parkville, VIC, Australia
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Bens M, Sahm A, Groth M, Jahn N, Morhart M, Holtze S, Hildebrandt TB, Platzer M, Szafranski K. FRAMA: from RNA-seq data to annotated mRNA assemblies. BMC Genomics 2016; 17:54. [PMID: 26763976 PMCID: PMC4712544 DOI: 10.1186/s12864-015-2349-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/22/2015] [Indexed: 11/25/2022] Open
Abstract
Background Advances in second-generation sequencing of RNA made a near-complete characterization of transcriptomes affordable. However, the reconstruction of full-length mRNAs via de novo RNA-seq assembly is still difficult due to the complexity of eukaryote transcriptomes with highly similar paralogs and multiple alternative splice variants. Here, we present FRAMA, a genome-independent annotation tool for de novo mRNA assemblies that addresses several post-assembly tasks, such as reduction of contig redundancy, ortholog assignment, correction of misassembled transcripts, scaffolding of fragmented transcripts and coding sequence identification. Results We applied FRAMA to assemble and annotate the transcriptome of the naked mole-rat and assess the quality of the obtained compilation of transcripts with the aid of publicy available naked mole-rat gene annotations. Based on a de novo transcriptome assembly (Trinity), FRAMA annotated 21,984 naked mole-rat mRNAs (12,100 full-length CDSs), corresponding to 16,887 genes. The scaffolding of 3488 genes increased the median sequence information 1.27-fold. In total, FRAMA detected and corrected 4774 misassembled genes, which were predominantly caused by fusion of genes. A comparison with three different sources of naked mole-rat transcripts reveals that FRAMA’s gene models are better supported by RNA-seq data than any other transcript set. Further, our results demonstrate the competitiveness of FRAMA to state of the art genome-based transcript reconstruction approaches. Conclusion FRAMA realizes the de novo construction of a low-redundant transcript catalog for eukaryotes, including the extension and refinement of transcripts. Thereby, results delivered by FRAMA provide the basis for comprehensive downstream analyses like gene expression studies or comparative transcriptomics. FRAMA is available at https://github.com/gengit/FRAMA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2349-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Bens
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Arne Sahm
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Marco Groth
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Niels Jahn
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Michaela Morhart
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
| | - Matthias Platzer
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
| | - Karol Szafranski
- Leibniz Institute on Ageing - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany.
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Moroz LL. Biodiversity Meets Neuroscience: From the Sequencing Ship (Ship-Seq) to Deciphering Parallel Evolution of Neural Systems in Omic's Era. Integr Comp Biol 2015; 55:1005-17. [PMID: 26163680 DOI: 10.1093/icb/icv084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The origins of neural systems and centralized brains are one of the major transitions in evolution. These events might occur more than once over 570-600 million years. The convergent evolution of neural circuits is evident from a diversity of unique adaptive strategies implemented by ctenophores, cnidarians, acoels, molluscs, and basal deuterostomes. But, further integration of biodiversity research and neuroscience is required to decipher critical events leading to development of complex integrative and cognitive functions. Here, we outline reference species and interdisciplinary approaches in reconstructing the evolution of nervous systems. In the "omic" era, it is now possible to establish fully functional genomics laboratories aboard of oceanic ships and perform sequencing and real-time analyses of data at any oceanic location (named here as Ship-Seq). In doing so, fragile, rare, cryptic, and planktonic organisms, or even entire marine ecosystems, are becoming accessible directly to experimental and physiological analyses by modern analytical tools. Thus, we are now in a position to take full advantages from countless "experiments" Nature performed for us in the course of 3.5 billion years of biological evolution. Together with progress in computational and comparative genomics, evolutionary neuroscience, proteomic and developmental biology, a new surprising picture is emerging that reveals many ways of how nervous systems evolved. As a result, this symposium provides a unique opportunity to revisit old questions about the origins of biological complexity.
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Affiliation(s)
- Leonid L Moroz
- The Whitney Laboratory for Marine Bioscience and Department of Neuroscience and McKnight Brain Institute, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
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6
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Cantacessi C, Hofmann A, Campbell BE, Gasser RB. Impact of next-generation technologies on exploring socioeconomically important parasites and developing new interventions. Methods Mol Biol 2015; 1247:437-474. [PMID: 25399114 DOI: 10.1007/978-1-4939-2004-4_31] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-throughput molecular and computer technologies have become instrumental for systems biological explorations of pathogens, including parasites. For instance, investigations of the transcriptomes of different developmental stages of parasitic nematodes give insights into gene expression, regulation and function in a parasite, which is a significant step to understanding their biology, as well as interactions with their host(s) and disease. This chapter (1) gives a background on some key parasitic nematodes of socioeconomic importance, (2) describes sequencing and bioinformatic technologies for large-scale studies of the transcriptomes and genomes of these parasites, (3) provides some recent examples of applications and (4) emphasizes the prospects of fundamental biological explorations of parasites using these technologies for the development of new interventions to combat parasitic diseases.
