Environmental Survey of Drinking Water Sources in Kampala, Uganda, during a Typhoid Fever Outbreak.

In 2015, a typhoid fever outbreak began in downtown Kampala, Uganda, and spread into adjacent districts. In response, an environmental survey of drinking water source types was conducted in areas of the city with high case numbers. A total of 122 samples was collected from 12 source types and tested for Escherichia coli, free chlorine, and conductivity. An additional 37 grab samples from seven source types and 16 paired large volume (20 liter) samples from wells and springs were also collected and tested for the presence of Salmonella enterica serovar Typhi. Escherichia coli was detected in 60% of kaveras (drinking water sold in plastic bags) and 80% of refilled water bottles; free chlorine was not detected in either source type. Most jerry cans (68%) contained E. coli and had free chlorine residuals below the WHO-recommended level of 0.5 mg/liter during outbreaks. Elevated conductivity readings for kaveras, refilled water bottles, and jerry cans (compared to treated surface water supplied by the water utility) suggested that they likely contained untreated groundwater. All unprotected springs and wells and more than 60% of protected springs contained E. coli Water samples collected from the water utility were found to have acceptable free chlorine levels and no detectable E. coli While S Typhi was not detected in water samples, Salmonella spp. were detected in samples from two unprotected springs, one protected spring, and one refilled water bottle. These data provided clear evidence that unregulated vended water and groundwater represented a risk for typhoid transmission.IMPORTANCE Despite the high incidence of typhoid fever globally, relatively few outbreak investigations incorporate drinking water testing. During waterborne disease outbreaks, measurement of physical-chemical parameters, such as free chlorine residual and electrical conductivity, and of microbiological parameters, such as the presence of E. coli or the implicated etiologic agent, in drinking water samples can identify contaminated sources. This investigation indicated that unregulated vended water and groundwater sources were contaminated and were therefore a risk to consumers during the 2015 typhoid fever outbreak in Kampala. Identification of contaminated drinking water sources and sources that do not contain adequate disinfectant levels can lead to rapid targeted interventions.

Copy number variation in schizophrenia in Sweden.

Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500 kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry--genome-wide screens for CNVs, common variation and exonic variation--are converging on similar sets of pathways and/or genes.

Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample.

Although copy number variants (CNVs) are important in genomic medicine, CNVs have not been systematically assessed for many complex traits. Several large rare CNVs increase risk for schizophrenia (SCZ) and autism and often demonstrate pleiotropic effects; however, their frequencies in the general population and other complex traits are unknown. Genotyping large numbers of samples is essential for progress. Large cohorts from many different diseases are being genotyped using exome-focused arrays designed to detect uncommon or rare protein-altering sequence variation. Although these arrays were not designed for CNV detection, the hybridization intensity data generated in each experiment could, in principle, be used for gene-focused CNV analysis. Our goal was to evaluate the extent to which CNVs can be detected using data from one particular exome array (the Illumina Human Exome Bead Chip). We genotyped 9100 Swedish subjects (3962 cases with SCZ and 5138 controls) using both standard genome-wide association study (GWAS) and exome arrays. In comparison with CNVs detected using GWAS arrays, we observed high sensitivity and specificity for detecting genic CNVs 400 kb including known pathogenic CNVs along with replicating the literature finding that cases with SCZ had greater enrichment for genic CNVs. Our data confirm the association of SCZ with 16p11.2 duplications and 22q11.2 deletions, and suggest a novel association with deletions at 11q12.2. Our results suggest the utility of exome-focused arrays in surveying large genic CNVs in very large samples; and thereby open the door for new opportunities such as conducting well-powered CNV assessment and comparisons between different diseases. The use of a single platform also minimizes potential confounding factors that could impact accurate detection.

A possible association between schizophrenia and GRIK3 polymorphisms in a multicenter sample of Scandinavian origin (SCOPE).

