Comprehensive detection of genomic duplications and deletions in the DMD gene,by use of multiplex amplifiable probe hybridization

Duplications and deletions are known to cause a number of genetic disorders, yet technical difficulties and financial considerations mean that screening for these mutations, especially duplications, is often not performed. We have adapted multiplex amplifiable probe hybridization (MAPH) for the screening of the DMD gene, mutations in which cause Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy. MAPH involves the quantitative recovery of specifically designed probes following hybridization to immobilized genomic DNA. We have engineered probes for each of the 79 exons of the DMD gene, and we analyzed them by using a 96-capillary sequencer. We screened 24 control individuals, 102 patients, and 23 potential carriers and detected a large number of novel rearrangements, especially small, one- and two-exon duplications. A duplication of exon 2 alone was the most frequently occurring mutation identified. Our analysis indicates that duplications occur in 6% of patients with DMD. The MAPH technique as modified here is simple, quick, and accurate; furthermore, it is based on existing technology (i.e., hybridization, PCR, and electrophoresis) and should not require new equipment. Together, these features should allow easy implementation in routine diagnostic laboratories. Furthermore, the methodology should be applicable to any genetic disease, it should be easily expandable to cover >200 probes, and its characteristics should facilitate high-throughput screening.     

Structure of the human argininosuccinate synthetase gene and an improved system for molecular diagnostics in patients with classical and mild citrullinemia

Deficiency of argininosuccinate synthetase (ASS) causes citrullinemia, an autosomal recessive inherited defect of the urea cycle. Most patients described so far have presented with the classical form of the disease. There are also patients with a mild form of citrullinemia in whom the exact molecular basis and clinical relevance are uncertain. Mutations in the human ASS gene have not yet been described in mildly affected or asymptomatic patients with citrullinemia. The genomic sequence of the human ASS gene is not precisely known making mutation analysis difficult. Here, the entire genomic DNA sequence and mutations in the ASS gene of patients with the classical and mild form of the disease are described. The mutations c.1168G-->A (G390R) and IVS13+5 G-->A and the novel mutation c.323G-->T (R108L) have been found to be associated with classical citrullinemia, whereas the novel mutations c.535T-->G (W179R), and c.1085G-->T (G362V) have been detected on alleles of the mildly affected patients. Thus, mutations found in the human ASS gene of asymptomatic children with biochemical abnormalities and in some cases enzymatically proven citrullinemia have allowed us to classify these cases as ASS-deficient patients. The elucidation of the structure of the human ASS gene has made possible the use of intronic primers for molecular analysis of patients with mild disease and the classical form, and provides another option for prenatal diagnostics in affected families with the severe type.     

Understanding fragile X syndrome: insights from animal models

The fragile X mental retardation syndrome is caused by large methylated expansions of a CGG repeat in the FMR1 gene leading to the loss of expression of FMRP, an RNA-binding protein. FMRP is proposed to act as a regulator of mRNA transport or translation that plays a role in synaptic maturation and function. To study the physiological function of the FMR1 protein, mouse and Drosophila models have been developed. The loss-of-function mouse model shows slightly enlarged testes, a subtle behavioral phenotype, and discrete anomalies of dendrite spines similar to those observed in brains of patients. Studies in Drosophila indicate that FXMR plays an important role in synaptogenesis and axonal arborization, which may underlie the observed deficits in flight ability and circadian behavior of FXR mutant flies. The relevance of these studies to our understanding of fragile X syndrome is discussed.     

