Pairwise Similarity Coefficient Research Articles

MOLECULAR CHARACTERIZATION AND ANALYSIS OF GEOGRAPHICAL DIFFERENTIATION OF INDIAN MANGO (MANGIFERA INDICA L.) GERMPLASM

ISHS I International Symposium on Biotechnology of Fruit Species: BIOTECHFRUIT2008 MOLECULAR CHARACTERIZATION AND ANALYSIS OF GEOGRAPHICAL DIFFERENTIATION OF INDIAN MANGO (MANGIFERA INDICA L.) GERMPLASM

Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs

To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleen-deficient) rats and to evaluate traditional Chinese drugs. Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats. A molecular marker was identified for Pi-deficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon's index for diversity of intestinal microflora, and Sorenson's pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora. Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats.

AFLP analysis among Ethiopian arabica coffee genotypes

Knowledge of genetic diversity is vital for genetic improvement and germplasm conservation. The genetic relationship of 28 Coffea arabica genotypes from Ethiopia was assessed using 10 Amplified Fragment Length Polymorphism (AFLP) primer combinations. The level of polymorphism was 30.9% and 18 markers were unique to 10 genotypes. Pair-wise genetic similarity coefficients ranged from 0.851 to 0.982, AD1491 being the most divergent and AD5091 the most closely related to all genotypes. All genotypes were independently distinguished and did not cluster according to collection region, demonstrating the presence of coffee genetic resource diversity within each region. Results of this study will be utilised for germplasm collection, conservation as well as in variety development efforts.

Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes

AbstractTea plant [Camellia sinensis (L.) O. Kuntze] is an important beverage crop in the world. In recent years many clonal tea cultivars have been released, and they play major roles in improving the production and quality of tea. It is important to understand the genetic diversity and relatedness of these cultivars to avoid inbreeding and narrow genetic basis in future tea breeding. In the present study, genetic diversity and relationship of 48 tea cultivars from China, Japan and Kenya were evaluated by inter‐simple sequence repeat (ISSR) markers. A total of 382 ISSR bands were scored, of which 381 (99.7%) were polymorphic. The ISSR primers showed high ability to distinguish between tea cultivars according to their high Resolving Power (RP) with an average of 7.4. The mean of Nei’s gene diversity (H) and Shannon’s information index (I) were 0.22 and 0.35, respectively. More abundant diversity was revealed among cultivars in China than those in Japan and Kenya. Within Chinese populations, the level of diversity in east China was higher than that in other regions. The coefficient of genetic differentiation (GST) was 0.202, which indicates a high degree of genetic variation within populations. This result was further confirmed by analysis of molecular variance, which revealed the variance component within the populations (92.07%) was obviously larger than that among populations (7.93%). The level of gene flow (Nm) was estimated to be 2.0. This could be explained by frequent natural cross‐pollination and seed dispersal among tea populations. The pairwise similarity coefficient between the cultivars varied from 0.162 to 0.538. A dendrogram of 48 tea cultivars was constructed where all the tested cultivars were divided into two groups. Our data show that the genetic relationship among tea cultivars can be determined by the ISSR markers. This will provide valuable information to assist parental selection in current and future tea breeding programmes.

A comparative measure of biodiversity based on species composition

In conservation planning, species richness and species endemism are the most often used metrics for describing the biodiversity importance of areas. However, when it comes to prioritizing regions for conservation actions these measures alone are insufficient because they do not reveal how similar or different the actual composition of species may be from one area to another. For comparative analysis an additional useful metric would be one that indicates the degree to which the species assemblage in one area is also represented in—or is distinct from—species assemblages of other areas. Here we describe a method for quantifying the compositional representativeness of species assemblages among geographic regions. The method generates asymmetric pairwise similarity coefficients that are then used to calculate separate measures for the representativeness and the distinctiveness of species assemblages in the regions being compared. We demonstrate the method by comparing fish communities among freshwater ecoregions of the Mississippi Basin, and then among smaller hydrological units within two individual freshwater ecoregions. At both scales of analysis, our measures of representativeness and distinctiveness reveal patterns of fish species composition that differ from patterns of species richness. This information can enhance conservation planning processes by ensuring that priority-setting explicitly consider the most representative and distinctive species assemblages.

