Bias correction with a single null marker for population stratification in candidate gene association studies

Population stratification is a form of confounding by ethnicity that may cause bias to effect estimates and inflate test statistics in genetic association studies. Unlinked genetic markers have been used to adjust for test statistics, but their use in correcting biased effect estimates has not been addressed. We evaluated the potential of bias correction that could be achieved by a single null marker (M) in studies involving one candidate gene (G). When the distribution of M varied greatly across ethnicities, controlling for M in a logistic regression model substantially reduced biases on odds ratio estimates. When M had same distributions as G across ethnicities, biases were further reduced or eliminated by subtracting the regression coefficient of M from the coefficient of G in the model, which was fitted either with or without a multiplicative interaction term between M and G. Correction of bias due to population stratification depended specifically on the distributions of G and M, the difference between baseline disease risks across ethnicities, and whether G had an effect on disease risk or not. Our results suggested that marker choice and the specific treatment of that marker in analysis greatly influenced bias correction.     

NK cells can trigger allograft vasculopathy: the role of hybrid resistance in solid organ allografts

Progressive arterial stenosis (cardiac allograft vasculopathy (CAV)) is a leading cause of long-term failure of organ transplants. CAV remains intractable, in part because its mechanisms are insufficiently understood. A central proposition is that MHC-driven alloimmune processes play a necessary role in CAV, as shown by the absolute requirement for histoincompatibility between donor and recipient for its production. Two immunological pathways have been implicated involving reactivity to donor MHC Ags by either T or B cells. In this study, we use a novel system of semiallogeneic cardiac transplants between parental donors and F1 hybrid recipients to provide evidence that NK cells, members of the innate immune system, also contribute to the generation of CAV in mice. This finding marks the first demonstration that the hybrid resistance phenomenon occurs in solid organ allografts. Extension of these experiments to recipients deficient in T cells demonstrates that this third pathway of CAV, the NK cell-triggered pathway, involves the recruitment of T cells not responsive to donor alloantigens. Finally, transplants performed with donors or recipients deficient in IFN-gamma revealed that recipient-derived IFN-gamma is necessary for CAV formation in parental to F1 transplants, suggesting a possible effector mechanism by which NK cells can promote CAV. Together, these results define a previously unknown pathway toward CAV and assign a novel role to NK cells in organ allograft rejection.     

No evidence for inbreeding avoidance through postcopulatory mechanisms in the black field cricket, Teleogryllus commodus

Several studies suggest that females mate multiply so that they can preferentially fertilize eggs with the sperm of genetically more compatible males. Unrelated males are expected to be genetically more compatible with a female than her close relatives. We tested whether black field crickets, Teleogryllus commodus, can bias sperm usage toward unrelated males by comparing egg hatching success of females mated to two of their siblings (SS), two sibling males unrelated to the female (NN) or to one unrelated male and a sibling male (NS or SN). Egg hatching success was highly repeatable. Hatching success varied significantly among females of the three mating types (P = 0.011, n = 245 females). The estimated mean hatching success of 36.8% for SS females was significantly less that the 43.4% of NN females, indicating an effect of inbreeding on hatching success. If females preferentially use the sperm of a less closely related male, the hatching success of NS/SN females should be closer to 43.4% than 36.8%. It was, in fact, only 34.9%. This does not differ significantly from the value expected if the two males contributed an equal amount of sperm that was then used randomly. Although polyandry may confer indirect genetic benefits, our results provide no evidence that female T. commodus gain these benefits by biasing paternity toward genetically more compatible males through postcopulatory mechanisms.     

A microsatellite genetic linkage map for Xiphophorus

Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between "male" and "female" maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.     

Selective roles for tumor necrosis factor alpha-converting enzyme/ADAM17 in the shedding of the epidermal growth factor receptor ligand family: the juxtamembrane stalk determines cleavage efficiency

