Genomes and Genes
Summary: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
- Costa J, Lilley C, Atkinson H, Urwin P. Functional characterisation of a cyst nematode acetylcholinesterase gene using Caenorhabditis elegans as a heterologous system. Int J Parasitol. 2009;39:849-58 pubmed publisher..elegans as a heterologous system to study neuronal aspects of plant-parasitic nematode biology. ..
- Wu L, Zhang Q, Li T, Chen S, Cao J. [DNA purification methods of Cryptosporidium oocysts]. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi. 2009;27:365-7 pubmed..The preparation of template DNA is important for PCR detection. Before DNA purification, the oocysts should be purified and splitted. This paper summarizes the ordinary purification and splitting methods for Cryptosporidium oocysts. ..
- Kim S, Choung S. Whole genomic expression analysis of octachlorostyrene-induced chronic toxicity in Caenorhabditis elegans. Arch Pharm Res. 2009;32:1585-92 pubmed publisher..elegans genes. Dye swaps were performed. After data analysis, we identified a total of 1,294 genes that were differentially expressed through generations. ..
- Zhong M, Niu W, Lu Z, Sarov M, Murray J, Janette J, et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010;6:e1000848 pubmed publisher..These results indicate distinct roles for this regulator in two different biological processes and demonstrate the versatility of transcription factors in mediating diverse biological roles. ..
- Cutter A, Choi J. Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Res. 2010;20:1103-11 pubmed publisher..briggsae, Arabidopsis thaliana, Lycopersicon, human). These results illustrate how recombination, mutation, selection, and population history interact in important ways to shape molecular heterogeneity within and between genomes. ..
- ..High throughput methods such as proteomics, transcriptomics and genome sequencing are now generating vast amounts of new data. The challenge for the future is to interpret and understand the biological relevance of this new information. ..
- Pontier D, Tijsterman M. A robust network of double-strand break repair pathways governs genome integrity during C. elegans development. Curr Biol. 2009;19:1384-8 pubmed publisher..Our results demonstrate profound versatility in DSB repair pathways for somatic cells of C. elegans, which are thus extremely fit to deal with chromosomal breaks. ..
- Panowski S, Dillin A. Signals of youth: endocrine regulation of aging in Caenorhabditis elegans. Trends Endocrinol Metab. 2009;20:259-64 pubmed publisher..elegans, the insulin/IGF-1 and germline signalling pathways, in which endocrine signalling is clearly important. We also incorporate recent data to create a model of how endocrine signalling in these pathways might occur. ..
- Zarlenga D, Gasbarre L. From parasite genomes to one healthy world: Are we having fun yet?. Vet Parasitol. 2009;163:235-49 pubmed publisher..Advancements in non-parasite systems are also presented with the proviso that applications to parasite research are in the making. ..
- Copeland C, Marz M, Rose D, Hertel J, Brindley P, Santana C, et al. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics. 2009;10:464 pubmed publisher..This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large. ..
- Ludtmann M, Rollinson D, Emery A, Walker A. Protein kinase C signalling during miracidium to mother sporocyst development in the helminth parasite, Schistosoma mansoni. Int J Parasitol. 2009;39:1223-33 pubmed publisher..These results highlight the dynamic nature of PKC signalling during S. mansoni postembryonic development and support a role for active PKC in restricting transformation of S. mansoni miracidia into mother sporocysts. ..
- Raboin M, Timko A, Howe D, Felix M, Denver D. Evolution of Caenorhabditis mitochondrial genome pseudogenes and Caenorhabditis briggsae natural isolates. Mol Biol Evol. 2010;27:1087-96 pubmed publisher..Our findings provide new insights into the mode and tempo of mitochondrial genome and pseudogene evolution both within and between Caenorhabditis nematode species. ..
- McVeigh P, Mair G, Atkinson L, Ladurner P, Zamanian M, Novozhilova E, et al. Discovery of multiple neuropeptide families in the phylum Platyhelminthes. Int J Parasitol. 2009;39:1243-52 pubmed publisher..Our dataset provides a springboard for investigation of the functional biology and therapeutic potential of neuropeptides in flatworms, simultaneously launching flatworm neurobiology into the post-genomic era. ..
- Struwe W, Warren C. High-throughput RNAi screening for N-glycosylation dependent loci in Caenorhabditis elegans. Methods Enzymol. 2010;480:477-93 pubmed publisher..elegans, its susceptibility to genetic silencing and its recognizable phenotypes, is a suitable model to dissect the complex phenomenon of glycosylation and identify genes that are required for N-glycan biosynthesis. ..
