61 results on '"Andrew P. Morgan"'
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2. The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC
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Robert Verity, Ozkan Aydemir, Nicholas F. Brazeau, Oliver J. Watson, Nicholas J. Hathaway, Melchior Kashamuka Mwandagalirwa, Patrick W. Marsh, Kyaw Thwai, Travis Fulton, Madeline Denton, Andrew P. Morgan, Jonathan B. Parr, Patrick K. Tumwebaze, Melissa Conrad, Philip J. Rosenthal, Deus S. Ishengoma, Jeremiah Ngondi, Julie Gutman, Modest Mulenga, Douglas E. Norris, William J. Moss, Benedicta A. Mensah, James L. Myers-Hansen, Anita Ghansah, Antoinette K. Tshefu, Azra C. Ghani, Steven R. Meshnick, Jeffrey A. Bailey, and Jonathan J. Juliano
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Science - Abstract
The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.
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- 2020
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3. Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
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Andrew P. Morgan, Nicholas F. Brazeau, Billy Ngasala, Lwidiko E. Mhamilawa, Madeline Denton, Mwinyi Msellem, Ulrika Morris, Dayne L. Filer, Ozkan Aydemir, Jeffrey A. Bailey, Jonathan B. Parr, Andreas Mårtensson, Anders Bjorkman, and Jonathan J. Juliano
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Plasmodium ,Malaria ,Population genetics ,Arctic medicine. Tropical medicine ,RC955-962 ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools. Methods Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. Results Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation. Conclusions These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
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- 2020
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4. Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice
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Lisa E. Gralinski, Vineet D. Menachery, Andrew P. Morgan, Allison L. Totura, Anne Beall, Jacob Kocher, Jessica Plante, D. Corinne Harrison-Shostak, Alexandra Schäfer, Fernando Pardo-Manuel de Villena, Martin T. Ferris, and Ralph S. Baric
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SARS-CoV ,Collaborative Cross ,F2 ,Ticam2 ,host susceptibility genes ,Multi-parent Advanced Generation Inter-Cross (MAGIC) ,multiparental populations ,MPP ,Genetics ,QH426-470 - Abstract
Host genetic variation is known to contribute to differential pathogenesis following infection. Mouse models allow direct assessment of host genetic factors responsible for susceptibility to Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). Based on an assessment of early stage lines from the Collaborative Cross mouse multi-parent population, we identified two lines showing highly divergent susceptibilities to SARS-CoV: the resistant CC003/Unc and the susceptible CC053/Unc. We generated 264 F2 mice between these strains, and infected them with SARS-CoV. Weight loss, pulmonary hemorrhage, and viral load were all highly correlated disease phenotypes. We identified a quantitative trait locus of major effect on chromosome 18 (27.1–58.6 Mb) which affected weight loss, viral titer and hemorrhage. Additionally, each of these three phenotypes had distinct quantitative trait loci [Chr 9 (weight loss), Chrs 7 and 12 (virus titer), and Chr 15 (hemorrhage)]. We identified Ticam2, an adaptor protein in the TLR signaling pathways, as a candidate driving differential disease at the Chr 18 locus. Ticam2−/− mice were highly susceptible to SARS-CoV infection, exhibiting increased weight loss and more pulmonary hemorrhage than control mice. These results indicate a critical role for Ticam2 in SARS-CoV disease, and highlight the importance of host genetic variation in disease responses.
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- 2017
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5. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection
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Elissa J. Chesler, Daniel M. Gatti, Andrew P. Morgan, Marge Strobel, Laura Trepanier, Denesa Oberbeck, Shannon McWeeney, Robert Hitzemann, Martin Ferris, Rachel McMullan, Amelia Clayshultle, Timothy A. Bell, Fernando Pardo Manuel de Villena, and Gary A. Churchill
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transmission ratio distortion ,meiotic drive ,aneuploidy ,Multiparent Advanced Generation Inter-Cross (MAGIC) ,multiparental populations MPP ,Genetics ,QH426-470 - Abstract
Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.
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- 2016
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6. Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers
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Andrew P. Morgan, John P. Didion, Anthony G. Doran, James M. Holt, Leonard McMillan, Thomas M. Keane, and Fernando Pardo-Manuel de Villena
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inbred mouse strains ,wild-derived mouse strains ,Robertsonian translocations ,karyotype evolution ,Genetics ,QH426-470 - Abstract
Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction.
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- 2016
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7. The Mouse Universal Genotyping Array: From Substrains to Subspecies
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Andrew P. Morgan, Chen-Ping Fu, Chia-Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti-Rodriguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark Keller, Alan D. Attie, Gary A. Churchill, Petko Petkov, Patrick F. Sullivan, Jennifer R. Brennan, Leonard McMillan, and Fernando Pardo-Manuel de Villena
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microarrays ,genetic mapping ,inbred strains ,Genetics ,QH426-470 - Abstract
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.
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- 2016
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8. argyle: An R Package for Analysis of Illumina Genotyping Arrays
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Andrew P. Morgan
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SNP microarrays ,genotyping ,software ,Genetics ,QH426-470 - Abstract
Genotyping microarrays are an important and widely-used tool in genetics. I present argyle, an R package for analysis of genotyping array data tailored to Illumina arrays. The goal of the argyle package is to provide simple, expressive tools for nonexpert users to perform quality checks and exploratory analyses of genotyping data. To these ends, the package consists of a suite of quality-control functions, normalization procedures, and utilities for visually and statistically summarizing such data. Format-conversion tools allow interoperability with popular software packages for analysis of genetic data including PLINK, R/qtl and DOQTL. Detailed vignettes demonstrating common use cases are included as supporting information. argyle bridges the gap between the low-level tasks of quality control and high-level tasks of genetic analysis. It is freely available at https://github.com/andrewparkermorgan/argyle and has been submitted to Bioconductor.
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- 2016
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9. Robust whole-hand spatial manipulation via energy maps with caging, rolling, and sliding
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Walter G. Bircher, Andrew S. Morgan, and Aaron M. Dollar
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spatial manipulation ,dexterous manipulation ,whole-hand manipulation ,potential energy ,caging ,design ,Mechanical engineering and machinery ,TJ1-1570 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Humans regularly use all inner surfaces of the hand during manipulation, whereas traditional formulations for robots tend to use only the tips of their fingers, limiting overall dexterity. In this paper, we explore the use of the whole hand during spatial robotic dexterous within-hand manipulation. We present a novel four-fingered robotic hand called the Model B, which is designed and controlled using a straight-forward potential energy-based motion model that is based on the hand configuration and applied actuator torques. In this way the hand-object system is driven to a new desired configuration, often through sliding and rolling between the object and hand, and with the fingers “caging” the object to prevent ejection. This paper presents the first ever application of the energy model in three dimensions, which was used to compare the theoretical manipulability of popular robotic hands, which then inspired the design of the Model B. We experimentally validate the hand’s performance with extensive benchtop experimentation with test objects and real world objects, as well as on a robotic arm, and demonstrate complex spatial caging manipulation on a variety of objects in all six object dimensions (three translation and three rotation) using all inner surfaces of the fingers and the palm.
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- 2023
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10. Epigenetic drugs induce the potency of classic chemotherapy, suppress post-treatment re-growth of breast cancer, but preserve the wound healing ability of stem cells
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Andrew Zheng, Michelle Bilbao, Janhvi Sookram, Kimberly M. Linden, Andrew B. Morgan, and Olga Ostrovsky
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triple negative breast cancer ,epigenetic drugs ,adipose-derived stem cells ,wound healing ,neoadjuvant chemotherapy ,breast conserving therapy ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Epigenetic therapy augments neoadjuvant chemotherapy (NACT) in breast cancer and may aid post-surgical wound healing affected by NACT. Our study investigates: (1) The cytotoxicity of classic paclitaxel chemotherapy on triple negative breast cancer (TNBC) independently and in combination with epigenetic drugs. (2) The sustainable inhibition of breast cancer regrowth following paclitaxel and epigenetic therapies. (3) The effects of paclitaxel with and without epigenetic therapy on the post-treatment viability and wound healing potential of adipose stem cells (ASCs). Cytotoxicity assays were performed on TNBC and ASCs. Cells were treated and recovered in drug-free medium. Cell viability was measured via cell counts and MTT assays. W -ound healing was tested with scratch assays. The combination of epigenetic drugs shows increased toxicity against TNBC cells compared to standard chemotherapy alone. Moreover, the combination of paclitaxel with epigenetic treatments causes cancer toxicity that is sustainable to TNBC cells after the drugs’ removal with minimal effect on ASCs wound healing ability. The use of epigenetic drugs in addition to standard chemotherapy is cytotoxic to TNBC cells and prevents post-treatment recovery of TNBC while maintaining ASC wound healing ability. This strategy may be useful in maximizing post-surgical wound healing following NACT in TNBC.
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- 2022
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11. Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers
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Susannah Holmes, Henry J. Kirkwood, Richard Bean, Klaus Giewekemeyer, Andrew V. Martin, Marjan Hadian-Jazi, Max O. Wiedorn, Dominik Oberthür, Hugh Marman, Luigi Adriano, Nasser Al-Qudami, Saša Bajt, Imrich Barák, Sadia Bari, Johan Bielecki, Sandor Brockhauser, Mathew A. Coleman, Francisco Cruz-Mazo, Cyril Danilevski, Katerina Dörner, Alfonso M. Gañán-Calvo, Rita Graceffa, Hans Fanghor, Michael Heymann, Matthias Frank, Alexander Kaukher, Yoonhee Kim, Bostjan Kobe, Juraj Knoška, Torsten Laurus, Romain Letrun, Luis Maia, Marc Messerschmidt, Markus Metz, Thomas Michelat, Grant Mills, Serguei Molodtsov, Diana C. F. Monteiro, Andrew J. Morgan, Astrid Münnich, Gisel E. Peña Murillo, Gianpietro Previtali, Adam Round, Tokushi Sato, Robin Schubert, Joachim Schulz, Megan Shelby, Carolin Seuring, Jonas A. Sellberg, Marcin Sikorski, Alessandro Silenzi, Stephan Stern, Jola Sztuk-Dambietz, Janusz Szuba, Martin Trebbin, Patrick Vagovic, Thomas Ve, Britta Weinhausen, Krzysztof Wrona, Paul Lourdu Xavier, Chen Xu, Oleksandr Yefanov, Keith A. Nugent, Henry N. Chapman, Adrian P. Mancuso, Anton Barty, Brian Abbey, and Connie Darmanin
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Science - Abstract
Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.
