Genomes and Genes
Summary: The functional hereditary units of HELMINTHS.
- Ithal N, Recknor J, Nettleton D, Hearne L, Maier T, Baum T, et al. Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol Plant Microbe Interact. 2007;20:293-305 pubmed
- Kim Y, Sun H. Functional genomic approach to identify novel genes involved in the regulation of oxidative stress resistance and animal lifespan. Aging Cell. 2007;6:489-503 pubmed..Our screen has also identified a group of genes that potentially function in a nutrient-sensing pathway to regulate lifespan in C. elegans. Our study provides a novel approach to identify genes involved in the regulation of aging. ..
- Lublin A, Evans T. The RNA-binding proteins PUF-5, PUF-6, and PUF-7 reveal multiple systems for maternal mRNA regulation during C. elegans oogenesis. Dev Biol. 2007;303:635-49 pubmed..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. ..
- Das P, Bagijn M, Goldstein L, Woolford J, Lehrbach N, Sapetschnig A, et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell. 2008;31:79-90 pubmed publisher..elegans. Instead, we demonstrate that Piwi acts upstream of an endogenous siRNA pathway in Tc3 silencing. These data might suggest a link between piRNA and siRNA function. ..
- de Voer G, Peters D, Taschner P. Caenorhabditis elegans as a model for lysosomal storage disorders. Biochim Biophys Acta. 2008;1782:433-46 pubmed publisher..Screens for genes involved in lysosomal biogenesis and function have been performed successfully resulting in the cup and glo mutants, but screens involving subtle phenotypes are likely to be difficult. ..
- Berriman M, Haas B, LoVerde P, Wilson R, Dillon G, Cerqueira G, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 2009;460:352-8 pubmed publisher..The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease. ..
- Gosney R, Liau W, LaMunyon C. A novel function for the presenilin family member spe-4: inhibition of spermatid activation in Caenorhabditis elegans. BMC Dev Biol. 2008;8:44 pubmed publisher..hc196 is a hypomorphic allele of spe-4, and its newly-discovered role inhibiting spermiogenesis may involve known proteolytic and/or calcium regulatory aspects of presenilin function, or it may involve yet-to-be discovered functions. ..
- Xue H, Xian B, Dong D, Xia K, Zhu S, Zhang Z, et al. A modular network model of aging. Mol Syst Biol. 2007;3:147 pubmed..Network simulations further suggest that aging might preferentially attack key regulatory nodes that are important for the network stability, implicating a potential molecular basis for the stochastic nature of aging. ..
- Knox D, Geldhof P, Visser A, Britton C. RNA interference in parasitic nematodes of animals: a reality check?. Trends Parasitol. 2007;23:105-7 pubmed..elegans) is fully functional in some parasitic nematodes. ..
- Aragon A, Imani R, Blackburn V, Cunningham C. Microarray based analysis of temperature and oxidative stress induced messenger RNA in Schistosoma mansoni. Mol Biochem Parasitol. 2008;162:134-41 pubmed publisher..Seventy-two elements were common to both stressors and could potentially be exploited in the development of novel anti-schistosomal therapeutics. ..
- Dillon G, Illes J, Isaacs H, Wilson R. Patterns of gene expression in schistosomes: localization by whole mount in situ hybridization. Parasitology. 2007;134:1589-97 pubmed..We believe that method of WISH will find broad application, in synergy with other emerging post-genomic techniques, such as RNA interference, to studies focused at increasing our molecular understanding of schistosomes. ..
- Tarailo M, Kitagawa R, Rose A. Suppressors of spindle checkpoint defect (such) mutants identify new mdf-1/MAD1 interactors in Caenorhabditis elegans. Genetics. 2007;175:1665-79 pubmed..elegans. The such-1/APC5-like mutation, h1960, significantly delays anaphase onset both in germline and in early embryonic cells. ..
- Hillier L, Reinke V, Green P, Hirst M, Marra M, Waterston R. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009;19:657-66 pubmed publisher..Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei. ..