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Affiliation(s)
- Cinzia Cantacessi
- Department of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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7
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Cantacessi C, Campbell BE, Gasser RB. Key strongylid nematodes of animals — Impact of next-generation transcriptomics on systems biology and biotechnology. Biotechnol Adv 2012; 30:469-88. [DOI: 10.1016/j.biotechadv.2011.08.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/09/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
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Blaxter M, Kumar S, Kaur G, Koutsovoulos G, Elsworth B. Genomics and transcriptomics across the diversity of the Nematoda. Parasite Immunol 2012; 34:108-20. [PMID: 22044053 DOI: 10.1111/j.1365-3024.2011.01342.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The diversity of biology in nematodes is reflected in the diversity of their genomes. Parasitic species in particular have evolved mechanisms to invade and outwit their hosts, and these offer opportunities for the development of control measures. Genomic analyses can reveal the molecular underpinnings of phenotypes such as parasitism and thus, initiate and support research programmes that explore the manipulation of host and parasite physiologies to achieve favourable outcomes. Wide sampling across nematode diversity allows phylogenetically informed formulation of research hypotheses, identification of core features shared by all species or important evolutionary novelties present in isolated clades. Many nematode species have been investigated through the use of the expressed sequence tag approach, which samples from the transcribed genome. Gene catalogues generated in this way can be explored to reveal the patterns of expression associated with parasitism and candidates for testing as drug targets or vaccine components. Analysis environments, such as NEMBASE facilitate exploitation of these data. The development of new high-throughput DNA-sequencing technologies has facilitated transcriptomic and genomic approaches to parasite biology. Whole genome sequencing offers more complete catalogues of genes and assists a systems approach to phenotype dissection. These efforts are being coordinated through the 959 Nematode Genomes initiative.
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Affiliation(s)
- M Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, UK.
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9
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Drumm ML, Ziady AG, Davis PB. Genetic variation and clinical heterogeneity in cystic fibrosis. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2011; 7:267-82. [PMID: 22017581 DOI: 10.1146/annurev-pathol-011811-120900] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis (CF), a lethal genetic disease, is characterized by substantial clinical heterogeneity. Work over the past decade has established that much of the variation is genetically conferred, and recent studies have begun to identify chromosomal locations that identify specific genes as contributing to this variation. Transcriptomic and proteomic data, sampling hundreds and thousands of genes and their products, point to pathways that are altered in the cells and tissues of CF patients. Genetic studies have examined more than half a million polymorphic sites and have identified regions, and probably genes, that contribute to the clinical heterogeneity. The combination of these approaches has great potential because genetic profiling identifies putative disease-modifying processes, and transcript and protein profiling is shedding light on the biology involved. Such studies are providing new insights into the disease, such as altered apoptotic responses, oxidative stress dysregulation, and neuronal involvement, all of which may open new therapeutic avenues to exploration.
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Affiliation(s)
- Mitchell L Drumm
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.
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10
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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11
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Margam VM, Coates BS, Bayles DO, Hellmich RL, Agunbiade T, Seufferheld MJ, Sun W, Kroemer JA, Ba MN, Binso-Dabire CL, Baoua I, Ishiyaku MF, Covas FG, Srinivasan R, Armstrong J, Murdock LL, Pittendrigh BR. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011; 6:e21388. [PMID: 21754987 PMCID: PMC3130784 DOI: 10.1371/journal.pone.0021388] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 05/26/2011] [Indexed: 01/31/2023] Open
Abstract
The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs) were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.
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Affiliation(s)
- Venu M. Margam
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Brad S. Coates
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Darrell O. Bayles
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Richard L. Hellmich
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Tolulope Agunbiade
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Manfredo J. Seufferheld
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Weilin Sun
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jeremy A. Kroemer
- United States Department of Agriculture – Agricultural Research Service, Corn Insect and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, Iowa, United States of America
| | - Malick N. Ba
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Clementine L. Binso-Dabire
- Institut de l'Environnement et de Recherches Agricoles (INERA), Station de Kamboinsé, Ouagadougou, Burkina Faso
| | - Ibrahim Baoua
- Institut National de Recherche Agronomique du Niger, Maradi, Niger
| | - Mohammad F. Ishiyaku
- Department of Plant Science, Institute for Agricultural Research, Ahmadu Bello University, Zaria, Nigeria
| | | | | | - Joel Armstrong
- Ecosystem Sciences, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, Australian Capital Territory, Australia
| | - Larry L. Murdock
- Department of Entomology, Purdue University, West Lafayette, Indiana, United States of America
| | - Barry R. Pittendrigh
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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12
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Lu FH, Cho MC, Park YJ. Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol Biol Rep 2011; 39:3327-35. [PMID: 21706160 DOI: 10.1007/s11033-011-1102-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 06/15/2011] [Indexed: 12/01/2022]
Abstract
Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.
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Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-802, Republic of Korea
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13
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Lamm AT, Stadler MR, Zhang H, Gent JI, Fire AZ. Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res 2011; 21:265-75. [PMID: 21177965 PMCID: PMC3032930 DOI: 10.1101/gr.108845.110] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 10/11/2010] [Indexed: 02/06/2023]
Abstract
We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.
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Affiliation(s)
- Ayelet T. Lamm
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Michael R. Stadler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Huibin Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Jonathan I. Gent
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
| | - Andrew Z. Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5324, USA
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Bowden P, Pendrak V, Zhu P, Marshall JG. Meta sequence analysis of human blood peptides and their parent proteins. J Proteomics 2010; 73:1163-75. [PMID: 20170764 DOI: 10.1016/j.jprot.2010.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 01/23/2010] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
Abstract
Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and gene ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human ENSEMBL, SwissProt and RefSeq databases by SQL. The reported peptide and protein sequences were organized into an SQL database with full protein sequences and up to five unique peptides in order of prevalence along with the peptide count for each protein. Structured query language or BLAST was used to acquire descriptive information in current databases. Sampling error at the level of peptides is the largest source of disparity between groups. Chi Square analysis of peptide to protein distributions confirmed the significant agreement between groups on identified proteins.