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- 2022
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12. Evaluation of data-driven respiratory gating waveforms for clinical PET imaging
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Matthew D. Walker, Andrew J. Morgan, Kevin M. Bradley, and Daniel R. McGowan
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PET/CT ,Motion ,Respiratory gating ,Data-driven gating ,Imaging ,Medical physics. Medical radiology. Nuclear medicine ,R895-920 - Abstract
Abstract Background We aimed to evaluate the clinical robustness of a commercially developed data-driven respiratory gating algorithm based on principal component analysis, for use in routine PET imaging. Methods One hundred fifty-seven adult FDG PET examinations comprising a total of 1149 acquired bed positions were used for the assessment. These data are representative of FDG scans currently performed at our institution. Data were acquired for 4 min/bed position (3 min/bed for legs). The data-driven gating (DDG) algorithm was applied to each bed position, including those where minimal respiratory motion was expected. The algorithm provided a signal-to-noise measure of respiratory-like frequencies within the data, denoted as R. Qualitative evaluation was performed by visual examination of the waveforms, with each waveform scored on a 3-point scale by two readers and then averaged (score S of 0 = no respiratory signal, 1 = some respiratory-like signal but indeterminate, 2 = acceptable signal considered to be respiratory). Images were reconstructed using quiescent period gating and compared with non-gated images reconstructed with a matched number of coincidences. If present, the SUVmax of a well-defined lesion in the thorax or abdomen was measured and compared between the two reconstructions. Results There was a strong (r = 0.86) and significant correlation between R and scores S. Eighty-six percent of waveforms with R ≥ 15 were scored as acceptable for respiratory gating. On average, there were 1.2 bed positions per patient examination with R ≥ 15. Waveforms with high R and S were found to originate from bed positions corresponding to the thorax and abdomen: 90% of waveforms with R ≥ 15 had bed centres in the range 5.6 cm superior to 27 cm inferior from the dome of the liver. For regions where respiratory motion was expected to be minimal, R tended to be
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- 2019
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13. Multi-centre, multi-vendor reproducibility of 7T QSM and R2* in the human brain: Results from the UK7T study
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Catarina Rua, William T. Clarke, Ian D. Driver, Olivier Mougin, Andrew T. Morgan, Stuart Clare, Susan Francis, Keith W. Muir, Richard G. Wise, T. Adrian Carpenter, Guy B. Williams, James B. Rowe, Richard Bowtell, and Christopher T. Rodgers
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7 tesla ,MRI ,Quantitative susceptibility mapping ,R2* mapping ,Multi-centre ,Reproducibility ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Introduction: We present the reliability of ultra-high field T2* MRI at 7T, as part of the UK7T Network's “Travelling Heads” study. T2*-weighted MRI images can be processed to produce quantitative susceptibility maps (QSM) and R2* maps. These reflect iron and myelin concentrations, which are altered in many pathophysiological processes. The relaxation parameters of human brain tissue are such that R2* mapping and QSM show particularly strong gains in contrast-to-noise ratio at ultra-high field (7T) vs clinical field strengths (1.5–3T). We aimed to determine the inter-subject and inter-site reproducibility of QSM and R2* mapping at 7T, in readiness for future multi-site clinical studies. Methods: Ten healthy volunteers were scanned with harmonised single- and multi-echo T2*-weighted gradient echo pulse sequences. Participants were scanned five times at each “home” site and once at each of four other sites. The five sites had 1× Philips, 2× Siemens Magnetom, and 2× Siemens Terra scanners. QSM and R2* maps were computed with the Multi-Scale Dipole Inversion (MSDI) algorithm (https://github.com/fil-physics/Publication-Code). Results were assessed in relevant subcortical and cortical regions of interest (ROIs) defined manually or by the MNI152 standard space. Results and Discussion: Mean susceptibility (χ) and R2* values agreed broadly with literature values in all ROIs. The inter-site within-subject standard deviation was 0.001–0.005 ppm (χ) and 0.0005–0.001 ms−1 (R2*). For χ this is 2.1–4.8 fold better than 3T reports, and 1.1–3.4 fold better for R2*. The median ICC from within- and cross-site R2* data was 0.98 and 0.91, respectively. Multi-echo QSM had greater variability vs single-echo QSM especially in areas with large B0 inhomogeneity such as the inferior frontal cortex. Across sites, R2* values were more consistent than QSM in subcortical structures due to differences in B0-shimming. On a between-subject level, our measured χ and R2* cross-site variance is comparable to within-site variance in the literature, suggesting that it is reasonable to pool data across sites using our harmonised protocol. Conclusion: The harmonized UK7T protocol and pipeline delivers on average a 3-fold improvement in the coefficient of reproducibility for QSM and R2* at 7T compared to previous reports of multi-site reproducibility at 3T. These protocols are ready for use in multi-site clinical studies at 7T.
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- 2020
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14. Multi-site harmonization of 7 tesla MRI neuroimaging protocols
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William T. Clarke, Olivier Mougin, Ian D. Driver, Catarina Rua, Andrew T. Morgan, Michael Asghar, Stuart Clare, Susan Francis, Richard G. Wise, Christopher T. Rodgers, Adrian Carpenter, Keith Muir, and Richard Bowtell
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7 tesla ,MRI ,Harmonization ,Anatomical ,Functional ,Scanner calibration ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Increasing numbers of 7 T (7 T) magnetic resonance imaging (MRI) scanners are in research and clinical use. 7 T MRI can increase the scanning speed, spatial resolution and contrast-to-noise-ratio of many neuroimaging protocols, but technical challenges in implementation have been addressed in a variety of ways across sites. In order to facilitate multi-centre studies and ensure consistency of findings across sites, it is desirable that 7 T MRI sites implement common high-quality neuroimaging protocols that can accommodate different scanner models and software versions.With the installation of several new 7 T MRI scanners in the United Kingdom, the UK7T Network was established with an aim to create a set of harmonized structural and functional neuroimaging sequences and protocols. The Network currently includes five sites, which use three different scanner platforms, provided by two different vendors.Here we describe the harmonization of functional and anatomical imaging protocols across the three different scanner models, detailing the necessary changes to pulse sequences and reconstruction methods. The harmonized sequences are fully described, along with implementation details. Example datasets acquired from the same subject on all Network scanners are made available. Based on these data, an evaluation of the harmonization is provided. In addition, the implementation and validation of a common system calibration process is described.
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- 2020
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15. The Evolutionary Fates of a Large Segmental Duplication in Mouse
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Fernando Pardo-Manuel de Villena, Amelia M.-F. Clayshulte, Liran Yadgary, John P. Didion, Duncan T. Odom, Andrew P. Morgan, Leonard McMillan, Rachel C. McMullan, James Holt, Paul Flicek, Timothy A. Bell, and David Thybert
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Genetics ,0303 health sciences ,Biology ,Genome ,meiotic drive ,Structural variation ,03 medical and health sciences ,0302 clinical medicine ,Meiotic drive ,copy-number variation ,Gene duplication ,Gene conversion ,segmental duplications ,Gene ,030217 neurology & neurosurgery ,030304 developmental biology ,Segmental duplication ,Reference genome - Abstract
Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127 kbp segmental duplication,R2d, in the house mouse (Mus musculus). R2dcontains a single protein-coding gene,Cwc22. De novoassembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to non-allelic gene conversion events spanning tens of kilobases.R2d2is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to more than 80 in wild mice sampled from around the globe. Hemizgyosity for high-copy-number alleles ofR2d2is associated inciswith meiotic drive, suppression of meiotic crossovers, and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in laboratory populations. We identify an additional 57 loci covering 0.8% of the mouse genome with patterns of sequence variation similar to those atR2d1andR2d2. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value ofde novoassembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.
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- 2023
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16. The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning
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Ana C. Conrado, Hugo Arruda, David W.G. Stanton, Samuel W. James, Peter Kille, George Brown, Elodie Silva, Lise Dupont, Shabnam Taheri, Andrew J. Morgan, Nelson Simões, Armindo Rodrigues, Rafael Montiel, and Luis Cunha
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Zoology ,QL1-991 - Abstract
Pontoscolex corethrurus (Müller, 1857) plays an important role in tropical soil ecosystems and has been widely used as an animal model for a large variety of ecological studies in particular due to its common presence and generally high abundance in human-disturbed tropical soils. In this study we describe the complete mitochondrial genome of the peregrine earthworm P. corethrurus. This is the first record of a mitochondrial genome within the Rhinodrilidae family. Its mitochondrial genome is 14 835 bp in length containing 37 genes (13 protein-coding genes (PCG) 2 rRNA genes and 22 tRNA genes). It has the same gene content and structure as in other sequenced earthworms but unusual among invertebrates it hasseveral overlapping open reading frames. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND3 which uses GTG as the start codon. The A+T content of the mitochondrial genome is 59.9% (31.8% A 28.1% T 14.6% G and 25.6% for C). The annotated genome sequence has been deposited in GenBank under the accession number KT988053.
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- 2017
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17. Investigating cell autonomy in microorganisms
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Sarah Piccirillo, Andrew P. Morgan, Andy Y. Leon, Annika L. Smith, and Saul M. Honigberg
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Saccharomyces cerevisiae Proteins ,Protein Biosynthesis ,Codon, Terminator ,Genetics ,Saccharomyces cerevisiae ,General Medicine ,Article - Abstract
Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.
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- 2022
18. The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo
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Corinna Keeler, Molly Deutsch-Feldman, Steven R. Meshnick, Kyaw L. Thwai, Valerie Gartner, Oliver J Watson, Jonathan J. Juliano, Jessie K. Edwards, Cedar L Mitchell, Ben Redelings, Michael Emch, Antoinette Tshefu, Andrew P. Morgan, Jonathan B. Parr, Nicholas F Brazeau, Gregory A. Wray, Andreea Waltmann, Joris L. Likwela, Robert Verity, Pere Gelabert, Lucy van Dorp, and Melchior K. Mwandagalirwa
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0301 basic medicine ,Adult ,Male ,medicine.medical_specialty ,Adolescent ,Epidemiology ,Science ,030231 tropical medicine ,Plasmodium vivax ,General Physics and Astronomy ,Parasitemia ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Risk Factors ,parasitic diseases ,medicine ,Malaria, Vivax ,Prevalence ,Humans ,Mass Screening ,Clade ,Multidisciplinary ,biology ,Age Factors ,General Chemistry ,biology.organism_classification ,medicine.disease ,Malaria ,Phylogenetics ,030104 developmental biology ,Carriage ,Cross-Sectional Studies ,Carrier State ,Democratic Republic of the Congo ,Forward propagation ,Female ,Demographic health survey ,Demography - Abstract
Reports of P. vivax infections among Duffy-negative hosts have accumulated throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa have been performed. To overcome this gap in knowledge, we screened over 17,000 adults in the Democratic Republic of the Congo (DRC) for P. vivax using samples from the 2013-2014 Demographic Health Survey. Overall, we found a 2.97% (95% CI: 2.28%, 3.65%) prevalence of P. vivax infections across the DRC. Infections were associated with few risk-factors and demonstrated a relatively flat distribution of prevalence across space with focal regions of relatively higher prevalence in the north and northeast. Mitochondrial genomes suggested that DRC P. vivax were distinct from circulating non-human ape strains and an ancestral European P. vivax strain, and instead may be part of a separate contemporary clade. Our findings suggest P. vivax is diffusely spread across the DRC at a low prevalence, which may be associated with long-term carriage of low parasitemia, frequent relapses, or a general pool of infections with limited forward propagation., Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.
