Secondary literature sources for Col_cuticle_N

The following references were automatically generated.

E Silva JP, Furtado AP, Dos Santos JN
Proteomic profile of Ortleppascaris sp.: A helminth parasite of Rhinella marina in the Amazonian region.
Int J Parasitol Parasites Wildl. 2014; 3: 67-74
Display abstract
Ortleppascaris sp. is a helminth that, in its larval stage, infects the liver parenchyma of the amphibian Rhinella marina, resulting in severe physiological and pathological changes. This study used a proteomic approach to determine the overall profile of proteins expressed in a somatic extract from the nematodes to investigate the relationship between the parasite and its host. A total of 60 abundant proteins were selected from the two-dimensional electrophoresis, identified by peptide mass fingerprinting, and grouped based on their Gene Ontology by the biological processes in which they are potentially involved. Important helminthic derivatives, such as the immunoreactive As37 antigen, guanylyl cyclases, proteolytic enzymes, and other proteins conserved among different parasites, were identified through homology. This study represents a new approach to helminth-related proteomic studies using an amphibian animal model. Furthermore, this study identified protein markers that are important to the host-parasite relationship and the viability, development, infectivity, and virulence of helminths.

Laing R et al.
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.
PLoS One. 2011; 6: 23216-23216
Display abstract
The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes.

Davies KG, Curtis RH
Cuticle surface coat of plant-parasitic nematodes.
Annu Rev Phytopathol. 2011; 49: 135-56
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The surface coat (SC) of the plant-parasitic nematode cuticle is an understudied area of current research, even though it likely plays key roles in both nematode-plant and nematode-microbe interactions. Although in several ways Caenorhabditis elegans is a poor model for plant-parasitic nematodes, it is a useful starting point for investigations of the cuticle and its SC, especially in the light of recent work using this species as a model for innate immunity and the generic biology underpinning much host-parasite biology. We review the research focused on the involvement of the SC of plant-parasitic nematodes. Using the insights gained from animal-parasitic nematodes and other sequenced nematodes, we discuss the key roles that the SC may play.

Liu G, Rogers J, Murphy CT, Rongo C
EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.
EMBO J. 2011; 30: 2990-3003
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Epidermal growth factor (EGF) signalling regulates growth and differentiation. Here, we examine the function of EGF signalling in Caenorhabditis elegans lifespan. We find that EGF signalling regulates lifespan via the Ras-MAPK pathway and the PLZF transcription factors EOR-1 and EOR-2. As animals enter adulthood, EGF signalling upregulates the expression of genes involved in the ubiquitin proteasome system (UPS), including the Skp1-like protein SKR-5, while downregulating the expression of HSP16-type chaperones. Using reporters for global UPS activity, protein aggregation, and oxidative stress, we find that EGF signalling alters protein homoeostasis in adults by increasing UPS activity and polyubiquitination, while decreasing protein aggregation. We show that SKR-5 and the E3/E4 ligases that comprise the ubiquitin fusion degradation (UFD) complex are required for the increase in UPS activity observed in adults, and that animals that lack SKR-5 or the UFD have reduced lifespans and indications of oxidative stress. We propose that as animals enter fertile adulthood, EGF signalling switches the mechanism for maintaining protein homoeostasis from a chaperone-based approach to an approach involving protein elimination via augmented UPS activity.

Rao VT, Accardi MV, Siddiqui SZ, Beech RN, Prichard RK, Forrester SG
Characterization of a novel tyramine-gated chloride channel from Haemonchus contortus.
Mol Biochem Parasitol. 2010; 173: 64-8
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Tyramine (TA), a trace amine, is becoming accepted as a main stream neurotransmitter in invertebrates. Recent evidence indicates that part of the function of TA in nematodes involves a novel receptor (Cel-LGC-55) from the ligand-gated chloride channel class of ionotropic receptors. However, the role of TA or its receptors in the biology of nematode parasites is limited. Haemonchus contortus is a deadly parasitic worm which causes significant economic burden in the production of small ruminants in many parts of the world. In this study, we have cloned and characterized a novel LGCC from H. contortus which we have named Hco-LGC-55. This receptor subunit is a clear orthologue of Cel-LGC-55 and is able to form a homomeric chloride channel that is gated by tyramine, dopamine and octopamine. Semi-quantitative reverse transcription-polymerase chain reaction (sqRT-PCR) shows that this subunit is expressed in all life-cycle stages of the worm, but appears to have reduced mRNA expression in the adult male.

Castagnone-Sereno P, Danchin EG, 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: 598-598
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BACKGROUND: Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. RESULTS: Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus) ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (AT)n, (AG)n and (CT)n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AAT)n and (ATT)n being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. CONCLUSIONS: Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species. 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.

Hu M, Zhong W, Campbell BE, Sternberg PW, Pellegrino MW, Gasser RB
Elucidating ANTs in worms using genomic and bioinformatic tools--biotechnological prospects?
Biotechnol Adv. 2010; 28: 49-60
Display abstract
Adenine nucleotide translocators (ANTs) belong to the mitochondrial carrier family (MCF) of proteins. ATP production and consumption are tightly linked to ANTs, the kinetics of which have been proposed to play a key regulatory role in mitochondrial oxidative phosphorylation. ANTs are also recognized as a central component of the mitochondrial permeability transition pore associated with apoptosis. Although ANTs have been investigated in a range of vertebrates, including human, mouse and cattle, and invertebrates, such as Drosophila melanogaster (vinegar fly), Saccharomyces cerevisiae (yeast) and Caenorhabditis elegans (free-living nematode), there has been a void of information on these molecules for parasitic nematodes of socio-economic importance. Exploring ANTs in nematodes has the potential lead to a better understanding of their fundamental roles in key biological pathways and might provide an avenue for the identification of targets for the rational design of nematocidal drugs. In the present article, we describe the discovery of an ANT from Haemonchus contortus (one of the most economically important parasitic nematodes of sheep and goats), conduct a comparative analysis of key ANTs and their genes (particularly ant-1.1) in nematodes and other organisms, predict the functional roles utilizing a combined genomic-bioinformatic approach and propose ANTs and associated molecules as possible drug targets, with the potential for biotechnological outcomes.

