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Miller DR, Borden JH, Slessor KN. Inter- and intrapopulation variation of the pheromone, ipsdienol produced by male pine engravers,Ips pini (Say) (Coleoptera: Scolytidae). J Chem Ecol 2013; 15:233-47. [PMID: 24271438 DOI: 10.1007/bf02027785] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/1987] [Accepted: 11/10/1987] [Indexed: 11/26/2022]
Abstract
We determined the chirality of ipsdienol in individual male pine engravers,Ips pini (Say), from New York, California, and two localities in British Columbia (BC). Both quantity and chirality of ipsdienol varied significantly between and within populations ofI. pini. Beetles from California and southeastern BC produced primarily (R)-(-)-ipsdienol with mean ratios of (S)-(+) : (R)-(-) of 9 : 91 and 11 : 89, respectively, while beetles from New York produced primarily (S)-(+)-ipsdienol with a mean (S)-(+) : (R)-(-) ratio of 57 : 43. A population from southwestern BC was unlike any other known western population, producing primarily (S)-(+)-ipsdienol with a mean (S)-(+) : (R)-(-) ratio of 66 : 34. In contrast to the unimodal chirality profiles for ipsdienol production in populations from California and southeastern BC, the profiles of the populations from southwestern BC and New York were bimodal, with a common mode at approximately 44 : 56 (S)-(+) : (R)-(-). Bimodality in the profiles of ipsdienol chirality in two populations ofI. pini and remarkably high levels of intrapopulation variation in pheromone chirality in all four populations suggest that evolutionary change in pheromone channels of communication could occur, possibly in response to artificial selection pressures such as mass trapping.
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Miller DR, Borden JH, Slessor KN. Enantiospecific pheromone production and response profiles for populations of pine engraver,Ips pini (Say) (Coleoptera: Scolytidae), in British Columbia. J Chem Ecol 2013; 22:2157-72. [PMID: 24227221 DOI: 10.1007/bf02040100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/1995] [Accepted: 07/03/1996] [Indexed: 11/30/2022]
Abstract
Analyses of the enantiomeric composition of ipsdienol produced by individual male pine engravers,Ips pini (Say), from six populations in British Columbia, support the hypothesis that New York and Idaho races of this species hybridize in southeastern British Columbia. Production profiles, expressed as frequency distributions of (+):(-) ipsdienol ratios [= ratio of (S)-(+)-ipsdienol to (R)-(-)-ipsdienol], were bimodal for four western British Columbia populations. The (+):(-) ratios ranged from 63:37 to 71:29. consistent with those previously found for the New York race. The profile for a southeastern population from Radium, British Columbia, was intermediate between those for the four western British Columbia populations and that from one population in Kimberley, British Columbia, just south of Radium. Males in the Kimberley population produce predominantly (R)-(-)-ipsdienol, typical of California nad Idaho males. Response profiles of different individuals ofI. pini, determined by captures of beetles in multiple-funnel traps baited with ipsdienol of 11 different (+):(-) ratios, were not consistent with production profiles. Populations in Williams Lake and Princeton, in western British Columbia, and Radium, in southeastern British Columbia, had response profiles with maximal attraction to ipsdienol over a broad range of (+):(-) ratios, falling off as enantiomeric purity was approached at either end of the spectrum. This type of response profile is consistent with that for the New York race, which has been shown to respond optimally to (+):(-) ratios ranging from 40:60 to 70:30. The response profile of the Kimberley population gradually declined from maximal attraction to ipsdienol with a (+):(-) ratio of 2:98 to the lowest response at a (+):(-) ratio of 98:2. The attraction ofI. pini to chemical stimuli in California is interrupted by ipsdienol with a (+):(-) ratio >5:95, a pheromone of a host competitor, the California five-spined ips,Ips paraconfusus Lanier. We hypothesie that the Idaho race, which does not compete withI. paraconfusus due to geographical separation, is characterized by a Kimberley-type enantiomeric response profile, intermediate between those of the New York and California races.