Determination of Ileum Microbial Diversity of Broilers Fed Triticale- or Corn-Based Diets and Colonized by Salmonella

Diversity of the bacterial communities in the ileum of broilers was characterized using denaturing gradient gel electrophoresis. Denaturing gradient gel electrophoresis separation of polymerase chain reaction amplicons of the V2–V3 variable regions of the 16S rDNA is a common method to profile community diversity and has been used to assess the effects of diet and antibiotics on the ileal bacterial community of chickens. Broilers raised either on litter floor or in cage batteries were fed either a finely ground corn- (control), a finely ground triticale-, or a whole triticale-based diet from 0 to 42 d. Microbial DNA was extracted from the ileum content of 42-d-old broilers, and the 16S rDNA gene was amplified by polymerase chain reaction and the amplicons separated by denaturing gradient gel electrophoresis. Diversity indexes including richness, evenness, diversity, and pairwise similarity coefficients were calculated. Diversity indexes were related to the dietary treatments, housing designs, and to changes in Salmonella colonization of broiler ceca as characterized by the most probable number method. Higher microbial diversity indexes were observed among birds fed whole triticale-based diets and reared on litter floors. In contrast, finely ground grain treatments had lower diversity and higher Salmonella prevalence than the whole triticale treatment. The data indicated that combination of high dietary fiber content and increased coarseness of the diet by feeding whole triticale stimulated microbial community diversity and discouraged Salmonella colonization, perhaps through a competitive exclusion-type mechanism.

Genetic diversity of 38 spinach (Spinacia oleracea L.) germplasm accessions and 10 commercial hybrids assessed by TRAP markers

Target region amplification polymorphism (TRAP) markers were used to assess genetic variability among 38 germplasm accessions and 10 commercial hybrids of spinach (Spinacia oleracea L.), an economically important leafy vegetable crop in many countries. Germplasm accessions with different geographic origins and 10 commercial hybrids were examined. For assessing genetic diversity within accessions, DNA was extracted from 12 individual seedlings from six germplasm accessions and two hybrids. A relatively high level of polymorphism was found within accessions based on 59 polymorphic TRAP markers generated from one fixed primer derived from the Arabidopsis-like telomere repeat sequence and two arbitrary primers. For evaluating interaccession variability, DNA was extracted from a bulk of six to 13 seedlings of each accession. Of the 492 fragments amplified by 12 primer combinations, 96 (19.5%) were polymorphic and discriminated the 48 accessions from each other. The average pair-wise genetic similarity coefficient (Dice) was 57.5% with a range from 23.2 to 85.3%. A dendrogram indicated that the genetic relationships among the accessions were not highly associated with the geographic locations in which the germplasms were collected. The seven commercial hybrids were grouped in three separate clusters, suggesting that the phenotype-based breeding activities tended to reduce the genetic variability. This preliminary study demonstrated that TRAP markers are effective for fingerprinting and evaluating genetic variability among spinach germplasms.

Genotyping and drug resistance profile of Candida spp. in recurrent and one-off vaginitis, and high association of non-albicans species with non-pregnant status

Recurrent vulvovaginal candidiasis affects women worldwide and the resistance to azole drugs may be an important factor. The extent of strain-to-strain variation within a species and its relationship to the ability of the organism to colonize the vulvovaginal mucosa is not well established. The aims of this study were to compare: (i) the genotypes of Candida strains in sequential infections in patients with recurrent vaginitis, (ii) the genotypes of strains in patients with only one episode of infection in a period of 1 year and (iii) determine the in vitro antifungal susceptibilities of strains that cause recurrent vaginitis. Fifty-one cultured specimens from six distinct Candida species were genotyped via random amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR) method using the ERIC1 and ERIC2 primers (ERIC, enterobacterial repetitive intergenic consensus). Statistical analyses allowed three different scenarios to be discerned for recurrent cases: (i) strain maintenance without genetic variation, (ii) strain maintenance with minor genetic variation and (iii) outright strain replacement. The genetic relatedness between strains from patients with recurrent vaginitis and patients with single episode of vaginitis were demonstrated by the dendogramme and the mean pairwise similarity coefficient S AB for the intergroup comparison was 0.223. However, intragroup genetic relatedness was slightly higher than intergroup comparison, with mean S AB of 0.261 and 0.331 for Groups I and II, respectively. A high proportion of Group I isolates (87.5%) causing recurrent infections were resistant to ketoconazole, whereas 41.7% of these isolates were cross-resistant to both clotrimazole and ketoconazole as shown by the in vitro antifungal susceptibility test, especially for C. glabrata isolates. Pregnancy status of patients displayed a highly significant association with C. albicans species whereas non- albicans species had a markedly higher prevalence in non-pregnant patients ( p < 0.001). These results may have a profound impact on the management of vaginal candidiasis, especially in recurrent cases.