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- 2021
19. Distribution and Temporal Dynamics of Plasmodium falciparum Chloroquine Resistance Transporter Mutations Associated With Piperaquine Resistance in Northern Cambodia
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Soklyda Chann, Mariusz Wojnarski, Brian Vesely, Piyaporn Saingam, Prom Satharath, Nonlawat Boonyalai, Chaiyaporn Chaisatit, Paphavee Lertsethtakarn, Michele D. Spring, Somethy Sok, Zalak Shah, Panita Gosi, Huy Rekol, Matthew Adams, Biraj Shrestha, David L. Saunders, Molly Deutsch-Feldman, Andrew P. Morgan, Darapiseth Sea, Chantida Praditpol, Philip L. Smith, Shannon Takala-Harrison, Dysoley Lek, Chanthap Lon, Jessica T. Lin, Norman C. Waters, Stuart D. Tyner, Charlotte A. Lanteri, and Suwanna Chaorattanakawee
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0301 basic medicine ,Plasmodium falciparum ,030106 microbiology ,Drug Resistance ,Protozoan Proteins ,Real-Time Polymerase Chain Reaction ,medicine.disease_cause ,Piperazines ,Antimalarials ,Major Articles and Brief Reports ,03 medical and health sciences ,Chloroquine ,Piperaquine ,parasitic diseases ,Prevalence ,medicine ,Animals ,Immunology and Allergy ,Malaria, Falciparum ,Allele ,Whole genome sequencing ,Mutation ,biology ,Mefloquine ,fungi ,Membrane Transport Proteins ,medicine.disease ,biology.organism_classification ,Virology ,030104 developmental biology ,Infectious Diseases ,Quinolines ,Cambodia ,Biomarkers ,Malaria ,medicine.drug - Abstract
Background Newly emerged mutations within the Plasmodium falciparum chloroquine resistance transporter (PfCRT) can confer piperaquine resistance in the absence of amplified plasmepsin II (pfpm2). In this study, we estimated the prevalence of co-circulating piperaquine resistance mutations in P. falciparum isolates collected in northern Cambodia from 2009 to 2017. Methods The sequence of pfcrt was determined for 410 P. falciparum isolates using PacBio amplicon sequencing or whole genome sequencing. Quantitative polymerase chain reaction was used to estimate pfpm2 and pfmdr1 copy number. Results Newly emerged PfCRT mutations increased in prevalence after the change to dihydroartemisinin-piperaquine in 2010, with >98% of parasites harboring these mutations by 2017. After 2014, the prevalence of PfCRT F145I declined, being outcompeted by parasites with less resistant, but more fit PfCRT alleles. After the change to artesunate-mefloquine, the prevalence of parasites with amplified pfpm2 decreased, with nearly half of piperaquine-resistant PfCRT mutants having single-copy pfpm2. Conclusions The large proportion of PfCRT mutants that lack pfpm2 amplification emphasizes the importance of including PfCRT mutations as part of molecular surveillance for piperaquine resistance in this region. Likewise, it is critical to monitor for amplified pfmdr1 in these PfCRT mutants, as increased mefloquine pressure could lead to mutants resistant to both drugs.
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- 2021
20. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales
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Andrew P. Morgan, Jonathan J. Hughes, John P. Didion, Wesley J. Jolley, Karl J. Campbell, David W. Threadgill, Francois Bonhomme, Jeremy B. Searle, and Fernando Pardo-Manuel de Villena
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Europe ,Mice ,Genome ,Genetics ,Animals ,Humans ,Inbreeding ,Biological Evolution ,Genetics (clinical) ,New Zealand - Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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- 2022
21. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales
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Andrew P Morgan, Jonathan J Hughes, John P Didion, Wesley J Jolley, Karl J Campbell, David W Threadgill, Francois Bonhomme, Jeremy B Searle, and Fernando Pardo-Manuel de Villena
- Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely-used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand and various small offshore islands is of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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- 2022
22. The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse.
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Andrew P Morgan, James J Crowley, Randal J Nonneman, Corey R Quackenbush, Cheryl N Miller, Allison K Ryan, Molly A Bogue, Sur Herrera Paredes, Scott Yourstone, Ian M Carroll, Thomas H Kawula, Maureen A Bower, R Balfour Sartor, and Patrick F Sullivan
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Medicine ,Science - Abstract
The second-generation antipsychotic olanzapine is effective in reducing psychotic symptoms but can cause extreme weight gain in human patients. We investigated the role of the gut microbiota in this adverse drug effect using a mouse model. First, we used germ-free C57BL/6J mice to demonstrate that gut bacteria are necessary and sufficient for weight gain caused by oral delivery of olanzapine. Second, we surveyed fecal microbiota before, during, and after treatment and found that olanzapine potentiated a shift towards an "obesogenic" bacterial profile. Finally, we demonstrated that olanzapine has antimicrobial activity in vitro against resident enteric bacterial strains. These results collectively provide strong evidence for a mechanism underlying olanzapine-induced weight gain in mouse and a hypothesis for clinical translation in human patients.
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- 2014
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23. The Epidemiology of Plasmodium vivax Among Adults in the Democratic Republic of the Congo: A Nationally-Representative, Cross-Sectional Survey
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Benjamin D. Redelings, Melchior K. Mwandagalirwa, Jonathan B. Parr, Nicholas F Brazeau, Gartner, Jessie K. Edwards, Jonathan J. Juliano, Meshnick, Gregory A. Wray, Cedar L Mitchell, Kyaw L. Thwai, Oliver J Watson, Andrew P. Morgan, Antoinette Tshefu, Molly Deutsch-Feldman, Robert Verity, Andreea Waltmann, Joris L. Likwela, and Michael Emch
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0303 health sciences ,medicine.medical_specialty ,Critical gap ,education.field_of_study ,biology ,Cross-sectional study ,Plasmodium vivax ,Population ,medicine.disease ,biology.organism_classification ,3. Good health ,03 medical and health sciences ,0302 clinical medicine ,Geography ,030220 oncology & carcinogenesis ,Epidemiology ,parasitic diseases ,medicine ,Malaria risk ,Clade ,education ,Malaria ,030304 developmental biology ,Demography - Abstract
BackgroundReports of P. vivax infections among Duffy-negative hosts have begun to accumulate throughout sub-Saharan Africa. Despite this growing body of evidence, no nationally representative epidemiological surveys of P. vivax in sub-Saharan Africa nor population genetic analyses to determine the source of these infections have been performed.MethodsTo overcome this critical gap in knowledge, we screened nearly 18,000 adults in the Democratic Republic of the Congo (DRC) for P. vivax using samples from the 2013-2014 Demographic Health Survey. Infections were identified by quantitative PCR and confirmed with nested-PCR. P. vivax mitochondrial genomes were constructed after short-read sequencing. Risk factors, spatial distributions and population genetic analyses were explored.FindingsOverall, we found a 2.96% (95% CI: 2.28%, 3.65%) prevalence of P. vivax infections across the DRC. Nearly all infections were among Duffy-negative adults (486/489). Infections were not associated with typical malaria risk-factors and demonstrated small-scale heterogeneity in prevalence across space. Mitochondrial genomes suggested that DRC P. vivax is an older clade that shares its most recent common ancestor with South American isolates.InterpretationP. vivax is more prevalent across the DRC than previously believed despite widespread Duffy-negativity. Comparison to global and historical P. vivax sequences suggests that historic DRC P. vivax may have been transported to the New World on the wave of European expansion. Our findings suggest congolese P. vivax is an innocuous threat given its relatively flat distribution across space, lack of malaria risk factors, and potentially ancestral lineage.FundingNational Institutes of Health and the Wellcome Trust.
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- 2020
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24. Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago
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Madeline Denton, Andrew P. Morgan, Jonathan B. Parr, Billy Ngasala, Mwinyi I. Msellem, Dayne L. Filer, Jonathan J. Juliano, Anders Björkman, Ozkan Aydemir, Jeffrey A. Bailey, Andreas Mårtensson, Nicholas F Brazeau, Ulrika Morris, and Lwidiko E. Mhamilawa
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0301 basic medicine ,Plasmodium ,Population genetics ,Infektionsmedicin ,Haploidy ,Tanzania ,Cohort Studies ,0302 clinical medicine ,Effective population size ,Malaria, Falciparum ,Islands ,0303 health sciences ,Travel ,education.field_of_study ,geography.geographical_feature_category ,biology ,Incidence ,3. Good health ,Infectious Diseases ,Archipelago ,Mainland ,Infectious Medicine ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,Plasmodium falciparum ,030231 tropical medicine ,Population ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,parasitic diseases ,medicine ,Humans ,lcsh:RC109-216 ,education ,030304 developmental biology ,Demography ,Gene Library ,geography ,Genetic diversity ,Whole Genome Sequencing ,Research ,Genetic Variation ,biology.organism_classification ,medicine.disease ,Malaria ,030104 developmental biology ,Haplotypes ,Evolutionary biology ,Mutation ,Parasitology - Abstract
Background Tanzania’s Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieved. Importation of parasites from outside of the archipelago is thought to be an important cause of malaria’s persistence, but this paradigm has not been studied using modern genetic tools. Methods Whole-genome sequencing (WGS) was used to investigate the impact of importation, employing population genetic analyses of Plasmodium falciparum isolates from both the archipelago and mainland Tanzania. Ancestry, levels of genetic diversity and differentiation, patterns of relatedness, and patterns of selection between these two populations were assessed by leveraging recent advances in deconvolution of genomes from polyclonal malaria infections. Results Significant decreases in the effective population sizes were inferred in both populations that coincide with a period of decreasing malaria transmission in Tanzania. Identity by descent analysis showed that parasites in the two populations shared long segments of their genomes, on the order of 5 cM, suggesting shared ancestry within the last 10 generations. Even with limited sampling, two of isolates between the mainland and Zanzibar were identified that are related at the expected level of half-siblings, consistent with recent importation. Conclusions These findings suggest that importation plays an important role for malaria incidence on Zanzibar and demonstrate the value of genomic approaches for identifying corridors of parasite movement to the island.
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- 2020
25. The relationship between early childhood blood lead levels and performance on end-of-grade tests
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Miranda, Marie Lynn, Kim, Dohyeong, Overstreet Galeano, M. Alicia, Paul, Christopher J., and Hull, Andrew P. Morgan, S. Philip
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Children -- Health aspects ,Children -- Research ,Lead poisoning -- Research ,Lead poisoning -- Complications and side effects ,United States -- Environmental aspects - Abstract
BACKGROUND: Childhood lead poisoning remains a critical environmental health concern. Lowlevel lead exposure has been linked to decreased performance on standardized IQ tests for schoolaged children. OBJECTIVE: In this study we sought to determine whether blood lead levels in early childhood are related to educational achievement in early elementary school as measured by performance on endof-grade (EOG) testing. METHODS: Educational testing data for 4th-grade students from the 2000--2004 North Carolina Education Research Data Center were linked to blood lead surveillance data for seven counties in North Carolina and then analyzed using exploratory and multivariate statistical methods. RESULTS: The discernible impact of blood lead levels on EOG testing is demonstrated for early childhood blood lead levels as low as 2 [micro]g/dL. A blood lead level of 5 [micro]g/dL is associated with a decline in EOG reading (and mathematics) scores that is roughly equal to 15% (14%) of the interquartile range, and this impact is very significant in comparison with the effects of covariates typically considered profoundly influential on educational outcomes. Early childhood lead exposures appear to have more impact on performance on the reading than on the mathematics portions of the tests. CONCLUSIONS: Our emphasis on population-level analyses of children who are roughly the same age linked to previous (rather than contemporaneous) blood lead levels using achievement (rather than aptitude) outcome complements the important work in this area by previous researchers. Our results suggest that the relationship between blood lead levels and cognitive outcomes are robust across outcome measures and at low levels of lead exposure. KEY WORDS: disparities, lead levels, school performance. Environ Health Perspect 115:1242--1247 (2007). doi:10.1289/ehp.9994 available via http://dx.doi.org/ [Online 27 April 2007], Although much progress has been made, childhood lead poisoning remains a critical environmental health concern. Since the late 1970s, mounting research demonstrates that lead causes irreversible, asymptomatic effects far below [...]