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Affiliation(s)
- Peter Bowden
- Department of Chemistry and Biology, Ryerson University, Toronto, Canada
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15
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Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 2009; 10:135-51. [PMID: 19715439 DOI: 10.1146/annurev-genom-082908-145957] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptome analysis has been a key area of biological inquiry for decades. Over the years, research in the field has progressed from candidate gene-based detection of RNAs using Northern blotting to high-throughput expression profiling driven by the advent of microarrays. Next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency, Genome Sciences Center, Vancouver, BC V5Z 4S6, Canada.
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Bowden P, Beavis R, Marshall J. Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system. J Proteomics 2009; 73:103-11. [PMID: 19703602 DOI: 10.1016/j.jprot.2009.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 08/04/2009] [Accepted: 08/17/2009] [Indexed: 01/23/2023]
Abstract
A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.
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Affiliation(s)
- Peter Bowden
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON, Canada M5B 2K3
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17
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Abstract
A common task in EST projects is the conversion of sequence chromatograms originating from gel-based or capillary sequencers into annotated sequence objects. Here we describe the usage of a software pipeline (available from http://www.nematodes.org/bioinformatics/ ), which has been developed to make the most of EST datasets. This modular software solution is targeted toward small- to medium-sized EST projects and comprises a series of Perl scripts. The software design is based on our experience during EST projects for parasitic nematodes and other species. The trace2dbest module processes sequence trace files and prepares the text files necessary for the submission of the sequences to the public repository dbEST. PartiGene provides facilities for clustering and assembling the ESTs into putative gene objects or unigenes and organizes the data in a relational database. Additional tools are available for annotation and for making the data accessible via the World Wide Web.
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Affiliation(s)
- Ralf Schmid
- Department of Biochemistry, University of Leicester, Leicester, UK
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18
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Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J. Sequence assembly. Comput Biol Chem 2008; 33:121-36. [PMID: 19152793 DOI: 10.1016/j.compbiolchem.2008.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 11/28/2008] [Accepted: 11/28/2008] [Indexed: 01/20/2023]
Abstract
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.
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Affiliation(s)
- K Scheibye-Alsing
- Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
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19
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Jankowski A, Zhu P, Marshall JG. Capture of an activated receptor complex from the surface of live cells by affinity receptor chromatography. Anal Biochem 2008; 380:235-48. [DOI: 10.1016/j.ab.2008.05.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 05/16/2008] [Accepted: 05/18/2008] [Indexed: 11/30/2022]
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20
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Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008; 92:255-64. [PMID: 18703132 DOI: 10.1016/j.ygeno.2008.07.001] [Citation(s) in RCA: 665] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 07/04/2008] [Accepted: 07/09/2008] [Indexed: 12/17/2022]
Abstract
A new generation of sequencing technologies, from Illumina/Solexa, ABI/SOLiD, 454/Roche, and Helicos, has provided unprecedented opportunities for high-throughput functional genomic research. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted resequencing, discovery of transcription factor binding sites, and noncoding RNA expression profiling. This review discusses applications of next-generation sequencing technologies in functional genomics research and highlights the transforming potential these technologies offer.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency Genome Sciences Centre, Vancouver, BC, Canada
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21
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Wan KH, Yu C, George RA, Carlson JW, Hoskins RA, Svirskas R, Stapleton M, Celniker SE. High-throughput plasmid cDNA library screening. Nat Protoc 2007; 1:624-32. [PMID: 17406289 DOI: 10.1038/nprot.2006.90] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Libraries of cDNA clones are valuable resources for analyzing the expression, structure and regulation of genes, and for studying protein functions and interactions. Full-length cDNA clones provide information about intron and exon structures, splice junctions, and 5' and 3' untranslated regions (UTRs). Open reading frames (ORFs) derived from cDNA clones can be used to generate constructs allowing the expression of both wild-type proteins and proteins tagged at their amino or carboxy terminus. Thus, obtaining full-length cDNA clones and sequences for most or all genes in an organism is essential for understanding genome functions. EST sequencing samples cDNA libraries at random, an approach that is most useful at the beginning of large-scale screening projects. As projects progress towards completion, however, the probability of identifying unique cDNAs by EST sequencing diminishes, resulting in poor recovery of rare transcripts. Here we describe an adapted, high-throughput protocol intended for the recovery of specific, full-length clones from plasmid cDNA libraries in 5 d.
