Diversities and similarities in PFGE profiles of Campylobacter jejuni isolated from migrating birds and humans

AIMS: To genetically sub-type Campylobacter jejuni strains isolated from migratory birds, and to compare these with clinical strains collected in the same area and corresponding time period, with the aim to increase our knowledge on sub-types occurring among wild birds and their possible impact on human disease. METHODS AND RESULTS: We sub-typed C. jejuni strains from migrating birds (n = 89) and humans (n = 47), using macrorestriction profiling by pulsed-field gel electrophoresis. Isolates from migrant birds often exhibited sub-types with higher levels of similarity to isolates from birds of the same species or feeding guild, than to isolates from other groups of birds. Likewise, could the vast majority of sub-types found among the migrant bird isolates not be identified among sub-types from human cases. Only two bird strains, one from a starling (Sturnus vulgaris) and one from a blackbird (Turdus merula), had sub-types that were similar to some of the human strain sub-types. CONCLUSIONS: Isolates from one bird species, or feeding guild, often exhibited high similarities, indicating a common transmission source for individuals, or an association between certain sub-types of C. jejuni and certain ecological guilds or phylogenetic groups of birds. Sub-types occurring among wild birds were in general distinctively different from those observed in patients. The two bird isolates that were similar to human strains were isolated from bird species that often live in close associations with human settlements. SIGNIFICANCE AND IMPACT OF STUDY: Wild birds have often been mentioned as a potential route for transmission of C. jejuni to humans. Our study demonstrates that strains isolated from birds most often are different from clinical strains, but that some strain similarities occur, notably in birds strongly associated with human activities.     

Characterization of human crossover interference

We present an analysis of crossover interference over the entire human genome, on the basis of genotype data from more than 8,000 polymorphisms in eight CEPH families. Overwhelming evidence was found for strong positive crossover interference, with average strength lying between the levels of interference implied by the Kosambi and Carter-Falconer map functions. Five mathematical models of interference were evaluated: the gamma model and four versions of the count-location model. The gamma model fit the data far better than did any of the other four models. Analysis of intercrossover distances was greatly superior to the analysis of crossover counts, in both demonstrating interference and distinguishing between the five models. In contrast to earlier suggestions, interference was found to continue uninterrupted across the centromeres. No convincing differences in the levels of interference were found between the sexes or among chromosomes; however, we did detect possible individual variation in interference among the eight mothers. Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms.     

Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements

The olfactory receptor (OR)-gene superfamily is the largest in the mammalian genome. Several of the human OR genes appear in clusters with > or = 10 members located on almost all human chromosomes, and some chromosomes contain more than one cluster. We demonstrate, by experimental and in silico data, that unequal crossovers between two OR gene clusters in 8p are responsible for the formation of three recurrent chromosome macrorearrangements and a submicroscopic inversion polymorphism. The first two macrorearrangements are the inverted duplication of 8p, inv dup(8p), which is associated with a distinct phenotype, and a supernumerary marker chromosome, +der(8)(8p23.1pter), which is also a recurrent rearrangement and is associated with minor anomalies. We demonstrate that it is the reciprocal of the inv dup(8p). The third macrorearrangment is a recurrent 8p23 interstitial deletion associated with heart defect. Since inv dup(8p)s originate consistently in maternal meiosis, we investigated the maternal chromosomes 8 in eight mothers of subjects with inv dup(8p) and in the mother of one subject with +der(8), by means of probes included between the two 8p-OR gene clusters. All the mothers were heterozygous for an 8p submicroscopic inversion that was delimited by the 8p-OR gene clusters and was present, in heterozygous state, in 26% of a population of European descent. Thus, inversion heterozygosity may cause susceptibility to unequal recombination, leading to the formation of the inv dup(8p) or to its reciprocal product, the +der(8p). After the Yp inversion polymorphism, which is the preferential background for the PRKX/PRKY translocation in XX males and XY females, the OR-8p inversion is the second genomic polymorphism that confers susceptibility to the formation of common chromosome rearrangements. Accordingly, it may be possible to develop a profile of the individual risk of having progeny with chromosome rearrangements.     

Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3

Autosomal dominant renal Fanconi syndrome is a genetic model for the study of proximal renal tubular transport pathology. We were able to map the locus for this disease to human chromosome 15q15.3 by genotyping a central Wisconsin pedigree with 10 affected individuals. After a whole-genome scan with highly polymorphic simple sequence repeat markers, a maximum LOD score of 3.01 was calculated for marker D15S659 on chromosome 15q15.3. Linkage and haplotype analysis for an additional 24 markers flanking D15S659 narrowed the interval to approximately 3 cM, with the two highest single-point LOD scores observed being 4.44 and 4.68 (for D15S182 and D15S537, respectively). Subsequently, a complete bacterial artificial chromosome contig was constructed, from the High Throughput Genomic Sequence Database, for the region bounded by D15S182 and D15S143. The identification of the gene and gene product altered in autosomal dominant renal Fanconi syndrome will allow the study of the physiology of proximal renal tubular transport.     

Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis

Nonalchoholic fatty liver disease (NAFLD) is the most common cause of liver dysfunction and is associated with metabolic diseases, including obesity, insulin resistance, and type 2 diabetes. We mapped a quantitative trait locus (QTL) for NAFLD to chromosome 17 in a cross between C57BL/6 (B6) and BTBR mouse strains made genetically obese with the Lep(ob/ob) mutation. We identified Tsc2 as a gene underlying the chromosome 17 NAFLD QTL. Tsc2 functions as an inhibitor of mammalian target of rapamycin, which is involved in many physiological processes, including cell growth, proliferation, and metabolism. We found that Tsc2(+/-) mice have increased lipogenic gene expression in the liver in an insulin-dependent manner. The coding single nucleotide polymorphism between the B6 and BTBR strains leads to a change in the ability to inhibit the expression of lipogenic genes and de novo lipogenesis in AML12 cells and to promote the proliferation of Ins1 cells. This difference is due to a different affinity of binding to Tsc1, which affects the stability of Tsc2.     

Effects of age,replicative lifespan and growth rate of human nucleus pulposus cells on selecting age range for cell-based biological therapies for degenerative disc diseases

Autologous disc cell implantation, growth factors and gene therapy appear to be promising therapies for disc regeneration. Unfortunately, the replicative lifespan and growth kinetics of human nucleus pulposus (NP) cells related to host age are unclear. We investigated the potential relations among age, replicative lifespan and growth rate of NP cells, and determined the age range that is suitable for cell-based biological therapies for degenerative disc diseases. We used NP tissues classified by decade into five age groups: 30s, 40s, 50s, 60s and 70s. The mean cumulative population doubling level (PDL) and population doubling rate (PDR) of NP cells were assessed by decade. We also investigated correlations between cumulative PDL and age, and between PDR and age. The mean cumulative PDL and PDR decreased significantly in patients in their 60s. The mean cumulative PDL and PDR in the younger groups (30s, 40s and 50s) were significantly higher than those in the older groups (60s and 70s). There also were significant negative correlations between cumulative PDL and age, and between PDR and age. We found that the replicative lifespan and growth rate of human NP cells decreased with age. The replicative potential of NP cells decreased significantly in patients 60 years old and older. Young individuals less than 60 years old may be suitable candidates for NP cell-based biological therapies for treating degenerative disc diseases.     

Binary Trait Mapping in Experimental Crosses With Selective Genotyping

Selective genotyping is an efficient strategy for mapping quantitative trait loci. For binary traits, where there are only two distinct phenotypic values (e.g., affected/unaffected or present/absent), one may consider selective genotyping of affected individuals, while genotyping none or only some of the unaffecteds. If selective genotyping of this sort is employed, the usual method for binary trait mapping, which considers phenotypes conditional on genotypes, cannot be used. We present an alternative approach, instead considering genotypes conditional on phenotypes, and compare this to the more standard method of analysis, both analytically and by example. For studies of rare binary phenotypes, we recommend performing an initial genome scan with all affected individuals and an equal number of unaffecteds, followed by genotyping the full cross in genomic regions of interest to confirm results from the initial screen.WE consider the problem of mapping genetic loci contributing to a binary trait in an experimental cross with selective genotyping. There are two clear approaches for linkage analysis with a binary trait. Typically, we compare the proportion of affected individuals across genotype groups (Xu and Atchley 1996). Alternatively, we can compare genotype frequencies between affected and unaffected individuals, similar to Henshall and Goddard (1999). Beyond these two basic approaches, binary trait mapping has seen fundamental advances in regression models (McIntyre et al. 2001; Deng et al. 2006), extensions to multiple-QTL mapping (Coffman et al. 2005; Chen and Liu 2009), and the development of Bayesian algorithms (Yi and Xu 2000; Huang et al. 2007). However, the original data structure and approach have remained intact. Existing methods for binary trait mapping largely require the availability of genotype and phenotype data for a representative sample of both affected and unaffected individuals, and we have not yet seen a well-developed framework for binary trait mapping in the presence of selective genotyping.It is not uncommon to see genotype data on affected individuals only, in which case the above methods cannot be used. Instead, we can compare observed genotype frequencies to the expected segregation ratios given the cross type, in a test for segregation distortion (see Faris et al. 1998; Lambrides et al. 2004). For example, the expected segregation proportions for an intercross are 1:2:1. The observed genotypes can then be described by a multinomial model, and statistically significant deviation from the expected segregation ratios among the genotyped affected individuals would suggest genotype–phenotype association. Gene mapping approaches that model genotypes rather than phenotypes have been developed extensively in the analysis of affected human relative pairs (see, for example, Risch 1990; Holmans 1993; Hauser and Boehnke 1998). In the analysis of experimental crosses, however, this type of approach has been developed primarily for the identification of monogenic mutants (Moran et al. 2006).Once all affected individuals are genotyped, an investigator may go on to genotype unaffected individuals. With this genotyping strategy in mind, we present several potential methods of analysis that might be applied in this context. First, we consider a standard analysis of the genotyped individuals, with disease proportions compared across genotype groups (Xu and Atchley 1996). Having omitted ungenotyped individuals, this method of analysis appears invalid because the estimated disease proportions are biased upward, reflecting an overrepresentation of affecteds in the set of genotyped individuals under consideration. As an alternative, we develop a reverse approach with genotype frequencies compared across phenotype groups. Because selective genotyping does provide a representative sample of genotypes for each phenotype group, this reverse approach does not face the bias in parameter estimation seen with the standard approach. We further extend the reverse approach to incorporate a segregation assumption, as is necessary for an affecteds only analysis. Finally, we present a full-likelihood analysis accounting for selective genotyping, similar to that suggested by Lander and Botstein (1989) for quantitative traits. We develop the full-likelihood approach both with and without incorporating an assumption on the genotype segregation proportions.Having put forth each of these methods, we derive analytic relationships among them. These relationships provide important insight regarding application of the presented methods under selective genotyping. Most notably, we find that making a segregation assumption can lead to spurious evidence of a QTL, but is necessary to treat the case of affecteds only genotyping. We demonstrate properties of the methods in an analysis of recovery from infection by Listeria monocytogenes in intercross mice and further compare power of the methods through computer simulations. Finally, we synthesize our analytical and simulation results to offer more general suggestions for the analysis of binary trait data with selective genotyping.     