There is considerable evidence of altered glutamatergic signalling in schizophrenia and a polymorphic variant of the GRIK3 glutamate receptor gene on 1p34-33 has previously been associated to this psychotic disorder. We therefore conducted a systematic association study with 30 HapMap-selected tagging SNPs across GRIK3 in three independent samples of Scandinavian origin from the Scandinavian Collaboration of Psychiatric Etiology (SCOPE), including a total of 839 cases with schizophrenia spectrum and 1473 healthy controls. Four markers (rs6671364, rs17461259, rs472188, and rs535620) attained nominally significant P-values in both the genotypic (0.002, 0.02, 0.03, and 0.05, respectively) and allelic (0.001, 0.006, 0.03, and 0.02, respectively) association tests for the combined sample, and 2 additional markers (rs481047and rs1160751) displayed significance for the genotype (P-values: 0.03 and 0.04). Several haplotypes, that all included at least one of the four SNPs implicated by the single marker analysis, remained significant after adjustment for multiple testing using permutations with 10,000 shuffles. In addition we observed an association for two of the four significant GRIK3 markers (rs472188 and rs535620) to scores for negative symptoms on the PANSS scale. The present results, although not robust, support the importance of more extensive investigations of GRIK3, given its potential role in mediating risk for schizophrenia.

Administration of non-pathogenic isolates of Escherichia coli and Clostridium perfringens type A to piglets in a herd affected with a high incidence of neonatal diarrhoea.

A bacterial cocktail of living strains of Clostridium perfringens type A (CPA) without ß2-toxin gene and non-pathogenic Escherichia coli was administered orally to newborn piglets before first colostrum intake and on 2 consecutive days on a farm with a high incidence of diarrhoea and antibiotic treatment in suckling piglets associated with E. coli and CPA. This clinical field study was driven by the hypothetic principle of competitive exclusion of pathogenic bacteria due to prior colonization of the gut mucosal surface by non-pathogenic strains of the same bacterial species with the aim of preventing disease. Although CPA strains used in this study did not produce toxins in vitro, their lack of pathogenicity cannot be conclusively confirmed. The health status of the herd was impaired by a high incidence of postpartum dysgalactia syndrome in sows (70%) and a high incidence of neonatal diarrhoea caused by enterotoxigenic E. coli and CPA during the study. No obvious adverse effect of the bacterial treatment occurred. On average, more piglets were weaned in litters treated (P=0.009). Visual pathological alterations in the small intestinal wall were more frequent in dead piglets of the control group (P=0.004) and necrotizing enteritis was only found in that group. A higher average daily weight gain of piglets in the control group (P<0.001) may be due to an increased milk uptake due to less competition in the smaller litters. The bacterial cocktail was tested under field conditions for its potential to stabilize gut health status in suckling piglets before disease development due to colibacillosis and clostridial infections; however, the gut flora stabilizing effect of the bacterial cocktail was not clearly discernible in this study. Further basic research is needed to confirm the positive effects of the bacterial treatment used and to identify additional potential bacterial candidates for competitive exclusion.

Nonrandom mating in an open-pollinated maize population.

Randomness of fertilization was studied in an open-pollinated population of maize (Zea mays L.) through allozyme assays of seedlings from open-pollinated seeds produced on both tasseled and detasseled plants. Mixed-mating-model estimates of the amount of outcrossing (t) were not significantly different from t = 1.00 for four enzyme loci ( Adh1, Idh2, Got1 and Acp1), indicating that fertilizations were at random in the population. However, for loci Prx1 and Est4 , estimates of t were significantly smaller than unity-0.80 and 0.70 for tasseled plants and 0.81 and 0.80 for detasseled plants. The excesses of homogametic fertilizations detected on the detasseled plants could not have been due to selffertilization, s = 1 - t, because the detasseled plants shed no pollen. Analyses of allelic frequencies in the pollen that produced seed on the detasseled plants established that different maternal plants sampled genetically different populations of pollen from the outcross pollen pool. It was suggested that the causes of the differential sampling were temporal variation in the pollen pool, and/or gametophytic selection, correlated with marker-locus genotype. Two-, three- and four-locus interactions among the marker loci were often statistically significant, indicating that the factors responsible for the nonrandom gametic unions observed in the maize population studied were complexly interactive.

Further analysis of complex allozyme polymorphisms in a barley population.

New theory has recently been developed for two-locus models. In the light of this theory, an earlier analysis of esterase allozyme data from an experimental barley population has been modified to take proper account of initial gametic phase (linkage) disequilibria. The results show that the directions in which two-locus genotypic frequencies deviated from products of one-locus frequencies in this population followed those predicted by neutral descent theory. The observed departures were, however, much larger in size than predicted by the new descent measure theory, indicating that selection is operating in the population.