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Affiliation(s)
- Kenneth H Wan
- Department of Genome Sciences, Earnest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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22
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Dornelas MC, Camargo RLB, Berger IJ, Takita MA. Towards the identification of flower-specific genes in Citrus spp. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000500005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJM. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 2006; 7:246. [PMID: 17010196 PMCID: PMC1592491 DOI: 10.1186/1471-2164-7-246] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 09/29/2006] [Indexed: 11/10/2022] Open
Abstract
Background High throughput sequencing-by-synthesis is an emerging technology that allows the rapid production of millions of bases of data. Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell. Results We present the utility of massively parallel sequencing by synthesis for profiling the transcriptome of a human prostate cancer cell-line, LNCaP, that has been treated with the synthetic androgen, R1881. Through the generation of approximately 20 megabases (MB) of EST data, we detect transcription from over 10,000 gene loci, 25 previously undescribed alternative splicing events involving known exons, and over 1,500 high quality single nucleotide discrepancies with the reference human sequence. Further, we map nearly 10,000 ESTs to positions on the genome where no transcription is currently predicted to occur. We also characterize various obstacles with using sequencing by synthesis for transcriptome analysis and propose solutions to these problems. Conclusion The use of high-throughput sequencing-by-synthesis methods for transcript profiling allows the specific and sensitive detection of many of a cell's transcripts, and also allows the discovery of high quality base discrepancies, and alternative splice variants. Thus, this technology may provide an effective means of understanding various disease states, discovering novel targets for disease treatment, and discovery of novel transcripts.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Alternative Splicing
- Androgens
- Cell Line, Tumor/chemistry
- Cell Line, Tumor/drug effects
- Chromosome Mapping
- Chromosomes, Human/genetics
- DNA, Complementary/genetics
- Exons/genetics
- Expressed Sequence Tags
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Male
- Metribolone/pharmacology
- Neoplasms, Hormone-Dependent/genetics
- Neoplasms, Hormone-Dependent/pathology
- Polymorphism, Single Nucleotide
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Sequence Alignment
- Sequence Analysis, DNA/methods
- Sequence Homology, Nucleic Acid
- Transcription, Genetic
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Affiliation(s)
- Matthew N Bainbridge
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - René L Warren
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin Hirst
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Tammy Romanuik
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Thomas Zeng
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Anne Go
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Allen Delaney
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Malachi Griffith
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Matthew Hickenbotham
- Washington University School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA
| | - Vincent Magrini
- Washington University School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA
| | - Elaine R Mardis
- Washington University School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA
| | - Marianne D Sadar
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Asim S Siddiqui
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Marco A Marra
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven JM Jones
- British Columbia Cancer Agency (BCCA) Genome Sciences Centre, Vancouver, British Columbia, Canada
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24
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Hillier LW, Coulson A, Murray JI, Bao Z, Sulston JE, Waterston RH. Genomics in C. elegans: so many genes, such a little worm. Genome Res 2006; 15:1651-60. [PMID: 16339362 DOI: 10.1101/gr.3729105] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and analyses, including a curated set of 19,735 protein-coding genes--with >90% directly supported by experimental evidence--and >1300 noncoding RNA genes. High-throughput efforts are under way to complete the gene sets, along with studies to characterize gene expression, function, and regulation on a genome-wide scale. The success of the worm project has had a profound effect on genome sequencing and on genomics more broadly. We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health.
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Affiliation(s)
- Ladeana W Hillier
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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25
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Hoskins RA, Stapleton M, George RA, Yu C, Wan KH, Carlson JW, Celniker SE. Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). Nucleic Acids Res 2005; 33:e185. [PMID: 16326860 PMCID: PMC1301602 DOI: 10.1093/nar/gni184] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5′- and 3′-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequence Tag (EST) sequencing is the method of choice for recovering cDNAs representing many of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a cDNA library at random, and it recovers transcripts with low expression levels inefficiently. We describe a PCR-based method for directed screening of plasmid cDNA libraries. We demonstrate its utility in a screen of libraries used in our Drosophila EST projects for 153 transcription factor genes that were not represented by full-length cDNA clones in our Drosophila Gene Collection. We recovered high-quality, full-length cDNAs for 72 genes and variously compromised clones for an additional 32 genes. The method can be used at any scale, from the isolation of cDNA clones for a particular gene of interest, to the improvement of large gene collections in model organisms and the human. Finally, we discuss the relative merits of directed cDNA library screening and RT–PCR approaches.
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Affiliation(s)
| | | | | | | | | | | | - Susan E. Celniker
- To whom correspondence should be addressed at Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, One Cyclotron Road MS 64-121, Berkeley, CA 94720, USA. Tel: 510 486 6258; Fax: 510 486 6798;
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26
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Abstract
This is the first of a projected series of canonic reviews covering all invertebrate muscle literature prior to 2005 and covers muscle genes and proteins except those involved in excitation-contraction coupling (e.g., the ryanodine receptor) and those forming ligand- and voltage-dependent channels. Two themes are of primary importance. The first is the evolutionary antiquity of muscle proteins. Actin, myosin, and tropomyosin (at least, the presence of other muscle proteins in these organisms has not been examined) exist in muscle-like cells in Radiata, and almost all muscle proteins are present across Bilateria, implying that the first Bilaterian had a complete, or near-complete, complement of present-day muscle proteins. The second is the extraordinary diversity of protein isoforms and genetic mechanisms for producing them. This rich diversity suggests that studying invertebrate muscle proteins and genes can be usefully applied to resolve phylogenetic relationships and to understand protein assembly coevolution. Fully achieving these goals, however, will require examination of a much broader range of species than has been heretofore performed.
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Affiliation(s)
- Scott L Hooper
- Neuroscience Program, Department of Biological Sciences, Irvine Hall, Ohio University, Athens, Ohio 45701, USA.
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27
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Abstract
Our knowledge of gene and genome organization in nematodes is growing rapidly, partly as a result of the Caenorhabditis elegans genome project. Here Martin Hammond and Ted Bianco review what is known about the organization of genes and genomes in parasitic nematode species, using information gained from molecular and cytological approaches. They suggest that there are implications not only for a wide range of problems in parasitology but also for our understanding of genome evolution in eukaryotes.
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Affiliation(s)
- M P Hammond
- Department of Biochemistry, University of the West Indies, Mona, Kingston 7, Jamaica
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28
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Abstract
A long-term goal of the field of interactome modeling is to understand how global and local properties of complex macromolecular networks impact on observable biological properties, and how changes in such properties can lead to human diseases. The information available at this stage of development of the field provides strong evidence for the existence of such interesting global and local properties, but also demonstrates that many more datasets will be needed to provide accurate models with increasingly predictive capacity. This review focuses on an early attempt at mapping a multicellular interactome network and on the lessons learned from that attempt.
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Affiliation(s)
- Marc Vidal
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.
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29
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Zhou Y, Tang J, Walker MG, Zhang X, Wang J, Hu S, Xu H, Deng Y, Dong J, Ye L, Lin L, Li J, Wang X, Xu H, Pan Y, Lin W, Tian W, Liu J, Wei L, Liu S, Yang H, Yu J, Wang J. Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome. GENOMICS PROTEOMICS & BIOINFORMATICS 2005; 1:26-42. [PMID: 15626331 PMCID: PMC5172415 DOI: 10.1016/s1672-0229(03)01005-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.