Lack of association of Mycobacterium avium subsp. paratuberculosis with oocytes and embryos from moderate shedders of the pathogen

Paratuberculosis is a chronic and progressive disease of the intestine in ruminants caused by Mycobacterium avium subsp. paratuberculosis (Map). The bacterium is transmitted to young animals, becomes manifest in adulthood and leads to economic losses. The aim of this study is to investigate if cows shedding Map possess oocytes and embryos that are carriers of the bacterium. New genetical material can enter the dairy farm using embryo transfer but the question as to whether this technique is safe with respect to transmission of paratuberculosis has yet to be addressed. We selected and bought 16 cows, all proven to be moderate shedders of the bacterium in the faeces immediately prior to the experiment but none were clinically sick. One sample of uterine content was collected from each animal by flushing the uterus on the day of heat and five samples of homogenised uterine tissue were collected on the eighth day of the same cycle by biopsy. In addition, 217 cumulus-oocyte complexes (COCs), ranging from 3 to 35 COCs per animal, were collected using ultrasound guided transvaginal puncture of the ovarian follicles (OPU). On the seventh day of the subsequent cycle 31 embryos were obtained using the classic technique of super ovulation induction, artificial insemination (AI), followed by flushing of the uterus. These embryos have been washed and trypsinised. Fourteen of the 16 cows were treated again for super ovulation in the subsequent cycle and 19 foetuses were collected by opening of the uterus after euthanasia on Days 35-49 of the cycle. All samples were cultured for presence of Map and checked every 2 months during 1 year for bacterial growth. None of the samples showed growth of Map after 12 months of culture. Pathological examination of the cows revealed different degrees of severity of pathological alterations of the intestinal tract and mesenteric lymph nodes. However, the results suggest that neither in vivo embryo's nor oocytes are carriers of the bacteria and do not form an extra risk at transfer. However, due to the limited size of the experiment (sample size of 16 cows), a certain margin for error remains.     

Comparison of velocity profiles for different flow chamber designs used in studies of microbial adhesion to surfaces

Flow chambers are commonly used to study microbial adhesion to surfaces under environmentally relevant hydrodynamic conditions. The parallel plate flow chamber (PPFC) is the most common design, and mass transport occurs through slow convective diffusion. In this study, we analyzed four different PPFCs to determine whether the expected hydrodynamic conditions, which control both mass transport and detachment forces, are actually achieved. Furthermore, the different PPFCs were critically evaluated based on the size of the area where the velocity profile was established and constant with a range of flow rates, indicating that valid observations could be made. Velocity profiles in the different chambers were calculated by using a numerical simulation model based on the finite element method and were found to coincide with the profiles measured by particle image velocimetry. Environmentally relevant shear rates between 0 and 10,000 s(-1) could be measured over a sizeable proportion of the substratum surface for only two of the four PPFCs. Two models appeared to be flawed in the design of their inlets and outlets and allowed development of a stable velocity profile only for shear rates up to 0.5 and 500 s(-1). For these PPFCs the inlet and outlet were curved, and the modeled shear rates deviated from the calculated shear rates by up to 75%. We concluded that PPFCs used for studies of microbial adhesion to surfaces should be designed so that their inlets and outlets are in line with the flow channel. Alternatively, the channel length should be increased to allow a greater length for the establishment of the desired hydrodynamic conditions.     

Direct random insertion mutagenesis of Helicobacter pylori

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or instability of the cloned DNA, or toxicity of the encoded products. We therefore created two mutant libraries in the human pathogen Helicobacter pylori using a simple, direct mutagenesis technique, which does not require E. coli as intermediate. H. pylori total DNA was digested, circularized and digested again with a frequently cutting restriction enzyme, and the resulting fragments were ligated to a kanamycin antibiotic resistance cassette. Subsequently, the ligation mixture was transformed into the parental H. pylori strain 1061. Insertion of the kanamycin cassette by double homologous recombination into the genome of H. pylori 1061 resulted in approximately 2500 kanamycin resistant colonies. Heterogeneity of kanamycin cassette insertion was confirmed by Southern blotting. The isolation of two independent H. pylori mutants defective in production of urease from this library underlines the potential of this mutagenesis strategy.     