(276) Assessing Genetic Diversity of Spinach Germplasm using TRAP Markers

Target region amplified polymorphism (TRAP) markers were used to evaluate genetic variability among 48 accessions of spinach (Spinacia oleracea L.), an economically important leafy vegetable crop in many countries. Thirty-eight accessions collected and preserved by the USDA National Plant Germplasm System (NPGS) and 10 commercial hybrids were used in the current study. For assessing genetic diversity within accessions, DNA samples were prepared from nine to 12 individual seedlings from six germplasm accessions and two hybrids. Relatively high levels of polymorphism was found within accessions based on 61 polymorphic TRAP markers generated with two fixed primers derived from the Arabidopsis-type telomere repeat sequence and two arbitrary primers. For evaluating inter-accession variability, DNA was extracted from a bulk of six to 10 seedlings of each accession. Of the 1092 fragments amplified by 14 primer combinations, 96 (8.8%) were polymorphic and discriminated the 48 accessions from each other. The average pair-wise genetic similarity coefficient (Dice, Nei) was 57.5% with a range from 23.2 to 85.3%. A dendrogram was constructed based on the similarity matrix. It was found that the genetic relationships were not highly correlated with the geographic locations in which the accessions were collected. However, seven commercial hybrids were grouped in three separate clusters, suggesting that the phenotype-based breeding activities have effect on the genetic variability. This study demonstrated that TRAP markers are effective for fingerprinting and evaluating genetic variability of spinach germplasm.

Recurrent candidaemia in a neonate with Hirschsprung's disease: fluconazole resistance and genetic relatedness of eight Candida tropicalis isolates

The incidence of candidaemia among immunocompromised patients in Malaysia is increasing at an alarming rate. Isolation of clinical strains that are resistant to fluconazole has also risen markedly. We report here the repeated isolation of Candida tropicalis from the blood of a neonatal patient with Hirschsprung's disease. In vitro fluconazole susceptibility tests of the eight isolates obtained at different time points showed that seven of the isolates were resistant and one isolate was scored as susceptible dose-dependent. Random amplification of polymorphic DNA fingerprinting of the isolates using three primers and subsequent phylogenetic analysis revealed that these isolates were highly similar strains having minor genetic divergence, with a mean pairwise similarity coefficient of 0.893+/-0.041. The source of the infectious agent was thought to be the central venous catheter, as culture of its tip produced fluconazole-resistant C. tropicalis. This study demonstrates the utility of applying molecular epidemiology techniques to complement traditional mycological culture and drug susceptibility tests for accurate and appropriate management of recurrent candidaemia and highlights the need for newer antifungals that can combat the emergence of fluconazole-resistant C. tropicalis strains.

Assessment of genetic diversity in Turkish oregano (Origanum onites L.) germplasm by AFLP analysis

SummaryOriganum onites (L.) is one of the most widely traded culinary herb species in Turkey. Despite limited knowledge on the level of genetic diversity, its use as a source of seed for planting is widespread. To initiate a selective breeding programme, Amplified Fragment Length Polymorphism (AFLP) analysis was used to estimate genetic diversity within the oregano germplasm collection of the Aegean Agricultural Research Institute of the Ministry of Agriculture and Rural Affairs, Turkey. Forty-four Origanum accessions were analysed with ten Eco RI-Mse I primer combinations. In total, 365 unambiguous, selectively amplified polymorphic fragments were detected and 294 polymorphic bands were scored for analysis. Seven main groups were identified by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering using Jaccard’s pairwise similarity coefficient. When this genetic analysis was compared with the sites of collection of the accessions, there was no close genetic similarity among accessions related to their growing region. Relatively low genetic similarity (0.396 – 0.725%) between accessions indicated that the rate of gene flow between Origanum species was high, as a result of cross-pollination. The results of this study indicate that a broad range of genetic variability exists between accessions of oregano and that future breeding programmes could be improved, based on these data, by selecting materials with maximally different AFLP fingerprints.