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Affiliation(s)
- Yan Zhou
- Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China.
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30
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Clegg N, Abbott D, Ferguson C, Coleman R, Nelson PS. Characterization and comparative analyses of transcriptomes from the normal and neoplastic human prostate. Prostate 2004; 60:227-39. [PMID: 15176052 DOI: 10.1002/pros.20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The prostate gland is a highly specialized organ with functional attributes that serve to enhance the fertility of mammalian species. Pathological processes affecting the prostate include benign prostate hypertrophy and prostate carcinoma; diseases that account for major morbidity and mortality in middle-aged and elderly men. To facilitate studies of biological processes uniquely represented in the prostate and assess molecular alterations associated with prostate carcinoma, we sought to establish the diversity of gene expression in the normal and neoplastic prostate through the compilation and analysis of a prostate transcriptome. METHODS We assembled and annotated ESTs derived from prostate cDNA libraries that were either produced in our laboratory or available from public sequence repositories such as CGAP, dbEST, and Unigene. Determinations of differential gene expression between the normal prostate, other normal tissues, and neoplastic prostate tissues was performed using statistical algorithms. Confirmation of differential expression was performed by quantitative PCR and Northern analysis. RESULTS A total of 99,448 high-quality ESTs were assembled and annotated to produce a prostate transcriptome comprised of 24,580 distinct TUs. Comparative analyses of gene expression levels identified 61 TUs with exclusive expression in the prostate and 45 TUs with high levels of expression in the prostate relative to at least 25 other normal tissues (P > 0.99). Comparative analyses of ESTs derived from neoplastic prostate tissues identified 75 genes with dysregulated expression in cancer (P > 0.99). CONCLUSIONS The human prostate expresses a diverse repertoire of genes that reflect a functionally complex organ. The identification of genes with prostate-restricted or enhanced expression may provide additional insights into the biochemical processes that interact to form the developmental, signaling, and metabolic pathways of the normal and neoplastic gland.
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Affiliation(s)
- Nigel Clegg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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31
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Rabinowicz PD, McCombie WR, Martienssen RA. Gene enrichment in plant genomic shotgun libraries. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:150-156. [PMID: 12667872 DOI: 10.1016/s1369-5266(03)00008-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.
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Affiliation(s)
- Pablo D Rabinowicz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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32
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Sorek R, Safer HM. A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res 2003; 31:1067-74. [PMID: 12560505 PMCID: PMC149192 DOI: 10.1093/nar/gkg170] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A key goal of the Human Genome Project was to understand the complete set of human proteins, the proteome. Since the genome sequence by itself is not sufficient for predicting new genes and alternative splicing events that lead to new proteins, expressed sequence tags (ESTs) are used as the primary tool for these purposes. The high prevalence of artifacts in dbEST, however, often leads to invalid predictions. Here we describe a novel method for recognizing genomic DNA contamination and other artifacts that cannot be identified using current EST cleaning techniques. Our method uses the alignment of the entire set of ESTs to the human genome to identify highly contaminated EST libraries. We discovered 53 highly contaminated libraries and a subset of 24 766 ESTs from these libraries that probably represent contamination with genomic DNA, pre-mRNA, and ESTs that span non-canonical introns. Although this is only a small fraction of the entire EST dataset, each contaminating sequence could create a spurious transcript prediction. Indeed, in the clustering and assembly tool that we used, these sequences would have caused incorrect inference of 9575 new splice variants and 6370 new genes. Conclusions based on EST analysis, including prediction of alternative splicing, should be re-evaluated in light of these results. Our method, along with the identified set of contaminated sequences, will be essential for applications that depend on large EST datasets.
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Affiliation(s)
- Rotem Sorek
- Compugen Ltd, 72 Pinchas Rosen Street, Tel Aviv 69512, Israel.
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33
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McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol 2003; 4:R26. [PMID: 12702207 PMCID: PMC154577 DOI: 10.1186/gb-2003-4-4-r26] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2002] [Revised: 02/17/2003] [Accepted: 02/28/2003] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita. RESULTS From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases. CONCLUSIONS With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses.
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Affiliation(s)
- James P McCarter
- Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St, Louis, MO 63108, USA.
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34
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Maddouri M, Elloumi M. A data mining approach based on machine learning techniques to classify biological sequences. Knowl Based Syst 2002. [DOI: 10.1016/s0950-7051(01)00143-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Blaxter M, Daub J, Guiliano D, Parkinson J, Whitton C. The Brugia malayi genome project: expressed sequence tags and gene discovery. Trans R Soc Trop Med Hyg 2002; 96:7-17. [PMID: 11925998 DOI: 10.1016/s0035-9203(02)90224-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To advance and facilitate molecular studies of Brugia malayi, one of the causative agents of human lymphatic filariasis, an expressed sequence tag (EST)-based gene discovery programme has been carried out. Over 22,000 ESTs have been produced and deposited in the public databases by a consortium of laboratories from endemic and non-endemic countries. The ESTs have been analysed using custom informatic tools to reveal patterns of individual gene expression that may point to potential targets for future research on anti-filarial drugs and vaccines. Many genes first discovered as ESTs are now being analysed by researchers for immunodiagnostic, vaccine and drug target potential. Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species.
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Affiliation(s)
- Mark Blaxter
- Institute of Cell, Animal and Population Biology, Ashworth Laboratories, Kings Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK.
