A cluster of highly polymorphic dinucleotide repeats in intron 17b of the cystic fibrosis transmembrane conductance regulator (CFTR) gene

A cluster of highly polymorphic dinucleotide repeats has been detected in intron 17b of the CFTR gene, 200 bp downstream from the preceding exon. At least 24 alleles, with sizes ranging from 7 to 56 units of a TA repeat, have been identified in a panel of 92 unrelated carriers of cystic fibrosis (CF). The common ones are those with 7, 30, and 31 dinucleotide units, with frequencies of .22, .19, and .12, respectively, among the non-CF chromosomes. Mendelian, codominant segregation of the alleles has been demonstrated in family studies, as expected. A less polymorphic dinucleotide (CA repeat) cluster has also been detected in a region 167 bp downstream from the TA repeat. The length of the CA repeat cluster varies from 11 to 17 dinucleotide units, and it appears to have an inverse relationship to that of the TA repeats. These dinucleotide repeats should be useful in genetic linkage studies, in counseling for CF families with unknown mutations, and in tracing the origins of the various mutant CF alleles.published_or_final_versio

CFTR gene variant for patients with congenital absence of vas deferens [3]

published_or_final_versio

Molecular consequences of cystic fibrosis transmembrane regulator (CFTR) gene mutations in the exocrine pancreas

Background and aims: We tested the hypothesis that the actual or predicted consequences of mutations in the cystic fibrosis transmembrane regulator gene correlate with the pancreatic phenotype and with measures of quantitative exocrine pancreatic function. Methods: We assessed 742 patients with cystic fibrosis for whom genotype and clinical data were available. At diagnosis, 610 were pancreatic insufficient, 110 were pancreatic sufficient, and 22 pancreatic sufficient patients progressed to pancreatic insufficiency after diagnosis. Results: We identified mutations on both alleles in 633 patients (85.3%), on one allele in 95 (12.8%), and on neither allele in 14 (1.9%). Seventy six different mutations were identified. The most common mutation was ΔF508 (71.3%) followed by G551D (2.9%), G542X (2.3%), 621+1G→T (1.2%), and W1282X (1.2%). Patients were categorized into five classes according to the predicted functional consequences of each mutation. Over 95% of patients with severe class I, II, and III mutations were pancreatic insufficient or progressed to pancreatic insufficiency. In contrast, patients with mild class IV and V mutations were consistently pancreatic sufficient. In all but four cases each genotype correlated exclusively with the pancreatic phenotype. Quantitative data of acinar and ductular secretion were available in 93 patients. Patients with mutations belonging to classes I, II, and III had greatly reduced acinar and ductular function compared with those with class IV or V mutations. Conclusion: The predicted or known functional consequences of specific mutant alleles correlate with the severity of pancreatic disease in cystic fibrosis.published_or_final_versio

Spectrum of mutations in the CFTR gene of patients with classical and atypical forms of cystic fibrosis from southwestern Sweden: Identification of 12 novel mutations

Cystic fibrosis (CF) is caused by mutations in the CFTR gene. The spectrum of CFTR mutations varies between populations and depends on different factors, such as ethnic background and geographical location. The extensive CFTR mutation screening of 129 patients with classical or atypical CF from the south-western region of Sweden revealed the presence of 37 CFTR mutations, including 12 novel alleles. The overall mutation detection rate in this study population was 92%, the highest among all tested regions in Sweden. Eight mutations with a frequency above 1% (ΔF508, 394delTT, R117C, 3659delC, E60X, 1112delT, R764X, and 621 + 1G → T) accounted for 78% of CF chromosomes and have been recommended for inclusion in the CFTR mutation screening panel for molecular diagnosis of CF in this region. The multiple occurrence of specific CFTR alleles less common than the predominant ΔF508 mutation (394delTT, R117C, 3659delC) allowed for genotype-phenotype comparisons and revealed consistent relationships between these mutations and disease severity.published_or_final_versio