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Phillippi J, Xie Y, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, de Villena FPM, Wang W, Valdar W, Frelinger JA. Using the emerging Collaborative Cross to probe the immune system. Genes Immun 2013; 15:38-46. [PMID: 24195963 PMCID: PMC4004367 DOI: 10.1038/gene.2013.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 12/21/2022]
Abstract
The Collaborative Cross (CC) is an emerging panel of recombinant inbred (RI) mouse strains. Each strain is genetically distinct but all descended from the same eight inbred founders. In 66 strains from incipient lines of the CC (pre-CC), as well as the 8 CC founders and some of their F1 offspring, we examined subsets of lymphocytes and antigen-presenting cells. We found significant variation among the founders, with even greater diversity in the pre-CC. Genome-wide association using inferred haplotypes detected highly significant loci controlling B-to-T cell ratio, CD8 T-cell numbers, CD11c and CD23 expression. Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology. For CD23, we found a strong QTL whose confidence interval contained the CD23 structural gene Fcer2a. Our data on the pre-CC demonstrate the utility of the CC for studying immunophenotypes and the value of integrating founder, CC and F1 data. The extreme immunophenotypes observed could have pleiotropic effects in other CC experiments.
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Marshall ADL, Miller DR, Smith LJ, Chetty M, Currie GP. A patient with concurrent primary lung cancer and lymphoma diagnosed using endobronchial ultrasound. QJM 2013; 106:389-90. [PMID: 23389432 DOI: 10.1093/qjmed/hct045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Miller DR, Mydin HH, Marshall ADL, Devereux GS, Currie GP. Fatal haemorrhage following endobronchial ultrasound-transbronchial needle aspiration: an unfortunate first. QJM 2013; 106:295-6. [PMID: 23359720 DOI: 10.1093/qjmed/hct005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT. Modeling host genetic regulation of influenza pathogenesis in the collaborative cross. PLoS Pathog 2013; 9:e1003196. [PMID: 23468633 PMCID: PMC3585141 DOI: 10.1371/journal.ppat.1003196] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 01/02/2013] [Indexed: 11/22/2022] Open
Abstract
Genetic variation contributes to host responses and outcomes following infection by influenza A virus or other viral infections. Yet narrow windows of disease symptoms and confounding environmental factors have made it difficult to identify polymorphic genes that contribute to differential disease outcomes in human populations. Therefore, to control for these confounding environmental variables in a system that models the levels of genetic diversity found in outbred populations such as humans, we used incipient lines of the highly genetically diverse Collaborative Cross (CC) recombinant inbred (RI) panel (the pre-CC population) to study how genetic variation impacts influenza associated disease across a genetically diverse population. A wide range of variation in influenza disease related phenotypes including virus replication, virus-induced inflammation, and weight loss was observed. Many of the disease associated phenotypes were correlated, with viral replication and virus-induced inflammation being predictors of virus-induced weight loss. Despite these correlations, pre-CC mice with unique and novel disease phenotype combinations were observed. We also identified sets of transcripts (modules) that were correlated with aspects of disease. In order to identify how host genetic polymorphisms contribute to the observed variation in disease, we conducted quantitative trait loci (QTL) mapping. We identified several QTL contributing to specific aspects of the host response including virus-induced weight loss, titer, pulmonary edema, neutrophil recruitment to the airways, and transcriptional expression. Existing whole-genome sequence data was applied to identify high priority candidate genes within QTL regions. A key host response QTL was located at the site of the known anti-influenza Mx1 gene. We sequenced the coding regions of Mx1 in the eight CC founder strains, and identified a novel Mx1 allele that showed reduced ability to inhibit viral replication, while maintaining protection from weight loss. Host responses to an infectious agent are highly variable across the human population, however, it is not entirely clear how various factors such as pathogen dose, demography, environment and host genetic polymorphisms contribute to variable host responses and infectious outcomes. In this study, a new in vivo experimental model was used that recapitulates many of the genetic characteristics of an outbred population, such as humans. By controlling viral dose, environment and demographic variables, we were able to focus on the role that host genetic variation plays in influenza virus infection. Both the range of disease phenotypes and the combinations of sets of disease phenotypes at 4 days post infection across this population exhibited a large amount of diversity, reminiscent of the variation seen across the human population. Multiple host genome regions were identified that contributed to different aspects of the host response to influenza infection. Taken together, these results emphasize the critical role of host genetics in the response to infectious diseases. Given the breadth of host responses seen within this population, several new models for unique host responses to infection were identified.