Campbell BE, Rabelo EM, Hofmann A, Hu M, Gasser RB
Characterization of a Caenorhabditis elegans glc seven-like phosphatase (gsp) orthologue from Haemonchus contortus (Nematoda).
Mol Cell Probes. 2010; 24: 178-89
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A full-length complementary DNA (cDNA; designated Hc-stp-1) encoding a serine/threonine phosphatase (Hc-STP-1) was isolated from Haemonchus contortus, a strongylid nematode parasite of small ruminants. Hc-stp-1 was shown to be transcribed in males of both adults and fourth-stage larvae, but not in females, early larval stages or eggs. The full-length gene (2854 bp) contained ten exons and nine introns, and encoded a cDNA of 951 bp. Comparisons of the conceptually translated protein (316 amino acids, estimated at approximately 35 kDa) with serine/threonine phosphatases (STPs) from other organisms revealed the presence of the conserved motif LRGNHE. Structural analysis, by comparative modelling, confirmed strict conservation of residues and features involved in catalytic activity, and variation in the ligand-binding interface. Phylogenetic analysis of amino acid sequence data revealed that Hc-STP-1 clustered with STPs from other nematodes (including Caenorhabditis elegans, Trichostrongylus vitrinus, Oesophagostomum dentatum, Ascaris suum and Brugia malayi) to the exclusion of STPs from other organisms. The protein was inferred to be most closely related to the PP1 class of STPs of C. elegans, within a group containing STPs encoded, amongst others, by the genes gsp-3 and gsp-4 in this free-living nematode. The functions of proteins GSP-3 and GSP-4 are known to be central to spermatogenesis and other male-specific processes in C. elegans. The findings from the present and previous studies support the proposal that Hc-stp-1 and its product play a significant role in reproductive and/or developmental processes in maturing or adult male H. contortus.

Choi YN et al.
Identification of cdc25 gene in pinewood nematode, Bursaphelenchus xylophilus, and its function in reproduction.
Mol Cells. 2010; 29: 195-201
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The cdc25 gene, which is highly conserved in many eukaryotes, encodes a phosphatase that plays essential roles in cell cycle regulation. We identified a cdc25 ortholog in the pinewood nematode, Bursaphelenchus xylophilus. The B. xylophilus ortholog (Bx-cdc25) was found to be highly similar to Caenorhabditis elegans cdc-25.2 in sequence as well as in gene structure, both having long intron 1. The Bx-cdc25 gene was determined to be composed of seven exons and six introns in a 2,580 bp region, and was shown to encode 360 amino acids of a protein containing a highly-conserved phosphatase domain. Bx-cdc25 mRNA was hardly detectable throughout the juvenile stages but was highly expressed in eggs and in both female and male adults. Functional conservation during germline development between C. elegans cdc25 and Bx-cdc25 was revealed by Bx-cdc25 RNA interference in C. elegans.

Yin Y et al.
Intestinal transcriptomes of nematodes: comparison of the parasites Ascaris suum and Haemonchus contortus with the free-living Caenorhabditis elegans.
PLoS Negl Trop Dis. 2008; 2: 269-269
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BACKGROUND: The nematode intestine is a major organ responsible for nutrient digestion and absorption; it is also involved in many other processes, such as reproduction, innate immunity, stress responses, and aging. The importance of the intestine as a target for the control of parasitic nematodes has been demonstrated. However, the lack of detailed knowledge on the molecular and cellular functions of the intestine and the level of its conservation across nematodes has impeded breakthroughs in this application. METHODS AND FINDINGS: As part of an extensive effort to investigate various transcribed genomes from Ascaris suum and Haemonchus contortus, we generated a large collection of intestinal sequences from parasitic nematodes by identifying 3,121 A. suum and 1,755 H. contortus genes expressed in the adult intestine through the generation of expressed sequence tags. Cross-species comparisons to the intestine of the free-living C. elegans revealed substantial diversification in the adult intestinal transcriptomes among these species, suggesting lineage- or species-specific adaptations during nematode evolution. In contrast, significant conservation of the intestinal gene repertories was also evident, despite the evolutionary distance of approximately 350 million years separating them. A group of 241 intestinal protein families (IntFam-241), each containing members from all three species, was identified based on sequence similarities. These conserved proteins accounted for approximately 20% of the sampled intestinal transcriptomes from the three nematodes and are proposed to represent conserved core functions in the nematode intestine. Functional characterizations of the IntFam-241 suggested important roles in molecular functions such as protein kinases and proteases, and biological pathways of carbohydrate metabolism, energy metabolism, and translation. Conservation in the core protein families was further explored by extrapolating observable RNA interference phenotypes in C. elegans to their parasitic counterparts. CONCLUSIONS: Our study has provided novel insights into the nematode intestine and lays foundations for further comparative studies on biology, parasitism, and evolution within the phylum Nematoda.

McVeigh P, Alexander-Bowman S, Veal E, Mousley A, Marks NJ, Maule AG
Neuropeptide-like protein diversity in phylum Nematoda.
Int J Parasitol. 2008; 38: 1493-503
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This study reports the identification of nematode neuropeptide-like protein (nlp) sequelogs from the GenBank expressed sequence tag (EST) database, using BLAST (Basic Local Alignment Search Tool) search methodology. Search strings derived from peptides encoded by the 45 known Caenorhabditis elegans nlp genes were used to identify more than 1000 ESTs encoding a total of 26 multi-species nlp sequelogs. The remaining 18 nlps (nlp-4, -16, -24 through -36, -39, -41 and -45) were identified only in C. elegans, while the sole EST representative of nlp-23 was from Caenorhabditis remanei. Several ESTs encoding putative antibacterial peptides similar to those encoded by the C. elegans genes nlp-24-33 were observed in several parasite species. A novel gene (nlp-46) was identified, encoding a single, amidated dodecapeptide (NIA[I/T]GR[G/A]DG[F/L]RPG) in eight species. Secretory signal peptides were identified in at least one species representing each nlp sequelog, confirming that all 46 nematode nlp genes encode secretory peptides. A random sub-set of C. elegans NLPs was tested physiologically in Ascaris suum ovijector and body wall muscle bioassays. None of the peptides tested were able to modulate ovijector activity, while only three displayed measurable myoactivity on somatic body wall muscle. AFAAGWNRamide (from nlp-23) and AVNPFLDSIamide (nlp-3) both produced a relaxation of body wall muscle, while AIPFNGGMYamide (nlp-10) induced a transient contraction. Numerical analyses of nlp-encoding ESTs demonstrate that nlp-3, -13, -14, -15 and -18 are amongst the most highly represented transcripts in the dataset. Using available bioinformatics resources, this study delineates the nlp complement of phylum Nematoda, providing a rich source of neuropeptide ligands for deorphanisation of nematode neuropeptide receptors.

