Identification of the Xenopus laevis cDNA for EXT1: a phylogenetic perspective.

The EXT family of genes is involved in the developmentally important biosynthesis of heparan sulfate molecules. Members of the EXT family have a demonstrated role in gastrulation, wing formation in flies, and proper bone development in vertebrates. EXT family members have been isolated from several phylogenetically diverse species. We report here, the isolation of the first Xenopus laevis EXT1 family member and discuss the evolutionary origins of this gene family.

Evaluation of dialysis as a technique for the removal of lipids prior to the GC determination of ortho- and non-ortho-chlorobiphenyls, using 14C-labelled congeners.

Dialysis was evaluated as a non-destructive clean-up technique to isolate chlorobiphenyls (CBs) from fish-oil prior to further analysis. 14C-CBs were used to study the transfer processes of the CBs across polyethylene membranes. Single step processes using equilibrium dialysis were compared to a dynamic method of refluxing solvent. The dynamic method reduced the duration of the separation to 8 h. The transfer of CBs and the lipids was dependent on temperature and nature of the analyte with smaller molecules being dialysed substantially faster than larger molecules. An optimised dynamic method was used to compare the dialytic clean-up with a traditional method using sulfuric acid-impregnated silica for the determination of CBs in a laboratory reference material. Labelled recovery standards for each individual congener are recommended in combination with dialysis as a method for clean-up.

An integrated physical map of 8q22-q24: use in positional cloning and deletion analysis of Langer-Giedion syndrome.

We have developed an integrated map for a 35-cM area of human chromosome 8 surrounding the Langer-Giedion syndrome deletion region. This map spans from approximately 8q22 to 8q24 and includes 10 hybrid cell intervals, 89 polymorphic STSs, 118 ESTs, and 37 known genes or inferred gene homologies. The map locations of 25 genes including osteoprotegerin, syndecan-2, and autotaxin have been refined from the general locations previously reported. In addition, the map has been used to indicate the location of nine deletions in patients with Langer-Giedion syndrome and trichorhinophalangeal syndrome type I to demonstrate the potential usefulness of the map in the analysis of these complex syndromes. The map will also be of interest to anyone trying to clone positionally disease genes in this region, such as Cohen syndrome (8q22-q23), Klip-Feil syndrome (8q22.2), hereditary spastic paraplegia (8q24), and benign adult familial myoclonic epilepsy (8q23.3-q24.1).

Disruption of gastrulation and heparan sulfate biosynthesis in EXT1-deficient mice.

Mutations in the EXT1 gene are responsible for human hereditary multiple exostosis type 1. The Drosophila EXT1 homologue, tout-velu, regulates Hedgehog diffusion and signaling, which play an important role in tissue patterning during both invertebrate and vertebrate development. The EXT1 protein is also required for the biosynthesis of heparan sulfate glycosaminoglycans that bind Hedgehog. In this study, we generated EXT1-deficient mice by gene targeting. EXT1 homozygous mutants fail to gastrulate and generally lack organized mesoderm and extraembryonic tissues, resulting in smaller embryos compared to normal littermates. RT-PCR analysis of markers for visceral endoderm and mesoderm development indicates the delayed and abnormal development of both of these tissues. Immunohistochemical staining revealed a visceral endoderm pattern of Indian hedgehog (Ihh) in wild-type E6.5 embryos. However, in both EXT1-deficient embryos and wild-type embryos treated with heparitinase I, Ihh failed to associate with the cells. The effect of the EXT1 deletion on heparan sulfate formation was tested by HPLC and cellular glycosyltransferase activity assays. Heparan sulfate synthesis was abolished in EXT1 -/- ES cells and decreased to less than 50% in +/- cell lines. These results indicate that EXT1 is essential for both gastrulation and heparan sulfate biosynthesis in early embryonic development.

Toxaphene in standard solutions and cleaned biota extracts--results of the first QUASIMEME interlaboratory studies. Quality Assurance of Information for Marine Environmental Monitoring in Europe.

