Detection and Integration of Genotyping Errors in Statistical Genetics

Detection of genotyping errors and integration of such errors in statistical analysis are relatively neglected topics, given their importance in gene mapping. A few inopportunely placed errors, if ignored, can tremendously affect evidence for linkage. The present study takes a fresh look at the calculation of pedigree likelihoods in the presence of genotyping error. To accommodate genotyping error, we present extensions to the Lander-Green-Kruglyak deterministic algorithm for small pedigrees and to the Markov-chain Monte Carlo stochastic algorithm for large pedigrees. These extensions can accommodate a variety of error models and refrain from simplifying assumptions, such as allowing, at most, one error per pedigree. In principle, almost any statistical genetic analysis can be performed taking errors into account, without actually correcting or deleting suspect genotypes. Three examples illustrate the possibilities. These examples make use of the full pedigree data, multiple linked markers, and a prior error model. The first example is the estimation of genotyping error rates from pedigree data. The second-and currently most useful-example is the computation of posterior mistyping probabilities. These probabilities cover both Mendelian-consistent and Mendelian-inconsistent errors. The third example is the selection of the true pedigree structure connecting a group of people from among several competing pedigree structures. Paternity testing and twin zygosity testing are typical applications.     

Metabolism of D-fructose by Arthrobacter pyridinolis

Previous studies showed that Arthrobacter pyridinolis can transport and utilize d-glucose only after prior growth on certain Krebs cycle intermediates. In contrast, we found that d-fructose was taken up and metabolized by A. pyridinolis without special prior conditions of growth. d-Fructose was first converted to d-fructose-1-phosphate by a phosphoenolpyruvate (PEP):D-fructose phosphotransferase. This activity required both supernatant and pellet fractions from d-fructose-grown cells centrifuged at 150,000 x g. The d-fructose-1-phosphate formed was converted to d-fructose-1, 6-diphosphate. Mutants deficient in PEP:d-fructose phosphotransferase and d-fructose-1-phosphate kinase, or d-fructose-1, 6-diphosphatase (FDPase) were unable to grow on d-fructose but retained the normal ability to use d-glucose. Mutants forming reduced amounts of FDPase were completely unable to grow on d-fructose but were still capable of limited growth on Krebs cycle intermediates. A requirement for higher levels of FDPase for growth on d-fructose than for growth on Krebs cycle intermediates was also indicated by the higher specific activities of FDPase in d-fructose-grown cells than in cells grown on l-malate or amino acids.     

A novel crosslinking reagent and its application for the detection and isolation of heparin-binding protein(s) on the platelet surface.

A new hetero-bifunctional photo crosslinking reagent, 2-(4-azidoanilyl)-4-(4-azabicyclo-[2,2, 2]hexylammonio)-6-morpholino-1,3,5-triazine chloride, was designed to detect and isolate heparin-binding protein(s) that may act as heparin-receptor(s) on the platelet surface. In a preliminary study using ethanol as a model substrate, the reagent was shown to react with the alcoholic hydroxy group under mild conditions and its crosslinking photoreactivity was high. The reagent effectively formed similar covalent bonds with heparin, while preserving its anticoagulant anti-Xa activity. [3H]Heparin labeled with this reagent crosslinked to antithrombin III very specifically but not to ovalbumin, as analyzed by the Bio-imaging Analyzer System (BAS, Fuji Photo Film, Tokyo). Affinity crosslinking of [3H]heparin was then used to detect heparin-binding proteins on the surface of intact platelets. Several discrete protein bands were detected by the BAS-imaging of SDS-PAGE.     

Amyotrophic lateral sclerosis and occupational exposure to electromagnetic fields

In an hypothesis-generating case-control study of amyotrophic lateral sclerosis, lifetime occupational histories were obtained. The patients (n = 28) were clinic based. The occupational exposure of interest in this report is electromagnetic fields (EMFs). This is the first and so far the only exposure analyzed in this study. Occupational exposure up to 2 years prior to estimated disease symptom onset was used for construction of exposure indices for cases. Controls (n = 32) were blood and nonblood relatives of cases. Occupational exposure for controls was through the same age as exposure for the corresponding cases. Twenty (71%) cases and 28 (88%) controls had at least 20 years of work experience covering the exposure period. The occupational history and task data were used to classify blindly each occupation for each subject as having high, medium/high, medium, medium/low, or low EMF exposure, based primarily on data from an earlier and unrelated study designed to obtain occupational EMF exposure information on workers in “electrical” and “nonelectrical” jobs. By using the length of time each subject spent in each occupation through the exposure period, two indices of exposure were constructed: total occupational exposure (E₁) and average occupational exposure (E₂). For cases and controls with at least 20 years of work experience, the odds ratio (OR) for exposure at the 75th percentile of the E₁ case exposure data relative to minimum exposure was 7.5 (P < 0.02; 95% Cl, 1.4–38.1) and the corresponding OR for E₂ was 5.5 (P < 0.02; 95% CI, 1.3–22.5). For all cases and controls, the ORs were 2.5 (P < 0.1; 95% CI, 0.9–8.1) for E₁ and 2.3 (P = 0.12; 95% CI, 0.8–6.6) for E₂. This study should be considered an hypothesis-generating study. Larger studies, using incident cases and improved exposure assessment, should be undertaken. Bioelectromagnetics 18:28–35, 1997. © 1997 Wiley-Liss, Inc.     

Predicting the receptive range of olfactory receptors

Although the family of genes encoding for olfactory receptors was identified more than 15 years ago, the difficulty of functionally expressing these receptors in an heterologous system has, with only some exceptions, rendered the receptive range of given olfactory receptors largely unknown. Furthermore, even when successfully expressed, the task of probing such a receptor with thousands of odors/ligands remains daunting. Here we provide proof of concept for a solution to this problem. Using computational methods, we tune an electronic nose to the receptive range of an olfactory receptor. We then use this electronic nose to predict the receptors' response to other odorants. Our method can be used to identify the receptive range of olfactory receptors, and can also be applied to other questions involving receptor–ligand interactions in non-olfactory settings.     

Sugar Chips immobilized with synthetic sulfated disaccharides of heparin/heparan sulfate partial structure

Carbohydrate chip technology has a great potential for the high-throughput evaluation of carbohydrate-protein interactions. Herein, we report syntheses of novel sulfated oligosaccharides possessing heparin and heparan sulfate partial disaccharide structures, their immobilization on gold-coated chips to prepare array-type Sugar Chips, and evaluation of binding potencies of proteins by surface plasmon resonance (SPR) imaging technology. Sulfated oligosaccharides were efficiently synthesized from glucosamine and uronic acid moieties. Synthesized sulfated oligosaccharides were then easily immobilized on gold-coated chips using previously reported methods. The effectiveness of this analytical method was confirmed in binding experiments between the chips and heparin binding proteins, fibronectin and recombinant human von Willebrand factor A1 domain (rh-vWf-A1), where specific partial structures of heparin or heparan sulfate responsible for binding were identified.     

Yeast Infections of the Lower Urinary Tract: Recommendations for Diagnosis and Treatment

Yeast infections of the lower urinary tract are common, with the vast majority due to Candida species. Though not life-threatening, candiduria may be a marker for overall severity of illness in hospitalized patients, as it appears to predict increased mortality, particularly in critically ill patients. Diagnosis is relatively simple through culture, but exact definitions of clinical disease are elusive. Management of asymptomatic patients is generally observation with reduction of predisposing factors, whereas symptomatic patients should be treated. Therapeutic options for these infections are limited and not well studied compared with therapies for systemic candidiasis. Further studies are needed to optimize management of these patients.