Wang X, Li H, Hu Y, Fu P, Xu J
Molecular cloning and analysis of a new venom allergen-like protein gene from the root-knot nematode Meloidogyne incognita.
Exp Parasitol. 2007; 117: 133-40
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A new venom allergen-like protein gene isolated from Meloidogyne incognita (designated Mi-vap-2) was cloned and analysed. The genomic clone of Mi-vap-2 is 1917-bp long, contains three introns, which range in size from 39 to 797 bp, and four exons ranging in size from 37 to 361 bp. The cDNA of Mi-vap-2 contains an open reading frame encoding 294 amino acids, being the first 16 residues a putative secretion signal. Southern blot analysis suggested that Mi-vp-2 is probably a member of a small multigene family. In situ hybridization analysis showed that the transcripts of Mi-vap-2 accumulated exclusively within the subventral oesophageal gland cells of M. incognita. RT-PCR analyses confirmed that Mi-vap-2 was transcribed mainly in the pre-parasitic second-stage and early post-inoculated juveniles. Results indicated that this venom allergen-like protein gene may play an important role in establishment of the parasitic relationship between plants and nematodes.

Nikolaou S et al.
Isolation and characterization of class II myosin genes from Haemonchus contortus.
Parasitol Res. 2006; 99: 200-3
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In this study, cDNAs encoding myosin from the parasitic nematode Haemonchus contortus were isolated and characterized. Several exhibited a considerable degree of sequence variation at the nucleotide and limited divergence at the amino acid levels within the various functional domains. The results suggest that the cDNAs isolated represented a single myosin heavy chain, which, by comparison with a number of other myosins, is inferred to represent a homologue of a muscle myosin (CeMHCA) of the free-living nematode Caenorhabditis elegans. The findings could have implications for investigating cytoskeletal dynamics and/or signalling pathways.

Huang G, Dong R, Allen R, Davis EL, Baum TJ, Hussey RS
Developmental expression and molecular analysis of two Meloidogyne incognita pectate lyase genes.
Int J Parasitol. 2005; 35: 685-92
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Proteinaceous secretions from the oesophageal glands of plant-parasitic nematodes have crucial roles in nematode parasitism of plants. Two cDNAs (designated Mi-pel-1 and Mi-pel-2) encoding pectate lyases were isolated from the root-knot nematode, Meloidogyne incognita, oesophageal gland-cell subtractive cDNA libraries, and the corresponding genomic DNAs were subsequently cloned. Southern blot analyses revealed that homologues to these pectate lyase genes were broadly distributed in Meloidogyne species, and present as members of a small multigene family. Mi-pel-1 and Mi-pel-2 encoded, respectively, predicted proteins of 271 and 280 amino acids, each of which was preceded by a signal peptide for secretion. Interestingly, these pectate lyases showed diversity at the amino acid level, with only 31% identity and 49% similarity. These pectate lyases were classified into the same family of pectate lyases with those of other phytoparasitic nematodes that contain four conserved regions characteristic of the class III pectate lyases of microbes. In situ mRNA hybridisation analyses showed the transcripts of Mi-pel-1 and Mi-pel-2 accumulated exclusively within the subventral oesophageal gland cells of M. incognita. RT-PCR analysis confirmed that their transcriptions were strong at the pre-parasitic and early parasitic second-stage juveniles, and not detectable at the late parasitic stages of the nematodes. These results indicated that these pectate lyases, like cellulases, could be secreted into plant tissues to facilitate the penetration and intercellular migration of M. incognita during the early stages of plant parasitism.

Bakhetia M, Charlton W, Atkinson HJ, McPherson MJ
RNA interference of dual oxidase in the plant nematode Meloidogyne incognita.
Mol Plant Microbe Interact. 2005; 18: 1099-106
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RNA interference (RNAi) is a powerful tool for the analysis of gene function in model organisms such as the nematode Caenorhabditis elegans. Recent demonstrations of RNAi in plant parasitic nematodes provide a stimulus to explore the potential of using RNAi to investigate disruption of gene function in Meloidogyne incognita, one of the most important nematode pests of global agriculture. We have used RNAi to examine the importance of dual oxidases (peroxidase and NADPH oxidase), a class of enzyme associated with extracellular matrix cross-linking in C. elegans. RNAi uptake by M. incognita juveniles is highly efficient. In planta infection data show that a single 4-h preinfection treatment with double-stranded RNA derived from the peroxidase region of a dual oxidase gene has effects on gene expression that are phenotypically observable 35 days postinfection. This RNAi effect results in a reduction in egg numbers at 35 days of up to 70%. The in vitro feeding strategy provides a powerful tool for identifying functionally important genes, including those that are potential targets for the development of new agrochemicals or transgenic resistance strategies.

Couthier A, Smith J, McGarr P, Craig B, Gilleard JS
Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence.
Mol Biochem Parasitol. 2004; 133: 241-53
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Comparative analysis between Caenorhabditis elegans and other nematode species offers a powerful approach to study gene function. C. elegans also has great potential as a surrogate expression system to study the function of genes from parasitic nematode species where transgenic methodologies are unavailable. However there is little information on the extent to which the biology of C. elegans is conserved with other nematode species and very few parasitic nematode genes have yet been functionally expressed in C. elegans. We have identified and characterised a homologue of the C. elegans GATA transcription factor elt-2, a central regulator of endoderm development, from the parasitic nematode Haemonchus contortus. The H. contortus ELT-2 polypeptide is present in endoderm nuclei throughout embryonic and post-embryonic development, except for in the infective L3 stage, and our experiments reveal that the development of the H. contortus endodermal lineage is strikingly similar to that of C. elegans. Sequence conservation between the H. contortus and C. elegans ELT-2 polypeptides broadly reflects function since the major region of sequence identity corresponds to the DNA binding domain. However, the overall level of sequence identity is remarkably low with the only other major region of identity corresponding to an unusual zinc finger domain. In spite of this, ectopic expression of the H. contortus elt-2 gene in transgenic C. elegans is sufficient to activate a programme of endodermal differentiation demonstrating that function is highly conserved. This approach of ectopic expression using an inducible promoter provides an effective way in which to use C. elegans for the in vivo functional analysis of parasitic nematode genes.

Davis MW, Birnie AJ, Chan AC, Page AP, Jorgensen EM
A conserved metalloprotease mediates ecdysis in Caenorhabditis elegans.
Development. 2004; 131: 6001-8
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Molting is required for progression between larval stages in the life cycle of nematodes. We have identified four mutant alleles of a Caenorhabditis elegans metalloprotease gene, nas-37, that cause incomplete ecdysis. At each molt the cuticle fails to open sufficiently at the anterior end and the partially shed cuticle is dragged behind the animal. The gene is expressed in hypodermal cells 4 hours before ecdysis during all larval stages. The NAS-37 protein accumulates in the anterior cuticle and is shed in the cuticle after ecdysis. This pattern of protein accumulation places NAS-37 in the right place and at the right time to degrade the cuticle to facilitate ecdysis. The nas-37 gene has orthologs in other nematode species, including parasitic nematodes, and they undergo a similar shedding process. For example, Haemonchus contortus molts by digesting a ring of cuticle at the tip of the nose. Incubating Haemonchus larvae in extracted exsheathing fluids causes a refractile ring of digested cuticle to form at the tip of the nose. When Haemonchus cuticles are incubated with purified NAS-37, a similar refractile ring forms. NAS-37 degradation of the Haemonchus cuticle suggests that the metalloproteases and the cuticle substrates involved in exsheathment of parasitic nematodes are conserved in free-living nematodes.