Estimation of life cycle components of selection in an experimental plant population.

Viability and fertility components of selection associated with linkage blocks marked by four electrophoretically detectable loci were estimated in an experimental population of barley [Composite Cross V (CCV)]. The intensity of selection affecting the distribution of pollen types in the outcross pool was also estimated and comparisons were made between the selective values of genes in the pools of uniting ovules and pollen. The estimates show that selection was intense at various stages of the life cycle and that viability and fertility components often opposed one another. Estimates of viability and fertility components of selection were also extended to the three-locus level. The multilocus estimates reveal large differences in viability and fertility among homozygous genotypes. It is concluded that strong selection operates at all life cycle stages in CCV, although often in differing directions.

Analysis of complex allozyme polymorphisms in a barley population.

Genotypes of 68,230 individuals taken from 10 generations (F(4)-F(6), F(14)-F(17), F(24)-F(26)) of an experimental population of barley were determined for four esterase loci. The results show that frequencies of gametic ditypes changed significantly over generations and that striking gametic phase disequilibrium developed within a few generations for each of the six pairwise combinations of loci which were monitored. The complex behavior of these four enzyme loci in the population is attributed to interactions between selection and restriction of recombination resulting from the effects of linkage and/or inbreeding.

The effect of selection on esterase allozymes in a barley population.

Changes in gene and genotypic frequencies at four esterase loci were monitored over 25 generations in Composite Cross V, an experimental population of barley, to obtain experimental evidence concerning the balance of forces responsible for: (1) the marked differences in allelic frequencies among barleys from different ecogeographical regions of the world; and (2) the extensive allelic variation found within local populations of barley. Analyses of the highly significant changes in allelic frequencies which occurred in CCV showed they were due to directional selection favoring particular alleles and not to mutation, migration or genetic drift. The results show that intense balancing selection, featuring consistent excesses of heterozygotes, also occurred in CCV. It is concluded that among the factors of neo-Darwinian evolution, natural selection plays the predominant role in determining the observed patterns of allelic variation in the barley species as a whole.

Mutation Rates for Enzyme and Morphological Loci in Barley ( HORDEUM VULGARE L.).

Spontaneous mutation rates were estimated by assaying 84,126 seedlings of a highly homozygous barley line (isogenic line 2025) for five enzyme loci. No mutants were observed in 841,260 allele replications. This result excludes, at probability level 0.95, a spontaneous mutation rate larger than 3.56 x 10(-6)/locus/gamete/generation for these enzyme loci. Isogenic line 2025 also was scored for mutants at four loci governing morphological variants. No mutants were observed in 3,386,850 allele replications which indicates that the upper bound for the mutation rate for these loci is 8.85 x 10(-7). It was concluded that, even though spontaneous mutation has been important in creating variability in the barley species at the loci scored, the rate is too low to have much affect on the short-term dynamics of barley populations.

RFLP genetic linkage maps from four F(2.3) populations and a joinmap of Gossypium hirsutum L.

An RFLP genetic linkage joinmap was constructed from four different mapping populations of cotton ( Gossypium hirsutum L.). Genetic maps from two of the four populations have been previously reported. The third genetic map was constructed from 199 bulk-sampled plots of an F(2.3) (HQ95-6x'MD51ne') population. The map comprises 83 loci mapped to 24 linkage groups with an average distance between markers of 10.0 centiMorgan (cM), covering 830.1 cM or approximately 18% of the genome. The fourth genetic map was developed from 155 bulk-sampled plots of an F(2.3) (119- 5 sub-okrax'MD51ne') population. This map comprises 56 loci mapped to 16 linkage groups with an average distance between markers of 9.3 cM, covering 520.4 cM or approximately 11% of the cotton genome. A core of 104 cDNA probes was shared between populations, yielding 111 RFLP loci. The constructed genetic linkage joinmap from the above four populations comprises 284 loci mapped to 47 linkage groups with the average distance between markers of 5.3 cM, covering 1,502.6 cM or approximately 31% of the total recombinational length of the cotton genome. The linkage groups contained from 2 to 54 loci each and ranged in distance from 1.0 to 142.6 cM. The joinmap provided further knowledge of competitive chromosome arrangement, parental relationships, gene order, and increased the potential to map genes for the improvement of the cotton crop. This is the first genetic linkage joinmap assembled in G. hirsutum with a core of RFLP markers assayed on different genetic backgrounds of cotton populations (Acala, Delta, and Texas plain). Research is ongoing for the identification of quantitative trait loci for agronomic, physiological and fiber quality traits on these maps, and the identification of RFLP loci lineage for G. hirsutum from its diploid progenitors (the A and D genomes).