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Marshall ADL, Miller DR, Chetty M, Miller J, Currie GP. Endobronchial ultrasound guided transbronchial needle aspiration--a sensitive and cost effective method of sampling mediastinal lymph nodes. Int J Clin Pract 2012; 66:1235. [PMID: 23163505 DOI: 10.1111/ijcp.12027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Thaisz J, Tsaih SW, Feng M, Philip VM, Zhang Y, Yanas L, Sheehan S, Xu L, Miller DR, Paigen B, Chesler EJ, Churchill GA, Dipetrillo K. Genetic analysis of albuminuria in collaborative cross and multiple mouse intercross populations. Am J Physiol Renal Physiol 2012; 303:F972-81. [PMID: 22859403 DOI: 10.1152/ajprenal.00690.2011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Albuminuria is an important marker of nephropathy that increases the risk of progressive renal and chronic cardiovascular diseases. The genetic basis of kidney disease is well-established in humans and rodent models, but the causal genes remain to be identified. We applied several genetic strategies to map and refine genetic loci affecting albuminuria in mice and translated the findings to human kidney disease. First, we measured albuminuria in mice from 33 inbred strains, used the data for haplotype association mapping (HAM), and detected 10 genomic regions associated with albuminuria. Second, we performed eight F(2) intercrosses between genetically diverse strains to identify six loci underlying albuminuria, each of which was concordant to kidney disease loci in humans. Third, we used the Oak Ridge National Laboratory incipient Collaborative Cross subpopulation to detect an additional novel quantitative trait loci (QTL) underlying albuminuria. We also performed a ninth intercross, between genetically similar strains, that substantially narrowed an albuminuria QTL on Chromosome 17 to a region containing four known genes. Finally, we measured renal gene expression in inbred mice to detect pathways highly correlated with albuminuria. Expression analysis also identified Glcci1, a gene known to affect podocyte structure and function in zebrafish, as a strong candidate gene for the albuminuria QTL on Chromosome 6. Overall, these findings greatly enhance our understanding of the genetic basis of albuminuria in mice and may guide future studies into the genetic basis of kidney disease in humans.
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Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, de Villena FPM. Status and access to the Collaborative Cross population. Mamm Genome 2012; 23:706-12. [PMID: 22847377 PMCID: PMC3463789 DOI: 10.1007/s00335-012-9410-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/04/2012] [Indexed: 12/03/2022]
Abstract
The Collaborative Cross (CC) is a panel of recombinant inbred lines derived from eight genetically diverse laboratory inbred strains. Recently, the genetic architecture of the CC population was reported based on the genotype of a single male per line, and other publications reported incompletely inbred CC mice that have been used to map a variety of traits. The three breeding sites, in the US, Israel, and Australia, are actively collaborating to accelerate the inbreeding process through marker-assisted inbreeding and to expedite community access of CC lines deemed to have reached defined thresholds of inbreeding. Plans are now being developed to provide access to this novel genetic reference population through distribution centers. Here we provide a description of the distribution efforts by the University of North Carolina Systems Genetics Core, Tel Aviv University, Israel and the University of Western Australia.