Vaccination-induced protection of lambs against the parasitic nematode Haemonchus contortus correlates with high IgG antibody responses to the LDNF glycan antigen

Lambs respond to vaccination against bacteria and viruses but have a poor immunological response to nematodes. Here we report that they are protected against the parasitic nematode Haemonchus contortus after vaccination with excretory/secretory (ES) glycoproteins using Alhydrogel as an adjuvant. Lambs immunized with ES in Alhydrogel and challenged with 300 L3 larvae/kg body weight had a reduction in cumulative egg output of 89% and an increased percentage protection of 54% compared with the adjuvant control group. Compared to the adjuvant dimethyl dioctadecyl ammonium bromide, Alhydrogel induced earlier onset and significantly higher ES- specific IgG, IgA, and IgE antibody responses. In all vaccinated groups a substantial proportion of the antibody response was directed against glycan epitopes, irrespective of the adjuvant used. In lambs vaccinated with ES in Alhydrogel but not in any other group a significant increase was found in antibody levels against the GalNAcbeta1,4 (Fucalpha1,3)GlcNAc (fucosylated LacdiNAc, LDNF) antigen, a carbohydrate antigen that is also involved in the host defense against the human parasite Schistosoma mansoni. In lambs the LDNF-specific response increased from the first immunization onward and was significantly higher in protected lambs. In addition, an isotype switch from LDNF-specific IgM to IgG was induced that correlated with protection. These data demonstrate that hyporesponsiveness of lambs to H. contortus can be overcome by vaccination with ES glycoproteins in a strong T-helper 2 type response-inducing aluminum adjuvant. This combination generated high and specific antiglycan antibody responses that may contribute to the vaccination-induced protection.     

An efficient cDNA-AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis

A new strategy has been designed to identify putative pathogenicity factors from the dorsal or subventral esophageal glands of the potato cyst nematode Globodera rostochiensis. Three independent criteria were used for selection. First, genes of interest should predominantly be expressed in infective second-stage juveniles, and not, or to a far lesser extent, in younger developmental stages. For this, gene expression profiles from five different developmental stages were generated with cDNA-AFLP (amplified fragment length polymorphism). Secondly, the mRNA corresponding to such a putative pathogenicity factor should predominantly be present in the esophageal glands of pre-parasitic juveniles. This was checked by in situ hybridization. As a third criterion, these proteinaceous factors should be preceded by a signal peptide for secretion. Expression profiles of more than 4,000 genes were generated and three up-regulated, dorsal gland-specific proteins preceded by signal peptide for secretion were identified. No dorsal gland genes have been cloned before from plant-parasitic nematodes. The partial sequence of these three factors, A4, A18, and A41, showed no significant homology to any known gene. Their presence in the dorsal glands of infective juveniles suggests that these proteins could be involved in feeding cell initiation, and not in migration in the plant root or in protection against plant defense responses. Finally, the applicability of this new strategy in other plant-microbe interactions is discussed.     

MODBASE, a database of annotated comparative protein structure models

MODBASE is a queryable database of annotated comparative protein structure models. The models are derived by MODPIPE, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. The database currently contains 3D models for substantial portions of approximately 17 000 proteins from 10 complete genomes, including those of Caenorhabditis elegans, Saccharomyces cerevisiae and Escherichia coli, as well as all the available sequences from Arabidopsis thaliana and Homo sapiens. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the quality of the models. ModBase is accessible through a web interface at http://guitar.rockefeller.edu/modbase/     

Highly efficient immobilization of glycosylated enzymes into polyurethane foams

Glycosylated enzymes, including aminoacylase from Aspergillus melleus, chloroperoxidase from Caldariomyces fumago, and phytase from Aspergillus ficuum, were covalently immobilized into polyurethane foams with very high enzyme loadings of up to 0.2 g protein per gram dry foam. The immobilization efficiency (retained activity) ranged from 100% at a low loading to 60% at high loadings. In contrast to many other immobilization methods no leaching of the enzyme from the support took place under the reaction conditions. In short, a universal method for the immobilization of enzymes from fungal sources was developed, affording a highly active, stable, and reusable biocatalyst.