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Jia L, Young MF, Powell J, Yang L, Ho NC, Hotchkiss R, Robey PG, Francomano CA. Gene expression profile of human bone marrow stromal cells: high-throughput expressed sequence tag sequencing analysis. Genomics 2002; 79:7-17. [PMID: 11827452 DOI: 10.1006/geno.2001.6683] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human bone marrow stromal cells (HBMSC) are pluripotent cells with the potential to differentiate into osteoblasts, chondrocytes, myelosupportive stroma, and marrow adipocytes. We used high-throughput DNA sequencing analysis to generate 4258 single-pass sequencing reactions (known as expressed sequence tags, or ESTs) obtained from the 5' (97) and 3' (4161) ends of human cDNA clones from a HBMSC cDNA library. Our goal was to obtain tag sequences from the maximum number of possible genes and to deposit them in the publicly accessible database for ESTs (dbEST of the National Center for Biotechnology Information). Comparisons of our EST sequencing data with nonredundant human mRNA and protein databases showed that the ESTs represent 1860 gene clusters. The EST sequencing data analysis showed 60 novel genes found only in this cDNA library after BLAST analysis against 3.0 million ESTs in NCBI's dbEST database. The BLAST search also showed the identified ESTs that have close homology to known genes, which suggests that these may be newly recognized members of known gene families. The gene expression profile of this cell type is revealed by analyzing both the frequency with which a message is encountered and the functional categorization of expressed sequences. Comparing an EST sequence with the human genomic sequence database enables assignment of an EST to a specific chromosomal region (a process called digital gene localization) and often enables immediate partial determination of intron/exon boundaries within the genomic structure. It is expected that high-throughput EST sequencing and data mining analysis will greatly promote our understanding of gene expression in these cells and of growth and development of the skeleton.
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Affiliation(s)
- Libin Jia
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Parkinson J, Whitton C, Guiliano D, Daub J, Blaxter M. 200000 nematode expressed sequence tags on the Net. Trends Parasitol 2001; 17:394-396. [PMID: 11700236 DOI: 10.1016/s1471-4922(01)01954-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- John Parkinson
- Institute of Cell, Animal and Population Biology, Ashworth Laboratories, Kings Buildings, University of Edinburgh, EH9 3JT, Edinburgh, UK
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38
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Jones D, Candido EP. The NED-8 conjugating system in Caenorhabditis elegans is required for embryogenesis and terminal differentiation of the hypodermis. Dev Biol 2000; 226:152-65. [PMID: 10993680 DOI: 10.1006/dbio.2000.9847] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This work has identified the enzymes involved in the activation and conjugation of the ubiquitin-like protein NED-8 in Caenorhabditis elegans. A C. elegans conjugating enzyme, UBC-12, is highly specific in its ability to utilize NED-8 as a substrate. Immunostaining shows that NED-8 is conjugated in vivo to a major target protein with a conjugate size of 90 kDa. While the amount of this conjugate is developmentally regulated with reduced levels in the larval stages, the mRNA encoding C. elegans UBC-12 is constitutively produced throughout development, as is NED-8 itself. The importance of the NED-8 conjugating system in C. elegans was determined by RNA interference (RNAi) assays using double-stranded RNA encoding NED-8, UBC-12, or the NED-8 activating enzyme component ULA-1. The progeny of both ned-8 and ubc-12 RNAi-treated hermaphrodites either arrested during embryonic development or underwent abnormal postembryonic development. The effect on postembryonic development was pleiotropic, the most frequent gross abnormality being vulval eversion during the L4 stage. Individuals with an everted vulva either burst at the L4 to adult molt or gave rise to adults incapable of egg laying. Additionally, both ned-8 and ubc-12 RNAi induced a striking abnormality in the alae, structures produced by the lateral hypodermal seam cells in the adult nematode. Affected alae were patchy and frequently diverged around a central space. Vulval defects were also produced by RNAi directed at C. elegans ula-1. This is the first demonstration of a requirement for NED-8 conjugation in metazoan development.
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Affiliation(s)
- D Jones
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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39
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Hoekstra R, Visser A, Otsen M, Tibben J, Lenstra JA, Roos MH. EST sequencing of the parasitic nematode Haemonchus contortus suggests a shift in gene expression during transition to the parasitic stages. Mol Biochem Parasitol 2000; 110:53-68. [PMID: 10989145 DOI: 10.1016/s0166-6851(00)00255-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expressed sequence tags from the parasitic nematode Haemonchus contortus were generated in order to identify anchor loci for comparative mapping between nematode genomes and candidate targets for future control measures. In total, 370 SL1 trans-spliced cDNAs from different developmental stages representing 195 different genes were partially sequenced. From these expressed sequence tags 50% were similar to genes with a known or predicted function and 19% were similar to nematode sequences with no ascribed function. From the first, free-living L1 and L3 stages relatively many cDNAs matched to housekeeping genes, and 11% (L1) or 23% (L3) of the encoded proteins were predicted to contain signal peptides. In contrast, no function could be ascribed to most of the cDNAs from the early L5 and adult parasitic stages, but for 30% (L5) or 55% (adult) of the encoded proteins a signal sequence was predicted. This limited analysis suggests that during the transition from the free-living to parasitic stages gene expression shifts towards the synthesis of less conserved extracellular proteins. These proteins offer the best perspectives for vaccine development and the development of anthelmintic drugs. In contrast, cDNAs from the first larval stages may be most suitable for comparative mapping with the free-living nematode Caenorhabditis elegans.
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Affiliation(s)
- R Hoekstra
- Department of Molecular Recognition, Institute for Animal Science and Health (ID-Lelystad), Lelystad, The Netherlands.