Two interlaboratory studies on individual toxaphene congeners have been organised by the project Quality Assurance of Information for Marine Environmental Monitoring in Europe (QUASIMEME). Fifteen laboratories analysed two standard solutions in the first study and 13 laboratories analysed a standard solution and two cleaned biota extracts in the second study. The coefficients of variation obtained for the standard solutions were 6-21% and for the cleaned extracts 16-39%. Although the results were comparable to those of other studies, further improvement in the level of agreement between the participating laboratories was considered possible.

Vg1 orthology in the direct developing frog, Syrrhophus cystignathoides campi.

Syrrhophus cystignathoides campi is a direct developing frog species that matures without passing through a larval (tadpole) stage. We have cloned and sequenced the Syrrhophus cDNA orthologous to the Xenopus Vg1 cDNA. The Syrrhophus Vg1 (sVg1) cDNA spans 1323 nucleotides and encodes a predicted protein of 345 amino acids which is 81% identical at its carboxyl terminal end to Xenopus Vg1. In addition, it contains seven conserved cysteine residues present in all Vg1 related proteins. Despite this high degree of similarity it is apparently missing a conserved N-linked glycosylation site and has an altered proteolytic processing sequence. Interestingly it is also missing a nine nucleotide sequence in its 3' UTR believed to be important for mRNA localization in Xenopus and Drosophila. These sequence variations could alter the functional expression and localization of the protein.

Chlorobiphenyl contaminants at Pladda and Garroch Head in the Firth of Clyde in relation to sewage sludge input.

Sewage sludge dumped at Garroch Head in the Firth of Clyde contains significant quantities of chlorinated hydrocarbons, such as polychlorinated biphenyls (CBs). These compounds are lipophilic and resistant to degradation. They accumulate in the biota either from the water column or through the food chain, particularly in tissue with a high lipid content. Bottom dwelling fish, such as plaice, in the vicinity of the dump site will accumulate CBs from their environment. Eighteen of the 209 CBs were measured in plaice livers from the Garroch Head dump site and from Pladda, a site reasonably remote from the dump site but also in the Clyde, over a 7 year period prior to the cessation of dumping in December 1998. Concentrations of the congeners in the liver of fish caught at the dump site were, in general, higher than those in the liver of fish caught at Pladda. Concentrations in the plaice livers for the sum of 18 CBs ranged from 1611 to 8471 micrograms kg-1 lipid for Garroch Head samples and from 336.9 to 2635 micrograms kg-1 lipid for samples from Pladda. The data were evaluated using principal component analysis (PCA). Pattern analysis was undertaken by normalising to the recalcitrant CB 153. Livers from the dump site were found to have a higher proportion of the lower chlorinated CBs. CB patterns were similar at the Garroch Head dump site from year to year, but multivariate techniques showed that there were differences in pattern when normalised to CB 153.

Human NDUFB9 gene: genomic organization and a possible candidate gene associated with deafness disorder mapped to chromosome 8q13.

Human NADH dehydrogenase (ubiquinone) 1beta-subcomplex, 9 (NDUFB9) is a nuclear encoded mitochondrial protein with the respiratory electron transport chain. It has been physically mapped to a 1-Mb deletion at chromosome 8q13 which also contains the gene for branchio-oto-renal (BOR) syndrome. BOR syndrome is characterized by branchial and renal abnormalities with hearing impairment. Since several hereditary deafness disorders have been associated with mitochondrial mutations, NDUFB9 was considered a candidate gene for BOR syndrome. Recently, EYA1 gene has been identified in the region which underlies the BOR syndrome but majority of BOR families did not show mutations in the EYA1 gene. Here we have determined the genomic structure of the NDUFB9 gene, including the nucleotide sequence, organization and the boundaries of the four coding exons. PCR primers were designed from the adjacent intron sequences that allow amplification of the four exons that encode the complete open reading frame. To identify whether mutations in NDUFB9 are involved in causing the BOR syndrome, we screened 9 BOR families which did not show mutations in the EYA1 gene by heteroduplex analysis; however, no mutations were found.