- Curran S, Ruvkun G. Lifespan regulation by evolutionarily conserved genes essential for viability. PLoS Genet. 2007;3:e56 pubmed..These results suggest that insulin-signaling pathways play a role in regulation of aging at any stage in life. ..
- MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T. A novel family of C. elegans snRNPs contains proteins associated with trans-splicing. RNA. 2007;13:511-20 pubmed..These phenotypic relationships, along with the association of SL26p with SL75p, imply that, like the SL1 RNA/Sm/SL75p/SL21p complex, the Sm Y/Sm/SL75p/SL26p complex is associated with trans-splicing. ..
- Reddien P, Andersen E, Huang M, Horvitz H. DPL-1 DP, LIN-35 Rb and EFL-1 E2F act with the MCD-1 zinc-finger protein to promote programmed cell death in Caenorhabditis elegans. Genetics. 2007;175:1719-33 pubmed..We propose that the DPL-1 DP, MCD-1 zinc finger, EFL-1 E2F, LIN-35 Rb, LIN-37 Mip40, and LIN-52 dLin52 proteins act together in transcriptional regulation to promote programmed cell death. ..
- Styer K, Singh V, Macosko E, Steele S, Bargmann C, Aballay A. Innate immunity in Caenorhabditis elegans is regulated by neurons expressing NPR-1/GPCR. Science. 2008;322:460-4 pubmed publisher..elegans, suggesting that GPCRs may participate in neural circuits that receive inputs from either pathogens or infected sites and integrate them to coordinate appropriate immune responses. ..
- Faghiri Z, Skelly P. The role of tegumental aquaporin from the human parasitic worm, Schistosoma mansoni, in osmoregulation and drug uptake. FASEB J. 2009;23:2780-9 pubmed publisher..These experiments reveal a heretofore unrecognized role of the schistosome tegument in controlling water and drug movement into the parasites and highlight the importance of the tegument in parasite osmoregulation and drug uptake. ..
- Davis M, Morton J, Carroll D, Jorgensen E. Gene activation using FLP recombinase in C. elegans. PLoS Genet. 2008;4:e1000028 pubmed publisher..We show that we can use this to inactivate synaptic transmission in all neurons or a subset of neurons in a FLP-dependent manner. ..
- Petersen C, Reddien P. Smed-betacatenin-1 is required for anteroposterior blastema polarity in planarian regeneration. Science. 2008;319:327-30 pubmed..Our data suggest that beta-catenin specifies the posterior character of the anteroposterior axis throughout the Bilateria and specifies regeneration polarity in planarians. ..
- Tachu B, Pillai S, Lucius R, Pogonka T. Essential role of chitinase in the development of the filarial nematode Acanthocheilonema viteae. Infect Immun. 2008;76:221-8 pubmed..RNAi also led to the death of 50% of female worms, revealing the essential role of chitinase in the life cycle of filarial nematodes. ..
- Gomes M, Cabral F, Jannotti Passos L, Carvalho O, Rodrigues V, Baba E, et al. Preliminary analysis of miRNA pathway in Schistosoma mansoni. Parasitol Int. 2009;58:61-8 pubmed publisher..mansoni. ..
- Dieterich C, Clifton S, Schuster L, Chinwalla A, Delehaunty K, Dinkelacker I, et al. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008;40:1193-8 pubmed publisher..Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle. ..
- Smith E, Tsuchiya M, Fox L, Dang N, Hu D, Kerr E, et al. Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. Genome Res. 2008;18:564-70 pubmed publisher..Together, these findings indicate that the genetic component of life span determination is significantly conserved between divergent eukaryotic species, and suggest pathways that are likely to play a similar role in mammalian aging. ..
- Hansen D, Schedl T. The regulatory network controlling the proliferation-meiotic entry decision in the Caenorhabditis elegans germ line. Curr Top Dev Biol. 2006;76:185-215 pubmed..For example, it is unknown if the entire population of proliferating cells are stem cells capable of self-renewal or if only a small portion are stem cells and the rest are transit amplifying cells. ..