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- 2007
26. Sequence and Structural Diversity of Mouse Y Chromosomes
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Andrew P. Morgan and Fernando Pardo-Manuel de Villena
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0106 biological sciences ,Male ,0301 basic medicine ,DNA Copy Number Variations ,Euchromatin ,Biology ,Y chromosome ,010603 evolutionary biology ,01 natural sciences ,Germline ,Evolution, Molecular ,Mice ,03 medical and health sciences ,Intragenomic conflict ,Y Chromosome ,Genetics ,Animals ,Allele ,Spermatogenesis ,Molecular Biology ,Gene ,X chromosome ,Discoveries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Sex Chromosomes ,Autosome ,Repertoire ,Chromosome ,Biological Evolution ,Population bottleneck ,Germ Cells ,030104 developmental biology ,Evolutionary biology ,House mice ,Databases, Nucleic Acid - Abstract
Over the 180 million years since their origin, the Y chromosomes of mammals have evolved a gene repertoire highly specialized for function in the male germline. The mouse Y chromosome is unique among mammal Y chromosomes studied to date in that it is large, gene-rich and almost entirely euchromatic. Yet little is known about its diversity in natural populations. Because the Y chromosome is passed only through the male germline and is obligately transmitted from fathers to sons without recombination, it provides a rich view into male-specific mutational, selective and demographic processes. We therefore took advantage of a recent high-quality assembly of the mouse Y to perform a systematic survey of a diverse sample of Y chromosomes using published whole-genome sequencing datasets. Sequence diversity in non-repetitive regions of Y chromosomes is
- Published
- 2017
27. Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice
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Vineet D. Menachery, Martin T. Ferris, Andrew P. Morgan, Alexandra Schäfer, Jessica A. Plante, D. Corinne Harrison-Shostak, Fernando Pardo-Manuel de Villena, Anne Beall, Jacob Kocher, Lisa E. Gralinski, Ralph S. Baric, and Allison L. Totura
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0301 basic medicine ,MPP ,Ticam2 ,host susceptibility genes ,Population ,Locus (genetics) ,Biology ,Quantitative trait locus ,QH426-470 ,Collaborative Cross ,Pathogenesis ,03 medical and health sciences ,0302 clinical medicine ,Genetic variation ,Genetics ,Genetics(clinical) ,Allele ,Multi-parent Advanced Generation Inter-Cross (MAGIC) ,education ,Molecular Biology ,Genetics (clinical) ,education.field_of_study ,SARS-CoV ,Phenotype ,3. Good health ,F2 ,030104 developmental biology ,Immunology ,multiparental populations ,Viral load ,030217 neurology & neurosurgery - Abstract
Host genetic variation is known to contribute to differential pathogenesis following infection. Mouse models allow direct assessment of host genetic factors responsible for susceptibility to Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). Based on an assessment of early stage lines from the Collaborative Cross mouse multi-parent population, we identified two lines showing highly divergent susceptibilities to SARS-CoV: the resistant CC003/Unc and the susceptible CC053/Unc. We generated 264 F2 mice between these strains, and infected them with SARS-CoV. Weight loss, pulmonary hemorrhage, and viral load were all highly correlated disease phenotypes. We identified a quantitative trait locus of major effect on chromosome 18 (27.1–58.6 Mb) which affected weight loss, viral titer and hemorrhage. Additionally, each of these three phenotypes had distinct quantitative trait loci [Chr 9 (weight loss), Chrs 7 and 12 (virus titer), and Chr 15 (hemorrhage)]. We identified Ticam2, an adaptor protein in the TLR signaling pathways, as a candidate driving differential disease at the Chr 18 locus. Ticam2−/− mice were highly susceptible to SARS-CoV infection, exhibiting increased weight loss and more pulmonary hemorrhage than control mice. These results indicate a critical role for Ticam2 in SARS-CoV disease, and highlight the importance of host genetic variation in disease responses.
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- 2017
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28. Structural Variation Shapes the Landscape of Recombination in Mouse
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Allan I. Pack, Andrew P. Morgan, Maya L. Najarian, Gary A. Churchill, Fernando Pardo-Manuel de Villena, Richard Mott, Daniel M. Gatti, Raymond J. Galante, and Thomas M. Keane
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Male ,0301 basic medicine ,DNA Copy Number Variations ,Genotype ,Population ,Biology ,Genome ,Chromosomes ,Structural variation ,Mice ,03 medical and health sciences ,Meiosis ,Multiparental Populations ,Genetic variation ,Genetics ,Animals ,Crossing Over, Genetic ,Copy-number variation ,Homologous Recombination ,education ,Recombination, Genetic ,education.field_of_study ,urogenital system ,Chromosome Mapping ,respiratory system ,humanities ,030104 developmental biology ,Haplotypes ,Homologous recombination ,human activities ,Recombination - Abstract
Meiotic recombination ensures the faithful segregation of chromosomes and influences patterns of genetic diversity. Morgan et al. used genotype data.. Meiotic recombination is an essential feature of sexual reproduction that ensures faithful segregation of chromosomes and redistributes genetic variants in populations. Multiparent populations such as the Diversity Outbred (DO) mouse stock accumulate large numbers of crossover (CO) events between founder haplotypes, and thus present a unique opportunity to study the role of genetic variation in shaping the recombination landscape. We obtained high-density genotype data from 6886 DO mice, and localized 2.2 million CO events to intervals with a median size of 28 kb. The resulting sex-averaged genetic map of the DO population is highly concordant with large-scale (order 10 Mb) features of previously reported genetic maps for mouse. To examine fine-scale (order 10 kb) patterns of recombination in the DO, we overlaid putative recombination hotspots onto our CO intervals. We found that CO intervals are enriched in hotspots compared to the genomic background. However, as many as 26% of CO intervals do not overlap any putative hotspots, suggesting that our understanding of hotspots is incomplete. We also identified coldspots encompassing 329 Mb, or 12% of observable genome, in which there is little or no recombination. In contrast to hotspots, which are a few kilobases in size, and widely scattered throughout the genome, coldspots have a median size of 2.1 Mb and are spatially clustered. Coldspots are strongly associated with copy-number variant (CNV) regions, especially multi-allelic clusters, identified from whole-genome sequencing of 228 DO mice. Genes in these regions have reduced expression, and epigenetic features of closed chromatin in male germ cells, which suggests that CNVs may repress recombination by altering chromatin structure in meiosis. Our findings demonstrate how multiparent populations, by bridging the gap between large-scale and fine-scale genetic mapping, can reveal new features of the recombination landscape.
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- 2017
29. Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross
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Sarah E. Cates, Fanny Odet, David L. Aylor, Andrew P. Morgan, Chia-Yu Kao, Seth Greenstein, Leonard McMillian, Wenqi Pan, Ginger D. Shaw, Alicia M. Stevans, John R. Shorter, Chen Ping Fu, Ryan W. Feathers, Deborah A. O'Brien, Darla R. Miller, Elissa J. Chesler, Sunny Patel, Timothy A. Bell, and Fernando Pardo-Manuel de Villena
- Subjects
Male ,0301 basic medicine ,Quantitative Trait Loci ,Population ,Mice, Inbred Strains ,Biology ,Chromosomes ,Male infertility ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Inbred strain ,Multiparental Populations ,Genetics ,medicine ,Animals ,Inbreeding ,Allele ,education ,Alleles ,Crosses, Genetic ,Infertility, Male ,X chromosome ,education.field_of_study ,Autosome ,Reproduction ,Haplotype ,Chromosome Mapping ,medicine.disease ,Phenotype ,030104 developmental biology ,Haplotypes ,Sperm Motility ,Female ,030217 neurology & neurosurgery - Abstract
The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.
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- 2017
30. Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers
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Leonard McMillan, John P. Didion, Thomas M. Keane, Andrew P. Morgan, Anthony G. Doran, Fernando Pardo-Manuel de Villena, and James Holt
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Male ,0106 biological sciences ,0301 basic medicine ,Animals, Wild ,Mice, Inbred Strains ,Genomics ,QH426-470 ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Mice ,03 medical and health sciences ,Inbred strain ,Phylogenetics ,Robertsonian translocations ,Genetic variation ,inbred mouse strains ,Genetics ,Animals ,Molecular Biology ,Phylogeny ,Genetics (clinical) ,Whole genome sequencing ,wild-derived mouse strains ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,karyotype evolution ,Karyotype ,Diploidy ,Genome Report ,030104 developmental biology ,Female ,Ploidy - Abstract
Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction.
- Published
- 2016
31. The Impact of Antimalarial Resistance on the Genetic Structure ofPlasmodium falciparumin the DRC
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Nicholas J. Hathaway, Patrick W Marsh, Nicholas F Brazeau, Patrick K Tumwebaze, Jonathan B. Parr, Melchior Kashamuka Mwandagalirwa, Azra C. Ghani, Travis Fulton, James L. Myers-Hansen, Jonathan J. Juliano, Steven R Meshnick, Julie Gutman, William J. Moss, Robert Verity, Jeffrey A. Bailey, Modest Mulenga, Deus S. Ishengoma, Jeremiah Ngondi, Melissa D. Conrad, Douglas E. Norris, Anita Ghansah, Andrew P. Morgan, Philip J. Rosenthal, Ozkan Aydemir, Benedicta A. Mensah, Kyaw L. Thwai, Oliver J Watson, Antoinette K. Tshefu, Madeline Denton, and National Institutes of Health
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0301 basic medicine ,Drug Resistance ,General Physics and Astronomy ,Drug resistance ,Gene flow ,Microbial ecology ,0302 clinical medicine ,Malaria, Falciparum ,lcsh:Science ,Genetics ,Principal Component Analysis ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Geography ,Chloroquine ,3. Good health ,Drug Combinations ,Pyrimethamine ,Genetic structure ,Democratic Republic of the Congo ,medicine.drug ,Genotype ,Science ,Plasmodium falciparum ,030231 tropical medicine ,Population ,Biology ,Polymorphism, Single Nucleotide ,Article ,General Biochemistry, Genetics and Molecular Biology ,Antimalarials ,03 medical and health sciences ,Sulfadoxine ,parasitic diseases ,medicine ,Humans ,Genetic variation ,education ,Genotyping ,030304 developmental biology ,Isolation by distance ,General Chemistry ,medicine.disease ,biology.organism_classification ,Sulfadoxine/pyrimethamine ,Malaria ,030104 developmental biology ,Haplotypes ,Mutation ,lcsh:Q ,Genome, Protozoan - Abstract
The Democratic Republic of the Congo (DRC) harbors 11% of global malaria cases, yet little is known about the spatial and genetic structure of the parasite population in that country. We sequence 2537 Plasmodium falciparum infections, including a nationally representative population sample from DRC and samples from surrounding countries, using molecular inversion probes - a high-throughput genotyping tool. We identify an east-west divide in haplotypes known to confer resistance to chloroquine and sulfadoxine-pyrimethamine. Furthermore, we identify highly related parasites over large geographic distances, indicative of gene flow and migration. Our results are consistent with a background of isolation by distance combined with the effects of selection for antimalarial drug resistance. This study provides a high-resolution view of parasite genetic structure across a large country in Africa and provides a baseline to study how implementation programs may impact parasite populations., The genome of the malaria parasite Plasmodium falciparum contains a record of past evolutionary forces. Here, using 2537 parasite sequences from the Democratic Republic of the Congo, the authors demonstrate how drug pressure and human movement have shaped the present-day parasite population.
- Published
- 2019
32. Instability of the pseudoautosomal boundary in house mice
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Andrew P. Morgan, Timothy A. Bell, James J. Crowley, and Fernando Pardo-Manuel de Villena
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Male ,X Chromosome ,Pseudoautosomal region ,Population ,Investigations ,Subspecies ,Biology ,Evolution, Molecular ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Meiosis ,Y Chromosome ,Genetics ,Homologous chromosome ,Animals ,education ,030304 developmental biology ,Pseudoautosomal Regions ,Recombination, Genetic ,0303 health sciences ,education.field_of_study ,Chromosome Mapping ,Evolutionary biology ,Female ,House mice ,030217 neurology & neurosurgery ,Heterogametic sex ,Recombination - Abstract
Faithful segregation of mammalian X and Y chromosomes in male meiosis depends on pairing and recombination in a short interval of residual sequence homology known as the pseudoautosomal region (PAR)... Faithful segregation of homologous chromosomes at meiosis requires pairing and recombination. In taxa with dimorphic sex chromosomes, pairing between them in the heterogametic sex is limited to a narrow interval of residual sequence homology known as the pseudoautosomal region (PAR). Failure to form the obligate crossover in the PAR is associated with male infertility in house mice (Mus musculus) and humans. Yet despite this apparent functional constraint, the boundary and organization of the PAR is highly variable in mammals, and even between subspecies of mice. Here, we estimate the genetic map in a previously documented expansion of the PAR in the M. musculus castaneus subspecies and show that the local recombination rate is 100-fold higher than the autosomal background. We identify an independent shift in the PAR boundary in the M. musculus musculus subspecies and show that it involves a complex rearrangement, but still recombines in heterozygous males. Finally, we demonstrate pervasive copy-number variation at the PAR boundary in wild populations of M. m. domesticus, M. m. musculus, and M. m. castaneus. Our results suggest that the intensity of recombination activity in the PAR, coupled with relatively weak constraints on its sequence, permit the generation and maintenance of unusual levels of polymorphism in the population of unknown functional significance.