QUASIMEME laboratory performance study of the biological effects of tributyltin (imposex and intersex) on two marine gastropod molluscs.

The disruption of the endocrine systems of gastropod molluscs and consequential physiological changes (imposex and intersex) are used as biomarkers for environmental contamination by tributyltin compounds. The first international laboratory performance study on the determination of imposex and intersex in neogastropod molluscs, Nucella lapillus and Littorina littorea has been undertaken by the QUASIMEME (Quality Assurance of Information for Marine Environmental Monitoring in Europe) project. Samples of live gastropods were distributed and participants were asked to record shell height and sex, together with penis length and vas deferens sequence stage (VDS) in Nucella or the intersex stage (IS) and prostate length in Littorina. Calculations were made of vas deferens sequence index (VDSI) and the relative penis size index (RPSI) in Nucella and of intersex stage index (ISI) and the average female prostate length (FPrL) in Littorina. Thirteen (87%) of the 15 participating laboratories returned data. The remaining two laboratories asked to participate in later exercises. For Nucella, seven laboratories reported sex ratios significantly different from the reference laboratory data. Differences in penis length measurements between laboratories were largely random, although there were indications of systematic errors affecting the data from three laboratories. Seven laboratories reported satisfactory data (Z-score magnitude of Z < 2) for VDSI. The inclusion of a high proportion of sub-adults in the Nucella samples may have made separation of the sexes more difficult than in mature adults. The sub-adults will have had smaller pene than mature adults in the same population, and therefore any errors (random or systematic) in the measurement of penis length or observation of reproductive organs would have a potentially greater impact on the final reported values of the summary imposex indices. The Littorina sample did not show a high degree of intersex (ISI = 0.41). The laboratories could determine the sex of Littorina reliably and only one laboratory reported data significantly different from the reference laboratory. All except two laboratories reported satisfactory data for ISI.

Evaluation of locus heterogeneity and EXT1 mutations in 34 families with hereditary multiple exostoses.

Hereditary multiple exostoses (EXT) is an autosomal dominant disorder characterized by growth of benign bone tumors. Three chromosomal loci have been implicated in this genetically heterogeneous disease: EXT1 at 8q24, EXT2 at 11p13, and EXT3 on 19p. EXT1 and EXT2 were recently cloned. We evaluated 34 families with EXT to estimate the proportion of disease attributable to EXT1, EXT2, and EXT3 and to investigate the spectrum of EXT1 mutations. Linkage analyses combined with heterogeneity testing provides strong evidence in favor of linkage of disease to both chromosomes 8 and 11, but does not support evidence of linkage to chromosome 19 in this data set. The 11 EXT1 exons were PCR-amplified and sequenced in all 11 isolated cases and in 20 of the 23 familial cases. Twelve different novel EXT1 mutations were detected, including 5 frame-shift deletions or insertions, 1 codon deletion, and 6 single base-pair substitutions distributed across 8 of the exons. Only 2 of the mutations were detected in more than one family. Three mutations affect sites in which alterations were previously reported. Nonchain-terminating missense mutations were identified in codons 280 and 340, both coding for conserved arginine residues. These residues may be crucial to the function of this protein. Although the prevalence of EXT has been estimated to be approximately 1/50,000 individuals, the disease has been reported to occur much more frequently in the Chamorro natives on Guam. Our detection of an EXT1 mutation in one Chamorro subject will allow investigation of a possible founder effect in this population. Combined mutational and heterogeneity analyses in this set of families with multiple exostoses suggest that 66% of our total sample, including 45% of isolated and 77% of familial cases, are attributable to abnormalities in EXT1.

Characterization and mapping to human chromosome 8q24.3 of Ly-6-related gene 9804 encoding an apparent homologue of mouse TSA-1.