- Antoshechkin I, Sternberg P. The versatile worm: genetic and genomic resources for Caenorhabditis elegans research. Nat Rev Genet. 2007;8:518-32 pubmed..We also hope that it will be helpful in identifying new research opportunities and will promote the development of additional resources. ..
- Curtis R. Plant parasitic nematode proteins and the host parasite interaction. Brief Funct Genomic Proteomic. 2007;6:50-8 pubmed..These methods should provide new data to help our understanding of how parasitic nematodes infect their hosts, leading to the identification of novel pathogenicity genes. ..
- Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, et al. WormBase 2007. Nucleic Acids Res. 2008;36:D612-7 pubmed..Improved search and display tools, wider cross-species comparisons and extended ontologies are some of the features that will help scientists extend their research and take advantage of other nematode species genome sequences. ..
- Pouchkina Stantcheva N, McGee B, Boschetti C, Tolleter D, Chakrabortee S, Popova A, et al. Functional divergence of former alleles in an ancient asexual invertebrate. Science. 2007;318:268-71 pubmed..The functional divergence of former alleles observed here suggests that adoption of asexual reproduction could itself be an evolutionary mechanism for the generation of diversity...
- DeMarco R, Verjovski Almeida S. Schistosomes--proteomics studies for potential novel vaccines and drug targets. Drug Discov Today. 2009;14:472-8 pubmed publisher..Successful preliminary trials of two vaccine candidates that have been detected at the parasite surface by proteomics give grounds for believing that such an approach may provide a fresh start for the field...
- Baum T, Hussey R, Davis E. Root-knot and cyst nematode parasitism genes: the molecular basis of plant parasitism. Genet Eng (N Y). 2007;28:17-43 pubmed
- Baugh L, Demodena J, Sternberg P. RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science. 2009;324:92-4 pubmed publisher..Therefore, accumulation of Pol II at promoters anticipates nutritionally controlled gene expression during C. elegans development. ..
- Kiefer J, Smith P, Mango S. PHA-4/FoxA cooperates with TAM-1/TRIM to regulate cell fate restriction in the C. elegans foregut. Dev Biol. 2007;303:611-24 pubmed..We propose that restriction of early blastomeres to the pharyngeal fate depends on both repression of ectodermal genes and activation of pharyngeal genes by PHA-4. ..
- Wang M, O Rourke E, Ruvkun G. Fat metabolism links germline stem cells and longevity in C. elegans. Science. 2008;322:957-60 pubmed publisher..This lipase is a key factor in the lipid hydrolysis and increased longevity that are induced by decreased insulin signaling. These results suggest a link between C. elegans fat metabolism and longevity. ..
- Fay D, Yochem J. The SynMuv genes of Caenorhabditis elegans in vulval development and beyond. Dev Biol. 2007;306:1-9 pubmed..Recent advances have led to a greater mechanistic understanding of how these genes function during vulval development and have also identified roles for these genes in diverse developmental processes. ..
- Klink V, Martins V, Alkharouf N, Overall C, MacDonald M, Matthews B. A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase. BMC Dev Biol. 2007;7:35 pubmed..glycines homologs of muscle gene decreases as the nematode becomes sedentary inside the root during its parasitic feeding stages. ..
- Whittle C, Lazakovitch E, Gronostajski R, Lieb J. DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I. Proc Natl Acad Sci U S A. 2009;106:12049-54 pubmed publisher..These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif. ..
- Derry W, Bierings R, van Iersel M, Satkunendran T, Reinke V, Rothman J. Regulation of developmental rate and germ cell proliferation in Caenorhabditis elegans by the p53 gene network. Cell Death Differ. 2007;14:662-70 pubmed..Further, we find that CEP-1 and PHG-1 mediate the decreased developmental rate and embryonic viability of mutations in the clk-2/TEL2 gene, which regulates lifespan and checkpoint responses. ..
- Bakhetia M, Urwin P, Atkinson H. QPCR analysis and RNAi define pharyngeal gland cell-expressed genes of Heterodera glycines required for initial interactions with the host. Mol Plant Microbe Interact. 2007;20:306-12 pubmed..Presoaking H. glycines J2 with double-stranded RNA has value for studying gene function during the nematode's early interaction with a plant. ..