- Published
- 2019
33. The Evolutionary Fates of a Large Segmental Duplication in Mouse
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Timothy A. Bell, James Holt, Rachel C. McMullan, David Thybert, Fernando Pardo-Manuel de Villena, Paul Flicek, Duncan T. Odom, Liran Yadgary, Leonard McMillan, John P. Didion, Amelia M.-F. Clayshulte, and Andrew P. Morgan
- Subjects
0301 basic medicine ,Gene Conversion ,Gene Dosage ,Animals, Wild ,Investigations ,Biology ,Genome ,Evolution, Molecular ,Structural variation ,Mice ,03 medical and health sciences ,Segmental Duplications, Genomic ,Genes, Duplicate ,Gene Duplication ,Gene duplication ,Genetics ,Animals ,Copy-number variation ,Gene conversion ,Alleles ,Phylogeny ,Segmental duplication ,Genetic Variation ,Nuclear Proteins ,RNA-Binding Proteins ,Biological Evolution ,030104 developmental biology ,Meiotic drive ,Reference genome - Abstract
Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22. De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.
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- 2016
34. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection
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Martin T. Ferris, Andrew P. Morgan, Amelia Clayshultle, Robert Hitzemann, Laura Trepanier, Denesa Oberbeck, Rachel C. McMullan, Timothy A. Bell, Fernando Pardo-Manuel de Villena, Daniel M. Gatti, Gary A. Churchill, Elissa J. Chesler, Marjorie Strobel, and Shannon K. McWeeney
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0301 basic medicine ,Male ,multiparental populations MPP ,Population ,Locus (genetics) ,Biology ,QH426-470 ,Breeding ,03 medical and health sciences ,Mice ,Effective population size ,Genetic drift ,Gene Frequency ,Genetic variation ,Multiparental Populations ,Genetics ,Animals ,aneuploidy ,Sex Ratio ,Allele ,Selection, Genetic ,education ,Molecular Biology ,Allele frequency ,Genetics (clinical) ,Alleles ,Crosses, Genetic ,Sex Chromosome Aberrations ,Genetic diversity ,education.field_of_study ,transmission ratio distortion ,Genome ,Computational Biology ,Genetic Variation ,Molecular Sequence Annotation ,Genomics ,meiotic drive ,Mitochondria ,030104 developmental biology ,Genetics, Population ,Phenotype ,Haplotypes ,Genetic Loci ,Mutation ,Female ,Multiparent Advanced Generation Inter-Cross (MAGIC) - Abstract
Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.
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- 2016
35. The Mouse Universal Genotyping Array: From Substrains to Subspecies
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Petko M. Petkov, John P. Didion, Gary A. Churchill, Patrick F. Sullivan, Paola Giusti-Rodríguez, J. Brennan, Kevin D. Cook, Lisa E. Gralinski, Fernando Pardo-Manuel de Villena, Darla R. Miller, Liran Yadgary, Alan D. Attie, Leeanna Hyacinth, Randal J. Nonneman, Martin T. Ferris, Andrew P. Morgan, Timothy A. Bell, Chen Ping Fu, Leonard McMillan, Mark P. Keller, Jason K. Whitmire, Chia-Yu Kao, and Catherine E. Welsh
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0301 basic medicine ,Genotype ,Gene Dosage ,inbred strains ,Population genetics ,Mice, Inbred Strains ,Genomics ,Single-nucleotide polymorphism ,Investigations ,QH426-470 ,Biology ,Polymorphism, Single Nucleotide ,Genome ,House mouse ,Mice ,03 medical and health sciences ,Gene mapping ,Inbred strain ,Genetics ,Animals ,microarrays ,Molecular Biology ,Genotyping ,Alleles ,Phylogeny ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,2. Zero hunger ,Chromosome Mapping ,Computational Biology ,biology.organism_classification ,Genetics, Population ,030104 developmental biology ,genetic mapping - Abstract
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.
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- 2016
36. argyle: An R Package for Analysis of Illumina Genotyping Arrays
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Andrew P. Morgan
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0106 biological sciences ,0301 basic medicine ,Quality Control ,Genotype ,Genotyping Techniques ,Interoperability ,QH426-470 ,Biology ,Investigations ,Web Browser ,computer.software_genre ,Bioinformatics ,01 natural sciences ,Polymorphism, Single Nucleotide ,Bioconductor ,03 medical and health sciences ,Software ,Gene Frequency ,SNP microarrays ,Genetics ,Humans ,Use case ,Molecular Biology ,Genotyping ,Genetics (clinical) ,Alleles ,Oligonucleotide Array Sequence Analysis ,Database ,business.industry ,software ,Suite ,Computational Biology ,Reproducibility of Results ,R package ,030104 developmental biology ,genotyping ,business ,computer ,010606 plant biology & botany - Abstract
Genotyping microarrays are an important and widely-used tool in genetics. I present argyle, an R package for analysis of genotyping array data tailored to Illumina arrays. The goal of the argyle package is to provide simple, expressive tools for nonexpert users to perform quality checks and exploratory analyses of genotyping data. To these ends, the package consists of a suite of quality-control functions, normalization procedures, and utilities for visually and statistically summarizing such data. Format-conversion tools allow interoperability with popular software packages for analysis of genetic data including PLINK, R/qtl and DOQTL. Detailed vignettes demonstrating common use cases are included as supporting information. argyle bridges the gap between the low-level tasks of quality control and high-level tasks of genetic analysis. It is freely available at https://github.com/andrewparkermorgan/argyle and has been submitted to Bioconductor.
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- 2015
37. Genetic characterization of invasive house mouse populations on small islands
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Andrew P. Morgan, John P. Didion, Jonathan J. Hughes, Karl J. Campbell, Jeremy B. Searle, Wesley J. Jolley, David W. Threadgill, and Fernando Pardo-Manuel de Villena
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0106 biological sciences ,0303 health sciences ,Resistance (ecology) ,Zoology ,Context (language use) ,15. Life on land ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,House mouse ,Predation ,03 medical and health sciences ,Colonization ,Mainland ,House mice ,030304 developmental biology - Abstract
House mice (Mus musculus) have dispersed to nearly every major landmass around the globe as a result of human activity. They are a highly successful invasive species, but their presence can be devastating for native ecosystems. This is particularly true on small offshore islands where mouse populations may grow unchecked by predators. Here we use genome-wide SNP genotypes to examine ancestry and population structure on two islands of ecological interest - Southeast Farallon Island, near San Francisco, CA; and Floreana Island in the Galápagos - in the context of a total cohort of 520 mice with diverse geographic origins, as a first step towards genetically-based eradication campaigns. We show that Farallon and Floreana mice, like those from previously-studied islands in both the Atlantic and Pacific Oceans, are of admixed European ancestry. We find that these populations are on average more inbred than mainland ones and passed through a strong colonization bottleneck with little subsequent genetic exchange. Finally we show that rodenticide resistance alleles present in parts of Europe are absent from all island populations studied. Our results add nuance to previous studies of island populations based on mitochondrial sequences or small numbers of microsatellites and will be useful for future eradication and monitoring efforts.
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- 2018
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38. Informatics resources for the Collaborative Cross and related mouse populations
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Andrew P. Morgan and Catherine E. Welsh
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Genetics ,Linkage disequilibrium ,Genetic diversity ,education.field_of_study ,Genome ,Population ,Haplotype ,Genetic Variation ,Mice, Inbred Strains ,Locus (genetics) ,Biology ,Identity by descent ,Article ,Gene flow ,Mice ,Phenotype ,Haplotypes ,Databases, Genetic ,Genetic variation ,Animals ,education ,Phylogeny - Abstract
RelatednessRelatedness in the genetic sense refers to the proportion of alleles shared between two individuals. The degree to which two individuals are genetically related depends on the number of common ancestors they share and the number of generations which have elapsed since they shared them. A pedigree describes the expected relatedness between individuals: first-degree relatives (parents or siblings) share, on average, half of their alleles; second-degree relatives (grandparents) one-fourth; and so on. With dense genotype data, we can instead compute realized relatedness as the proportion of shared, unlinked alleles. Using dense genotypes, we can define relatedness both at the genome-wide and at the local scale. In the presence of admixture or introgression (see below), local relatedness in different regions of the genome may deviate from the genome-wide average. Population structure A population is “structured” when it has experienced deviations from random mating, or equivalently, when it is divided into subpopulations with restricted genetic exchange between them. In a structured population, some groups of individuals are more closely related to (share more alleles with) each other than with other groups. Geography and mating behavior generate at least some degree of structure in most natural populations. Population structure in laboratory mouse strains is widespread: for instance, the 129 and C57BL strain groups form a genetic cluster distinct from so-called “Swiss mice” including FVB/NJ, the NOD substrains, and ICR outbred stock (Beck et al. 2000). Failure to account for population structure can lead to false-positive QTL in genetic mapping of complex traits. Linkage disequilibrium (LD) Two loci are said to be in LD if the frequencies of pairwise genotypes depart from those expected if alleles were sampled randomly at each locus. LD is decreased by recombination, and therefore generally decreases with time and with physical distance between loci. Unlinked markers are expected to be in linkage equilibrium, but non-random mating can produce “long-range” LD between unlinked loci in structured populations. Haplotype block A haplotype block is a chromosomal segment in which there is no evidence for recombination during the history of a sample of individuals. Within a block, individuals in a population can be collapsed into one of a small (relative to the population size) number of ancestral haplotypes (Wall et al. 2003). LD is relatively high between loci within a block, but relatively low between loci in adjacent blocks. Although many schemes have been proposed for defining haplotype blocks, the one discussed in this review is the four-gamete test (Hudson et al. 1985). Consider two loci A and B with alleles A,a and B,b, respectively. There are four possible haploid genotypes (gametes)—AB, aB, Ab, and ab—and if all four are observed in a sample, recombination between A and B must have occurred at least once in the past. Haplotype blocks are a useful means of investigating patterns of genetic diversity at intermediate timescales since a common ancestor, such as among classical inbred strains of mice (Yang et al. 2011). But because recombination events accumulate and LD decreases with time, haplotype blocks shared between two individuals with a common ancestor far in the past—for example, a wild-derived inbred strain and a classical laboratory strain—will be very short. For this reason, haplotype blocks were not inferred for the wild mice and wild-derived strains in Yang et al. (2011). Identity by descent (IBD) A chromosomal segment is shared identical-by-descent between two individuals if it was inherited from their common ancestor without recombination. The notion of IBD is closely related to the haplotype block. Admixture Admixture refers to inter-breeding between individuals from populations which were previously genetically isolated from one another. Admixture facilitates gene flow between populations, and in the process creates heterogeneity of relatedness across the genome. IntrogressionIntrogression refers to the introduction of a chromosomal segment from one population into a separate, genetically distinct population. It is often used to describe gene flow between species or subspecies which can still form fertile hybrids. Unlike admixture, which describes ongoing inter-breeding, introgression describes events which are episodic in nature. In this review, we refer to genetic exchange between mouse subspecies, which do not interbreed in the wild except at narrow hybrid zones (Ursin 1952), as introgression. Ancestry inference Broadly speaking, an ancestry-inference procedure steps along the genome of an individual and attempts to assign each segment to one of a few ancestral clusters. These clusters may represent ancestral population groups, for samples from natural populations, or founder haplotypes in laboratory populations. Examples of ancestry inference discussed in this review include assignment of subspecific origin in wild mice (Yang et al. 2011), which labels genomic regions with one of three subspecies; and haplotype reconstruction on the CC and DO (Fu et al. 2012), which assigns genomic regions to one of those populations’ 8 founder strains. Hidden Markov model (HMM) A hidden Markov model is a probabilistic model which describes how an observed sequence can be generated from an underlying, unknown sequence of “hidden states” (Baum and Petrie 1966; Rabiner 1989). Efficient algorithms can be used to “decode” the sequence of hidden states given an observed sequence. In this review, we discuss HMMs in which the observed sequences are genotypes along a chromosome, and the hidden states are founder haplotypes.