The 9804 gene, which encodes a human Ly-6 protein most similar to mouse differentiation Ag TSA-1/Sca-2, has also been called RIG-E. Like mouse TSA-1, it has a broad tissue distribution with varied expression levels in normal human tissues and tumor cell lines. Like some members of the murine Ly-6 family, the 9804 gene is responsive to IFNs, particularly IFN-alpha. Overlapping genomic fragments spanning the 9804 gene (5543 bp) have been isolated and characterized. The gene organization is analogous to that of known mouse Ly-6 genes. The first exon, 2296 bp upstream from exon II, is entirely untranslated. The three coding exons (II, III, and IV) are separated by short introns of 321 and 131 bp, respectively. Primers were developed for specific amplification of 9804 gene fragments. Screening of human-hamster somatic cell hybrids and yeast artificial chromosomes (YACs) indicated that the gene is distal to c-Myc, located in the q arm of human chromosome 8. No positives were detected from the Centre d'Etude du Polymorphisme Humain mega-YAC A or B panels, nor from bacterial artificial chromosome libraries; two positive cosmids (c101F1 and c157F6) were isolated from a human chromosome 8 cosmid library (LA08NC01). Fluorescence in situ hybridization of metaphase spreads of chromosome 8, containing hybrid cell line 706-B6 clone 17 (CL-17) with cosmid c101F1, placed the 9804 gene close to the telomere at 8q24.3. This mapping is significant, since the region shares a homology with a portion of mouse chromosome 15, which extends into band E where Ly-6 genes reside. Moreover, the gene encoding E48, the homologue of mouse Ly-6 molecule ThB, has also been mapped to 8q24.

Concentration-dependent changes of PCB patterns in fish-eating mammals: structural evidence for induction of cytochrome P450.

Data sets on CB concentrations in fish-eating mammals from five laboratories were combined to test and refine a pharmacokinetic model. Clear differences in PCB patterns were observed between species. The ability to metabolize chlorobiphenyl (CB) congeners with vicinal H-atoms only in the ortho- and meta-positions and with one ortho-chlorine substituent generally increased in the order otter < cetaceans (harbor porpoise, common dolphin) < phocid seals (harbor and grey seal), but the metabolism of congeners with vicinal H-atoms in the meta- and para-positions and with two ortho-chlorines increased in the order cetaceans < seals < otter. Both categories of congeners are probably metabolized by different families of cytochrome P450 (1A and 2B) of which levels apparently differed between the cetaceans, the pinnipeds, and the otter. Within-species CB patterns differed in a concentration-dependent manner. The induction of cytochrome P450 enzymes offers the most likely explanation for this phenomenon, but starvation could have a similar effect on occasion.

Mutation screening of the EXT1 and EXT2 genes in patients with hereditary multiple exostoses.

Hereditary multiple exostoses (HME), the most frequent of all skeletal dysplasias, is an autosomal dominant disorder characterized by the presence of multiple exostoses localized mainly at the end of long bones. HME is genetically heterogeneous, with at least three loci, on 8q24.1 (EXT1), 11p11-p13 (EXT2), and 19p (EXT3). Both the EXT1 and EXT2 genes have been cloned recently and define a new family of potential tumor suppressor genes. This is the first study in which mutation screening has been performed for both the EXT1 and EXT2 genes prior to any linkage analysis. We have screened 17 probands with the HME phenotype, for alterations in all translated exons and flanking intronic sequences, in the EXT1 and EXT2 genes, by conformation-sensitive gel electrophoresis. We found the disease-causing mutation in 12 families (70%), 7 (41%) of which have EXT1 mutations and 5 (29%) EXT2 mutations. Together with the previously described 1-bp deletion in exon 6, which is present in 2 of our families, we report five new mutations in EXT1. Two are missense mutations in exon 2 (G339D and R340C), and the other three alterations (a nonsense mutation, a frameshift, and a splicing mutation) are likely to result in truncated nonfunctional proteins. Four new mutations are described in EXT2. A missense mutation (D227N) was found in 2 different families; the other three alterations (two nonsense mutations and one frameshift mutation) lead directly or indirectly to premature stop codons. The missense mutations in EXT1 and EXT2 may pinpoint crucial domains in both proteins and therefore give clues for the understanding of the pathophysiology of this skeletal disorder.

