A dominant gene for garnet brown seed coats at the <Emphasis Type="Italic">Rk</Emphasis> locus in ‘Dorado’ common bean and mapping <Emphasis Type="Italic">Rk</Emphasis> to linkage group 1

The color of the seed coats of ‘Dorado’ (Phaseolus vulgaris L.) is garnet brown (dark red kidney bean color) and differs from most other dry bean varieties in the Honduran red bean market class. A genetic investigation of the color of ‘Dorado’ (same as DOR364) and G19833 (Liborino market class) seed coats was conducted. Crosses with genetic tester stocks demonstrated that the gene for garnet brown (GB) in ‘Dorado’ was not allelic with the R gene for dominant red (oxblood) seed coat. An allelism test between the ‘Dorado’ gene for GB seed coat and the rk ^drv gene for recessive expression of GB demonstrated allelism. We propose the gene symbol for Rk ^r for the ‘Dorado’ GB seed coat color gene. Rk ^r expresses partial dominance over Rk, where Rk ^r/Rk expresses a paler and highly variable intermediate red color. The interactions of Rk ^r, rk ^drv, and c ^u are discussed. Segregation analysis in the mapping population made up of DOR364 (same as ‘Dorado’) × G19833 recombinant inbred lines showed that the Rk ^r gene mapped to linkage group 1. The new allele at Rk was located at a distance of 17 cM from the RFLP marker Bng130 with a LOD > 3.0.     

Genetic relationships of Brassica vegetables determined using database derived simple sequence repeats

Sequence databases were screened to identify simple sequence repeats (SSRs) in Brassica oleracea sequences. A total of 512 B. oleracea DNA sequences were screened and 43 potential SSRs were identified. Thirty-six primer pairs were designed to amplify target sequences. Of the 36 primer pairs, six failed to amplify fragments of expected sizes, and 17 primer pairs failed to generate polymorphisms. Thirteen SSRs were used to assess genetic similarity between 54 B. oleracea cultivars, belonging to 3 variteal groups (cabbage, cauliflower, and broccoli). Pairwise genetic similarities were calculated for cultivars, and a dendrogram of relationships was produced. All cabbage cultivars were distinguished from each other and clustered in two separate groups. Five cauliflower cultivars could not be distinguished with SSR markers used in the study. Three broccoli cultivars clustered with cauliflower cultivars, and two cauliflower cultivars grouped with broccoli cultivars. The varietal group with the narrowest genetic variation in the study was cauliflower (B. oleracea var. botrytis) followed by broccoli (B. oleracea var. italica) and cabbage (B. oleracea var. capitata) groups. Polymorphism information content (PIC) values and number of alleles produced per marker ranged between 0.25 to 0.86 and 1 to 8, respectively, for database derived SSR markers.     

Long-term heathland restoration on former grassland: The results of a 17-year experiment

European lowland heaths have declined by up to 80% due to land use change and lack of management. There has been considerable research into the restoration of this threatened habitat. However, long-term outcomes of restoration are poorly understood, especially in situations where past agricultural land use imposes severe constraints on community re-assembly. In 1989 a large-scale experiment was established to examine the effectiveness of five treatments to restore heathland on formerly productive grassland: (i) natural regeneration; (ii) herbicide application to facilitate regeneration; (iii) cultivation and application of seed-rich heathland vegetation; (iv) soil removal and incorporation of heathland topsoil; and (v) heathland translocation. After 17 years the pH of the unamended agricultural soil remained significantly higher than that of the adjacent heathland. All treatments showed different trajectories of vegetation change in the long-term. Natural colonisation by heathland species was slow due to seed limitation, resulting in formation of an acid grassland community. Heathland community assembly was not facilitated by destruction of the initial grassland with herbicide. Incorporation of topsoil had an intermediate effect on pH reduction. This may explain the subsequent failure of the plant community to assemble in the anticipated proportions, and the dominance of leguminous scrub species (Ulex spp.). Turf translocation was effective in reducing pH to the required range and restoring the heathland community in the long-term. However, this technique should only be considered as a means of ‘rescue’ when habitat destruction is otherwise unavoidable. The only practical and sustainable means of increasing heathland extent on former farmland is the application of seed-bearing vegetation cut as part of routine management. However, this technique needs refining in order to establish the full range of characteristic heathland species.     

Effect of soil moisture and sample depth on pesticide photolysis

The effects of soil depth and moisture on pesticide photolysis were studied. Moist soil at depths of 3, 2.5, 2, 1.5, 1, and 0.5 mm were each dosed at 2.5 microg/g with (14)C-niclosamide and photolyzed under a xenon lamp at constant temperature. Samples were removed after 20, 40, 110, and 153 h of continuous irradiation. The decrease in percent of niclosamide and the appearance of degradates were followed by analyzing the soil extracts by HPLC. A corresponding set of experiments used air-dried soil. An experiment was also performed using initially moist soil which was permitted to dry during photolysis but returned to moist conditions at each sampling. Qualitative and quantitative differences were found in the rate and route of degradation of niclosamide under these conditions. These differences have resulted from a combination of reduced photochemical activity and microbial population in dry soil. The half-lives of niclosamide in the dry soils were 2 to 5 times longer than those in the moisture-maintained soil. There was also a noticeable difference in the half-lives in soil of different depths. Moisture-maintained soil showed a uniform linear increase in half-life from 95 to 195 h as soil depth increased from 0.5 mm to 3.0 mm. With air-dried soil the half-lives were greatly dependent on soil depth, showing a much broader range of 199 h at 0.5-mm to 1064 h in 3.0-mm soil. An experimental design is described which maintains soil temperature and moisture to preset conditions.     

