Genomes and Genes
Summary: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Publications186 found, 100 shown here
- Systematic functional analysis of the Caenorhabditis elegans genome using RNAiRavi S Kamath
Wellcome Trust Cancer Research UK Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
Nature 421:231-7. 2003..Our resulting data set and reusable RNAi library of 16,757 bacterial clones will facilitate systematic analyses of the connections among gene sequence, chromosomal location and gene function in C. elegans...
- The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegansB J Reinhart
Department of Molecular Biology, Massachusetts General Hospital, and Harvard Medical School, Boston 02114, USA
Nature 403:901-6. 2000..We propose that the sequential stage-specific expression of the lin-4 and let-7 regulatory RNAs triggers transitions in the complement of heterochronic regulatory proteins to coordinate developmental timing...
- Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNAA E Pasquinelli
Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
Nature 408:86-9. 2000..elegans and Drosophila, at 48 hours after fertilization in zebrafish, and in adult stages of annelids and molluscs. The let-7 regulatory RNA may control late temporal transitions during development across animal phylogeny...
- Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi libraryJean François Rual
Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Res 14:2162-8. 2004..The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans...
- Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegansB Sönnichsen
Cenix BioScience GmbH, Tatzberg 47 51, D 01307 Dresden, Germany
Nature 434:462-9. 2005....
- Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegansColeen T Murphy
Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 2200, USA
Nature 424:277-83. 2003....
- Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopyP Zipperlen
University of Cambridge, Wellcome CRC Institute and Department of Genetics, Tennis Court Road, Cambridge CB2 1QR, UK
EMBO J 20:3984-92. 2001....
- A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegansS W Knight
Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, 50 North Medical Drive, Room 211, Salt Lake City, UT 84132, USA
Science 293:2269-71. 2001..Mutant animals have germ line defects that lead to sterility, suggesting that cleavage of dsRNA to short pieces is a requisite event in normal development...
- The microRNAs of Caenorhabditis elegansLee P Lim
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
Genes Dev 17:991-1008. 2003..Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species...
- An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegansN C Lau
Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
Science 294:858-62. 2001..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals...
- Mechanistic insights and identification of two novel factors in the C. elegans NMD pathwayDasa Longman
Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, Scotland, United Kingdom
Genes Dev 21:1075-85. 2007..elegans that we have termed smgl (for smg lethal). We show that the encoded proteins are conserved throughout evolution and are required for NMD in C. elegans and also in human cells...
- Asymmetrically distributed PAR-3 protein contributes to cell polarity and spindle alignment in early C. elegans embryosB Etemad-Moghadam
Section of Genetics and Development, Cornell University, Ithaca, New York 14853, USA
Cell 83:743-52. 1995..In addition, the distribution of the PAR-3 protein correlates with differences in cleavage spindle orientation and suggests a mechanism by which PAR-3 contributes to control of cleavage pattern...
- Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPsP A Maroney
Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
RNA 2:735-45. 1996..Finally, we provide evidence that a SL RNP-containing multi-snRNP (SL, U4, U5, and U6 RNPs) may be a functional precursor in trans-spliceosome assembly...
- Two hypotheses to explain why RNA interference does not work in animal parasitic nematodesM E Viney
School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
Int J Parasitol 38:43-7. 2008....
- Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1William M Winston
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Science 295:2456-9. 2002..One of these loci, sid-1, encodes a conserved protein with predicted transmembrane domains. SID-1 is expressed in cells sensitive to RNAi, is localized to the cell periphery, and is required cell-autonomously for systemic RNAi...
- The complete mitochondrial genome of Anisakis simplex (Ascaridida: Nematoda) and phylogenetic implicationsKyu Heon Kim
Department of Parasitology and Medical Research Institute, College of Medicine, Chungbuk National University, Cheongju 361 763, South Korea
Int J Parasitol 36:319-28. 2006....
- Identification and characterization of novel microRNAs from Schistosoma japonicumXiangyang Xue
Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
PLoS ONE 3:e4034. 2008..Although a large number of miRNAs have been identified from plants to mammals, it remains no experimental proof whether schistosome exist miRNAs...
- Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypesNadim W Alkharouf
United States Department of Agriculture, ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705 2350, USA
Exp Parasitol 115:247-58. 2007..Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing...
- Repertoire and evolution of miRNA genes in four divergent nematode speciesElzo de Wit
Hubrecht Institute KNAW and University Medical Center Utrecht, Cancer Genomics Center, Utrecht 3584 CT, The Netherlands
Genome Res 19:2064-74. 2009..The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation...
- Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome IIIP GONCZY
Max Planck Institute for Cell Biology and Genetics, Dresden, Germany
Nature 408:331-6. 2000....
- Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAiErbay Yigit
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Cell 127:747-57. 2006..Interestingly, these AGO proteins lack key residues required for mRNA cleavage. Our findings support a two-step model for RNAi, in which functionally and structurally distinct AGOs act sequentially to direct gene silencing...
- Intronic microRNA precursors that bypass Drosha processingJ Graham Ruby
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 448:83-6. 2007..This suggests that other lineages with many similarly sized introns probably also have mirtrons, and that the mirtron pathway could have provided an early avenue for the emergence of miRNAs before the advent of Drosha...
- The rde-1 gene, RNA interference, and transposon silencing in C. elegansH Tabara
Department of Cell Biology, Program in Molecular Medicine, University of Massachusetts Cancer Center, Worcester 01605, USA
Cell 99:123-32. 1999..We discuss implications for the mechanism of RNAi and the possibility that one natural function of RNAi is transposon silencing...
- Suppression of cathepsin B expression in Schistosoma mansoni by RNA interferencePatrick J Skelly
Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
Int J Parasitol 33:363-9. 2003..This ability to manipulate gene expression represents a powerful new tool for investigating gene function in these debilitating human parasites...
- Genetics: a touch of elegance with RNAiC P Hunter
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
Curr Biol 9:R440-2. 1999..RNA-mediated gene interference (RNAi), a rapid, convenient tool for inhibiting gene function in Caenorhabditis elegans, has recently been shown to work in other organisms...
- Control of developmental timing in Caenorhabditis elegansV Ambros
Department of Biological Sciences, Dartmouth College, Hanover 03755, USA
Curr Opin Genet Dev 10:428-33. 2000..These regulators interact with each other to elaborate stage-specific regulatory switches and act through downstream effectors to control the timing of cell-type-specific developmental events...
- The Caenorhabditis elegans histone hairpin-binding protein is required for core histone gene expression and is essential for embryonic and postembryonic cell divisionJonathan Pettitt
Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, UK
J Cell Sci 115:857-66. 2002..In addition, we have observed defects in the specification of vulval cell fate in animals depleted for histone H3 and H4, which indicates that histone proteins are required for cell fate regulation during vulval development...
- The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events in Caenorhabditis elegansR Feinbaum
Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
Dev Biol 210:87-95. 1999..These results indicate that the temporal profile of lin-4 RNA accumulation specifies the timing of LIN-14 down-regulation and thereby controls the timing of postembryonic developmental events...
- Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genesKaveh Ashrafi
Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Nature 421:268-72. 2003....
- Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicumLili Hao
Laboratory of Parasitology, Institute of Pathogen Biology Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing 100730, PR China
BMC Genomics 11:55. 2010..The objective of this study is to investigate the transcriptional profile and potential function of the small non-coding RNAs in the development of S. japanicum...
- Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timingA Grishok
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
Cell 106:23-34. 2001..Our findings suggest that a common processing machinery generates guide RNAs that mediate both RNAi and endogenous gene regulation...
- Transcriptomics tool for the human Schistosoma blood flukes using microarray gene expression profilingGeoffrey N Gobert
Queensland Institute of Medical Research and Australian Centre for International Health and Nutrition, Brisbane, QLD, Australia
Exp Parasitol 114:160-72. 2006..This is the first microarray commercially manufactured for studying schistosomes, and the large size and verified quality of the resource demonstrate its power for characterising the schistosome transcriptome...
- Functional genomic analysis of RNA interference in C. elegansJohn K Kim
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
Science 308:1164-7. 2005..We demonstrate that some of these genes are also required for germline and somatic transgene silencing. Moreover, the physical interactions among these potential RNAi factors suggest links to other RNA-dependent gene regulatory pathways...
- The expression of the let-7 small regulatory RNA is controlled by ecdysone during metamorphosis in Drosophila melanogasterLorenzo F Sempere
Department of Genetics, Dartmouth College, Hanover, New Hampshire 03755, USA
Dev Biol 244:170-9. 2002..These results demonstrate an interaction between steroid hormone signaling and the heterochronic pathway in insects...