Olsen AN, Skriver K
Ligand mimicry? Plant-parasitic nematode polypeptide with similarity to CLAVATA3.
Trends Plant Sci. 2003; 8: 55-7

Warren CE, Krizus A, Dennis JW
Complementary expression patterns of six nonessential Caenorhabditis elegans core 2/I N-acetylglucosaminyltransferase homologues.
Glycobiology. 2001; 11: 979-88
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The Caenorhabditis elegans genome contains 18 sequences related to mammalian core 2/I N-acetylglucosaminyltransferases. The six most closely related genes (gly-1 and gly-15 to gly-19) likely encode active enzymes, because are all transcribed and do not appear to be pseudogenes. Polypeptide divergence and the gene structures are both concordant with a common ancestor at the time of radiation from mammals that underwent three rounds of duplication and, most recently, a tandem duplication. Polypeptide alignments with mammalian homologues do not indicate whether the enzyme specificities are core 2, 4, or I-like or novel, but do clearly demonstrate the secondary structure characteristics of glycosyltransferases. The six homologues have essentially nonoverlapping expression patterns, unrelated by tissue type or cell lineage. The extent varies widely; gly-15 is expressed only in two gland cells, whereas gly-18 is broadly expressed in diverse cell types. gly-1, -15, -18 and -19 are expressed during adulthood; gly-16 and gly-17 appear to be restricted to embryonic or early larval stages. The parsimonious interpretation of the expression pattern and sequence data is that the catalytic activities are similar but with diverged promoters. Null alleles of three of the genes were generated without causing gross abnormality in homozygous animals. RNA-mediated interference experiments also failed to induce defects in the four genes tested. Nevertheless, the nematode has evolved six diverged core 2 GlcNAc-T-like genes, and we postulate that these arose in response to selection pressures to which C. elegans is not ordinarily subjected in the laboratory.

Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS
Molecular characterisation and expression of two venom allergen-like protein genes in Heterodera glycines.
Int J Parasitol. 2001; 31: 1617-25
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Secretory proteins encoded by genes expressed in the oesophageal gland cells of plant-parasitic nematodes have key roles in nematode parasitism of plants. Two venom allergen-like protein cDNAs (designated hg-vap-1 and hg-vap-2)were isolated from Heterodera glycines gland cell cDNA libraries. Both cDNAs hybridised to genomic DNA of H. glycines in Southern blots. The hg-vap-1 cDNA contained an open reading frame encoding 215 amino acids with the first 25 amino acids being a putative secretion signal. The hg-vap-2 cDNA contained an open reading frame encoding 212 amino acids with the first 19 amino acids being a putative secretion signal. Genes of hg-vap-1 and hg-vap-2 contained four introns, which ranged in size from 44 to 574 bp, and five exons ranging in size from 43 to 279 bp. In situ hybridisation analyses showed that mRNAs of both vap genes accumulated specifically in the subventral gland cells of H. glycines during parasitism. The gland cell-specific expression and presence of predicted secretion signal peptides in both VAPs suggest that these proteins are secreted from the nematode and may play a role in the infection of host plants by this parasite.

Hoekstra R, Visser A, Otsen M, Tibben J, Lenstra JA, Roos MH
EST sequencing of the parasitic nematode Haemonchus contortus suggests a shift in gene expression during transition to the parasitic stages.
Mol Biochem Parasitol. 2000; 110: 53-68
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Expressed sequence tags from the parasitic nematode Haemonchus contortus were generated in order to identify anchor loci for comparative mapping between nematode genomes and candidate targets for future control measures. In total, 370 SL1 trans-spliced cDNAs from different developmental stages representing 195 different genes were partially sequenced. From these expressed sequence tags 50% were similar to genes with a known or predicted function and 19% were similar to nematode sequences with no ascribed function. From the first, free-living L1 and L3 stages relatively many cDNAs matched to housekeeping genes, and 11% (L1) or 23% (L3) of the encoded proteins were predicted to contain signal peptides. In contrast, no function could be ascribed to most of the cDNAs from the early L5 and adult parasitic stages, but for 30% (L5) or 55% (adult) of the encoded proteins a signal sequence was predicted. This limited analysis suggests that during the transition from the free-living to parasitic stages gene expression shifts towards the synthesis of less conserved extracellular proteins. These proteins offer the best perspectives for vaccine development and the development of anthelmintic drugs. In contrast, cDNAs from the first larval stages may be most suitable for comparative mapping with the free-living nematode Caenorhabditis elegans.

Brownlee DJ, Fairweather I
Exploring the neurotransmitter labyrinth in nematodes.
Trends Neurosci. 1999; 22: 16-24
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Nematodes include both free-living species such as Caenorhabditis elegans and major parasites of humans, livestock and plants. The apparent simplicity and uniformity of their nervous system belies a rich diversity of putative signalling molecules, particularly neuropeptides. This new appreciation stems largely from the genome-sequencing project with C. elegans, which is due to be completed by the end of 1998. The project has provided additional insights into other aspects of nematode neurobiology, as have studies on the mechanism of action of anthelmintics. Here, progress on the identification, localization, synthesis and physiological actions of transmitters identified in nematodes is explored.

Piotte C, Arthaud L, Abad P, Rosso MN
Molecular cloning of an acetylcholinesterase gene from the plant parasitic nematodes, Meloidogyne incognita and Meloidogyne javanica.
Mol Biochem Parasitol. 1999; 99: 247-56
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A gene encoding a protein with strong homology with Caenorhabditis elegans and C. briggsae acetylcholinesterase ACE-1 was cloned from Meloidogyne incognita and M. javanica pre-parasitic juveniles. Both cDNAs have an ORF of 1968 bp for a deduced translation product of 656 amino acid residues. The key residues essential to acetylcholinesterase (AChE) structure and function are conserved in both sequences. M. incognita and M. javanica AChE share a homology of 98.8% at the amino acid level and 97% at the nucleotide level. Phylogenetic analysis showed that Meloidogyne and Caenorhabditis AChE form a cluster among AChE of triploblastic organisms. This Meloidogyne AChE is expressed in eggs, pre-parasitic juveniles and males and AChE activity was detected in situ in amphids of pre-parasitic juveniles. The opportunity of using AChE as a target in new strategies of nematode control is discussed.