Suppression of hepatic fatty acid oxidation and food intake in men.

We investigated the effects of the fatty acid oxidation inhibitor etomoxir (ETO) on food intake and on fat and carbohydrate metabolism in two double-blind crossover studies in male, normal-weight subjects. In study 1, ETO (75 mg [+]-racemate) or placebo was given orally 30 min after completion of a standardized, fat-enriched (total energy: 2698 kJ, 40% from fat) lunch. The subjects (n = 15) were isolated from external time cues and free to choose when to eat dinner from an oversized serving (total energy: 6656 kJ, 60% from fat). In study 2, subjects (n = 13) were selected for habitually high fat intake (mean: 44% of energy intake). ETO (150 mg) or placebo was given after an overnight fast, 2.5 h before offering an oversized high fat breakfast (6960 kJ, 72% from fat). In both studies, blood samples were taken and the respiratory quotient (RQ) was measured several times during each test period. In study 1, ETO (75 mg) did not affect the timing and size of the dinner or subjective feelings of hunger and satiety. Although ETO (75 mg) did not affect the RQ, it decreased plasma beta-hydroxybutyrate (BHB) and increased plasma lactate compared with placebo. Plasma triacylglycerols (TG), free fatty acids (FFA), glucose, and insulin were not affected by ETO. In study 2, ETO (150 mg) enhanced hunger feelings and increased the size of the breakfast by 22.7%. ETO did not affect the RQ, but baseline RQ was lower in study 2 than in study 1 (0.83 versus 0.89, P < 0.01). Compared with placebo, ETO (150 mg) decreased plasma BHB and increased plasma FFA and plasma lactate. Baseline plasma concentrations of BHB, FFA, and lactate were higher in study 2 than in study 1 (BHB: 242 versus 81 mumol/L, P < 0.001; FFA: 0.674 versus 0.406 mmol/L, P < 0.01; lactate: 1.08 versus 0.74 mmol/L, P < 0.05). Plasma concentrations of TG, glucose, and insulin were not affected by ETO. The results suggest that inhibition of hepatic fatty acid oxidation stimulates eating in men when baseline fatty acid oxidation is sufficiently high and markedly suppressed by the treatment.

[Renal papillary necrosis in a diabetic patient]. / Cukorbeteg vesepapilla-necrosisa.

The authors present a case of a young diabetic patient with acute symptoms of pyelonephritis. The specific and permanent antibiotic treatment was ineffective and septic condition developed complicated by renal papillary necrosis. Because of the strong flank pain extensive examinations were done with negative result. The patient's condition was improving only slowly and there was need for treatment after her discharge as well. Long-term antibiotic treatment is an effective therapy to cure this previously deadly complication. Special attention should be given to diabetic patients because of frequent urinary tract infection and increased risk of renal damage among them.

A new coding mutation in the Tnf-alpha leader sequence in tuberculosis-sensitive I/St mice causes higher secretion levels of soluble TNF-alpha.

I/St and A/Sn mice are polar extremes in terms of several parameters defining sensitivity to Mycobacterium tuberculosis. TNF-alpha, mainly produced by activated macrophages, can mediate both physiological and pathophysiological processes. Adequate TNF-alpha levels are essential for a forceful protective response to M. tuberculosis. We have functionally characterized a nonsynonymous substitution, Arg8 His, in the highly conserved cytoplasmic domain of the pro-TNF-alpha leader peptide from extremely M. tuberculosis-sensitive I/St mice. This was compared to the common pro-TNF-alpha variant found in A/Sn mice. Using cDNA constructs, both variants were constitutively expressed in HEK293A cells. A significantly higher secretion level of Arg8 His TNF-alpha was shown using flow cytometry and ELISA analysis (P=0.0063), while intracellular levels were similar for both protein variants. An even TNF-alpha distribution throughout the cells was seen using confocal microscopy. This suggests that the Arg8 His substitution affects pro-TNF-alpha processing. The I/St mouse may serve as a model to further explore the function of the well-conserved cytoplasmic region of TNF-alpha. However, other identified substitutions in the I/St promoter, introns and 3'UTR of Tnf-alpha, as well as the cellular environment in vivo may affect the balance between soluble and intracellular Arg8 His TNF-alpha before and during M. tuberculosis infection.

Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid.

Univariate and multivariate analyses were used to identify associations between eight enzyme marker loci and 11 quantitative traits of maize (Zea mays L.). The material analyzed included inbred lines Wf9 and Pa405, single-cross hybrid Wf9 X Pa405, and the F2 generation of the selfed single-cross hybrid. Each enzyme locus assayed was associated with at least one quantitative trait, and all quantitative traits were associated with genotypes at particular enzyme loci. Significant associations also were found between the level of heterozygosity per individual and nine of 11 quantitative traits. The total contribution to heterosis, for seed yield per plant, of genes linked with the eight enzyme loci, was 27% of the F2 mean and 18% of the difference in mean between the F1 hybrid and the inbred parents. Genes linked with Glu1 accounted for nearly one third of the total dominance effect detected by the eight enzyme loci. The chromosome segments marked by loci with significant effects on seed yield were markedly overdominant. The large heterotic effects of chromosome segments marked by particular loci suggest that enzyme loci could be used to help transfer genes responsible for heterosis to inbred lines. We conclude that analyses of additional inbred lines, F1 hybrids, and F2 populations in more environments will halp identify specific associations between enzyme loci, or chromosome segments which they mark, and important agronomic traits.

Identification of a novel gene of pyrimidine nucleotide biosynthesis, pyrDII, that is required for dihydroorotate dehydrogenase activity in Bacillus subtilis.

An in-frame deletion in the coding region of a gene of previously unidentified function (which is called orf2 and which we propose to rename pyrDII) in the Bacillus subtilis pyr operon led to pyrimidine bradytrophy, markedly reduced dihydroorotate dehydrogenase activity, and derepressed levels of other enzymes of pyrimidine biosynthesis. The deletion mutation was not corrected by a plasmid encoding pyrDI, the previously identified gene encoding dihydroorotate dehydrogenase, but was complemented by a plasmid encoding pyrDII. We propose that pyrDII encodes a protein subunit of dihydroorotate dehydrogenase that catalyzes electron transfer from the pyrDI-encoded subunit to components of the electron transport chain.

Worldwide patterns of genetic variation among four esterase loci in Barley (Hordeum vulgare L.).

Electrophoretic assays of 1506 accessions of domestic (Hordeum vulgare L.) and wild (H. spontaneum Koch.) barley, maintained in the USDA World Barley Collection, led to the following conclusions: (1) worldwide the four esterase loci, Est 1, Est 2, Est 3, and Est 4, have a minimum of 7, 12, 6, and 7 alleles, respectively; (2) little or no genetic differentation has developed between H. vulgare and H. spontaneum at these four esterase loci; (3) substantial genetic polymorphism and heterozygosity occur within many of the accessions despite the heavy inbreeding which results from the mating system of predominant self fertilization and from genetic drift associated with maintenance in small populations; (4) patterns of geographical distribution of alleles at these four loci are not at random over both small and large geographical areas, including differences on a continental scale; (5) four among 16 four-locus combinations of alleles are found in excess and all other combinations occur in deficiency on a worldwide basis.

Evolutionary Changes in the Mating System of an Experimental Population of Barley (Hordeum vulgare L.).

An analysis is presented of the reproductive cycle in an experimental population of barley. The experimental design included growing three different generations of the population in the same year and environment, thus permitting an assessment of the mating system at three stages in the evolutionary history of the population, unconfounded by environmental differences. Gene frequencies sometimes differed significantly in adults and in the effective pollen pool. It was also found that out-crossing rate more than doubled during the twenty generations spanned by the study. These results provide evidence for selection during reproductive phases of the life cycle. They also demonstrate that evolution in this predominantly self-pollinating population was in the direction of increased recombinational potential.