- Developmental gene expression profiles of the human pathogen Schistosoma japonicumGeoffrey N Gobert
Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
BMC Genomics 10:128. 2009..Advanced analyses including ANOVA, principal component analysis, and hierarchal clustering provided a global synopsis of gene expression relationships among the different developmental stages of the schistosome parasite...
- Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegansJ Graham Ruby
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
Cell 127:1193-207. 2006..The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs)...
- An extensive class of small RNAs in Caenorhabditis elegansR C Lee
Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
Science 294:862-4. 2001..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
- Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-armMasayuki Sakurai
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo Kashiwa, Chiba 277 8562, Japan
Nucleic Acids Res 33:1653-61. 2005..Thus, m1A9 is indispensable for the structure and function of T-armless tRNAs of nematode mitochondrial origin...
- Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAiJoris Pothof
Hubrecht Laboratory, Center for Biomedical Genetics, 3584 CT, Utrecht, The Netherlands
Genes Dev 17:443-8. 2003..Because known mutator genes are causally involved in many hereditary and sporadic human cancers, it is likely that some of these new mutators are equally relevant in cancer etiology...
- Alternative splicing and sequence diversity of transcripts from the oncosphere stage of Taenia solium with homology to the 45W antigen of Taenia ovisC G Gauci
Molecular Parasitology Laboratory, The University of Melbourne, Princes Highway, Werribee, VIC 3030, Australia
Mol Biochem Parasitol 112:173-81. 2001..In this respect, the generation of sequence diversity and hence potential antigenic diversity through alternative splicing of TSO45 genes may have implications for the use of these proteins in vaccines against T. solium cysticercosis...
- Cathepsin B-like cysteine proteases and Caenorhabditis elegans homologues dominate gene products expressed in adult Haemonchus contortus intestineD P Jasmer
Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164 7040, USA
Mol Biochem Parasitol 116:159-69. 2001..The ESTs identified intestinal genes with potential application to immune control, understanding of basic intestinal regulatory processes and refinement of nematode genomic resources...
- An Argonaute transports siRNAs from the cytoplasm to the nucleusShouhong Guang
Department of Pharmacology, University of Wisconsin Madison, Madison, WI 53706, USA
Science 321:537-41. 2008..Thus, specific Argonaute proteins can transport specific classes of small regulatory RNAs to distinct cellular compartments to regulate gene expression...
- Profiling Schistosoma mansoni development using serial analysis of gene expression (SAGE)David L Williams
Department of Biological Sciences, Illinois State University, Normal, IL, USA
Exp Parasitol 117:246-58. 2007..A number of novel, differentially expressed genes have been identified, both within and between the different developmental stages found in the mammalian and snail hosts...
- A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegansM E Domeier
Huntsman Cancer Institute Center for Children and Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112, USA
Science 289:1928-31. 2000..The levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes...
- A global analysis of Caenorhabditis elegans operonsThomas Blumenthal
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Box B121, 4200 E 9th Avenue, Denver, Colorado 80262, USA
Nature 417:851-4. 2002..elegans genes. Numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal previously unknown functional relationships...
- Some molecular insights into schistosome evolutionD Rollinson
Department of Zoology, Natural History Museum, London, U K
Int J Parasitol 27:11-28. 1997..Gene discovery and gene mapping projects are leading to a better understanding of the schistosome genome and can be expected to contribute significantly to future comparative evolutionary studies...
- Brugia pahangi: in vivo tissue migration of early L3 alters gene expressionSharon R Chirgwin
Department of Pathobiological Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA 70803, USA
Exp Parasitol 118:89-95. 2008..These data suggest that migratory activity, exposure to potentially different host environments and/or host location may be important external factors in influencing larval gene expression...
- Efficacy and specificity of RNA interference in larval life-stages of Ostertagia ostertagiA Visser
Department of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium
Parasitology 133:777-83. 2006..In conclusion, the results indicate that the RNAi pathway is probably present in O. ostertagi but that the current RNAi techniques can not be used as a reliable screening method...
- Functional characterization of SR and SR-related genes in Caenorhabditis elegansD Longman
MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU
EMBO J 19:1625-37. 2000..RNAi with CeSRPK, an SR protein kinase, resulted in early embryonic lethality, suggesting an essential role for SR protein phosphorylation during development...
- DAF-16/FOXO targets genes that regulate tumor growth in Caenorhabditis elegansJulie Pinkston-Gosse
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, USA
Nat Genet 39:1403-9. 2007....