Metabolism of niclosamide in sediment and water systems

A series of experiments analyzed the kinetics and mechanisms of [(14)C]niclosamide degradation. The aerobic aquatic metabolism of [(14)C]niclosamide was studied in nonsterile river water/sediment mixtures. Test systems, maintained under aerobic conditions, were treated with niclosamide and incubated in the dark at 25.0 +/- 1.0 degrees C for 30 days. Half-lives of 4.9 and 5.4 days were calculated for the chlorosalicylic acid- and chloronitroaniline-labeled test systems, respectively. From 0 to 21 days after treatment (DAT), the only metabolism product observed in either test system was aminoniclosamide. At the final sampling interval, five peaks were resolved from the chlorosalicylic acid label, and three peaks were resolved from the chloronitroaniline label test substance. By 30 DAT, sediment-bound residues represented approximately 70% of the observed radioactivity. For the anaerobic aquatic metabolism of [(14)C]niclosamide, test systems were incubated under anaerobic conditions for 365 days. Half-lives of 0.65 day for the chlorosalicylic acid label and 2.79 days for the chloronitroaniline label were calculated. From 0 to 3 DAT, niclosamide was first transformed into aminoniclosamide. Aminoniclosamide is readily formed, as it was observed in the chlorosalicylic acid label 0 DAT sampling. Several minor metabolites were observed in the water and sediment extracts. None of these metabolites were formed to a significant amount until the parent niclosamide dissipated below the detection limit. Two of the byproducts from these metabolism studies are polar unknowns eluting at 3 and 5 min by HPLC, similar to the unknowns observed in aqueous photolysis studies.     

Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis

The intestinal microflora, typically equated with bacteria, influences diseases such as obesity and inflammatory bowel disease. Here, we show that the mammalian gut contains a rich fungal community that interacts with the immune system through the innate immune receptor Dectin-1. Mice lacking Dectin-1 exhibited increased susceptibility to chemically induced colitis, which was the result of altered responses to indigenous fungi. In humans, we identified a polymorphism in the gene for Dectin-1 (CLEC7A) that is strongly linked to a severe form of ulcerative colitis. Together, our findings reveal a eukaryotic fungal community in the gut (the "mycobiome") that coexists with bacteria and substantially expands the repertoire of organisms interacting with the intestinal immune system to influence health and disease.     

A common fold mediates vertebrate defense and bacterial attack

Proteins containing membrane attack complex/perforin (MACPF) domains play important roles in vertebrate immunity, embryonic development, and neural-cell migration. In vertebrates, the ninth component of complement and perforin form oligomeric pores that lyse bacteria and kill virus-infected cells, respectively. However, the mechanism of MACPF function is unknown. We determined the crystal structure of a bacterial MACPF protein, Plu-MACPF from Photorhabdus luminescens, to 2.0 angstrom resolution. The MACPF domain reveals structural similarity with poreforming cholesterol-dependent cytolysins (CDCs) from Gram-positive bacteria. This suggests that lytic MACPF proteins may use a CDC-like mechanism to form pores and disrupt cell membranes. Sequence similarity between bacterial and vertebrate MACPF domains suggests that the fold of the CDCs, a family of proteins important for bacterial pathogenesis, is probably used by vertebrates for defense against infection.     

Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection

Genetic diversity data were collected from a large population of common bean (Phaseolus vulgaris L.) landraces representing the United States Department of Agriculture core collection. The data were based on microsatellite data from all linkage groups. A procedure was developed to determine if we collected sufficient marker data to adequately estimated pairwise diversity. The diversity data were used to define populations using distance and model-based approaches. Genetic differentiation and genetic isolation by distance data were collected. Diversity was also compared for markers linked and unlinked to domestication loci. Using a model-based approach, the landraces were divided into the traditional Middle American and Andean gene pools. Diversity was greater for the Middle American gene pool. Six Middle American and three Andean subpopulations were defined, and the Middle American subpopulations exhibited strong geographic identity. Unlike other studies, seed size varied considerably with subpopulations, and a number of the subpopulations contained landraces from multiple common bean races. All of the subpopulations were highly differentiated, with the Middle American subpopulations showing the greatest differentiation. Genetic isolation by distance was observed among the Middle American and Andean subpopulations but not among subpopulations within a gene pool. Within each gene pool, diversity was lower for markers linked to domestication loci.