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40
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Cherkasova V, Ayyadevara S, Egilmez N, Shmookler Reis R. Diverse Caenorhabditis elegans genes that are upregulated in dauer larvae also show elevated transcript levels in long-lived, aged, or starved adults. J Mol Biol 2000; 300:433-48. [PMID: 10884342 DOI: 10.1006/jmbi.2000.3880] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Under adverse conditions, the nematode Caenorhabditis elegans undergoes reversible developmental arrest as dauer larvae, an alternative third larval stage adapted for dispersal and long-term survival. Following such arrest, which may exceed three times their usual life-span, worms resume development to form reproductive adults of normal subsequent longevity. Mutations of genes in the dauer-formation (daf) pathway can extend life-span two- to fourfold, even in adults that mature without diapause. To identify transcript-level changes that might contribute to extended survival, we prepared a subtractive cDNA library of messages more abundant in dauer than in non-dauer (L3) larvae. Six genes were confirmed as three- to ninefold upregulated in dauer larvae, after correction for mRNA load: genes encoding poly(A)-binding protein (PABP), heat-shock proteins hsp70 and hsp90, and three novel genes of uncertain function. The novel genes encode a partial homologue of human activating signal cointegrator 1 (ASC-1), a GTP-binding homologue of a ribosomal protein, and an SH3-domain protein. Transcript levels for all except hsp70 increased during aging in two C. elegans strains, whereas the three novel genes (and possibly PABP) were also induced to varying degrees by starvation of adults. All six genes are expressed at higher levels in young adults of long-lived daf mutant strains than in normal-longevity controls, suggesting that increased expression of these genes may play a protective function, thus favoring survival in diverse contexts.
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Affiliation(s)
- V Cherkasova
- Departments of Geriatrics, Medicine, and Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, and Central Arkansas Veterans Health Care System - Research 151, 4300 West 7th Street, Little Rock, AR, 72205, USA
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41
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Spence P. From genome to drug--optimising the drug discovery process. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2000; 53:157-91. [PMID: 10616298 DOI: 10.1007/978-3-0348-8735-9_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Current drug discovery and development practices are technologically sophisticated and highly efficient. At the same time the failure rate of compounds in both preclinical and clinical development is high. These failures can be attributed to many factors. Two predominant causes of failure are lack of efficacy and toxicity. Often lack of efficacy is only determined late in the clinical trial process and can be difficult if not impossible to explain, as well as being expensive. Toxicity accounts for many failures during preclinical development, which are less costly, but it also occurs in the clinic. Often the underlying cause of clinical toxicity is never identified. Studies of the structure and activity of the human and other genomes has over the last decade lead to a revolution in biological and medical research. Disease associated genes can now be identified through the application of human genetics, whole genomes have been sequenced and tools have been developed that allow the complete characterization of an organism's gene expression profile in a single experiment. These tools are now being applied to pharmaceutical research and development with the aim to increase the efficiency of the process and the quality of the product.
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Affiliation(s)
- P Spence
- G.D. Searle, St. Louis, MO 63198, USA
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43
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Quackenbush J, Liang F, Holt I, Pertea G, Upton J. The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 2000; 28:141-5. [PMID: 10592205 PMCID: PMC102391 DOI: 10.1093/nar/28.1.141] [Citation(s) in RCA: 271] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide significant additional functional, structural and evolutionary information. Our analysis of the public EST sequences, available through the TIGR Gene Indices (TGI; http://www.tigr.org/tdb/tdb.html ), is an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed for selected organisms by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.
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Affiliation(s)
- J Quackenbush
- The Institute for Genomic Research, Rockville, MD 20850, USA.
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Blaxter M, Ivens A. Reports from the cutting edge of parasitic genome analysis. PARASITOLOGY TODAY (PERSONAL ED.) 1999; 15:430-1. [PMID: 10511682 DOI: 10.1016/s0169-4758(99)01541-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This new feature in Parasitology Today will host reports from the laboratories involved in genomics of parasites, be that sequencing, mapping or 'functional genomics' - the mining and analysis of the sequence datasets, and the development of postgenomics tools to examine gene expression, response to drugs and population variability. It will publicize new technology to wider audiences, let communities of researchers know about novel resources (particularly those available through the World Wide Web) and highlight significant advances in the understanding of parasitic genomes through functional genomics.
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45
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Tetteh KK, Loukas A, Tripp C, Maizels RM. Identification of abundantly expressed novel and conserved genes from the infective larval stage of Toxocara canis by an expressed sequence tag strategy. Infect Immun 1999; 67:4771-9. [PMID: 10456930 PMCID: PMC96808 DOI: 10.1128/iai.67.9.4771-4779.1999] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/1999] [Accepted: 06/01/1999] [Indexed: 12/31/2022] Open
Abstract
Larvae of Toxocara canis, a nematode parasite of dogs, infect humans, causing visceral and ocular larva migrans. In noncanid hosts, larvae neither grow nor differentiate but endure in a state of arrested development. Reasoning that parasite protein production is orientated to immune evasion, we undertook a random sequencing project from a larval cDNA library to characterize the most highly expressed transcripts. In all, 266 clones were sequenced, most from both 3' and 5' ends, and similarity searches against GenBank protein and dbEST nucleotide databases were conducted. Cluster analyses showed that 128 distinct gene products had been found, all but 3 of which represented newly identified genes. Ninety-five genes were represented by a single clone, but seven transcripts were present at high frequencies, each composing >2% of all clones sequenced. These high-abundance transcripts include a mucin and a C-type lectin, which are both major excretory-secretory antigens released by parasites. Four highly expressed novel gene transcripts, termed ant (abundant novel transcript) genes, were found. Together, these four genes comprised 18% of all cDNA clones isolated, but no similar sequences occur in the Caenorhabditis elegans genome. While the coding regions of the four genes are dissimilar, their 3' untranslated tracts have significant homology in nucleotide sequence. The discovery of these abundant, parasite-specific genes of newly identified lectins and mucins, as well as a range of conserved and novel proteins, provides defined candidates for future analysis of the molecular basis of immune evasion by T. canis.