Mentha longifolia (L.) L.: A Model Species for Mint Genetic Research

Mentha longifolia, a wild relative of the polyploid, cultivated Mentha (mint) species, was evaluated as a potential model system for genetic research relevant to the cultivated mints. Fourteen Mentha longifolia accessions maintained by the US Department of Agriculture (USDA), Agricultural Research Service, National Clonal Germplasm Repository (NCGR), were highly diverse with respect to geographic origin, oil composition, verticillium wilt resistance, aspects of morphology, and molecular marker polymorphism. Accession CMEN 584 was the only carvone chemotype, while CMEN 682 was the only accession with high menthol content. Trans-piperitone oxide was the primary oil component of accessions CMEN 17 and CMEN 18, while pulegone was most abundant in CMEN 20, CMEN 500, CMEN 501, and CMEN 585. Four accessions—CMEN 585, CMEN 17, CMEN 501, and CMEN 81—were consistently resistant to verticillium wilt, while CMEN 584 and CMEN 516 were highly susceptible. Pairwise similarity coefficients were calculated and a UPGMA (unweighted pair-group analysis) tree was constructed on the basis of 63 informative randomly amplified polymorphic DNA (RAPD) marker bands. CMEN 585 and CMEN 584 shared the greatest number of bands (16), and formed a distinct cluster in the UPGMA tree. Seven pairs of accessions had no bands in common, emphasizing the high degree of molecular diversity represented by these accessions. The favorable features of diploid (2n = 2x = 24) genome constitution, comparatively small genome size (400 to 500 Mb), self-fertility, fecundity, and diversity with respect to economically relevant traits, contribute to M. longifolia's potential usefulness as a model system for the cultivated mints. As a perennial species amenable to vegetative propagation, M. longifolia's spectrum of susceptibility/resistance to an important vascular wilt disease encourages its further evaluation as a system for broader studies of plant–microbe interactions and disease resistance mechanisms.

Molecular ecological analysis of porcine ileal microbiota responses to antimicrobial growth promoters.

Cultivation-independent microbial molecular ecology approaches were used to examine the effects of antibiotic growth promoters on the pig ileal microbiota. Five-week-old barrows were fitted with a simple T-cannula at the distal ileum. Three diets meeting or exceeding the minimum nutrient requirements were fed for 5 wk and supplemented as follows: 1) negative control (no antibiotic; n = 5), 2) continuous tylosin administration (n = 5), and 3) an antibiotic rotation sequence (wk 1, chlorotetracycline sulfathiazole penicillin; wk 2, bacitracin and roxarsone; wk 3, lincomycin; wk 4, carbadox; wk 5, virginiamycin; n = 5). Ileal luminal contents were collected for DNA isolation at the end of each of the 5 wk of the testing period. The V3 region of 16S rDNA was amplified by PCR and analyzed via denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction (qPCR). Resulting PCR-DGGE band numbers (bacterial species) were counted, and the banding patterns analyzed by calculating Sorenson's pairwise similarity coefficients (C(S)), an index measuring bacterial species in common among samples. Band numbers and total bacterial DNA concentrations decreased (P < 0.05) temporally in antibiotic-treated pigs compared with controls. Comparisons between treatments yielded low intertreatment C(S) indices, indicating treatment-dependent alterations in banding patterns, whereas intratreatment comparisons revealed increased homogeneity in antibiotic-treated vs. control pigs. Sequence analysis of treatment-specific bands identified three Lactobacillus, one Streptococcus, and one Bacillus species that were diminished with antibiotic rotation treatment, whereas tylosin selected for the presence of L. gasseri. Lactobacillus-specific qPCR was performed and analyzed as a percentage of total bacteria to further evaluate the effects of antibiotic administration on this genus. Total bacteria were decreased (P < 0.05) by tylosin and rotation treatments, whereas the percentage of lactobacilli increased (P < 0.05) by d 14 and through d 28 in tylosin-treated pigs. The decrease in total bacteria by antibiotics may reduce host-related intestinal or immune responses, which would divert energy that could otherwise be used for growth. Conversely, the ability of tylosin to improve animal growth may relate to its apparent selection for lactobacilli, commensals known to competitively exclude potentially pathogenic species from colonizing the intestine.

Genetic relatedness of Candida strains isolated from women with vaginal candidiasis in Malaysia.

