02308nas a2200289   4500008004100000245007900041210006900120260005900189300001000248490000700258520139200265653001801657653001401675653001601689653002501705653002001730653002201750653001301772653001601785653001801801653000901819653002201828100001701850700001901867700001901886856011301905       2006                        eng d00aSentinel nematodes of land-use change and restoration in tallgrass prairie0 aSentinel nematodes of landuse change and restoration in tallgras  aPO BOX 311, MARCELINE, MO 64658 USAbSOC NEMATOLOGISTS  a20-270 v383 aChanges in land use and the associated changes in land cover are recognized as the most important component of human-induced global change. Much attention has been focused on deforestation, but grasslands are among the most endangered ecosystems on Earth. The North American tallgrass prairie is a dramatic example, exhibiting a greater than 95% decline in historical area. Renewed interest in prairie conservation and restoration has highlighted the need for ecological indicators of disturbance and recovery in native systems, including the belowground component. The tallgrass prairie differs from the agricultural systems that have replaced it in having greater diversity and heterogeneity of resources, less physical soil disturbance (although other disturbances, such as fire and grazing, are prominent), and greater nitrogen limitation. Understanding the responses of nematode taxa to these characteristic differences is crucial to the development and improvement of community indices, but while knowledge of disturbance responses by individual taxa is accumulating, the level of necessary taxonomic resolution remains in question. Although nematode communities generally are better described for temperate grasslands than for other natural ecosystems, identification of sentinel taxa is further confounded by high levels of diversity, and both spatial and temporal heterogeneity.10aagroecosystem10acommunity10adisturbance10aecological indicator10aland-use change10anatural ecosystem10anematode10arestoration10asentinel taxa10asoil10atallgrass prairie1 aTodd, T., C.1 aPowers, T., O.1 aMullin, P., G.  uhttps://nematoda.myspecies.info/content/sentinel-nematodes-land-use-change-and-restoration-tallgrass-prairie01812nas a2200229   4500008004100000245010400041210006900145260010100214300001400315490000700329520096500336653002101301653001701322653002201339653001301361653001901374653000901393100001501402700001901417700001601436856013001452       2009                        eng d00aNematode response to metal, PAHs and organic enrichment in tourist marinas of the mediterranean sea0 aNematode response to metal PAHs and organic enrichment in touris  aTHE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLANDbPERGAMON-ELSEVIER SCIENCE LTD  a1192-12010 v583 aThe structure of nematode assemblages was investigated in the sediments of two different tourist marinas in the Mediterranean Sea and related to pollution variables. Nematode densities and generic compositions were determined, as were concentrations of heavy metals, PAHs and organic matter. Results showed different assemblages at the two marinas, with a dominance of the genera Paralongicyatholaimus and Daptonema. Significant correlations between nematodes and concentrations of environmental contaminants were found. In particular, Paralongicyatholaimus showed a significant negative correlation with Cu concentrations and was almost absent at the stations where higher Cu concentrations were found. The presence of sensitive/tolerant nematode genera represents a promising tool to identify areas subjected to a higher level of disturbance and to define the correct environmental management strategy for harbors. (C) 2009 Elsevier Ltd. All rights reserved.10aHarbor sediments10aheavy metals10aMediterranean Sea10anematode10aorganic matter10aPAHs1 aMoreno, M.1 aAlbertelli, G.1 aFabiano, M.  uhttps://nematoda.myspecies.info/content/nematode-response-metal-pahs-and-organic-enrichment-tourist-marinas-mediterranean-sea02854nas a2200313   4500008004100000245010100041210006900142260008700211300001400298490000600312520175000318653002902068653001702097653001802114653003102132653001602163653001302179100002702192700002802219700001702247700002202264700002102286700002402307700002302331700002402354700001402378700001902392856012902411       2009                        eng d00aEvaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity0 aEvaluating highthroughput sequencing as a method for metagenomic  aCOMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USAbWILEY-BLACKWELL PUBLISHING, INC  a1439-14500 v93 aNematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving similar to 400-bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82% were > 199 bp in length. Among the reads > 199 bp, 86% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.10a454 genome sequencer FLX10aBiodiversity10aDNA barcoding10ahigh-throughput sequencing10ametagenomic10anematode1 aPorazinska, Dorota, L.1 aGiblin-Davis, Robin, M.1 aFaller, Lina1 aFarmerie, William1 aKanzaki, Natsumi1 aMorris, Krystalynne1 aPowers, Thomas, O.1 aTucker, Abraham, E.1 aSung, Way1 aThomas, Kelley  uhttps://nematoda.myspecies.info/content/evaluating-high-throughput-sequencing-method-metagenomic-analysis-nematode-diversity02222nas a2200193   4500008004100000245012000041210006900161260007500230300001200305490000700317520145700324653002601781653001301807653002001820653001901840100001501859700001701874856013701891       1998                        eng d00aUltrastructure of sperm development in the free-living marine nematode Enoplus anisospiculus (Enoplida : Enoplidae)0 aUltrastructure of sperm development in the freeliving marine nem  a23 RUE LINOIS, 75015 PARIS, FRANCEbGAUTHIER-VILLARS/EDITIONS ELSEVIER  a213-2250 v213 aThe development of sperm in testes of the free-living marine nematode Enoplus anisospiculus was studied with electron microscopy. The spermatogonia are undifferentiated polygonal cells with a large nucleus surrounded by a small cytoplasm. The cytoplasm of spermatocytes is filled with numerous Golgi bodies, cisternae of the RER, ribosomes, and mitochondria and it forms membranous organelles (MO). The development of MOs proceeds along two parallel lines that are characteristic of two different types of spermatocyte. In the first type, MOs begin as a system of cisternae; in the second type, MOs first appear as large vesicles filled with osmiophilic material. Later in the development of spermatocytes, all MOs are bipolar because of a large eccentric dense body associated with the system of cisternae. The nuclei of spermatids have a distinct nuclear envelope. During the collapse of the nucleus, mitochondria and MOs become closely associated with the nuclear envelope. In older spermatids, mitochondria form a layer at the future anterior end of the nucleus, all MOs are positioned posteriorly, and fibrous bodies with a marked radial orientation appear first between the anterior layer of the mitochondria and the nucleus. This cluster of organelles is retained in the immature sperm after detachment of the residual body. The distinctly external cytoplasm (ectoplasm) of the immature sperm is devoid of organelles. (C) Orstom/Elsevier, Paris.10aEnoplus anisospiculus10anematode10aspermatogenesis10aultrastructure1 aYushin, VV1 aMalakhov, VV  uhttps://nematoda.myspecies.info/content/ultrastructure-sperm-development-free-living-marine-nematode-enoplus-anisospiculus-enoplida-02314nas a2200229   4500008004100000245009600041210006900137260007100206300001200277490000700289520151200296653002501808653002001833653001301853653001701866653001001883653002001893653000901913653001901922100002101941856012201962       1998                        eng d00aUltrastructure of spermatozoa in the nematode Halalaimus dimorphus (Nemata : Oxystominidae)0 aUltrastructure of spermatozoa in the nematode Halalaimus dimorph  a3012 SKYVIEW DRIVE, LAKELAND, FL 33801-7072 USAbSOC NEMATOLOGISTS  a391-4030 v303 aThe ultrastructure of spermatozoa in the free-living marine nematode Halalaimus dimorphus was studied with transmission electron microscopy. Spermatozoa in the posterior testis of the male had a large cavity filled with cellular processes, which contained a variable number of small tubules. Mitochondria and small tubules were the only cell structures observed in the cytoplasm. The spermatozoa had a bipolar structure. The anteriorly situated nucleus, which was electron-dense and homogeneous, was surrounded by a single membrane. The size of the small tubules in the cytoplasm (diam. 12-13 nm) and their relatively thick wall structure suggested that they were not normal microtubules (diam. 25 nm). The material of the small tubules was assumed to be major sperm protein (MSP). The cavity appeared to open on the surface of the spermatozoon at the posterior extremity of the cell, and also medially, at the level of the anterior end of the cavity. The pores apparently were closed by a special plug-like