Rosso MN et al.
Isolation of a cDNA encoding a beta-1,4-endoglucanase in the root-knot nematode Meloidogyne incognita and expression analysis during plant parasitism.
Mol Plant Microbe Interact. 1999; 12: 585-91
Display abstract
A beta-1,4-endoglucanase encoding cDNA (EGases, E.C. 3.2.1.4), named Mi-eng-1, was cloned from Meloidogyne incognita second-stage juveniles (J2). The deduced amino acid sequence contains a catalytic domain and a cellulose-binding domain separated by a linker. In M. incognita, the gene is transcribed in the migratory J2, in males, and in the sedentary adult females. In pre-parasitic J2, endoglucanase transcripts are located in the cytoplasm of the subventral esophageal glands. The presence of beta-1,4-endoglucanase transcripts in adult females could be related to the expression of the gene in esophageal glands at this stage. However, cellulase activity within the egg matrix of adult females suggests that the endoglucanase may also be synthesized in the rectal glands and involved in the extrusion of the eggs onto the root surface. The maximum identity of the predicted MI-ENG-1 catalytic domain with the recently cloned cyst nematode beta-1,4-endoglucanases is 52.5%. In contrast to cyst nematodes, M. incognita pre-parasitic J2 were not found to express a beta-1,4-endoglucanase devoid of a cellulose-binding domain.

Hagg PM, Muona A, Lietard J, Kivirikko S, Pihlajaniemi T
Complete exon-intron organization of the human gene for the alpha1 chain of type XV collagen (COL15A1) and comparison with the homologous COL18A1 gene.
J Biol Chem. 1998; 273: 17824-31
Display abstract
The human gene for the alpha1 chain of type XV collagen (COL15A1) is about 145 kilobases in size and contains 42 exons. The promoter is characterized by the lack of a TATAA motif and the presence of several Sp1 binding sites, some of which appeared to be functional in transfected HeLa cells. Comparison with Col18a1, which encodes the alpha1(XVIII) collagen chain homologous with alpha1(XV), indicates marked structural homology spread throughout the two genes. The mouse Col18a1 contains one exon more than COL15A1, due to the fact that COL15A1 lacks sequences corresponding to exon 3 of Col18a1, which encodes a cysteine-rich sequence motif. Twenty-five of the exons of the two genes are almost identical in size, six of them contain conserved split codons, and the locations of the respective exon-intron junctions are identical or almost identical in the two genes. The homologous exons include the closely adjacent first pair of exons and the exons encoding a thrombospondin-1 homology found in the N-terminal noncollagenous domain 1, which are followed by the most variable part of the two genes, covering the C-terminal half of their noncollagenous domain 1 and the beginning of the collagenous portion, after which most of the exons are homologous. The lengths of the introns are not similar in these genes, with two exceptions, namely the first intron, which is very short, less than 100 base pairs, and the second intron, which is very large, about 50 kilobases, in both genes. It can be concluded that COL15A1 and Col18a1 are derived from a common ancestor.

Blaxter M
Caenorhabditis elegans is a nematode.
Science. 1998; 282: 2041-6
Display abstract
Caenorhabditis elegans is a rhabditid nematode. What relevance does this have for the interpretation of the complete genome sequence, and how will it affect the exploitation of the sequence for scientific and social ends? Nematodes are only distantly related to humans and other animal groups; will this limit the universality of the C. elegans story? Many nematodes are parasites; can knowledge of the C. elegans sequence aid in the prevention and treatment of disease?

Keddie EM, Higazi T, Unnasch TR
The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis.
Mol Biochem Parasitol. 1998; 95: 111-27
Display abstract
The complete DNA sequence of the mitochondrial genome of Onchocerca volvulus is described. The O. volvulus mitochondrial genome is 13747 bp, slightly smaller than the mitochondrial genomes of the nematodes Ascaris suum and Caenorhabditis elegans, and the smallest metazoan mitochondrial DNA molecule reported to date. The O. volvulus mitochondrial genome contains genes for two ribosomal RNAs, 22 transfer RNAs and 12 proteins. Consistent with the small size of the genome, four gene pairs overlap and eight contain no intergenic regions. Only 17 intergenic regions are found, ranging in size from 1 to 46 bp. As in C. elegans and A. suum, the O. volvulus mitochondrial genome lacks an open reading frame encoding ATPase subunit 8, and all genes are apparently transcribed in the same direction. However, the mitochondrial gene order of O. volvulus differs from that of A. suum, C. elegans and other metazoan mitochondrial genomes. A total of 20 of the 22 transfer RNAs encoded in the O. volvulus mitochondrial genome have the potential to fold into secondary structures lacking the TpsiC arm, as has been reported in other nematodes. The genome exhibits a striking codon bias, with 15/20 amino acids having a single codon preference of > 70%.

Liao VH, Freedman JH
Cadmium-regulated genes from the nematode Caenorhabditis elegans. Identification and cloning of new cadmium-responsive genes by differential display.
J Biol Chem. 1998; 273: 31962-70
Display abstract
The transition metal cadmium is a pervasive and persistent environmental contaminant that has been shown to be both a human toxicant and carcinogen. To inhibit cadmium-induced damage, cells respond by increasing the expression of genes encoding stress-response proteins. In most cases, the mechanism by which cadmium affects the expression of these genes remains unknown. It has been demonstrated in several instances that cadmium activates gene transcription through signal transduction pathways, mediated by protein kinase C, cAMP-dependent protein kinase, or calmodulin. A codicil is that cadmium should influence the expression of numerous genes. To investigate the ability of cadmium to affect gene transcription, the differential display technique was used to analyze gene expression in the nematode Caenorhabditis elegans. Forty-nine cDNAs whose steady-state levels of expression change 2-6-fold in response to cadmium exposure were identified. The nucleotide sequences of the majority of the differentially expressed cDNAs are identical to those of C. elegans cosmids, yeast artificial chromosomes, expressed sequence tags, or predicted genes. The translated amino acid sequences of several clones are identical to C. elegans metallothionein-1, HSP70, collagens, and rRNAs. In addition, C. elegans homologues of pyruvate carboxylase, DNA gyrase, beta-adrenergic receptor kinase, and human hypothetical protein KIAA0174 were identified. The translated amino acid sequences of the remaining differentially expressed cDNAs encode novel proteins.