The aims of this study were to compare the genetic relatedness of: (i) sequential and single isolates of Candida strains from women with recurrent vaginal candidiasis (RVC); and (ii) Candida strains from women who had only one episode of infection within a 1-year period. In total, 87 isolates from 71 patients were cultured, speciated and genotyped by random amplification of polymorphic DNA (RAPD) analysis. Patients were categorized into three groups, namely those with: (i) a history of RVC from whom two or more yeast isolates were obtained (group A); (ii) a history of RVC from whom only a single isolate was obtained (group B); and (iii) a single episode of vaginal candidiasis within a 1-year period (group C). Six yeast species were detected: Candida albicans, Candida glabrata, Candida lusitaniae, Candida famata, Candida krusei and Candida parapsilosis. Interestingly, the prevalence of non-albicans species was higher in group A patients (50 %) than in patients in groups B (36 %) or C (18.9 %). Eighty RAPD profiles were observed, with a total of 61 polymorphic PCR fragments of distinct sizes. Clustering analysis showed that, overall, the majority of patients in group A had recurrent infections caused by highly similar, but not identical, sequential strains [mean pairwise similarity coefficient (S(AB)) = 0.721 +/- 0.308]. The range of mean S(AB) values for intergroup comparisons for C. albicans isolates alone was 0.50-0.56, suggesting that there was no significant relatedness between strains from different groups. Genetic similarity of C. albicans isolates from patients in group A was lower than that of C. albicans isolates from patients in group C (mean S(AB) = 0.532 +/- 0.249 and 0.636 +/- 0.206, respectively); this difference was statistically significant (P = 0.036). These results demonstrate that the cause of recurrent infections varies among individuals and ranges between strain maintenance, strain microevolution and strain replacement; the major scenario is strain maintenance with microevolution. They also show that C. albicans strains that cause recurrent infections are less similar to each other than strains that cause one-off infections, suggesting that the former may represent more virulent subtypes.

Assessing genetic diversity of domestic populations of channel catfish ( Ictalurus punctatus) in Alabama using AFLP markers

Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of domestic stocks of channel catfish ( Ictalurus punctatus). Sixteen populations within Alabama (USA) were surveyed using five primer combinations. A total of 454 reproducible, polymorphic bands were detected from 282 individuals, with an average heterozygosity of 0.135. The percentage of polymorphic loci varied greatly within distinct populations, ranging from 18.26% to 100%. Research populations tended to have a lower percentage of loci polymorphic than farm populations. The estimated average F st value across all loci was 0.4456. However, this value dropped to 0.1763 when the Hicks Farm stock was excluded from the analysis. Cluster analysis by Jaccard's pairwise similarity coefficient indicated high similarity among individuals, with some population-specific clusters and with the Hicks Farm stock being highly distinctive. Nei's population-wise identity measures found all populations except the population from the Hick's Farm related with 96% similarity. The Hick's Farm stock was 34% similar to the other populations. The genotypic information derived from this study is consistent with the historical origins and management of catfish broodstocks. The results of this study suggest that many channel catfish farm strains in Alabama are genetically similar, but some very distinct differences exist. Such information has implications for future broodstock selection and management and for further analysis of interactions between domestic and wild populations of channel catfish.

Secretory antibodies do not affect the composition of the bacterial microbiota in the terminal ileum of 10-week-old mice.

Terminal restriction fragment length polymorphism (T-RFLP) analysis was conducted on the 16S rRNA genes of the bacterial communities colonizing the epithelial surfaces of the terminal ilea of open conventionally housed mice in an institutional small-animal facility. Polymeric-immunoglobulin-receptor-deficient (pIgR(-/-)) mice that were unable to secrete antibodies across mucosal surfaces were cohoused with normal and otherwise genetically identical wild-type (C57BL/6) mice for 4 weeks. If secretory antibodies played a role in modeling the gastrointestinal microbiota, C57BL/6 mice would have had a more distinct and uniform microbiota than their pIgR(-/-) cage mates. The T-RFLP profiles of the bacterial communities were compared by using Sorensen's pairwise similarity coefficient, a newly developed weighted pairwise similarity coefficient, and on the basis of Shannon's and Simpson's diversity indices. No systematic differences were observed between the dominant components of the mucosa-associated bacterial communities of the terminal ileal walls of the two types of mice, indicating that secretory antibodies do not control the composition of this microbiota. Similar analyses of experiments conducted at two different times, between which the bacterial community composition of the mouse colony in the small-animal facility appeared to have changed, showed that differences could have been detected, had they existed.