Large genomic rearrangements in the CFTR gene contribute to CBAVD

<p>Abstract</p> <p>Background</p> <p>By performing extensive scanning of whole coding and flanking sequences of the <it>CFTR (Cystic Fibrosis Transmembrane Conductance Regulator</it>) gene, we had previously identified point mutations in 167 out of 182 (91.7%) males with isolated congenital bilateral absence of the vas deferens (CBAVD). Conventional PCR-based methods of mutation analysis do not detect gross DNA lesions. In this study, we looked for large rearrangements within the whole <it>CFTR </it>locus in the 32 CBAVD patients with only one or no mutation.</p> <p>Methods</p> <p>We developed a semi-quantitative fluorescent PCR assay (SQF-PCR), which relies on the comparison of the fluorescent profiles of multiplex PCR fragments obtained from different DNA samples. We confirmed the gross alterations by junction fragment amplification and identified their breakpoints by direct sequencing.</p> <p>Results</p> <p>We detected two large genomic heterozygous deletions, one encompassing exon 2 (c.54-5811_c.164+2186del8108ins182) [or <it>CFTRdele2</it>], the other removing exons 22 to 24 (c.3964-3890_c.4443+3143del9454ins5) [or <it>CFTRdele 22_24</it>], in two males carrying a typical CBAVD mutation on the other parental <it>CFTR </it>allele. We present the first bioinformatic tool for exon phasing of the <it>CFTR </it>gene, which can help to rename the exons and the nomenclature of small mutations according to international recommendations and to predict the consequence of large rearrangements on the open reading frame.</p> <p>Conclusion</p> <p>Identification of large rearrangements further expands the <it>CFTR </it>mutational spectrum in CBAVD and should now be systematically investigated. We have designed a simple test to specifically detect the presence or absence of the two rearrangements identified in this study.</p

Limits of effective nutrient management in dairy farming: analyses of experimental farm De Marke

Key words: nutrient management, dairy, prototyping, organic matter, soil fertility, nitrogen, phosphor. Intensive dairy production in the Netherlands is associated with high farm nutrient (N and P) inputs and high losses to the environment. The Dutch government and the dairy sector stimulate farmers to reduce losses through more efficient use of N and P inputs on their farms. This study explores for a dairy farm on dry sandy soil with average Dutch production intensity (12,000 kg milk per ha) the possibilities to meet strict environmental standards related to N and P by maximizing N and P use efficiency at the level of the farm and of the soil. Moreover, the study addresses the effects of efficient nutrient management on soil fertility. The research was conducted on experimental dairy farm De Marke, that is designed to meet strict environmental standards, implemented in practice in 1989 and modified continuously to meet its targets by prototyping, i.e. a cyclic procedure of designing, implementing, testing and evaluating measures. The thesis evaluates system development since 2000, while results from 1993-1999 were used to analyse long-term developments. After implementation of the farming system in 1989, the nitrate concentration in groundwater ‘stabilized’ at a level exceeding the environmental standard: 55 mg l-1. Causes of excessive nitrate leaching were examined by relating measured nitrate concentrations to management. Grazing was associated with higher leaching in spite of careful management with rotational grazing. Leaching under permanent grassland was similar to the overall leaching in crop rotations in which grass was alternated with maize and grains. Spatial and temporal patterns of soil N mineralization were explored to improve the synchronization of N application and crop N requirements. This study indicated that fertilizing a 1st year maize crop, following grassland, is not necessary. Measures implemented since 2000 to improve nutrient efficiency, included reduced grazing, adoption of anaerobic digestion, application of manure in the rows of maize, growing spring barley as the last crop in the arable phase, and, since 2004, the abolishment of fertilizer N. These measures contributed to an increase in the manure-N utilization and to an increase in the farm-N use efficiency up to 2008 to values exceeding the value of 33% that was realized in the period 1993-1999. Farm-N use efficiency was 35% in 2000-2003, 43% in 2004-2008 and 37% in 2009-2010. Farm-P use efficiency also increased as compared to the 87% that was realized in 1993-1999, i.e., it was 103% in 2000-2003 and 91% in 2004-2008. In 2009-2010, however, the farm-P use efficiency decreased to 69%, lower than the value realized in 1993-1999. The lower N and P use efficiency in 2009-2010 can be attributed to the lower N and P yields in grassland as a delayed effect of N limitation resulting from the abolishment of fertilizer N in grassland since 2004. Hence, despite the increase in manure-N utilization, mineral-N use is not yet completely redundant. P-equilibrium fertilization seems to be compatible with highly efficient crop production, in the short and in the long term. Soil organic matter (SOM) percentage in the upper topsoil decreased by 0.03 yr-1 (average across all land uses) at a constant rate over the last 20 years. The possibilities to stop this decline by higher organic matter inputs to the soil seem conflicting with efficient nutrient use. Hence, the long term dynamics of SOM may become critical for future farm performance. It was concluded that N and P use efficiency can be enhanced substantially by on-farm nutrient management, but that efficient nutrient management may conflict with maintenance of SOM.</p

Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients

Identification of mutations causing cystic fibrosis (CF) in the Turkish population is essential for assessment of the molecular basis of CF in Turkey and the development of strategies for prenatal diagnosis and genetic counseling. Here, we present an updated report of mutations found in the Turkish CF population from an extensive screening study of the entire coding region, including exon-intron boundaries and the promoter region. Cases for which mutations could not be identified were also screened for previously defined large alterations and (TG) mT n-M470V loci. This study revealed a total of 27 different mutations accounting for almost 60% of disease genes in the Turkish population. In this study, we also identified the haplotypes associated with 17 mutations and those associated with unknown mutations. The mutation spectrum of CF in Turkey and its associated haplotypes indicated the presence of a major Mediterranean component in the contemporary Turkish population.published_or_final_versio

Mutations that permit residual CFTR function delay acquisition of multiple respiratory pathogens in CF patients

<p>Abstract</p> <p>Background</p> <p>Lung infection by various organisms is a characteristic feature of cystic fibrosis (CF). <it>CFTR </it>genotype effects acquisition of <it>Pseudomonas aeruginosa (Pa)</it>, however the effect on acquisition of other infectious organisms that frequently precede <it>Pa </it>is relatively unknown. Understanding the role of CFTR in the acquisition of organisms first detected in patients may help guide symptomatic and molecular-based treatment for CF.</p> <p>Methods</p> <p>Lung infection, defined as a single positive respiratory tract culture, was assessed for 13 organisms in 1,381 individuals with CF. Subjects were divided by predicted CFTR function: 'Residual': carrying at least one partial function <it>CFTR </it>mutation (class IV or V) and 'Minimal' those who do not carry a partial function mutation. Kaplan-Meier estimates were created to assess <it>CFTR </it>effect on age of acquisition for each organism. Cox proportional hazard models were performed to control for possible cofactors. A separate Cox regression was used to determine whether defining infection with <it>Pa</it>, mucoid <it>Pa </it>or <it>Aspergillus (Asp) </it>using alternative criteria affected the results. The influence of severity of lung disease at the time of acquisition was evaluated using stratified Cox regression methods by lung disease categories.</p> <p>Results</p> <p>Subjects with 'Minimal' CFTR function had a higher hazard than patients with 'Residual' function for acquisition of 9 of 13 organisms studied (HR ranging from 1.7 to 3.78 based on the organism studied). Subjects with minimal CFTR function acquired infection at a younger age than those with residual function for 12 of 13 organisms (p-values ranging: < 0.001 to 0.017). Minimal CFTR function also associated with younger age of infection when 3 alternative definitions of infection with <it>Pa</it>, mucoid <it>Pa </it>or <it>Asp </it>were employed. Risk of infection is correlated with CFTR function for 8 of 9 organisms in patients with good lung function (>90%ile) but only 1 of 9 organisms in those with poorer lung function (<50%ile).</p> <p>Conclusions</p> <p>Residual CFTR function correlates with later onset of respiratory tract infection by a wide spectrum of organisms frequently cultured from CF patients. The protective effect conferred by residual CFTR function is diminished in CF patients with more advanced lung disease.</p