Agulnik SI, Ruvinsky I, Silver LM
Three novel T-box genes in Caenorhabditis elegans.
Genome. 1997; 40: 458-64
Display abstract
The T-box gene family consists of members that share a unique DNA binding domain. The best characterized T-box gene, Brachyury or T, encodes a transcription factor that plays an important role in early vertebrate development. Seven other recently described mouse T-box genes are also expressed during development. In the nematode Caenorhabditis elegans, four T-box genes have been characterized to date. In this study, we describe three new C. elegans T-box genes, named Ce-tbx-11, Ce-tbx-12, and Ce-tbx-17. Ce-tbx-11 and Ce-tbx-17 were uncovered through the sequencing efforts of the C. elegans Genome Project. Ce-tbx-12 was uncovered through degenerate PCR analysis of C. elegans genomic DNA. Ce-tbx-11 and Ce-tbx-17 are located in close proximity to the four other previously described T-box genes in the central region of chromosome III. In contrast, Ce-tbx-12 maps alone to chromosome II. Phylogenetic analysis of all known T-box domain sequences provides evidence of an ancient origin for this gene family.

Johnstone IL, Shafi Y, Majeed A, Barry JD
Cuticular collagen genes from the parasitic nematode Ostertagia circumcincta.
Mol Biochem Parasitol. 1996; 80: 103-12
Display abstract
The nematode cuticle is a multifunctional structure whose roles include exoskeleton and barrier between the animal and its environment. It is an extracellular matrix which consists predominantly of small collagen-like proteins. For those species studied, these cuticular collagens are encoded by a multigene family. In the free living nematode Caenorhabditis elegans, this family has approximately 100 members. Our data indicate a gene family of similar size in the parasitic nematode Ostertagia circumcincta. We have characterised a pair of tandemly duplicated collagen genes from O. circumcincta, colost-1 and colost-2, which we believe to be the direct homologues of col-12 and col-13, a tandemly duplicated pair previously identified in C. elegans. The interspecies comparison of these homologues indicates regions of extreme conservation. We conclude that the gene duplication event that resulted in the creation of col-12 and col-13 in C. elegans is most likely the same duplication that generated colost-1 and colost-2 in O. circumcincta, and thus this particular gene duplication precedes the divergence of the two species. These two nematode species are deeply diverged, O. circumcincta belonging to the order Strongylata and C. elegans to Rhabditata. The ability to identify direct homologues of individual cuticular collagen genes between deeply diverged species provides a powerful method for determining regions of structural importance in these small collagens. Characteristics that are conserved between homologues in divergent species, but not conserved with other members of the multigene family within one species, must relate to the specific function of that particular cuticular collagen.

Kloek AP, McCarter JP, Setterquist RA, Schedl T, Goldberg DE
Caenorhabditis globin genes: rapid intronic divergence contrasts with conservation of silent exonic sites.
J Mol Evol. 1996; 43: 101-8
Display abstract
Globin genes from the Caenorhabditis species briggsae and remanei were identified and compared with a previously described C. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix. C. remanei was found to have two globin alleles, Crg1-1 and Crg1-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1% divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show that Crg1-1 and Crg1-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.

Lichtsteiner S, Tjian R
Cloning and properties of the Caenorhabditis elegans TATA-box-binding protein.
Proc Natl Acad Sci U S A. 1993; 90: 9673-7
Display abstract
The nematode Caenorhabditis elegans has become an organism of choice for the study of developmental processes at the genetic level. We have undertaken to develop an in vitro system to study transcription in C. elegans. As a first step we report here the cloning of the cDNA encoding the C. elegans TATA-box-binding protein (CeTBP). We used "touch-down PCR" to generate a specific DNA probe derived from the C-terminal region conserved in all TBP genes cloned to date. Several clones encoding an extended open reading frame were isolated from a phage lambda cDNA library. The complete amino acid sequence of CeTBP deduced from the cDNA reveals a protein of 37 kDa with an extended sequence similarity in the C-terminal region with all other TBP cDNAs sequenced so far. The N-terminal region of CeTBP (amino acids 1-153), however, does not show any homology with TBPs from other organisms. Interestingly, the N-terminal portion of the molecule contains three short direct repeats. Purified recombinant CeTBP binds specifically to the TATA box sequence, interacts with transcription factors TFIIA and TFIIB, and is able to substitute for the TFIID basal activity when assayed by in vitro transcription in both HeLa and C. elegans nuclear extracts. CeTBP is therefore a basal transcription factor.

Powers TO, Harris TS, Hyman BC
Mitochondrial DNA Sequence Divergence among Meloidogyne incognita, Romanomermis culicivorax, Ascaris suum, and Caenorhabditis elegans.
J Nematol. 1993; 25: 564-72
Display abstract
Mitochondrial DNA sequences were obtained from the NADH dehydrogenase subunit 3 (ND3), large rRNA, and cytochrome b genes from Meloidogyne incognita and Romanomermis culicivorax. Both species show considerable genetic distance within these same genes when compared with Caenorhabditis elegans or Ascaris suum, two species previously analyzed. Caenorhabditis, Ascaris, and Meloidogyne were selected as representatives of three subclasses in the nematode class Secernentea: Rhabditia, Spiruria, and Diplogasteria, respectively. Romanomermis served as a representative out-group of the class Adenophorea. The divergence between the phytoparasitic lineage (represented by Meloidogyne) and the three other species is so great that virtually every variable position in these genes appears to have accumulated multiple mutations, obscuring the phylogenetic information obtainable from these comparisons. The 39 and 42% amino acid similarity between the M. incognita and C. elegans ND3 and cytochrome b coding sequences, respectively, are approximately the same as those of C. elegans-mouse comparisons for the same genes (26 and 44%). This discovery calls into question the feasibility of employing cloned C. elegans probes as reagents to isolate phytoparasitic nematode genes. The genetic distance between the phytoparasitic nematode lineage and C. elegans markedly contrasts with the 79% amino acid similarity between C. elegans and A. suum for the same sequences. The molecular data suggest that Caenorhabditis and Ascaris belong to the same subclass.

Jacenko O, Olsen BR, LuValle P
Organization and regulation of collagen genes.
Crit Rev Eukaryot Gene Expr. 1991; 1: 327-53

Guo XD, Johnson JJ, Kramer JM
Embryonic lethality caused by mutations in basement membrane collagen of C. elegans.
Nature. 1991; 349: 707-9
Display abstract
Basement membranes are specialized forms of extracellular matrix with important functions in development. A major structural component of basement membranes is type IV collagen, a heterotrimer of two alpha 1(IV) and one alpha 2(IV) chains, which forms a complex, polygonal network associated with other basement membrane components. Here we report that the alpha 1(IV) collagen chain of Caenorhabditis elegans is encoded by the genetic locus emb-9. Mutations in emb-9 cause temperature-sensitive lethality during late embryogenesis. We have identified single nucleotide alterations that substitute glutamic acid for glycine in the triple-helical Gly-X-Y repeat region of the alpha 1(IV) collagen in three emb-9 mutant strains. These results are direct evidence that defects in basement membranes can disrupt embryonic development and form a basis for the genetic analysis of basement membrane function.