- Kalinna B, Brindley P. Manipulating the manipulators: advances in parasitic helminth transgenesis and RNAi. Trends Parasitol. 2007;23:197-204 pubmed..This situation is now changing in response to the availability of genome sequences and other advances. In this article, we review advances in the transgenesis and gene silencing of parasitic worms. ..
- Abad P, Gouzy J, Aury J, Castagnone Sereno P, Danchin E, Deleury E, et al. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. 2008;26:909-15 pubmed publisher..Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies...
- Kanazawa T, Zappaterra M, Hasegawa A, Wright A, Newman Smith E, Buttle K, et al. The C. elegans Opa1 homologue EAT-3 is essential for resistance to free radicals. PLoS Genet. 2008;4:e1000022 pubmed publisher..We conclude that free radicals contribute to the pathology of C. elegans eat-3 mutants. ..
- Arum O, Johnson T. Reduced expression of the Caenorhabditis elegans p53 ortholog cep-1 results in increased longevity. J Gerontol A Biol Sci Med Sci. 2007;62:951-9 pubmed..This study clarifies the inverse relationship between cep-1 expression and C. elegans life span, and, by extrapolation, that between p53 expression and mammalian life span. ..
- Jia K, Levine B. Autophagy is required for dietary restriction-mediated life span extension in C. elegans. Autophagy. 2007;3:597-9 pubmed..elegans life span. Since autophagy and longevity control are highly conserved from C. elegans to mammals, a similar role for autophagy in dietary restriction-mediated life span extension may also exist in mammals. ..
- Artieri C, Haerty W, Gupta B, Singh R. Sexual selection and maintenance of sex: evidence from comparisons of rates of genomic accumulation of mutations and divergence of sex-related genes in sexual and hermaphroditic species of Caenorhabditis. Mol Biol Evol. 2008;25:972-9 pubmed publisher..Our results provide empirical evidence of increased sexual selection pressure in dioecious animals, supporting the possibility that sexual selection may play an important role in the maintenance of sexual reproduction. ..
- Kumar S, Chaudhary K, Foster J, Novelli J, Zhang Y, Wang S, et al. Mining predicted essential genes of Brugia malayi for nematode drug targets. PLoS ONE. 2007;2:e1189 pubmed..By virtue of the selection procedure, the potential B. malayi drug targets highlight components of key processes in nematode biology such as central metabolism, molting and regulation of gene expression...
- Axäng C, Rauthan M, Hall D, Pilon M. The twisted pharynx phenotype in C. elegans. BMC Dev Biol. 2007;7:61 pubmed..The twisted pharynx is a useful and easy-to-score phenotype for genes required in extracellular adhesion or organ attachment, and perhaps forgenes required for cytoskeleton regulation. ..
- Ruzanov P, Riddle D, Marra M, McKay S, Jones S. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Exp Gerontol. 2007;42:825-39 pubmed..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. ..
- Cutter A, Dey A, Murray R. Evolution of the Caenorhabditis elegans genome. Mol Biol Evol. 2009;26:1199-234 pubmed publisher..We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns. ..
- Schulenburg H, Ewbank J. The genetics of pathogen avoidance in Caenorhabditis elegans. Mol Microbiol. 2007;66:563-70 pubmed..We propose that the selective pressure associated with avoidance behaviours influence both pathogen and host evolution. ..
- Gillan V, Maitland K, McCormack G, Him N, Devaney E. Functional genomics of hsp-90 in parasitic and free-living nematodes. Int J Parasitol. 2009;39:1071-81 pubmed publisher..These results indicate that factors other than the level of sequence identity are important for determining whether parasite genes can functionally complement in C. elegans...
- Troemel E, Chu S, Reinke V, Lee S, Ausubel F, Kim D. p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans. PLoS Genet. 2006;2:e183 pubmed..The contribution of the PMK-1 pathway to the enhanced lifespan of daf-2 mutants suggests that innate immunity is an important determinant of longevity. ..