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Rose AJ, Berlowitz DR, Miller DR, Hylek EM, Ozonoff A, Zhao S, Reisman JI, Ash AS. INR targets and site-level anticoagulation control: results from the Veterans AffaiRs Study to Improve Anticoagulation (VARIA). J Thromb Haemost 2012; 10:590-5. [PMID: 22288563 DOI: 10.1111/j.1538-7836.2012.04649.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Not all clinicians target the same International Normalized Ratio (INR) for patients with a guideline-recommended target range of 2-3. A patient's mean INR value suggests the INR that was actually targeted. We hypothesized that sites would vary by mean INR, and that sites of care with mean values nearest to 2.5 would achieve better anticoagulation control, as measured by per cent time in therapeutic range (TTR). OBJECTIVES To examine variations among sites in mean INR and the relationship with anticoagulation control in an integrated system of care. PATIENTS/METHODS We studied 103,897 patients receiving oral anticoagulation with an expected INR target between 2 and 3 at 100 Veterans Health Administration (VA) sites from 1 October 2006 to 30 September 2008. Key site-level variables were: proportion near 2.5 (that is, percentage of patients with mean INR between 2.3 and 2.7) and mean risk-adjusted TTR. RESULTS Site mean INR ranged from 2.22 to 2.89; proportion near 2.5, from 30 to 64%. Sites' proportions of patients near 2.5, below 2.3 and above 2.7 were consistent from year to year. A 10 percentage point increase in the proportion near 2.5 predicted a 3.8 percentage point increase in risk-adjusted TTR (P < 0.001). CONCLUSIONS Proportion of patients with mean INR near 2.5 is a site-level 'signature' of care and an implicit measure of targeted INR. This proportion varies by site and is strongly associated with site-level TTR. Our study suggests that sites wishing to improve TTR, and thereby improve patient outcomes, should avoid the explicit or implicit pursuit of non-standard INR targets.
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Miller DR, Chew D, Chetty M, Currie GP, Bissett D, McKean ME. Endobronchial ultrasound guided transbronchial needle aspiration: a novel way to diagnose metastatic urological cancer. QJM 2012; 105:292-4. [PMID: 22238431 DOI: 10.1093/qjmed/hcr273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Threadgill DW, Miller DR, Churchill GA, de Villena FPM. The collaborative cross: a recombinant inbred mouse population for the systems genetic era. ILAR J 2011; 52:24-31. [PMID: 21411855 DOI: 10.1093/ilar.52.1.24] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mouse is the most extensively used mammalian model for biomedical and aging research, and an extensive catalogue of laboratory resources is available to support research using mice: classical inbred lines, genetically modified mice (knockouts, transgenics, and humanized mice), selectively bred lines, consomics, congenics, recombinant inbred panels, outbred and heterogeneous stocks, and an expanding set of wild-derived strains. However, these resources were not designed or intended to model the heterogeneous human population or for a systematic analysis of phenotypic effects due to random combinations of uniformly distributed natural variants. The Collaborative Cross (CC) is a large panel of recently established multiparental recombinant inbred mouse lines specifically designed to overcome the limitations of existing mouse genetic resources for analysis of phenotypes caused by combinatorial allele effects. The CC models the complexity of the human genome and supports analyses of common human diseases with complex etiologies originating through interactions between allele combinations and the environment. The CC is the only mammalian resource that has high and uniform genomewide genetic variation effectively randomized across a large, heterogeneous, and infinitely reproducible population. The CC supports data integration across environmental and biological perturbations and across space (different labs) and time.
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Philip VM, Sokoloff G, Ackert-Bicknell CL, Striz M, Branstetter L, Beckmann MA, Spence JS, Jackson BL, Galloway LD, Barker P, Wymore AM, Hunsicker PR, Durtschi DC, Shaw GS, Shinpock S, Manly KF, Miller DR, Donohue KD, Culiat CT, Churchill GA, Lariviere WR, Palmer AA, O'Hara BF, Voy BH, Chesler EJ. Genetic analysis in the Collaborative Cross breeding population. Genome Res 2011; 21:1223-38. [PMID: 21734011 DOI: 10.1101/gr.113886.110] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations.