Epidermal growth factor (EGF) family ligands are derived by proteolytic cleavage of the ectodomains of integral membrane precursors. Previously, we established that tumor necrosis factor alpha-converting enzyme (TACE/ADAM17) is a physiologic transforming growth factor-alpha (TGF-alpha) sheddase, and we also demonstrated enhanced shedding of amphiregulin (AR) and heparin-binding (HB)-EGF upon restoration of TACE activity in TACE-deficient EC-2 fibroblasts. Here we extended these results by showing that purified soluble TACE cleaved single sites in the juxtamembrane stalks of mouse pro-HB-EGF and pro-AR ectodomains in vitro. For pro-HB-EGF, this site matched the C terminus of the purified human growth factor, and we speculate that the AR cleavage site is also physiologically relevant. In contrast, ADAM9 and -10, both implicated in HB-EGF shedding, failed to cleave the ectodomain or cleaved at a nonphysiologic site, respectively. Cotransfection of TACE in EC-2 cells enhanced phorbol myristate acetate-induced but not constitutive shedding of epiregulin and had no effect on betacellulin (BTC) processing. Additionally, soluble TACE did not cleave the juxtamembrane stalks of either pro-BTC or pro-epiregulin ectodomains in vitro. Substitution of the shorter pro-BTC juxtamembrane stalk or truncation of the pro-TGF-alpha stalk to match the pro-BTC length reduced TGF-alpha shedding from transfected cells to background levels, whereas substitution of the pro-BTC P2-P2' sequence reduced TGF-alpha shedding less dramatically. Conversely, substitution of the pro-TGF-alpha stalk or lengthening of the pro-BTC stalk, especially when combined with substitution of the pro-TGF-alpha P2-P2' sequence, markedly increased BTC shedding. These results indicate that efficient TACE cleavage is determined by a combination of stalk length and scissile bond sequence.     

Compound 800, a natural product isolated from genetically engineered Pseudomonas: proposed structure, reactivity, and putative relation to heme d1

Genetically engineered strains of Escherichia coli and Pseudomonas aeruginosa were prepared harboring the gene cluster nirFDLGH from Pseudomonas stutzeri substrain ZoBell on a high copy plasmid. These genes have been previously implicated as being essential for the biosynthesis of heme d(1), the prosthetic group of dissimilatory nitrite reductases in anaerobic, denitryfying bacteria. Tetrapyrroles detectable at steady-state levels were identified from both organisms, and cell-free extracts from each were also used to transform uroporphyrinogen in vitro. E. coli does not naturally produce d(1), and the engineered strain failed to produce d(1) or any tetrapyrrole foreign to E. coli. Therefore, while nirFDLGHmay be necessary for d(1) biosynthesis, it is not sufficient. In the denitrifier P. aeruginosa, the results were more positive. The presence of the plasmid led to increased levels of d(1). In addition, a previously unidentified tetrapyrrole was detected. This compound was characterized by visible absorption spectroscopy, infrared spectroscopy, X-ray photoelectron spectroscopy, mass spectrometry, and NMR, and a tentative structure was proposed for this compound. The tetrapyrrole has structural features similar to sirohydrochlorin (as precorrin-2 or sirotetrahydrochlorin, a known intermediate of d(1)) and d(1) itself. The most unusual substituents are epoxide and sulfoxide moieties. When this tetrapyrrole was treated with strong mineral acid and heat, it was converted into natural d(1).     

Sensitivity of Bayes estimators to hyper-parameters with an application to maximum yield from fisheries

Priors are seldom unequivocal and an important component of Bayesian modeling is assessment of the sensitivity of the posterior to the specified prior distribution. This is especially true in fisheries science where the Bayesian approach has been promoted as a rigorous method for including existing information from previous surveys and from related stocks or species. These informative priors may be highly contested by various interest groups. Here, formulae for the first and second derivatives of Bayes estimators with respect to hyper-parameters of the joint prior density are given. The formula for the second derivative provides a correction to a previously published result. The formulae are shown to reduce to very convenient and easily implemented forms when the hyper-parameters are for exponential family marginal priors. For model parameters with such priors it is shown that the ratio of posterior variance to prior variance can be interpreted as the sensitivity of the posterior mean to the prior mean. This methodology is applied to a nonlinear state-space model for the biomass of South Atlantic albacore tuna and sensitivity of the maximum sustainable yield to the prior specification is examined.     

Characterization of a small metal binding protein from Nitrosomonas europaea

A small metal-binding protein (SmbP) with no known similarity to other proteins in current databases was isolated and characterized from the periplasm of Nitrosomonas europaea. The primary structure of this small (9.9 kDa) monomeric protein is characterized by a series of 10 repeats of a seven amino acid motif and an unusually high number of histidine residues. The protein was isolated from N. europaea with Cu(II) bound but was found to be capable of binding multiple equivalents of a variety of divalent and trivalent metals. The protein was overexpressed in Escherichia coli and used for the study of its metal-binding properties by UV/vis, circular dichroism (CD), and electron paramagnetic resonance (EPR) spectroscopy and equilibrium dialysis and isothermal titration calorimetry. The protein was found to bind up to six Cu(II) atoms with dissociation constants of approximately 0.1 microM for the first two metal ions and approximately 10 microM for the next four. Binding of Cu(II) resulted in spectroscopic features illustrating two distinctive geometries, as determined by EPR spectroscopy. The levels of SmbP in the periplasm were found to increase by increasing the levels of copper in the growth media. This protein is proposed to have a role in cellular copper management in the ammonia-oxidizing bacterium N. europaea.