- Evolution of small nucleolar RNAs in nematodesAnja Zemann
Institute of Experimental Pathology ZMBE, University of Munster, D 48149 Munster, Germany
Nucleic Acids Res 34:2676-85. 2006..Some target sites modified by snoRNAs were changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs...
- Microarray analysis identifies genes preferentially expressed in the lung schistosomulum of Schistosoma mansoniGary P Dillon
Department of Biology, University of York, PO Box 373, York YO10 5YW, UK
Int J Parasitol 36:1-8. 2006..Two promising secreted molecules have homology to antigens with vaccine and/or immunomodulatory potential in other helminths...
- Gender-associated gene expression in two related strains of Schistosoma japonicumJennifer M Fitzpatrick
Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
Mol Biochem Parasitol 136:191-209. 2004..japonicum gender-associated gene transcripts that may be considered targets for improved intervention strategies...
- Testing the efficacy of RNA interference in Haemonchus contortusPeter Geldhof
Moredun Research Institute, Pentlands Science Park, Penicuik, Midlothian EH26 0PZ, UK
Int J Parasitol 36:801-10. 2006..elegans and other nematodes have limited efficacy in H. contortus. This may reflect differences between nematode species in dsRNA uptake and transport into cells and between cells...
- A stress-responsive glutathione S-transferase confers resistance to oxidative stress in Caenorhabditis elegansBritta Leiers
Institute for Genetics and Biological Medical Research Center, Heinrich Heine University, Dusseldorf, Germany
Free Radic Biol Med 34:1405-15. 2003..The Ce-GST-p24 was also localized in BL1 C. elegans by confocal laser-scanning microscopy, revealing a wide-spread distribution profile...
- A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopyN Ranjit
Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4006, Australia
Int J Parasitol 36:701-10. 2006..Expressed sequence tags corresponding to known and potential recombinant vaccines were identified and these included homologues of proteases, anti-clotting factors, defensins and integral membrane proteins involved in cell adhesion...
- Differential gene expression during desiccation stress in the insect-killing nematode Steinernema feltiae IS-6Tali Z Gal
Department of Nematology, ARO, The Volcani Center, Bet Dagan 50250, Israel
J Parasitol 89:761-6. 2003..feltiae IS-6. Our results unveiled some of the components of the genetic networks that are activated in S. feltiae IS-6 during dehydration and suggested a differing pattern of temporal regulation during nematode dehydration...
- In vivo and in vitro evidence that the four essential intermediate filament (IF) proteins A1, A2, A3 and B1 of the nematode Caenorhabditis elegans form an obligate heteropolymeric IF systemAnton Karabinos
Max Planck Institute for Biophysical Chemistry, Department of Biochemistry, Am Fassberg 11, 37077 Goettingen, Germany
J Mol Biol 333:307-19. 2003..Proteins A1 and B1 have a similar and rather slow turnover rate in photobleaching experiments of the pharynx tonofilaments...
- Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expressionWei Deng
Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Genome Res 16:20-9. 2006..Preliminary estimates indicate that the C. elegans transcriptome contains approximately 2700 small non-coding RNAs, potentially acting as regulatory elements in nematode development...
- SMG-5, required for C.elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2AKirk R Anders
Department of Genetics, University of Wisconsin Madison, Madison, WI 53706, USA
EMBO J 22:641-50. 2003..Our results suggest that PP2A is the SMG-2 phosphatase, and the role of SMG-5 is to direct PP2A to its SMG-2 substrate. We discuss cycles of SMG-2 phosphorylation and their roles in NMD...
- Short report: Echinococcus granulosus from Xinjiang, PR China: cDNAS encoding the EG95 vaccine antigen are expressed in different life cycle stages and are conserved in the oncosphereWenbao Zhang
Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, Queensland Institute of Medical Research and University of Queensland, Brisbane, Queensland, Australia
Am J Trop Med Hyg 68:40-3. 2003..Very limited sequence variation was evident in the EG95 protein from oncospheres. This high degree of sequence conservation predicts that the vaccine will continue to be effective in China and elsewhere...
- Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identificationUwe Ohler
Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
RNA 10:1309-22. 2004..The improved analysis supports our previous assertion that miRNA gene identification is nearing completion in C. elegans with apparently no more than 20 miRNA genes now remaining to be identified...
- Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposonClaudia S Copeland
Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin, Berlin, Germany
Gene 329:103-14. 2004..In addition, phylogenetic analysis targeting discrete domains of Boudicca revealed a generalized radiation in sequences among the multiple copies of Boudicca resident in the schistosome genome...
- Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicumClaudia S Copeland
Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany
BMC Genomics 10:464. 2009..The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available...
- A single histone H1 isoform (H1.1) is essential for chromatin silencing and germline development in Caenorhabditis elegansM A Jedrusik
Third Department of Zoology Developmental Biology, University of Gottingen, Humboldtalle 34A, D 37073 Gottingen, Germany
Development 128:1069-80. 2001..Our observations therefore support this interpretation of the mes phenotype and they identify a single histone H1 isoform (H1.1) as a new component specifically involved in chromatin silencing in the germline of C. elegans...
- Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilisKoushirou Suga
Nagasaki Industrial Promotion Foundation, Omura, Japan
PLoS ONE 2:e671. 2007..However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking...
- RNAi analysis of genes expressed in the ovary of Caenorhabditis elegansF Piano
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Curr Biol 10:1619-22. 2000..Furthermore, this approach is directly applicable to other organisms sensitive to RNAi and whose genomes have not yet been sequenced...
- Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarrayHousheng He
Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Genome Res 17:1471-7. 2007..After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed...
- SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeastM F Page
Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
Mol Cell Biol 19:5943-51. 1999..We discuss these results with regard to the in vivo functions of SMG-2 and NMD...
- The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factorF J Slack
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
Mol Cell 5:659-69. 2000..We suggest that late larval activation of let-7 RNA expression downregulates LIN-41 to relieve inhibition of lin-29...
- Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 familySebastian Greiss
Wellcome Trust Centre for Gene Regulation and Expression, School of Life Sciences, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
BMC Genomics 9:334. 2008..To address the function of p53 in global transcriptional regulation we investigate genome-wide transcriptional responses upon DNA damage and cep-1 deficiency...
- RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegansM K Montgomery
Carnegie Institution of Washington, Department of Embryology, 115 West University Parkway, Baltimore, MD 21210, USA
Proc Natl Acad Sci U S A 95:15502-7. 1998..elegans responsible for targeting and destroying aberrant messages. We suggest a model of how dsRNA might function in a catalytic mechanism to target homologous mRNAs for degradation...
- Atypical protein kinase C cooperates with PAR-3 to establish embryonic polarity in Caenorhabditis elegansY Tabuse
Fundamental Research Laboratories, NEC Corporation, Tsukuba, Ibaraki 305, Japan
Development 125:3607-14. 1998..We conclude that PKC-3 plays an indispensable role in establishing embryonic polarity through interaction with PAR-3...
- Caenorhabditis elegans SID-2 is required for environmental RNA interferenceWilliam M Winston
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 104:10565-70. 2007..elegans. SID-2, when expressed in the environmental RNAi defective species Caenorhabditis briggsae, confers environmental RNAi...
- Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegansMakedonka Mitreva
Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
Genome Res 14:209-20. 2004..We also provide functional classifications of S. stercoralis clusters...
- RNA interference in parasitic nematodes of animals: a reality check?David P Knox
Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian EH26 0PZ, UK
Trends Parasitol 23:105-7. 2007..elegans) is fully functional in some parasitic nematodes...
- Stop making nonSense: the C. elegans smg genesS E Mango
Huntsman Cancer Institute, 2000 Circle of Hope, University of Utah, Salt Lake City, UT 84112, USA
Trends Genet 17:646-53. 2001..Here I describe what is known about the smg genes and their potential functions in these two mRNA degradation pathways...
- A gene expression map for Caenorhabditis elegansS K Kim
Department of Developmental Biology and Genetics, Stanford University Medical School, Stanford, CA 94305, USA
Science 293:2087-92. 2001....
- Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNAIris Cheung
Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
Nat Genet 31:405-9. 2002..We propose that DOG-1 is required to resolve the secondary structures of guanine-rich DNA that occasionally form during lagging-strand DNA synthesis...
- Use of a 44k oligoarray to explore the transcriptome of Schistosoma mansoni adult wormsSergio Verjovski-Almeida
Laboratory of Gene Expression in Eukaryotes, Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, Av Prof Lineu Prestes, 748, 05508 000 Sao Paulo, SP, Brazil
Exp Parasitol 117:236-45. 2007..Moreover, detection of bi-directional transcription for 7% of the active "no match" genes in adults leads us to hypothesize a widespread production of antisense RNA in S. mansoni, with possible regulatory roles...
- Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegansM Hanazawa
Molecular Genetics Research Laboratory, University of Tokyo, Tokyo 113 0033, Japan
Proc Natl Acad Sci U S A 98:8686-91. 2001..These results demonstrate the efficacy of the screening strategy using the EST library combined with the RNAi technique in C. elegans...
- The RNA-binding proteins PUF-5, PUF-6, and PUF-7 reveal multiple systems for maternal mRNA regulation during C. elegans oogenesisAlex L Lublin
Department of Cell and Developmental Biology, University of Colorado School of Medicine, Mail Stop 8108, P O Box 6511, Aurora, CO 80045, USA
Dev Biol 303:635-49. 2007..Multiple sets of RNA-binding complexes function in different domains of the C. elegans germ line to maintain silencing of Notch/glp-1 and other mRNAs...
- Translational regulators maintain totipotency in the Caenorhabditis elegans germlineRafal Ciosk
Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Science 311:851-3. 2006....
- Isolation of eight novel Caenorhabditis elegans small RNAsM Wachi
Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo cho, Hirosaki, Aomori 036 8561, Japan
Gene 335:47-56. 2004..The results of our study suggest that there are more as-yet-unidentified small ncRNAs of which genes are located in the intron regions of protein-coding genes in C. elegans...
- mRNA sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity compared with other adult mammalian parasitic nematodesDouglas P Jasmer
Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 9916407040, USA
Mol Biochem Parasitol 137:297-305. 2004..contortus. Therefore, adaptations related to nutrient acquisition may vary markedly among these parasitic nematodes...
- Genomics: frontiers of gene functionSean M O'Rourke
Nature 434:444-5. 2005
- C. elegans dss-1 is functionally conserved and required for oogenesis and larval growthJohanna Pispa
Cellular Biotechnology Research Program, Institute of Biotechnology, University of Helsinki, Finland
BMC Dev Biol 8:51. 2008..While the fungal orthologues of Dss1 are not essential for viability, the significance of Dss1 in metazoans has remained unknown due to a lack of knockout animal models...
- The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25Gabriel D Hayes
Department of Genetics, Harvard Medical School and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
Development 133:4631-41. 2006..The synergistic action of miRNA paralogs in development may be a general feature of the diversified miRNA gene family...
- Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adultsPeter Ruzanov
Genome Sciences Centre, BC Cancer Research Centre, 570 West 7th Avenue, Vancouver, BC, Canada
Exp Gerontol 42:825-39. 2007..We propose a model for enhanced longevity through a cytochrome c oxidase-mediated reduction in reactive oxygen species commonly held to be a major contributor to aging...
- The expression of the Alzheimer's amyloid precursor protein-like gene is regulated by developmental timing microRNAs and their targets in Caenorhabditis elegansRyusuke Niwa
Department of Molecular, Cellular and Developmental Biology, KBT 936, Yale University, PO Box 208103, 266 Whitney Avenue, New Haven, CT 06520, USA
Dev Biol 315:418-25. 2008..Moreover, the levels of the apl-1 transcription are modulated by the activity of let-7 family microRNAs. Our work places apl-1 in a developmental timing pathway and may provide new insights into the time-dependent progression of AD...
- A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegansInsuk Lee
Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, MBB 3 210, Austin, Texas 78712, USA
Nat Genet 40:181-8. 2008..We conclude that an analogous network for human genes might be similarly predictive and thus facilitate identification of disease genes and rational therapeutic targets...
- RNA interference in Caenorhabditis elegansNathaniel R Dudley
Biology Department, University of North Carolina, Chapell Hill, USA
Methods Mol Biol 309:29-38. 2005
- Regulation of Caenorhabditis elegans RNA interference by the daf-2 insulin stress and longevity signaling pathwayD Wang
Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Cold Spring Harb Symp Quant Biol 69:429-31. 2004
- Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicing-related components with synMuv B activityJulian Ceron
Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
BMC Dev Biol 7:30. 2007..For instance, lin-35 Rb is a synthetic multivulva (synMuv) class B gene, which causes a multivulva phenotype when inactivated simultaneously with a class A or C synMuv gene...