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- 2015
39. Genomes of the Mouse Collaborative Cross
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Darla R. Miller, Vishal Kumar Sarsani, Leonard McMillan, Paola Giusti-Rodríguez, John R. Shorter, Pablo Hock, Rachel C. McMullan, Anwica Kashfeen, Gary A. Churchill, Patrick F. Sullivan, Anuj Srivastava, Fernando Pardo-Manuel de Villena, Martin T. Ferris, Andrew P. Morgan, Maya L. Najarian, Lucy H. Williams, Timothy A. Bell, and J. Sebastian Sigmon
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0301 basic medicine ,Male ,MPP ,Genotype ,Quantitative Trait Loci ,selection ,Mice, Inbred Strains ,Biology ,Investigations ,Genome ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Mice ,Inbred strain ,Genetic drift ,Multiparental Populations ,Genetics ,Animals ,Gene ,Genotyping ,Crosses, Genetic ,Whole genome sequencing ,drift ,genetic variants ,Haplotype ,Genetic Drift ,whole genome sequence ,Chromosome Mapping ,030104 developmental biology ,Haplotypes ,Mutation ,Imputation (genetics) - Abstract
The Collaborative Cross (CC) is a multiparent panel of recombinant inbred (RI) mouse strains derived from eight founder laboratory strains. RI panels are popular because of their long-term genetic stability, which enhances reproducibility and integration of data collected across time and conditions. Characterization of their genomes can be a community effort, reducing the burden on individual users. Here we present the genomes of the CC strains using two complementary approaches as a resource to improve power and interpretation of genetic experiments. Our study also provides a cautionary tale regarding the limitations imposed by such basic biological processes as mutation and selection. A distinct advantage of inbred panels is that genotyping only needs to be performed on the panel, not on each individual mouse. The initial CC genome data were haplotype reconstructions based on dense genotyping of the most recent common ancestors (MRCAs) of each strain followed by imputation from the genome sequence of the corresponding founder inbred strain. The MRCA resource captured segregating regions in strains that were not fully inbred, but it had limited resolution in the transition regions between founder haplotypes, and there was uncertainty about founder assignment in regions of limited diversity. Here we report the whole genome sequence of 69 CC strains generated by paired-end short reads at 30× coverage of a single male per strain. Sequencing leads to a substantial improvement in the fine structure and completeness of the genomes of the CC. Both MRCAs and sequenced samples show a significant reduction in the genome-wide haplotype frequencies from two wild-derived strains, CAST/EiJ and PWK/PhJ. In addition, analysis of the evolution of the patterns of heterozygosity indicates that selection against three wild-derived founder strains played a significant role in shaping the genomes of the CC. The sequencing resource provides the first description of tens of thousands of new genetic variants introduced by mutation and drift in the CC genomes. We estimate that new SNP mutations are accumulating in each CC strain at a rate of 2.4 ± 0.4 per gigabase per generation. The fixation of new mutations by genetic drift has introduced thousands of new variants into the CC strains. The majority of these mutations are novel compared to currently sequenced laboratory stocks and wild mice, and some are predicted to alter gene function. Approximately one-third of the CC inbred strains have acquired large deletions (>10 kb) many of which overlap known coding genes and functional elements. The sequence of these mice is a critical resource to CC users, increases threefold the number of mouse inbred strain genomes available publicly, and provides insight into the effect of mutation and drift on common resources.
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- 2017
40. The Collaborative Cross as a Resource for Modeling Human Disease: CC011/Unc, a New Mouse Model for Spontaneous Colitis
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Darla R. Miller, Virginia Godfrey, Terry J. Gooch, Timothy A. Bell, Fernando Pardo-Manuel de Villena, Allison R. Rogala, Alexis M. Christensen, and Andrew P. Morgan
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Genotype ,Quantitative Trait Loci ,Genome-wide association study ,Context (language use) ,Mice, Inbred Strains ,Disease ,Biology ,Quantitative trait locus ,Breeding ,Inflammatory bowel disease ,Polymerase Chain Reaction ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Genetics ,medicine ,Animals ,Humans ,Allele ,Crosses, Genetic ,030304 developmental biology ,DNA Primers ,0303 health sciences ,Chromosome Mapping ,medicine.disease ,Inflammatory Bowel Diseases ,Human genetics ,3. Good health ,Pedigree ,Mice, Inbred C57BL ,Disease Models, Animal ,Immunology ,030217 neurology & neurosurgery - Abstract
Inflammatory bowel disease (IBD) is an immune-mediated condition driven by improper responses to intestinal microflora in the context of environmental and genetic background. GWAS in humans have identified many loci associated with IBD, but animal models are valuable for dissecting the underlying molecular mechanisms, characterizing environmental and genetic contributions and developing treatments. Mouse models rely on interventions such as chemical treatment or introduction of an infectious agent to induce disease. Here, we describe a new model for IBD in which the disease develops spontaneously in 20-week-old mice in the absence of known murine pathogens. The model is part of the Collaborative Cross and came to our attention due to a high incidence of rectal prolapse in an incompletely inbred line. Necropsies revealed a profound proliferative colitis with variable degrees of ulceration and vasculitis, splenomegaly and enlarged mesenteric lymph nodes with no discernible anomalies of other organ systems. Phenotypic characterization of the CC011/Unc mice with homozygosity ranging from 94.1 to 99.8 % suggested that the trait was fixed and acted recessively in crosses to the colitis-resistant C57BL/6J inbred strain. Using a QTL approach, we identified four loci, Ccc1, Ccc2,Ccc3 and Ccc4 on chromosomes 12, 14, 1 and 8 that collectively explain 27.7 % of the phenotypic variation. Surprisingly, we also found that minute levels of residual heterozygosity in CC011/Unc have significant impact on the phenotype. This work demonstrates the utility of the CC as a source of models of human disease that arises through new combinations of alleles at susceptibility loci. Electronic supplementary material The online version of this article (doi:10.1007/s00335-013-9499-2) contains supplementary material, which is available to authorized users.
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- 2014
41. R2d2 drives selfish sweeps in the house mouse
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David W. Threadgill, Wesley J. Jolley, Maria da Graça Ramalhinho, James Holt, Amanda J. Chunco, Lydia Ortiz de Solorzano, Daniel W. Förster, Daniel Pomp, Andrew Holmes, Fernando Pardo-Manuel de Villena, Sofia A. Grize, Leonard McMillan, Sofia I. Gabriel, Mabel D. Giménez, John P. Didion, Jeremy S. Herman, Jeremy B. Searle, George M. Weinstock, Riccardo Castiglia, İslam Gündüz, Kunjie Hua, Timothy A. Bell, Karl J. Campbell, John E. French, Janice Britton-Davidian, Karen L. Svenson, Andrew P. Morgan, Elissa J. Chesler, Carol J. Bult, Maria da Luz Mathias, Daniel M. Gatti, George P. Mitsainas, James J. Crowley, Rachel C. McMullan, Pat Thomas-Laemont, Heidi C. Hauffe, Yung-Hao Ching, Meng Shin Shiao, Stephan P. Rosshart, Liran Yadgary, María José López-Fuster, Emanuela Solano, Barbara Rehermann, Gary A. Churchill, Jacint Ventura Queija, Eva B. Giagia-Athanasopoulou, Theodore Garland, Anna K. Lindholm, University of Zurich, de Villena, Fernando Pardo-Manuel, Lineberger Comprehensive Cancer Center (UNC Lineberger), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Carolina Center for Genome Sciences, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The Jackson Laboratory [Bar Harbor] (JAX), Island Conservation, University of Queensland [Brisbane], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Elon University [NC, USA], University of North Carolina System (UNC), Leibniz Institute for Zoo and Wildlife Research (IZW), Leibniz Association, National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH), Centre for Environmental and Marine Studies [Aveiro] (CESAM), Universidade de Aveiro, Universidade de Lisboa = University of Lisbon (ULISBOA), University of California [Riverside] (UC Riverside), University of California (UC), Department of Biology [Patras], University of Patras, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Universidad Nacional de Misiones, Universität Zürich [Zürich] = University of Zurich (UZH), Ondokuz Mayis University (OMU), National Institute on Alcohol Abuse and Alcoholism (NIAAA), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Department of Computer Science [Chapel Hill], Universitat de Barcelona (UB), National Institute of Diabetes and Digestive and Kidney Diseases [Bethesda], Department of Ecology and Evolutionary Biology [Ithaca], Cornell University [New York], Mahidol University [Bangkok], Texas A&M University [College Station], Universitat Autònoma de Barcelona (UAB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Universidade de Lisboa (ULISBOA), University of California [Riverside] (UCR), University of California, University of Patras [Patras], Ondokuz Mayis University, and OMÜ