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Gelinas R, Chesler EJ, Vasconcelos D, Miller DR, Yuan Y, Wang K, Galas D. A genetic approach to the prediction of drug side effects: bleomycin induces concordant phenotypes in mice of the collaborative cross. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2011; 4:35-45. [PMID: 23226052 PMCID: PMC3513218 DOI: 10.2147/pgpm.s22475] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Indexed: 12/19/2022]
Abstract
The antineoplastic drug bleomycin leads to the side effect of pulmonary fibrosis in both humans and mice. We challenged genetically diverse inbred lines of mice from the Collaborative Cross with bleomycin to determine the heritability of this phenotype. Sibling pairs of mice from 40 lines were treated with bleomycin. Lung disease was assessed by scoring lung pathology and by measuring soluble collagen levels in lavage fluid. Serum micro ribonucleic acids (miRNAs) were also measured. Inbred sibling pairs of animals demonstrated high coinheritance of the phenotypes of disease susceptibility or disease resistance. The plasma levels of one miRNA were clearly correlated in sibling mice. The results showed that, as in humans, the lines that comprise the Collaborative Cross exhibited wide genetic variation in response to this drug. This finding suggests that the genetically diverse Collaborative Cross animals may reveal drug effects that might be missed if a study were based on a conventional mouse strain.
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Mathes WF, Aylor DL, Miller DR, Churchill GA, Chesler EJ, de Villena FPM, Threadgill DW, Pomp D. Architecture of energy balance traits in emerging lines of the Collaborative Cross. Am J Physiol Endocrinol Metab 2011; 300:E1124-34. [PMID: 21427413 PMCID: PMC3118585 DOI: 10.1152/ajpendo.00707.2010] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32-10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5-38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2-83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4-48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9-89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance.
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Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R, Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D, de Villena FPM, Churchill GA. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 2011; 21:1213-22. [PMID: 21406540 DOI: 10.1101/gr.111310.110] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites-all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.
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Rung A, Miller DR, Scheffer SJ. Polymerase chain reaction-restriction fragment length polymorphism method to distinguish three mealybug groups within the Planococcus citri-P. minor species complex (Hemiptera: Coccoidea: Pseudococcidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2009; 102:8-12. [PMID: 19253611 DOI: 10.1603/029.102.0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The mealybug species Planococcus citri (Risso) and Planococcus minor (Maskell) (Hemiptera: Coccoidea: Pseudococcidae) have special significance to U.S. quarantine and U.S. agriculture. Commonly intercepted at U.S. ports-of-entry, they are difficult to identify based on morphological characters. This study presents a molecular method for distinguishing P. citri, P. minor, and a genetically distinct group that is morphologically identical to P. citri, from Hawaii. This method uses polymerase chain reaction (PCR) followed by restriction fragment polymorphism analysis (RFLP) using the restriction enzymes BspH1, BsmH1, and HpH1. The resulting band patterns can be visualized in a 2% agarose gel and are sufficient to differentiate between the three entities mentioned above. PCR-RFLP diagnostics can be used for all life stages and is cheaper and faster than DNA sequencing.
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Iqbal SU, Cunningham F, Lee A, Miller DR, Li NC, Cheung R, Kazis L. Persistence with hepatitis C therapy in the Department of Veterans Affairs. J Clin Pharm Ther 2008; 33:251-61. [PMID: 18452412 DOI: 10.1111/j.1365-2710.2008.00912.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Persistence with Hepatitis C therapy has been identified as a key variable for predicting treatment success. The primary purpose of this study was to assess the persistence with therapy for patients undergoing hepatitis C treatment in the VA healthcare system with two forms of combination therapies: peginterferon alfa-2a with Ribavirin (peg-IFN alpha-2a/Rib) and peginterferon alpha-2b with Ribavirin (peg-IFN alpha-2b/Rib). METHODS A retrospective cohort study design was used to analyse persistence in VA patients undergoing hepatitis C therapy during FY 2003-2004 using a large national VA data set. Stringent inclusion and exclusion criteria along with various defining variables were used to identify the inception cohort. Persistence rates were calculated for each of the two treatment groups at 3, 6, 9 and 11 months using the Kaplan-Meier method. Likelihood ratio test of equality between the two treatment groups was performed to detect any differences in persistence rates. RESULTS A total of 5816 hepatitis C patients formed the inception cohort. Persistence rates for the overall duration showed significantly higher rates for patients on peg-IFN alpha-2a/Rib than peg-IFN alpha-2b/Rib. Cox regression analysis also showed favourable hazard ratio of persistence (0.88) for peg-IFN alpha-2a/Rib over peg-IFN alpha-2b/Rib. CONCLUSION Peg alfa-2A/Rib showed slightly higher persistence rates for the overall duration of treatment as compared to Peg alfa-2B/Rib. However the differences, even though statistically significant, are small and not likely to translate into any substantial clinical advantage. Further research involving other approaches is required to confirm these findings.