- Reinke V, Cutter A. Germline expression influences operon organization in the Caenorhabditis elegans genome. Genetics. 2009;181:1219-28 pubmed publisher..These analyses demonstrate that mechanisms governing germline gene expression influence operon origination and/or maintenance. Thus, gene expression in a specific tissue can have profound effects on the evolution of genome organization. ..
- Barrière A, Yang S, Pekarek E, Thomas C, Haag E, Ruvinsky I. Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 2009;19:470-80 pubmed publisher..Our results highlight the impact of mating systems on genome sequencing projects. ..
- Sleumer M, Bilenky M, He A, Robertson G, Thiessen N, Jones S. Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. Nucleic Acids Res. 2009;37:1323-34 pubmed publisher..The annotated motifs provide novel binding site candidates for both characterized transcription factors and orthologues of characterized mammalian transcription factors. ..
- Castagnone Sereno P, Danchin E, Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics. 2010;11:598 pubmed publisher..2,245 di- to hexanucleotide loci were identified in the genome of M. incognita, providing adequate material for the future development of a wide range of microsatellite markers in this major plant parasite. ..
- Jones M, Chua S, O Neil N, Johnsen R, Rose A, Baillie D. High-resolution array comparative genomic hybridization analysis reveals unanticipated complexity of genetic deficiencies on chromosome V in Caenorhabditis elegans. Mol Genet Genomics. 2009;282:37-46 pubmed publisher..Our observations highlight the use of array-based approaches for the analysis of rearranged genomes, revealing previously unidentified deficiency characteristics and addressing biologically relevant questions. ..
- Doroszuk A, Snoek L, Fradin E, Riksen J, Kammenga J. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res. 2009;37:e110 pubmed publisher..Overall, the presented IL library provides a versatile resource toward easier and efficient fine mapping and functional analyses of loci and genes underlying complex traits in C. elegans. ..
- Webster J, Oliviera G, Rollinson D, Gower C. Schistosome genomes: a wealth of information. Trends Parasitol. 2010;26:103-6 pubmed publisher..We comment on these breakthroughs and their potential applications in the study and control of schistosomes. ..
- Vohanka J, SimeckovÃ¡ K, MachalovÃ¡ E, BehenskÃ½ F, Krause M, Kostrouch Z, et al. Diversification of fasting regulated transcription in a cluster of duplicated nuclear hormone receptors in C. elegans. Gene Expr Patterns. 2010;10:227-36 pubmed publisher..Our results reveal the diversification of the temporal, spatial, and metabolic gene expression patterns coupled with evolutionary drift within supnr family members. ..
- Usmanova N, Kazakov V. The DL1 repeats in the genome of Diphyllobothrium latum. Parasitol Res. 2010;107:449-52 pubmed publisher..latum genomic DNA with one specific primer was sequenced. In discussion, several evidences that DL1 repeat is a member of the SINE family of retroposons were adduced...
- Jans J, Gladden J, Ralston E, Pickle C, Michel A, Pferdehirt R, et al. A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev. 2009;23:602-18 pubmed publisher..DCC disruption causes opposite effects on expression of X and autosomal genes. The DCC thus acts at a distance to impact expression throughout the genome. ..
- Brindley P, Mitreva M, Ghedin E, Lustigman S. Helminth genomics: The implications for human health. PLoS Negl Trop Dis. 2009;3:e538 pubmed publisher..They are likely also to predict new potential vaccine candidates and drug targets. In this review, we present an overview of these efforts and emphasize the potential impact and importance of these new findings. ..
- Dolgin E, Charlesworth B, Cutter A. Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes. Genet Res (Camb). 2008;90:317-29 pubmed publisher..elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against TEs in selfing populations, but may in part be explained by non-equilibrium TE dynamics. ..
- Smith M, Boyd W, Kissling G, Rice J, Snyder D, Portier C, et al. A discrete time model for the analysis of medium-throughput C. elegans growth data. PLoS ONE. 2009;4:e7018 pubmed publisher..In addition, extraneous matter and the inability to assign specific measurements to specific nematodes made it difficult to estimate growth rates. The present model addresses these problems through a population-based Markov model. ..
- Jex A, Hall R, Littlewood D, Gasser R. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res. 2010;38:522-33 pubmed publisher..These mt genomic data provide a rich source of markers for studies of the systematics and population genetics of a group of socioeconomically important pathogens of humans and other animals...
- Lu Y, Smielewska M, Palakodeti D, Lovci M, Aigner S, Yeo G, et al. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. RNA. 2009;15:1483-91 pubmed publisher..Together, these results increase the known repertoire of S. mediterranea miRNAs and identify numerous regulated miRNAs that may play important roles in regeneration, homeostasis, neoblast function, and reproduction...