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Male ,0301 basic medicine ,MESH: Selection, Genetic ,Meiotic Drive ,House Mouse ,purl.org/becyt/ford/1 [https] ,Mice ,Settore BIO/05 - ZOOLOGIA ,0302 clinical medicine ,Darwinian Fitness ,MUS MUSCULUS DOMESTICUS ,MESH: Animals ,MESH: Genetic Variation ,MESH: Models, Genetic ,Selective sweep ,MESH: Evolution, Molecular ,2. Zero hunger ,Genetics ,Selfish Genes ,education.field_of_study ,Nuclear Proteins ,RNA-Binding Proteins ,Meiotic drive ,Adaptation, Physiological ,Biological Evolution ,Fixation (population genetics) ,Fast Track ,590 Animals (Zoology) ,Female ,MESH: DNA Copy Number Variations ,CIENCIAS NATURALES Y EXACTAS ,Selective Sweep ,Selfish genes ,MESH: Mutation ,DNA Copy Number Variations ,Otras Ciencias Biológicas ,Population ,MESH: Genetics, Population ,MESH: Biological Evolution ,Biology ,R2d2 ,Evolution, Molecular ,Ciencias Biológicas ,03 medical and health sciences ,10127 Institute of Evolutionary Biology and Environmental Studies ,Genetic drift ,1311 Genetics ,Genetic variation ,1312 Molecular Biology ,Animals ,Selection, Genetic ,purl.org/becyt/ford/1.6 [https] ,education ,Molecular Biology ,MESH: Mice ,Alleles ,Ecology, Evolution, Behavior and Systematics ,Repetitive Sequences, Nucleic Acid ,MESH: Repetitive Sequences, Nucleic Acid ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Models, Genetic ,MESH: Alleles ,Genetic Variation ,MESH: Adaptation, Physiological ,MESH: Male ,House mouse ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Genetics, Population ,030104 developmental biology ,MESH: RNA-Binding Proteins ,1105 Ecology, Evolution, Behavior and Systematics ,Mutation ,570 Life sciences ,biology ,MESH: Nuclear Proteins ,MESH: Female ,030217 neurology & neurosurgery - Abstract
Mitsainas, George/0000-0003-4976-8275; Lindholm, Anna K/0000-0001-8460-9769; Mathias, Maria da Luz/0000-0003-3876-958X; Foerster, Daniel/0000-0002-6934-0404; Hauffe, Heidi Christine C/0000-0003-3098-8964; Threadgill, David W/0000-0003-3538-1635; Gabriel, Sofia I/0000-0003-3702-4631; Chesler, Elissa/0000-0002-5642-5062; Didion, John/0000-0002-8111-6261; solano, emanuela/0000-0001-8482-9243; Weinstock, George/0000-0002-2997-4592; McMullan, Rachel/0000-0003-0297-4549; Holt, James/0000-0001-6411-9236; Rehermann, Barbara/0000-0001-6832-9951 WOS: 000376170300001 PubMed: 26882987 A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether "selfish" genes are capable of fixation-thereby leaving signatures identical to classical selective sweeps-despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes nonrandom segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2(HC)) in natural populations. We replicate this finding inmultiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2(HC) rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2(HC) is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution. National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [T32GM067553, F30MH103925, P50GM076468, K01MH094406, DK-076050, DK-056350, AG038070]; National Science FoundationNational Science Foundation (NSF) [IOS-1121273]; Vaadia-BARD Postdoctoral Fellowship AwardUS-Israel Binational Science Foundation [FI-478-13]; U.S. Army Medical Research and Materiel CommandU.S. Army Medical Research & Materiel Command (USAMRMC) [W81XWH-11-1-0762]; Jackson Laboratory new investigator funds; National Center for Scientific Research, France [ISEM 2016-002]; University of Rome "La Sapienza"; Claraz-Stiftung; Natural Environment Research Council (UK)NERC Natural Environment Research Council; EU Human Capital and Mobility Programme [CHRX-CT93-0192]; Foundation for Science and Technology, PortugalPortuguese Foundation for Science and Technology [PTDC/BIA-EVF/116884/2010, UID/AMB/50017/2013]; Spanish "Ministerio de Ciencia y Tecnologia"Spanish Government [CGL2007-62111]; "Ministerio de Economia y Competitividad"Spanish Government [CGL2010-15243]; School of Medicine at University of North Carolina We wish to thank all the scientists and research personnel who collected and processed the samples used in this study. In particular we acknowledge Luanne Peters and Alex Hong-Tsen Yu for providing critical samples; Ryan Buus and T. Justin Gooch for isolating DNA for high-density genotyping of wild-caught mice; and Vicki Cappa, A. Cerveira, Guila Ganem, Ron and Annabelle Lesher, K. Said, Toni Schelts, Dan Small, and J. Tapisso for aiding in mouse trapping. We thank Muriel Davisson at the Jackson Laboratory for maintaining, for several decades, tissue samples from breeding colonies used to generate wild-derived inbred strains. We also thank Francis Collins, Jim Evans, Matthew Hahn, and Corbin Jones for comments on an earlier version of this manuscript. This work was supported by the National Institutes of Health T32GM067553 to J.P.D. and A.P.M., F30MH103925 to A.P.M., P50GM076468 to E.J.C., G.A.C., and F.P.M.V., K01MH094406 to J.J.C., DK-076050 and DK-056350 to D.P., AG038070 to G.A.C, and the intramural research program to B.R. and S.P.R.; National Science Foundation IOS-1121273 to T.G.; Vaadia-BARD Postdoctoral Fellowship Award FI-478-13 to L.Y.; U.S. Army Medical Research and Materiel Command W81XWH-11-1-0762 to C.J.B.; The Jackson Laboratory new investigator funds to E.J.C.; The National Center for Scientific Research, France to J.B.D. (this is contribution no ISEM 2016-002); the University of Rome "La Sapienza" to R.C. and E.S.; Claraz-Stiftung to S.G. and A.L.; Natural Environment Research Council (UK) to M.D.G., H.C.H., and J.B.S.; EU Human Capital and Mobility Programme (CHRX-CT93-0192) to H.C.H. and J.B.S.; Foundation for Science and Technology, Portugal PTDC/BIA-EVF/116884/2010 and UID/AMB/50017/2013 to S.I.G., M.L.M., and J.B.S.; Spanish "Ministerio de Ciencia y Tecnologia" CGL2007-62111 and "Ministerio de Economia y Competitividad" CGL2010-15243 to J.V.;and the Oliver Smithies Investigator funds provided by the School of Medicine at University of North Carolina to F.P.M.V. All data are made available at http://csbio.unc.edu/r2d2/. The authors declare no competing financial interests. Correspondence and requests for materials should be addressed to F.P.M.V. (fernando@med.unc.edu).
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- 2016
42. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance
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Kazuyo Takeda, Stephan P. Rosshart, Davide Angeletti, Andrew P. Morgan, Nadim J. Ajami, Diane S. Hutchinson, Brian G. Vassallo, Heather D. Hickman, Barbara Rehermann, Giorgio Trinchieri, John A. McCulloch, Fernando Pardo-Manuel de Villena, Jonathan H. Badger, and Jonathan W. Yewdell
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Male ,0301 basic medicine ,Carcinogenesis ,Animals, Wild ,Inflammation ,Gut flora ,Plant disease resistance ,Article ,General Biochemistry, Genetics and Molecular Biology ,Virus ,Microbiology ,Mice ,03 medical and health sciences ,Peromyscus ,0302 clinical medicine ,Animals, Laboratory ,medicine ,Animals ,Microbiome ,Physiological Phenomenon ,Disease Resistance ,Maryland ,biology ,Host (biology) ,Laboratory mouse ,biology.organism_classification ,Gastrointestinal Microbiome ,Mice, Inbred C57BL ,030104 developmental biology ,Virus Diseases ,030220 oncology & carcinogenesis ,Female ,medicine.symptom - Abstract
Summary Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. Video Abstract
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- 2017
43. R2d2 drives selfish sweeps in the house mouse
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George M. Weinstock, Amanda J. Chunco, Lydia Ortiz de Solorzano, Meng-Shin Shiao, Sofia I. Gabriel, Daniel Pomp, David W. Threadgill, Riccardo Castiglia, Mabel D. Giménez, Stephan P. Rosshart, Wesley J. Jolley, John P. Didion, Heidi C. Hauffe, Fernando Pardo-Manuel de Villena, John E. French, Jeremy B. Searle, İslam Gündüz, Eva B. Giagia-Athanasopoulou, Emanuela Solano, Yung-Hao Ching, Kunji Hua, María J López-Fuster, Janice Britton-Davidian, Karen L. Svenson, Theodore Garland, Carol J. Bult, M Graça Ramalhinho, Andrew P. Morgan, Anna K. Lindholm, James J. Crowley, James Holt, Liran Yadgary, Barbara Rehermann, Pat Thomas-Laemont, Gary A. Churchill, Timothy A. Bell, Karl J. Campbell, Jacint Ventura Queija, Leonard McMillan, Daniel M. Gatti, Maria da Luz Mathias, George P. Mitsainas, Sofia A. Grize, Andrew Holmes, Rachel C. McMullan, Elissa J. Chesler, and Jeremy S. Herman
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0106 biological sciences ,0303 health sciences ,education.field_of_study ,Selfish Genes ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Fixation (population genetics) ,Meiotic drive ,Genetic drift ,Evolutionary biology ,Darwinian Fitness ,Allele ,education ,Selective sweep ,030304 developmental biology - Abstract
A selective sweep is the result of strong positive selection rapidly driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population or species. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little empirical evidence addresses whether "selfish" genes are capable of fixation -- thereby leaving signatures identical to classical selective sweeps -- despite being neutral or deleterious to organismal fitness. We previously reported the discovery of R2d2, a large copy-number variant that causes non-random segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a "selfish" sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations of mice. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygosity, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.
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- 2015
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44. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
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KyungSu Kim, Chen Ping Fu, John P. Didion, Leonard McMillan, Corey R. Quackenbush, James Holt, Yunjung Kim, William Valdar, Mark Calaway, Fernando Pardo-Manuel de Villena, Timothy A. Bell, Lisa M. Tarantino, Yuying Xie, Ginger D. Shaw, Cordelia J. Barrick, Darla R. Miller, Alan B. Lenarcic, James J. Crowley, Terry J. Gooch, Jeremy Wang, Vasyl Zhabotynsky, Zhishan Guo, Zhaojun Zhang, John D. Calaway, Patrick F. Sullivan, Wei Wang, Stephanie D. Hansen, Shunping Huang, Zaining Yun, David W. Threadgill, Wei Sun, Fei Zou, Jason S. Spence, James G. Xenakis, Randal J. Nonneman, Ryan J. Buus, David L. Aylor, Andrew P. Morgan, Nashiya N. Robinson, Isa Kemal Pakatci, and Catherine E. Welsh
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Male ,Genetic Speciation ,1.1 Normal biological development and functioning ,Knockout ,Gene Expression ,Single-nucleotide polymorphism ,Biology ,Crosses ,Allelic Imbalance ,eQTL ,Polymorphism, Single Nucleotide ,Medical and Health Sciences ,Article ,Mice ,Genetic ,Phylogenetics ,Dosage Compensation, Genetic ,Genetics ,Animals ,Humans ,Imprinting (psychology) ,Allele ,Polymorphism ,Gene ,Crosses, Genetic ,mouse ,Phylogeny ,Alleles ,Mice, Knockout ,Dosage compensation ,Human Genome ,Single Nucleotide ,Biological Sciences ,allelic imbalance ,Expression quantitative trait loci ,dosage compensation ,Dosage Compensation ,Female ,Generic health relevance ,imprinting ,Biotechnology ,Developmental Biology - Abstract
Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.