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Fraedrich SW, Harrington TC, Rabaglia RJ, Ulyshen MD, Mayfield AE, Hanula JL, Eickwort JM, Miller DR. A Fungal Symbiont of the Redbay Ambrosia Beetle Causes a Lethal Wilt in Redbay and Other Lauraceae in the Southeastern United States. PLANT DISEASE 2008; 92:215-224. [PMID: 30769391 DOI: 10.1094/pdis-92-2-0215] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Extensive mortality of redbay has been observed in the coastal plain counties of Georgia and southeastern South Carolina since 2003 and northeastern Florida since 2005. We show that the redbay mortality is due to a vascular wilt disease caused by an undescribed Raffaelea sp. that is a fungal symbiont of Xyleborus glabratus, an exotic ambrosia beetle. Trees affected by the disease exhibit wilt symptoms that include a black discoloration of the sapwood. Redbay trees and containerized seedlings died within 5 to 12 weeks after inoculation with the Raffaelea sp. When redbay seedlings were challenged with X. glabratus, the beetles tunneled into 96% of the plants, 70% died, and the Raffaelea sp. was recovered from 91%. X. glabratus and the Raffaelea sp. have also been associated with mortality of sassafras, and the Raffaelea sp. has been isolated from wilted pondberry and pondspice. Additional inoculation studies have shown that the Raffaelea sp. is pathogenic to sassafras, spicebush, and avocado, but not to red maple. Female adults of X. glabratus have paired mycangia near the mandibles, and the Raffaelea sp. is routinely isolated from the heads of beetles. The fungus is apparently introduced into healthy redbay during beetle attacks on stems and branches. The wilt currently affecting redbay and sassafras represents a major threat to other members of the Lauraceae indigenous to the Americas, including avocado in commercial production.
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Iqbal SU, Cunningham F, Lee A, Wang S, Hamed A, Miller DR, Ren X, Kazis L. Divalproex sodium vs. valproic acid: drug utilization patterns, persistence rates and predictors of hospitalization among VA patients diagnosed with bipolar disorder. J Clin Pharm Ther 2008; 32:625-32. [PMID: 18021341 DOI: 10.1111/j.1365-2710.2007.00876.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVES To compare divalproex sodium and valproic acid for therapeutic patterns, persistence rates and predictors of hospitalization among bipolar patients on monotherapy in the Veterans Affairs (VA) healthcare system. METHODS Using VA administrative data bases, we conducted a retrospective inception cohort study of VA patients'>or= 18 years of age who had at least one outpatient diagnoses of bipolar disorder and two continuous prescription records for the study drugs in the VA PBM pharmacy database during the study period of 1st April 2001 to 30th September 2003. Persistence for the comparative drugs was reported as continuous variable and compared using t-tests. Logistic regression models were used to examine the risk of hospitalization whereas Cox proportional hazard regression models were used to evaluate the time to hospitalization and time to interruption of therapy for the two drug groups. RESULTS We identified 4624 bipolar patients on monotherapy with valproic acid (n = 4036) and divalproex sodium (n = 588) during the study period. The descriptive statistics included sociodemographics, disability and comorbidity status and were similar for the two groups. For the crude persistence rates there were no statistically significant differences between divalproex sodium (120 days) and valproic acid (110 days). The logistic regression model for risk of hospitalization showed no statistically significant difference between the two comparators [odds ratio = 1.06, 95% confidence interval (CI) = 0.787-1.444]. The Cox model for time to interruption of therapy showed an insignificant hazard ratio (HR) for divalproex sodium vs. valproic acid (HR = 0.928, 95% CI = 0.844-1.020) and for time to hospitalization also no statistically significant difference in the HR for the two drugs (HR = 0.984, 95% CI = 0.784-1.295). CONCLUSION The study showed a comparable profile of generic valproic acid with divalproex sodium for persistence and predictors of hospitalization for bipolar patients on monotherapy in the VA. Results have important healthcare implications for treatment and costs.