DNA fingerprinting of individual species and intergeneric and interspecific hybrids of genera Bos and Bison, subfamily Bovinae

Genome fingerprinting with a hypervariable minisatellite sequence of phage M13 DNA was used to study the genetic variation in individual species of the genera Bos and Bison (subfamily Bovinae) and in their interspecific and intergeneric hybrids. DNA fingerprints were obtained for domestic cow Bos taurus primigenius, vatussy Bos taurus macroceros, banteng Bos javanicus, gaur Bos gaurus, wisent Bison bonasus, bison Bison bison, and for the interspecific and intergeneric hybrids. Compared with the original species, most hybrids showed a greater variation in number and size of hybridization fragments. An association was revealed between the number of hybridization fragments and blood composition of interspecific hybrids resulting from unique crossing of domestic cow and banteng. Pairwise similarity coefficients were calculated to construct a dendrogram of genetic similarity, which reflected the relationships between the parental species and hybrids varying in blood composition. The applicability of the method for identifying interspecific and intergeneric hybrids and for studying the consequences of distant hybridization in the subfamily Bovinae is discussed.

Molecular Ecological Analysis of Dietary and Antibiotic-Induced Alterations of the Mouse Intestinal Microbiota

A cultivation-independent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), was used to characterize changes in fecal bacterial populations resulting from consumption of a low residue diet or oral administration of a broad-spectrum antibiotic. C57BL/6NHsd mice were weaned to either a standard nonpurified diet (LC-diet) or a low residue diet (LR-diet) and at 17 wk of age were randomly assigned to receive drinking water with or without 25 ppm cefoxitin for 14 d. On d 1, 2, 7 and 14, microbial DNA was extracted from feces, and the V3 region of the 16S rDNA gene was amplified by PCR and analyzed by DGGE. The diversity of fecal microbial populations, assessed using Shannon's index (H'), which incorporates species richness (number of species, or in this case, PCR-DGGE bands) and evenness (the relative distribution of species), was not affected by cefoxitin. However, use of Sorenson's pairwise similarity coefficient (C(s)), an index that measures the species in common between different habitats, indicated that the species composition of fecal bacterial communities was altered by cefoxitin in mice fed either diet. Dietary effects on fecal microbial communities were more pronounced, with greater H' values (P < 0.05) in mice fed the LR-diet (1.9 +/- 0.1) compared with the LC-diet (1.6 +/- 0.1). The C(s) values were also greater (P < 0.05) in fecal bacterial populations from mice fed the LR-diet (C(s) = 69.8 +/- 2.0%) compared with mice fed the LC-diet (C(s) = 50.1 +/- 3.8%), indicating greater homogeneity of fecal bacterial communities in mice fed the LR-diet. These results demonstrate the utility of cultivation-independent PCR-DGGE analysis combined with measurements of ecological diversity for monitoring diet- and antibiotic-induced alterations of the complex intestinal microbial ecosystem.

The Reindeer Oestrids Hypoderma tarandi and Cephenemyia trompe (Diptera: Oestridae): Batesian Mimics of Bumblebees (Hymenoptera: Apidae: Bombus spp.)?

The color pattern (two areas on each of 20 transverse bands along the dorsal surface of the body) in two reindeer oestrids, Hypoderma tarandi and Cephenemyia trompe (Diptera: Oestridae), was analyzed and compared with that of different bumblebee species found in an oestrid study area in northern Norway. A clustering analysis and multidimensional scaling analysis of the resulting matrix of pairwise similarity coefficients indicated that Bombus lapponicus, B. alpinus, and B. monticola (Hymenoptera: Bombinae) comprise a Mullerian guild whose members serve as Batesian models for H. tarandi, and that B. pratorum, B. jonellus, and B. lucorum comprise a Mullerian guild whose members may serve as Batesian models for C. trompe. The oestrid mimics also resemble their models in size.

Assignment of tools to machines in a flexible manufacturing system

Subgradient optimization is employed to solve the problem of assigning tools to machines in a flexible manufacturing system (FMS). Machines in the FMS have a limited number of slots in the tool mafazine, and tools may require multiple slots. Tools are grouped based upon a pairwise similarity coefficient that indicates the frequency of successive operations that require both tools. Typical solution strategies have included graph theoretic heuristics. Lagrangian relaxation is utilized in the algorithm developed in this article. The problem is formulated as a linear integer program. After dualizing two sets of constraints, two integer subproblems are formed in which the first is further decomposed into several knapsack subproblems. The second subproblem can be solved by a linear network code. A subgradient algorithm is developed to solve the dual problem. The algorithm is compared to a graph theoretic heuristic that utilizes cluster analysis. For most test problems, the subgradient algorithm is superior, but is sensitive to convergence parameters.