Increased Rho activation and PKC-mediated smooth muscle contractility in the absence of caveolin-1

Caveolae are omega-shaped membrane invaginations that are abundant in smooth muscle cells. Since many receptors and signaling proteins co-localize with caveolae, these have been proposed to integrate important signaling pathways. The aim of this study was to test whether RhoA/Rho-kinase and protein kinase C (PKC)-mediated Ca²⁺ sensitization depends on caveolae using caveolin (Cav)-1-deficient (KO) and wild-type (WT) mice. In WT smooth muscle, caveolae were detected and Cav-1, -2 and -3 proteins were expressed. Relative mRNA expression levels were 15:1:1 for Cav-1, -2, and -3, respectively. Caveolae were absent in KO and reduced levels of Cav-2 and Cav-3 proteins were seen. In intact ileum longitudinal muscle, no differences in the responses to 5-HT or the muscarinic agonist carbachol were found, whereas contraction elicited by endothelin-1 was reduced. Rho activation by GTPS was increased in KO compared with WT as shown using a pull-down assay. Following -toxin permeabilization, no difference in Ca²⁺ sensitivity or in Ca²⁺ sensitization was detected. In KO femoral arteries, phorbol 12,13-dibutyrate (PDBu)-induced and PKC-mediated contraction was increased. This was associated with increased ₁-adrenergic contraction. Following inhibition of PKC, ₁-adrenergic contraction was normalized. PDBu-induced Ca²⁺ sensitization was not increased in permeabilized femoral arteries. In conclusion, Rho activation, but not Ca²⁺ sensitization, depends on caveolae in the ileum. Moreover, PKC driven arterial contraction is increased in the absence of caveolin-1. This depends on an intact plasma membrane and is not associated with altered Ca²⁺ sensitivity. Ca²⁺ sensitization; Rho-associated kinase; myosin phosphatase target protein; lipid rafts; CPI-17; G protein-coupled receptor     

siRNA-induced caveolin-1 knockdown in mice increases lung vascular permeability via the junctional pathway

Caveolin-1, the principal integral membrane protein of caveolae, has been implicated in regulating the structural integrity of caveolae, vesicular trafficking, and signal transduction. Although the functions of caveolin-1 are beginning to be explored in caveolin-1-/- mice, these results are confounded by unknown compensatory mechanisms and the development of pulmonary hypertension, cardiomyopathy, and lung fibrosis. To address the role of caveolin-1 in regulating lung vascular permeability, in the present study we used small interfering RNA (siRNA) to knock down caveolin-1 expression in mouse lung endothelia in vivo. Intravenous injection of siRNA against caveolin-1 mRNA incorporated in liposomes selectively reduced the expression of caveolin-1 by approximately 90% within 96 h of injection compared with wild-type mice. We observed the concomitant disappearance of caveolae in lung vessel endothelia and dilated interendothelial junctions (IEJs) as well as increased lung vascular permeability to albumin via IEJs. The reduced caveolin-1 expression also resulted in increased plasma nitric oxide concentration. The nitric oxide synthase inhibitor L-NAME, in part, blocked the increased vascular albumin permeability. These morphological and functional effects of caveolin-1 knockdown were reversible within 168 h after siRNA injection, corresponding to the restoration of caveolin-1 expression. Thus our results demonstrate the essential requirement of caveolin-1 in mediating the formation of caveolae in endothelial cells in vivo and in negatively regulating IEJ permeability.