Kurz EM, Holstein TW, Petri BM, Engel J, David CN
Mini-collagens in hydra nematocytes.
J Cell Biol. 1991; 115: 1159-69
Display abstract
We have isolated and characterized four collagen-related c-DNA clones (N-COL 1, N-COL 2, N-COL 3, N-COL 4) that are highly expressed in developing nematocytes in hydra. All four c-DNAs as well as their corresponding transcripts are small in size (600-1,000 bp). The deduced amino acid sequences show that they contain a central region consisting of 14 to 16 Gly-X-Y triplets. This region is flanked amino-terminal by a stretch of 14-23 proline residues and carboxy-terminal by a stretch of 6-9 prolines. At the NH2- and COOH-termini are repeated patterns of cysteine residues that are highly conserved between the molecules. A model is proposed which consists of a central stable collagen triple helix of 12-14 nm length from which three 9-22 nm long polyproline II type helices emerge at both ends. Disulfide linkage between cysteine-rich segments in these helices could lead to the formation of oligomeric network structures. Electrophoretic characterization of nematocyst extracts allows resolution of small proline-rich polypeptides that correspond in size to the cloned sequences.

Hawkins NC, McGhee JD
Homeobox containing genes in the nematode Caenorhabditis elegans.
Nucleic Acids Res. 1990; 18: 6101-6
Display abstract
We designed a unique 36-mer oligonucleotide probe, based on the most highly conserved amino acid sequences of Antennapedia-like homeodomains and the codon bias of Caenorhabditis elegans. This probe was then used to isolate four classes of genes from a C. elegans genomic library. Sequencing reveals that we have isolated three new homeobox genes, designated ceh-1, ceh-9 and ceh-10. The fourth homeobox gene, ceh-11, has recently been described by Schaller et al (Nucleic Acids Res. 18, 2033-2036). The amino acid sequence of ceh-1 is 87% similar to the honeybee H40 homeodomain, 85% similar to the Drosophila NK-1 homeodomain and 82% similar to the chicken CHox3 homeodomain. The sequence ceh-10 appears to be a member of the paired class of homeodomains. The other two sequences, ceh-9 and ceh-11, remain unclassified. Three of the four sequences have at least one intron within the homeobox region. Transcripts of ceh-10 and ceh-11 are present in embryonic RNA but are greatly diminished in later developmental stages. Three of the four new genes have been placed on the C. elegans genomic map.

Exposito JY, Garrone R
Characterization of a fibrillar collagen gene in sponges reveals the early evolutionary appearance of two collagen gene families.
Proc Natl Acad Sci U S A. 1990; 87: 6669-73
Display abstract
We have characterized cDNA and genomic clones coding for a sponge collagen. The partial cDNA has an open reading frame encoding 547 amino acid residues. The conceptual translation product contains a probably incomplete triple-helical domain (307 amino acids) with one Gly-Xaa-Yaa-Zaa imperfection in the otherwise perfect Gly-Xaa-Yaa repeats and a carboxyl propeptide (240 amino acids) that includes 7 cysteine residues. Amino acid sequence comparisons indicate that this sponge collagen is homologous to vertebrate and sea urchin fibrillar collagens. Partial characterization of the corresponding gene reveals an intron-exon organization clearly related to the fibrillar collagen gene family. The exons coding for the triple-helical domain are 54 base pairs (bp) or multiples thereof, except for a 57-bp exon containing the Gly-Xaa-Yaa-Zaa coding sequence and for two unusual exons of 126 and 18 bp, respectively. This latter 18-bp exon marks the end of the triple-helical domain, contrary to the other known fibrillar collagen genes that contain exons coding for the junction between the triple-helical domain and the carboxyl propeptide. Compared to other fibrillar collagen genes, the introns are remarkably small. Hybridization to blotted RNAs established that the gene transcript is 4.9 kilobases. Together with previous results that showed the existence of a nonfibrillar collagen in the same species, these data demonstrate that at least two collagen gene families are represented in the most primitive metazoa.

Kingston IB, Pettitt J
Structure and expression of Ascaris suum collagen genes: a comparison with Caenorhabditis elegans.
Acta Trop. 1990; 47: 283-7
Display abstract
We are interested in the structure and organization of collagen and collagen genes in the parasitic nematode Ascaris suum and in the control of collagen gene expression in Ascaris. In this nematode, as in all others studied, collagens constitute the major component of the extracellular cuticle and ultimately we would like to correlate the expression pattern of Ascaris cuticular collagen genes with the structure of the nematode cuticle. We would also like to see if there is any correlation between differential collagen gene expression and the biology and life-cycle of the parasite. In addition, we are also interested in comparing our data with the more extensive data available on collagen genes in the free living nematode Caenorhabditis elegans.

Guo XD, Kramer JM
The two Caenorhabditis elegans basement membrane (type IV) collagen genes are located on separate chromosomes.
J Biol Chem. 1989; 264: 17574-82
Display abstract
We have identified and characterized the two genes, clb-1 and clb-2, that encode basement membrane collagen (IV) in Caenorhabditis elegans. Both genes encode 5.5-kilobase mRNAs, similar in size to the mammalian and Drosophila type IV collagen gene transcripts but much larger than the cuticle collagen transcripts of C. elegans. The nucleotide sequences of the NC1 regions of both genes were determined. Comparisons of the clb-1 and clb-2 NC1 amino acid sequences with those of mouse and human show that clb-1 shares 72% identity with mammalian alpha 2(IV) and clb-2 shares 63% identity with mammalian alpha 1(IV), suggesting that clb-1 is the alpha 2(IV) homologue and clb-2 is the alpha 1(IV) homologue. The presence of two type IV collagen genes in C. elegans and the mammals, but a single gene in Drosophila, indicates that the primordial type IV collagen gene had already duplicated early in the evolution of the invertebrates and that one of the genes has been subsequently lost from Drosophila. The mouse and human alpha 1(IV) and alpha 2(IV) genes are separated by only about 130 base pairs and are transcribed in opposite directions from overlapping promoters. We show that the C. elegans genes are located on separate chromosomes, clb-1 on X and clb-2 on III, demonstrating that the mammalian arrangement is not a requirement for all type IV collagen genes. We have identified a candidate genetic locus for the clb-2 basement membrane collagen gene, which will allow us to pursue a genetic analysis of basement membrane structure and function in C. elegans.