- Dcp2 Decaps m2,2,7GpppN-capped RNAs, and its activity is sequence and context dependentLeah S Cohen
Department of Biology, City University of New York Graduate Center, CSI, Staten Island, 10314, USA
Mol Cell Biol 25:8779-91. 2005..Overall, the data suggest that Dcp2 activity can be influenced by both sequence and context and that Dcp2 may contribute to gene regulation in multiple RNA pathways, including monomethyl- and trimethylguanosine-capped RNAs...
- Uncover genetic interactions in Caenorhabditis elegans by RNA interferenceAngelo Fortunato
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA, Cambridge, Hinxton, UK
Biosci Rep 25:299-307. 2005..In this review, we illustrate how RNAi has been used to analyse gene function in C. elegans as well as pointing to some future directions for using RNAi to examine genetic interactions in a systematic manner...
- Deficiency of the Caenorhabditis elegans DNA polymerase eta homologue increases sensitivity to UV radiation during germ-line developmentTsuyoshi Ohkumo
Graduate School of Frontier Biosciences, Osaka University, SORST, Japan Science and Technology Agency, Japan
Cell Struct Funct 31:29-37. 2006..elegans in early embryogenesis but only modestly at later stages. As early embryogenesis is characterized by high levels of DNA replication, Poleta may confer UV resistance in C. elegans, perhaps by catalyzing TLS in early embryogenesis...
- Successful transgenesis of the parasitic nematode Strongyloides stercoralis requires endogenous non-coding control elementsXinshe Li
Department of Pathobiology, School of Veterinary Medicine and University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104 6050, USA
Int J Parasitol 36:671-9. 2006..This system has the potential to significantly advance the molecular and cellular biological study of S. stercoralis and of parasitic nematodes generally...
- A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodesAshwin Hajarnavis
RNA 12:1786-9. 2006..We suggest that this signal may be involved in translation or other message-level regulation of ribosomal genes in C. elegans...
- The Caenorhabditis elegans odr-2 gene encodes a novel Ly-6-related protein required for olfactionJ H Chou
Howard Hughes Medical Institute, Program in Developmental Biology, Department of Anatomy, University of California, San Francisco, California 94143 0452, USA
Genetics 157:211-24. 2001..The AWC neurons are superficially normal in their development and structure in odr-2 mutants, but their function is impaired. Our results suggest that ODR-2 may regulate AWC signaling within the neuronal network required for chemotaxis...
- TRICHINELLOSIS AND REGULATION OF HOST GENE EXPRESSIONDouglas Jasmer; Fiscal Year: 2001..Understanding these mechanisms may also contribute unique insight on mechanisms of muscle differentiation and cell cycle regulation in mammalian cells. ..
- Mild Ol - Toward Better Understanding and TreatmentPeter Byers; Fiscal Year: 2004..abstract_text> ..
- 2003/2005 INTERNATIONAL C. ELEGANS MEETINGSGeraldine Seydoux; Fiscal Year: 2004..Previous C. elegans meetings have led to the exchange of knowledge, ideas, methods, mutants, and clones and have been vital in fostering the sense of excitement and the collegiality and cooperativity that characterize this field. ..
- Disulfide redox balance in Schistosoma mansoniDavid Williams; Fiscal Year: 2003..Because disulfide redox balance in schistosomes is centered on a single, key enzyme and is fundamentally different from host mechanisms we propose that this pathway is a promising target for novel, rational drug design. ..
- Genetic and Biochemical Analysis of SID-1 and SID-2Craig Hunter; Fiscal Year: 2007..Although RNAi has been shown to be effective, a major obstacle remains delivery of dsRNA into human cells both in culture and in vivo. ..
- Mechanisms of anti-schistosome artemisinin chemotherapyDavid Williams; Fiscal Year: 2006..mansoni translationally controlled tumor protein. The critical conclusions of this study will direct subsequent future experiments into the molecular mechanism of artemisinin's anti-parasitic activity. ..
- Computational methods to identify noncoding RNA genesElena Rivas; Fiscal Year: 2006..abstract_text> ..
- HTS Inhibitors:Schistosoma Mansoni Peroxiredoxins(RMI)David Williams; Fiscal Year: 2005..This will be the first step in the development of novel antischistosome chemotherapies, which are essential for continued public health measures. ..
- Integrated Studies of 3'-UTR Mediated Gene RegulationJOEL GRABER; Fiscal Year: 2009..Our work will generate resources that facilitate the connection between regulatory activity and health implications. ..