structure, which was an evagination of the cell. The wall of the cavity was characterized by longitudinal folds, which were mushroom-shaped in transverse section. Spermatids in the anterior testis of H. dimorphus were characterized by fibrous bodies packed with small tubules and by cellular processes also containing small tubules. H. dimorphus sperm seem to perform swimming movements based on liquid currents commonly present in turbin-like systems. Spermatogenesis resembled that found in ticks.10aHalalaimus dimorphus10amarine nematode10anematode10areproduction10asperm10aspermatogenesis10atick10aultrastructure1 aTurpeenniemi, TA  uhttps://nematoda.myspecies.info/content/ultrastructure-spermatozoa-nematode-halalaimus-dimorphus-nemata-oxystominidae03040nas a2200289   4500008004100000245013500041210006900176260007600245300001000321490000600331520198800337653002202325653001302347653001102360653002802371653002202399100002302421700002502444700002402469700002102493700001802514700002602532700001702558700001702575700002102592856013702613       2008                        eng d00aA ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats0 aribosomal DNAbased framework for the detection and quantificatio  a9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLANDbBLACKWELL PUBLISHING  a23-340 v83 aIndigenous communities of soil-resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under-exploitation as soil health indicators, and a user-friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress-sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full-length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA-based systematics, Mononchida families (indicated here as M1-M5) are relatively well-supported and, consequently, family-specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (approximate to 1000 bp from the 5'-end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1-D9, PP1-PP3) that shows only distant similarity with 'classical' Dorylaimid systematics. Most subclades were trophically homogeneous, and - in most cases - specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real-time polymerase chain reaction). Our results constitute proof-of-principle for the concept of DNA sequence signatures-based monitoring of stress sensitive nematode families in environmental samples.10aLSU ribosomal DNA10anematode10aRT-PCR10asoil community analysis10aSSU ribosomal DNA1 aHolterman, Martijn1 aRybarczyk, Katarzyna1 avan den Elsen, Sven1 avan Megen, Hanny1 aMooyman, Paul1 aSantiago, Reyes, Pena1 aBongers, Tom1 aBakker, Jaap1 aHelder, Johannes  uhttps://nematoda.myspecies.info/content/ribosomal-dna-based-framework-detection-and-quantification-stress-sensitive-nematode-familie01836nas a2200241   4500008004100000245007600041210006900117260005900186300001200245490000700257520101400264653002701278653001401305653002201319653002501341653001301366653003301379653001601412653002701428100001201455700001401467856011301481       2005                        eng d00aRolling circle amplification of complete nematode mitochondrial genomes0 aRolling circle amplification of complete nematode mitochondrial   aPO BOX 311, MARCELINE, MO 64658 USAbSOC NEMATOLOGISTS  a236-2410 v373 aTo enable investigation of nematode mitochondrial DNA evolution, methodology has been developed to amplify intact nematode mitochondrial genomes in preparative yields using a rolling circle replication strategy. Successful reactions were generated from whole cell template DNA prepared by alkaline lysis of the rhabditid nematode Caenorhabditis elegans and a mermithid nematode, Thaumamerinis cosgrovei. These taxa, representing the two major nematode classes Chromodorea and Enoplea, maintain mitochondrial genomes of 13.8 kb and 20.0 kb, respectively. Efficient amplifications were conducted on template DNA isolated from individual or pooled nematodes that were alive or stored at -80 degrees C. Unexpectedly, these experiments revealed that multiple T. cosgrovei mitochondrial DNA haplotypes are maintained in our local population. Rolling circle amplification products can be used as templates for standard PCR reactions with specific primers that target mitochondrial genes or for direct DNA sequencing.10aCaenorhabditis elegans10amermithid10amitochondrial DNA10amolecular nematology10anematode10arolling circle amplification10asystematics10aThaumamermis cosgrovei1 aTang, S1 aHyman, BC  uhttps://nematoda.myspecies.info/content/rolling-circle-amplification-complete-nematode-mitochondrial-genomes