Burglin TR, Finney M, Coulson A, Ruvkun G
Caenorhabditis elegans has scores of homoeobox-containing genes.
Nature. 1989; 341: 239-43
Display abstract
Homoeobox-containing genes control cell identities in particular spatial domains, cell lineages, or cell types during the development of Drosophila and Caenorhabditis elegans, and they probably control similar processes in vertebrates. More than 80 genes with homoeoboxes that have sequence similarities ranging from 25 to 100% have been isolated by genetic means or by DNA hybridization to previously isolated genes. We synthesized 500-2,000-fold degenerate oligonucleotides corresponding to a set of well-conserved eight amino acid sequences from the helix-3 region of the homoeodomain. We screened C. elegans genomic libraries with these probes and identified 49 putative homoeobox-containing loci. DNA sequencing confirmed that eight out of ten selected loci had sequences corresponding to the conserved helix-3 region plus additional flanking sequence similarity. One of these genes contained a sequence corresponding to a complete pou-domain and another was closely related to the homoeobox-containing genes caudal/cdx-1. The putative homoeobox loci were mapped to the physical contig map of C. elegans, allowing the identification of potentially corresponding genes from the correlated genetic map. We estimate that the number of homoeobox-containing genes in C. elegans is at least 60, constituting approximately 1% of the estimated total number of genes.

Martin RE, Foster LA, Kester AS, Donahue MJ
Ascaris lumbricoides suum: morphological characterization of apparent cuticular pores by ionic permeability and electron microscopy.
Exp Parasitol. 1987; 63: 329-36
Display abstract
The cuticle of the parasitic roundworm Ascaris lumbricoides suum has been found to contain apparent pores, using scanning and transmission electron microscopy. However, X-ray spectral analysis and dot mapping analysis of diffusing divalent cations in the cuticle found these ions to be randomly distributed on the pseudocoelomic surface of the cuticle. This indicates that the pores seen with the electron microscope were not true structural pores and that the cuticle is homogeneously permeable to ions.

Russnak RH, Candido EP
Locus encoding a family of small heat shock genes in Caenorhabditis elegans: two genes duplicated to form a 3.8-kilobase inverted repeat.
Mol Cell Biol. 1985; 5: 1268-78
Display abstract
The genes coding for hsp 16-48, previously identified by cDNA cloning, and for another 16-kilodalton heat shock protein designated hsp16-1 were characterized by DNA sequencing. The two genes were arranged in a head-to-head orientation. Both the coding and flanking regions were located within a 1.9-kilobase module which was duplicated exactly to form a 3.8-kilobase inverted repeat structure. The inverted repeat structure ended in an unusual guanine-plus-cytosine-rich sequence 24 nucleotides in length. The identity of the two modules at the nucleotide sequence level implies that the duplication event may have occurred recently. Alternatively, gene conversion between the two modules could also maintain homology of the two gene pairs. The small heat shock genes of Caenorhabditis elegans contained TATA boxes and heat-inducible promoters, the latter agreeing closely with the Drosophila melanogaster consensus sequence described by Pelham (Cell 30:517-528, 1982). Unlike the homologous D. melanogaster genes, each of these C. elegans genes contained a short intron, the position of which has been conserved in a related murine alpha-crystallin gene. The intron separated variable and conserved regions within the amino acid sequences of the encoded heat shock polypeptides.

Kramer JM, Cox GN, Hirsh D
Comparisons of the complete sequences of two collagen genes from Caenorhabditis elegans.
Cell. 1982; 30: 599-606
Display abstract
Several collagen genes have been isolated from the nematode Caenorhabditis elegans. The complete nucleotide sequences of two of these genes, col-1 and col-2, have been determined. These collagen genes differ from vertebrate collagen genes in that they contain only one or two introns, their triplehelical regions are interrupted by nonhelical amino acid sequences and they are smaller. A high degree of nucleotide and amino acid homology exists between col-1 and col-2. In particular, the regions around cysteines and lysines are most highly conserved. The C. elegans genome contains 50 or more collagen genes, the majority of which probably encode cuticle collagens; col-1 and col-2 apparently are members of this large family of cuticle collagen genes.

Prockop DJ
Recombinant DNA and collagen research. Is amino acid sequencing obsolete? Can we study diseases involving collagen by analysis of the genes?
Coll Relat Res. 1981; 1: 129-35

Maggenti AR
The role of cuticular strata nomenclature in the systematics of nemata.
J Nematol. 1979; 11: 94-8
Display abstract
A system of cuticular nomenclature based on the strata observed in Enoplia is proposed. Nematode cuticle is divided into four fundamental strata: epicuticle, exocuticle, mesocuticle, and endocuticle. Application of this system allows the correlation of complementary strata throughout Nemata. The major taxonomic categories within Nemata are differentiated on the basis of their cuticular strata as compared with the Enoplia model cuticle.

Noble S, Leushner J, Pasternak J
In vitro translation of nematode cuticular collagens.
Biochim Biophys Acta. 1978; 520: 219-28
Display abstract
Phenanthroline treatment of growing cultures of the free-living nematode Panagrellus silusiae was used to lower the degree of hydroxylation of nascent collagen chains at the polysomal level. Under these conditions, the bound pentasome-hexasome fraction provided substrate for prolyl hydroxylase. When this polysomal fraction was subsequently tested in a cell-free wheat germ system, collagenase-susceptible translation products were observed after sodium dodecyl sulfate-acrylamide gel electrophoresis. The electrophoretic mobilities of each of these four major collagen products were similar to four collagens that are isolated from intact cuticles. In addition, purified polysomal RNA that adhered to unmodified cellulose directed the synthesis of four pepsin-resistant polypeptides that had molecular weights that coincided with four pepsin-resistant collagens that can be purified from the cuticle of this species. Thus, the polysomal site of the messenger RNAs for the cuticular collagens of P. silusiae was located. Although precursor forms of the cuticular collagens were not produced in the cell-free system, the question whether additional amino acid segments occur on the primary translational products of the cuticular collagens in vivo remains open.

Searcy DG, Kisiel MJ, Zuckerman BM
Age-related increase of cuticle permeability in the nematode Caenorhabditis briggsae.
Exp Aging Res. 1976; 2: 293-301
Display abstract
The external cuticular surface of nematodes, which resembles cellular membranes in certain ways, appears to deteriorate with age. For example, when the permeabilities to radioactive water of young and old nematodes were compared, and the data were corrected for the different surface: volume ratios, the older nematodes were significantly more permeable. In both living and dead nematodes, the same rates of water exchange were observed, indicating that the major route of exchange was probably by passive diffusion through the cuticle rather than by active processes such as swallowing or excreting water.

Jackson GJ, Bradbury PC
Cuticular fine structure and molting of Neoaplectana glaseri (Nematoda), after prolonged contact with rat peritoneal exudate.
J Parasitol. 1970; 56: 108-15