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Affiliation(s)
- K K Tetteh
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, Scotland, United Kingdom
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46
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Hresko MC, Schriefer LA, Shrimankar P, Waterston RH. Myotactin, a novel hypodermal protein involved in muscle-cell adhesion in Caenorhabditis elegans. J Cell Biol 1999; 146:659-72. [PMID: 10444073 PMCID: PMC2150558 DOI: 10.1083/jcb.146.3.659] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In C. elegans, assembly of hypodermal hemidesmosome-like structures called fibrous organelles is temporally and spatially coordinated with the assembly of the muscle contractile apparatus, suggesting that signals are exchanged between these cell types to position fibrous organelles correctly. Myotactin, a protein recognized by monoclonal antibody MH46, is a candidate for such a signaling molecule. The antigen, although expressed by hypodermis, first reflects the pattern of muscle elements and only later reflects the pattern of fibrous organelles. Confocal microscopy shows that in adult worms myotactin and fibrous organelles show coincident localization. Further, cell ablation studies show the bodywall muscle cells are necessary for normal myotactin distribution. To investigate myotactin's role in muscle-hypodermal signaling, we characterized the myotactin locus molecularly and genetically. Myotactin is a novel transmembrane protein of approximately 500 kd. The extracellular domain contains at least 32 fibronectin type III repeats and the cytoplasmic domain contains unique sequence. In mutants lacking myotactin, muscle cells detach when embryonic muscle contraction begins. Later in development, fibrous organelles become delocalized and are not restricted to regions of the hypodermis previously contacted by muscle. These results suggest myotactin helps maintain the association between the muscle contractile apparatus and hypodermal fibrous organelles.
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Affiliation(s)
- M C Hresko
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
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47
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Williams SA. Deep within the filarial genome: progress of the filarial genome project. PARASITOLOGY TODAY (PERSONAL ED.) 1999; 15:219-24. [PMID: 10366827 DOI: 10.1016/s0169-4758(99)01454-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Four years ago, a WHO/United Nations Development Programme/World Bank-sponsored genome project to study the filarial lymphatic nematode parasite Brugia malayi was initiated. The project took as its aims gene discovery for drug target and vaccine candidate identification, genome mapping, dissemination of genomic data to the world community and training of endemic country partners in genomic research. In this article, the principal investigators in the laboratories behind the project describe the background to the project, the data now emerging and goals for the future. Open access to filarial genome data is emphasized.
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Affiliation(s)
- S A Williams
- Department of Biological Sciences, Clark Science Center, Smith College, Northampton, MA 01063, USA.
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48
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Marra M, Hillier L, Kucaba T, Allen M, Barstead R, Beck C, Blistain A, Bonaldo M, Bowers Y, Bowles L, Cardenas M, Chamberlain A, Chappell J, Clifton S, Favello A, Geisel S, Gibbons M, Harvey N, Hill F, Jackson Y, Kohn S, Lennon G, Mardis E, Martin J, Mila L, McCann R, Morales R, Pape D, Person B, Prange C, Ritter E, Soares M, Schurk R, Shin T, Steptoe M, Swaller T, Theising B, Underwood K, Wylie T, Yount T, Wilson R, Waterston R. An encyclopedia of mouse genes. Nat Genet 1999; 21:191-4. [PMID: 9988271 DOI: 10.1038/5976] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The laboratory mouse is the premier model system for studies of mammalian development due to the powerful classical genetic analysis possible (see also the Jackson Laboratory web site, http://www.jax.org/) and the ever-expanding collection of molecular tools. To enhance the utility of the mouse system, we initiated a program to generate a large database of expressed sequence tags (ESTs) that can provide rapid access to genes. Of particular significance was the possibility that cDNA libraries could be prepared from very early stages of development, a situation unrealized in human EST projects. We report here the development of a comprehensive database of ESTs for the mouse. The project, initiated in March 1996, has focused on 5' end sequences from directionally cloned, oligo-dT primed cDNA libraries. As of 23 October 1998, 352,040 sequences had been generated, annotated and deposited in dbEST, where they comprised 93% of the total ESTs available for mouse. EST data are versatile and have been applied to gene identification, comparative sequence analysis, comparative gene mapping and candidate disease gene identification, genome sequence annotation, microarray development and the development of gene-based map resources.
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Affiliation(s)
- M Marra
- Washington University Genome Sequencing Center, St. Louis, Missouri 63108, USA.
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Sluder AE, Mathews SW, Hough D, Yin VP, Maina CV. The Nuclear Receptor Superfamily Has Undergone Extensive Proliferation and Diversification in Nematodes. Genome Res 1999. [DOI: 10.1101/gr.9.2.103] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of theC. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. Most of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF083222–AF083225 and AF083251–AF083234.]
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50
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Abstract
Caenorhabditis elegans is a rhabditid nematode. What relevance does this have for the interpretation of the complete genome sequence, and how will it affect the exploitation of the sequence for scientific and social ends? Nematodes are only distantly related to humans and other animal groups; will this limit the universality of the C. elegans story? Many nematodes are parasites; can knowledge of the C. elegans sequence aid in the prevention and treatment of disease?
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Affiliation(s)
- M Blaxter
- Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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