Chromosomal localization of the human and mouse hyaluronan synthase genes.

We have recently identified a new vertebrate gene family encoding putative hyaluronan (HA) synthases. Three highly conserved related genes have been identified, designated HAS1, HAS2, and HAS3 in humans and Has1, Has2, and Has3 in the mouse. All three genes encode predicted plasma membrane proteins with multiple transmembrane domains and approximately 25% amino acid sequence identity to the Streptococcus pyogenes HA synthase, HasA. Furthermore, expression of any one HAS gene in transfected mammalian cells leads to high levels of HA biosynthesis. We now report the chromosomal localization of the three HAS genes in human and in mouse. The genes localized to three different positions within both the human and the mouse genomes. HAS1 was localized to the human chromosome 19q13.3-q13.4 boundary and Has1 to mouse Chr 17.HAS2 was localized to human chromosome 8q24.12 and Has2 to mouse Chr 15. HAS3 was localized to human chromosome 16q22.1 and Has3 to mouse Chr 8. The map position for HAS1 reinforces the recently reported relationship between a small region of human chromosome 19q and proximal mouse chromosome 17. HAS2 mapped outside the predicted critical region delineated for the Langer-Giedion syndrome and can thus be excluded as a candidate gene for this genetic syndrome.

Identification of novel mutations in the human EXT1 tumor suppressor gene.

Hereditary multiple exostoses (EXT) is a genetically heterogeneous bone disorder caused by genes segregating on human chromosomes 8, 11, and 19 and designated EXT1, EXT2 and EXT3, respectively. Recently, the EXT1 gene has been isolated and partially characterized and appears to encode a tumor suppressor gene. We have identified six mutations in the human EXT1 gene from six unrelated multiple exostoses families segregating for the EXT gene on chromosome 8. One of the mutations we detected is the same 1-bp deletion in exon 6 that was previously reported in two independent EXT families. The other five mutations, in exons 1, 6, 9, and the splice junction at the 3' end of exon 2, are novel. In each case, the mutation is likely to result in a truncated or nonfunctional EXT1 protein. These results corroborate and extend the previous report of mutations in this gene in two EXT families, and provide additional support for the EXT1 gene as the cause of hereditary multiple exostoses in families showing linkage to chromosome 8.

Genomic organization and promoter structure of the human EXT1 gene.

Hereditary predisposition to multiple exostoses is a genetically heterogeneous disease. Recently, we have reported the identification of the EXT1 gene on human chromosome 8. We have now isolated a cDNA clone from a human adult lung cDNA library and have determined the genomic organization and promoter structure of the EXT1 gene. The gene is composed of 11 exons, ranging from 90 to 1735 bp, and spans approximately 350 kb of genomic DNA. Sequence analysis of the promoter region revealed the presence of a CpG island containing GC and CAAT boxes, but no TATA box. Such a promoter is characteristic for housekeeping genes. This finding is in good agreement with the ubiquitous expression of the EXT1 gene.

Concentrations and patterns of organic contaminants in Atlantic white-sided dolphins (Lagenorhynchus acutus) from Irish and Scottish coastal waters.

Chlorobiphenyls (CBs) and organochlorine pesticides (OCPs) have been determined in the blubber of 17 Atlantic white-sided dolphins stranded at Killala Bay, Co Mayo, Ireland and five from the Scottish coast. The concentrations of the contaminants measured range from 773 to 63,400 microg kg(-1) for sigmaCB and from 160 to 54,600 microg kg(-1) for sigmaDDT. The concentrations of the CBs and OCPs is highly dependent on the age, sex, reproductive state and nutritional condition of the animals in addition to the intake via the food web. Principal Components Analysis (PCA) has been used to study the variation of chemical patterns (data ratioed to CB 153). Immature animals (< 6 years), mature males and primogravid females, and lactating females could be distinguished on the basis of their contaminant patterns. This paper describes the different processes of bioaccumulation and metabolism of organochlorine contaminants (OCs) in this species.