- Yuan Z, Zhao B, Zhang J, Zhang S. Expression pattern of DjPreb gene during the planarian Dugesia japonica embryonic development. Mol Biol (Mosk). 2010;44:650-5 pubmed
- Vergara I, Chen N. Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genomics. 2010;11:516 pubmed publisher..We have demonstrated that OrthoCluster can be used to accurately identify synteny blocks and have found that synteny blocks between C. elegans and C. briggsae are almost three-folds larger than previously identified. ..
- Morales Hojas R. Molecular systematics of filarial parasites, with an emphasis on groups of medical and veterinary importance, and its relevance for epidemiology. Infect Genet Evol. 2009;9:748-59 pubmed publisher..Furthermore, it is also intended to highlight the relevance of molecular systematic studies in the molecular epidemiology research area...
- Bai X, Adams B, Ciche T, Clifton S, Gaugler R, Hogenhout S, et al. Transcriptomic analysis of the entomopathogenic nematode Heterorhabditis bacteriophora TTO1. BMC Genomics. 2009;10:205 pubmed publisher..This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora...
- Mbeunkui F, Scholl E, Opperman C, Goshe M, Bird D. Proteomic and bioinformatic analysis of the root-knot nematode Meloidogyne hapla: the basis for plant parasitism. J Proteome Res. 2010;9:5370-81 pubmed publisher..Collectively, the analyzed protein set provides an initial foundation to experimentally dissect the basis of plant parasitism by M. hapla. ..
- Bird D, Williamson V, Abad P, McCarter J, Danchin E, Castagnone Sereno P, et al. The genomes of root-knot nematodes. Annu Rev Phytopathol. 2009;47:333-51 pubmed publisher..Acquisition of these genes, apparently via horizontal gene transfer, and their subsequent expansion and diversification point to the evolutionary history of these parasites. It also suggests new routes to their control. ..
- Thomas M, Macias F, Alonso C, Lopez M. The biology and evolution of transposable elements in parasites. Trends Parasitol. 2010;26:350-62 pubmed publisher..This review addresses how TEs are organized, how they colonize the genomes of mammalian parasites, the functional role these elements play in parasite biology, and the interactions between these elements and the parasite genome. ..
- Zakaria C, Kassahun H, Yang X, Labbé J, Nilsen H, Ramotar D. Caenorhabditis elegans APN-1 plays a vital role in maintaining genome stability. DNA Repair (Amst). 2010;9:169-76 pubmed publisher..Finally, we showed that depletion of APN-1 by RNAi partially rescued the lethality resulting from uracil misincorporation, suggesting that APN-1 is an important AP endonuclease for repair of misincorporated uracil. ..
- Shim Y, Paik Y. Caenorhabditis elegans proteomics comes of age. Proteomics. 2010;10:846-57 pubmed publisher..Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode. ..
- Ramani A, Nelson A, Kapranov P, Bell I, Gingeras T, Fraser A. High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans. Genome Biol. 2009;10:R101 pubmed publisher..elegans and used it to identify endogenous targets of NMD. We find that these transcripts arise principally through splicing errors, strengthening the prevailing view that splicing and NMD are highly interlinked processes. ..
- Rose A, O Neil N, Bilenky M, Butterfield Y, Malhis N, Flibotte S, et al. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010;11:131 pubmed publisher..In this study, we observed no evidence of a mutator effect at the nucleotide level attributable to the Rec-1 mutation. ..
- Atkinson H, Babbitt P, Sajid M. The global cysteine peptidase landscape in parasites. Trends Parasitol. 2009;25:573-81 pubmed publisher..This snapshot of the landscape of parasite cysteine peptidases is complex and highly populated, suggesting that expansion of research beyond the few 'model' parasite peptidases is now timely. ..
- Bos D, Mayfield C, Minchella D. Analysis of regulatory protease sequences identified through bioinformatic data mining of the Schistosoma mansoni genome. BMC Genomics. 2009;10:488 pubmed publisher..This work provides a foundation for expanding knowledge of proteases in Schistosoma species and examining their diverse function and potential as targets for new chemotherapies. ..
- Parihar M, Minton R, Flowers S, Holloway A, Morehead B, Paille J, et al. The genome of the nematode Pristionchus pacificus encodes putative homologs of RXR/Usp and EcR. Gen Comp Endocrinol. 2010;167:11-7 pubmed publisher..The identification of a putative ecdysone receptor in a nematode amenable to genetic analysis provides a powerful system to investigate the function and evolution of ecdysone receptor signaling in the Nematoda. ..