- Computational approaches to noncoding RNAsElena Rivas; Fiscal Year: 2006..How to improve RNA similarity searches by taking into account the structure as well as the sequence information. (5) RNA-based phylogenetic methods. (6) ncRNA families and RNA databases. [unreadable] [unreadable]..
- Developmental Genomics in C. elegansCraig Hunter; Fiscal Year: 2006..This analysis, although limited to those genes that are transcriptional targets of pal-1 activity, is the necessary first step to a complete description of the activity of a master regulator. ..
- Trans-splicing in C. elegansThomas Blumenthal; Fiscal Year: 2007..We will determine what functions these proteins have in 3' end formation. These studies should provide important new insight into how 3' end cleavage can occur without accompanying transcription termination. ..
- Gordon Conference-Autophagy/Stress/Development/DiseaseAna Cuervo; Fiscal Year: 2007....
- New Research Strategies in Osteogenesis ImperfectaPeter Byers; Fiscal Year: 2006..unreadable] [unreadable] [unreadable] [unreadable]..
- MAP kinase signal specificity in the C. elegans germlineValerie Reinke; Fiscal Year: 2007..Together these experiments should build toward a comprehensive understanding of the mechanisms used to produce a specific cell fate in response to a generally used signaling pathway. ..
- Developmental Gene Regulation in Schistosoma mansoniDavid Williams; Fiscal Year: 2006..mansoni genome and studies using DNA micro arrays. Furthermore, we will validate the use of SAGE technology to study differential global gene expression in S. mansoni. ..
- PROTEOMIC ANALYSIS OF DECREASED AUTOPHAGY IN AGINGAna Cuervo; Fiscal Year: 2005..abstract_text> ..
- IDENTIFICATION AND EXPRESSION OF SKIN SPECIFIC GENESPeter Byers; Fiscal Year: 2002....
- Functional Genomics:Complex Biological SystemsStuart Kim; Fiscal Year: 2003..The goal of the meeting is to integrate advances in human disease, modeling of genetic networks, quantitative trait mapping, and data mining techniques. ..
- Gordon Research Conferences: Collagen 2003, 2005, 2007Peter Byers; Fiscal Year: 2003..The funds will be used to partially defray conferee travel expenses and registration fees for invited speakers and for young members of the research community. ..
- Probabilistic methods to identify noncoding RNA genesElena Rivas; Fiscal Year: 2003..elegans and E. coli. ..
- Genetic and Biochemical Analysis of SID-1and SID-2Craig Hunter; Fiscal Year: 2008..4). To isolate and characterize endogenous extracellular RNAs in C. elegans. This work may identify an ancient, gene-specific mechanism for intercellular communication in animals. ..
- Regulatory and functional RNAs: computational approachesElena Rivas; Fiscal Year: 2003..Inference of RNA function. (3) RNA structural alignments and homology searches. How to improve RNA similarity searches by taking into account the structure as well as the sequence information. ..
- Fluorescent Activated Cell Sorter for C. elegans (worms)Susan Mango; Fiscal Year: 2004..elegans researchers at the University of Utah. It would both facilitate existing research projects and permit the development of new projects that could not function without this novel instrument. ..
- Control of cell polarity in the C. elegans zygoteGeraldine Seydoux; Fiscal Year: 2005..We anticipate that our studies will provide significant insights into these processes by taking advantage of the experimental attributes of a simple model system...
- TRANSLATIONAL CONTROL IN C. ELEGANS EMBRYOSCraig Hunter; Fiscal Year: 2004..abstract_text> ..
- High Throughput Proteome Analysis of Schistosoma mansoniDavid Williams; Fiscal Year: 2005..Completion of this project will provide information on significant protein complements of S. mansoni and also validate the use of MudPIT in future proteomic studies to define a comprehensive view of the S. mansoni proteomes. ..
- The Challenges of Autosomal Recessive and Other New Forms of OIPeter Byers; Fiscal Year: 2008..It also will facilitate identification of new OI genes, identify new paths of research to benefit patients, and increase progress of the Linked Clinical Research Centers. [unreadable] [unreadable] [unreadable] [unreadable]..
- Genetic Control of Development in C elegansStuart Kim; Fiscal Year: 2006..abstract_text> ..
- DEVELOPMENT OF DNA MICROARRAYS RESOURCE FOR C ELEGANSStuart Kim; Fiscal Year: 2003..elegans microarrays can play an important part in developing this technology because these miroarrays will be the only one containing the complete genome from a metazoan. ..