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Cook MN, Dunning JP, Wiley RG, Chesler EJ, Johnson DK, Miller DR, Goldowitz D. Neurobehavioral mutants identified in an ENU-mutagenesis project. Mamm Genome 2007; 18:559-72. [PMID: 17629744 DOI: 10.1007/s00335-007-9035-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
We report on a battery of behavioral screening tests that successfully identified several neurobehavioral mutants among a large-scale ENU-mutagenized mouse population. Large numbers of ENU-mutagenized mice were screened for abnormalities in central nervous system function based on abnormal performance in a series of behavior tasks. We developed and used a high-throughput screen of behavioral tasks to detect behavioral outliers. Twelve mutant pedigrees, representing a broad range of behavioral phenotypes, have been identified. Specifically, we have identified two open-field mutants (one displaying hyperlocomotion, the other hypolocomotion), four tail-suspension mutants (all displaying increased immobility), one nociception mutant (displaying abnormal responsiveness to thermal pain), two prepulse inhibition mutants (displaying poor inhibition of the startle response), one anxiety-related mutant (displaying decreased anxiety in the light/dark test), and one learning-and-memory mutant (displaying reduced response to the conditioned stimulus). These findings highlight the utility of a set of behavioral tasks used in a high-throughput screen to identify neurobehavioral mutants. Further analysis (i.e., behavioral and genetic mapping studies) of mutants is in progress with the ultimate goal of identification of novel genes and mouse models relevant to human disorders as well as the identification of novel therapeutic targets.
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Manning JM, Cerami A, Gillette PN, De Furia FG, Miller DR. Biochemical and physiological properties of carbamylated hemoglobin S. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 40:1-27. [PMID: 4600763 DOI: 10.1002/9780470122853.ch1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Ren XS, Qian S, Lee AF, Herz L, Miller DR, Kazis LE. Treatment persistence: a comparison among patients with schizophrenia who were initiated on atypical antipsychotic agents. J Clin Pharm Ther 2006; 31:57-65. [PMID: 16476121 DOI: 10.1111/j.1365-2710.2006.00711.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Although clinical trials have demonstrated the efficacy of atypical antipsychotic agents in reducing symptoms of schizophrenia, the likelihood of sustaining control of schizophrenic symptoms may depend on treatment persistence. OBJECTIVE In this study, we compared treatment persistence between patients who were initiated on risperidone or olanzapine, the two most widely prescribed atypical antipsychotic agents. METHOD We identified patients with schizophrenia by ICD-9-CM codes (> or =1 inpatient or > or =2 outpatient ICD-9-CM codes > or =7 days apart) between 1 July 1998 and 30 June 1999. We further selected those who were prescribed the target drug during 1 April 1999 through 31 March 2000 provided that they were not on any antipsychotic agents during the prior 6 months. Using event history analysis, we compared the treatment persistence in terms of hazard ratio between olanzapine and risperidone initiators, adjusting for patient's sociodemographic and clinical characteristics. RESULTS Following the initiation of the target drug, more patients switched from risperidone to olanzapine than vice versa. However, among patients with schizophrenia who had comorbid diabetes, there were more patients who made a switch from olanzapine to risperidone; whereas among those who used anxiolytics, there were more patients who switched from risperidone to olanzapine. Finally, olanzapine initiators had decreased hazards of discontinuation by 14% (unadjusted; P < 0.001) and 12% (adjusted; P = 0.002), respectively, than risperidone initiators. CONCLUSIONS Compared with risperidone, olanzapine seems to be better tolerated by patients as indicated by better treatment persistence. As such, initiation of olanzapine may increase the likelihood of sustaining control of symptoms of schizophrenia. Future research needs to provide a more comprehensive assessment of treatment persistence by considering other antipsychotic agents in the study and developing models to assess treatment persistence and switching as two interdependent competing risks.
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Jablonski MM, Wang X, Lu L, Miller DR, Rinchik EM, Williams RW, Goldowitz D. The Tennessee Mouse Genome Consortium: identification of ocular mutants. Vis Neurosci 2006; 22:595-604. [PMID: 16332270 DOI: 10.1017/s0952523805225087] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 06/17/2005] [Indexed: 11/05/2022]
Abstract
The Tennessee Mouse Genome Consortium (TMGC) is in its fifth year of a ethylnitrosourea (ENU)-based mutagenesis screen to detect recessive mutations that affect the eye and brain. Each pedigree is tested by various phenotyping domains including the eye, neurohistology, behavior, aging, ethanol, drug, social behavior, auditory, and epilepsy domains. The utilization of a highly efficient breeding protocol and coordination of various universities across Tennessee makes it possible for mice with ENU-induced mutations to be evaluated by nine distinct phenotyping domains within this large-scale project known as the TMGC. Our goal is to create mutant lines that model human diseases and disease syndromes and to make the mutant mice available to the scientific research community. Within the eye domain, mice are screened for anterior and posterior segment abnormalities using slit-lamp biomicroscopy, indirect ophthalmoscopy, fundus photography, eye weight, histology, and immunohistochemistry. As of January 2005, we have screened 958 pedigrees and 4800 mice, excluding those used in mapping studies. We have thus far identified seven pedigrees with primary ocular abnormalities. Six of the mutant pedigrees have retinal or subretinal aberrations, while the remaining pedigree presents with an abnormal eye size. Continued characterization of these mutant mice should in most cases lead to the identification of the mutated gene, as well as provide insight into the function of each gene. Mice from each of these pedigrees of mutant mice are available for distribution to researchers for independent study.
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Miller DR, Asaro C. Ipsenol and ipsdienol attract Monochamus titillator (Coleoptera: Cerambycidae) and associated large pine woodborers in southeastern United States. JOURNAL OF ECONOMIC ENTOMOLOGY 2005; 98:2033-40. [PMID: 16539130 DOI: 10.1603/0022-0493-98.6.2033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We determined the responses of the southern pine sawyer, Monochamus titillator (F.) (Coleoptera: Cerambycidae), to the pheromones (ipsenol, ipsdienol, and lanierone) used by pine engraver beetles (Coleoptera: Scolytidae) in the southeastern United States. (+/-)-Ipsenol, (+/-)-ipsdienol, or a combination increased catches of M. titillator in Florida, Louisiana, Georgia, and North Carolina. Catches of Acanthocinus obsoletus (Olivier) (Cerambycidae) were increased by (+/-)-ipsenol and (+/-)-ipsdienol in Florida and North Carolina, whereas only (+/-)-ipsenol was attractive in Georgia. (+/-)-Ipsenol and (+/-)-ipsdienol were attractive to Pachylobius picivorus (Germar) (Coleoptera: Curculionidae) in Florida, whereas only (+/-)-ipsdienol was active in Louisiana. In Florida, catches of M. titillator, A. obsoletus, and P. picivorus were greatest in traps baited with both (+/-)-ipsenol and (+/-)-ipsdienol. In Louisiana, catches of the woodborer Chalcophora virginiensis (Drury) (Buprestidae) were increased by (+/-)-ipsenol. Lanierone did not affect trap catches of the aforementioned species. The combination of (+/-)-ipsenol and (+/-)-ipsdienol may be a cost-effective lure for these four species because we found no evidence of interruption in attraction to baited traps, and the cost of the lure combination is relatively low.
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