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- 2015
45. The 28th International Mammalian Genome Conference--meeting report
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Linda D. Siracusa, Andrew P. Morgan, and William T. Barrington
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Aging ,Population ,Library science ,Biology ,Mouse Genome Informatics ,Article ,International Knockout Mouse Consortium ,Evolution, Molecular ,03 medical and health sciences ,Annotation ,Mice ,0302 clinical medicine ,Chapel ,Genetics ,Animals ,education ,Summer vacation ,030304 developmental biology ,computer.programming_language ,Mammals ,0303 health sciences ,education.field_of_study ,Genome ,GENCODE ,Home page ,Stem Cells ,Computational Biology ,Genomics ,Congresses as Topic ,Disease Models, Animal ,Genetics, Population ,030220 oncology & carcinogenesis ,computer - Abstract
The 28th International Mammalian Genome Conference (IMGC) was held October 26–29th, 2014 in scenic Bar Harbor, Maine. In addition to being the home of The Jackson Laboratory, Mount Desert Island is a popular summer vacation destination. More than 200 attendees of the conference enjoyed the last few days of the tourist season as the autumn leaves fell and the local residents prepared for winter. Darla Miller and Dasha Li Kappe organized the meeting, with the help of local organizers Ron Korstanje, Karen Svenson, Erin McDevitt, and Nancy Place. Scientists presented cutting-edge research in the fields of mammalian genetics and genomics that highlighted the importance of mammalian models for human genetics and disease research. The plenary presentations demonstrated the broad applicability of mammalian models to study a range of topics from gene evolution to rare human diseases. Meanwhile, the Verne Chapman lecture provided a historical account of mouse genetics research and encouraged a new, automated approach to forward genetics. Bioinformatics and Systems Genetics Workshops gave participants hands-on opportunities to become familiar with genetic and genomic tools. A student satellite symposium afforded budding scientists the chance to share their work and two poster sessions encouraged interaction among researchers. The meeting program and abstracts are available online at www.imgs.org/Archive/abstracts/2014Abstracts/IMGS2014Program.pdfwww.imgs.org. Online resources presented at the meeting are listed in Table 1. Table 1 Databases, resources, and tools Bioinformatics workshops Several workshops provided conference attendees with opportunities for hands-on guided tours of publicly available informatics resources relevant to IMGS members. The pre-conference Bioinformatics Workshop offered three mini-sessions: (1) a guide to genome annotations produced by the GENCODE consortium, and differences between annotation sets provided by popular databases (Laurens Wilming, Wellcome Trust Sanger Institute); (2) an overview of the International Knockout Mouse Consortium's pipeline and progress (Mark Thomas, Wellcome Trust Sanger Institute); and (3) a tour of the International Mouse Phenotyping Consortium's database of mutant mouse phenotypes (www.mousephenotype.org). An online link to these workshop powerpoint presentations can be found under the “History” tab on the IMGS home page (www.imgs.org). The System Genetics Workshops, led by Dan Gatti (The Jackson Laboratory), Marty Ferris (University of North Carolina at Chapel Hill), Gary Churchill (The Jackson Laboratory) along with Andrew Morgan and Fernando Pardo-Manuel de Villena (University of North Carolina at Chapel Hill) featured talks on the design and status of two important multiparental genetic reference populations, the Collaborative Cross (CC) and the Diversity Outbred (DO) mice. Didactic sessions were supplemented with small-group discussions on rational experimental designs using these populations and available online tools for analyses (www.csbio.unc.edu/CCstatus/index.py) were described by Leonard McMillan, Chen-Ping Fu, and Chia-yu Kao (University of North Carolina at Chapel Hill). This year's Mouse Genome Informatics(MGI) Workshops (www.informatics.jax.org) were led by Joanne Berghout and David Shaw (The Jackson Laboratory). The hands-on workshops included seminar-style demonstrations followed by the opportunity to navigate MGI using self-guided exercises. Participants were instructed on how to locate biological information by performing a variety of searches, and were also introduced to new tools such as the Human-Mouse: Disease Connection portal (www.informatics.jax.org/humanDisease.shtml), the Recombinase (Cre) Activity portal (www.informatics.jax.org/recombinase.shtml), and the MouseMine computational access platform (www.mousemine.org/mousemine/begin.do). In celebration of the 25th birthday of the MGI database, Janan Eppig (The Jackson Laboratory; O-30) tracked the history of the MGI from a pre-web version distributed on floppy disks to the MGI website (www.informatics.jax.org) that we know today. Janan emphasized the continued commitment of MGI to provide integrated genetic, genomic, and biological data for mouse and to provide increased access to translational data views to support discovery and hypothesis building for studies of human disease. Janan also recognized the contributions of many individuals who worked to develop MGI over the years and described future plans as MGI evolves to meet the growing needs of the scientific community.
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- 2015
46. A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2
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David L. Aylor, John P. Didion, Petko M. Petkov, Timothy A. Bell, Karen L. Svenson, Fernando Pardo-Manuel de Villena, Elissa J. Chesler, Kent W. Hunter, Matt Holt, Petr Simecek, Darla R. Miller, Lucy B. Rowe, Rachel C. McMullan, Ginger D. Shaw, Alison H. Harrill, Daniel Pomp, Kenneth Paigen, David W. Threadgill, Patrick F. Sullivan, Mark Calaway, John E. French, George M. Weinstock, Amelia M.-F. Clayshulte, Andrew P. Morgan, Theodore Garland, Leonard McMillan, Terry J. Gooch, Kunjie Hua, Thomas R. Geiger, James J. Crowley, Daniel M. Gatti, Gary A. Churchill, Ling Bai, Wenqi Pan, Liran Yadgary, and Deborah A. O'Brien
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Male ,Cancer Research ,DNA Copy Number Variations ,Genotyping Techniques ,lcsh:QH426-470 ,Inheritance Patterns ,Biology ,Chromosomes ,03 medical and health sciences ,symbols.namesake ,Mice ,0302 clinical medicine ,Inbred strain ,Genetics ,Animals ,Allele ,Molecular Biology ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Alleles ,Crosses, Genetic ,030304 developmental biology ,0303 health sciences ,Haplotype ,Chromosome ,Genomics ,Meiosis ,lcsh:Genetics ,Meiotic drive ,Haplotypes ,Mutation (genetic algorithm) ,Mutation ,Mendelian inheritance ,symbols ,Female ,030217 neurology & neurosurgery ,Research Article - Abstract
Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 – 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system., Author Summary One of the strongest expectations in genetics is that chromosomes segregate randomly during meiosis. However, genetic loci that exhibit transmission ratio distortion (TRD) are sometimes observed in offspring of F1 hybrids. Meiotic drive is a type of non-Mendelian inheritance in which a “selfish” genetic element exploits asymmetric female meiotic cell division to promote its preferential inclusion in ova. We previously reported TRD on Chr 2 in the CC, a mouse recombinant inbred panel with contributions from three Mus musculus subspecies. Here we show that maternal TRD consistent with a novel meiotic drive system is caused by a copy number gain. This mutation is similar in size and structure to other known meiotic drive responders, such as the knobs of maize. A deletion of most of the copies is sufficient to restore Mendelian segregation, proving that the copy number variant is causative of the observed TRD. In the CC, and also the related DO population, the transmission frequency of the favored allele varies dependent on genetic background, demonstrating that this system is under genetic control. In conclusion, we describe a novel wild-derived meiotic drive locus on mouse Chr 2 that exploits female meiosis asymmetry to violate the Laws of Mendelian inheritance.
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- 2015
47. Genetic architecture of atherosclerosis dissected by QTL analyses in three F2 intercrosses of apolipoprotein E-null mice on C57BL6/J, DBA/2J and 129S6/SvEvTac backgrounds
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Svetlana Zhilicheva, Sylvia Hiller, Yukako Kayashima, Andrei Makhanov, Andrew P. Morgan, Longquan Xu, Natalia Makhanova, Nobuyo Maeda, and Fernando Pardo-Manuel de Villena
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0301 basic medicine ,Apolipoprotein E ,Heredity ,Apolipoprotein B ,030105 genetics & heredity ,Vascular Medicine ,Mice ,Mathematical and Statistical Techniques ,Medicine and Health Sciences ,Aorta ,Genetics ,Mammalian Genomics ,Multidisciplinary ,Chromosome Mapping ,Genomics ,Lipids ,Phenotype ,Plaque, Atherosclerotic ,Genetic Mapping ,Mice, Inbred DBA ,Physical Sciences ,Medicine ,Statistics (Mathematics) ,Research Article ,Permutation ,Science ,Transgene ,Quantitative Trait Loci ,Mice, Transgenic ,Variant Genotypes ,Locus (genetics) ,Quantitative trait locus ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,Apolipoproteins E ,Animals ,Statistical Methods ,Crosses, Genetic ,Alleles ,Analysis of Variance ,Discrete Mathematics ,Biology and Life Sciences ,Atherosclerosis ,Genetic architecture ,Mice, Inbred C57BL ,030104 developmental biology ,Genetic Loci ,Combinatorics ,Animal Genomics ,biology.protein ,Epistasis ,Mathematics - Abstract
Quantitative trait locus (QTL) analyses of intercross populations between widely used mouse inbred strains provide a powerful approach for uncovering genetic factors that influence susceptibility to atherosclerosis. Epistatic interactions are common in complex phenotypes and depend on genetic backgrounds. To dissect genetic architecture of atherosclerosis, we analyzed F2 progeny from a cross between apolipoprotein E-null mice on DBA/2J (DBA-apoE) and C57BL/6J (B6-apoE) genetic backgrounds and compared the results with those from two previous F2 crosses of apolipoprotein E-null mice on 129S6/SvEvTac (129-apoE) and DBA-apoE backgrounds, and B6-apoE and 129-apoE backgrounds. In these round-robin crosses, in which each parental strain was crossed with two others, large-effect QTLs are expected to be detectable at least in two crosses. On the other hand, observation of QTLs in one cross only may indicate epistasis and/or absence of statistical power. For atherosclerosis at the aortic arch, Aath4 on chromosome (Chr)2:66 cM follows the first pattern, with significant QTL peaks in (DBAx129)F2 and (B6xDBA)F2 mice but not in (B6x129)F2 mice. We conclude that genetic variants unique to DBA/2J at Aath4 confer susceptibility to atherosclerosis at the aortic arch. A similar pattern was observed for Aath5 on chr10:35 cM, verifying that the variants unique to DBA/2J at this locus protect against arch plaque development. However, multiple loci, including Aath1 (Chr1:49 cM), and Aath2 (Chr1:70 cM) follow the second type of pattern, showing significant peaks in only one of the three crosses (B6-apoE x 129-apoE). As for atherosclerosis at aortic root, the majority of QTLs, including Ath29 (Chr9:33 cM), Ath44 (Chr1:68 cM) and Ath45 (Chr2:83 cM), was also inconsistent, being significant in only one of the three crosses. Only the QTL on Chr7:37 cM was consistently suggestive in two of the three crosses. Thus QTL analysis of round-robin crosses revealed the genetic architecture of atherosclerosis.
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- 2017
48. Wild mouse gut microbiome protects laboratory mice against lethal influenza virus infection and colorectal cancer
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Stephan Patrick Rosshart, Brian G. Vassallo, Davide Angeletti, Diane S. Hutchinson, Andrew P. Morgan, Kazuyo Takeda, Heather D. Hickman, Nadim J. Ajami, Fernando Pardo-Manuel de Villena, Jonathan W. Yewdell, and Barbara Rehermann
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Immunology ,Immunology and Allergy - Abstract
Mouse models are paramount for understanding basic immunological mechanisms, but can be limited in recapitulating human diseases. The microbiome has been identified as a main factor influencing host physiology as illustrated by many studies that disrupt or modify host-microbe interactions in laboratory mice. Differences in the gut microbiome contribute to the variability of research results obtained with genetically identical animals from different vendors. In an effort to identify an external reference that better recapitulates physiologically important interactions found in a natural habitat, we asked how far removed the gut microbiome of laboratory mice is from that of their outbred, wild-living relative. Through genetic analysis we identify the closest wild relatives to classical laboratory strains among 21 distinct populations from Europe, Asia and the Americas. We establish that their gut microbiome differs significantly from that of C57BL/6 mice from the leading breeders worldwide, and that it can be transferred and maintained over several generations under vivarium conditions. Offspring of pregnant germ-free C57BL/6 mice reconstituted with the gut microbiome of wild mice exhibit a significantly reduced inflammatory response and increased survival following influenza A virus infection. This restoration of the natural ‘microbial identity’ of laboratory mice also improved their resistance against mutagen- and inflammation-induced colorectal cancer. Collectively, these data show the beneficial effects of the wild mouse microbiome in two diseases of global relevance. They also illustrate a novel approach towards developing animal models of greater biological relevance and translational research value.
- Published
- 2017
49. High-resolution sex-specific linkage maps of the mouse reveal polarized distribution of crossovers in male germline
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Elissa J. Chesler, Wei Wang, Andrew P. Morgan, Fernando Pardo-Manuel de Villena, Eric Yi Liu, and Gary A. Churchill
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Male ,Genotyping Techniques ,cold regions ,1.1 Normal biological development and functioning ,sex effects ,mouse CC ,Biology ,Investigations ,Genetic recombination ,Chromosomal crossover ,Genome Integrity and Transmission ,Mice ,Species Specificity ,Genetic ,Genetic linkage ,Crossing Over ,Genetics ,Animals ,Copy-number variation ,Crossing Over, Genetic ,X chromosome ,Segmental duplication ,Sex Characteristics ,Autosome ,Siblings ,Contraception/Reproduction ,Human Genome ,Chromosome ,Chromosome Mapping ,Genomics ,Spermatozoa ,linkage map ,recombination ,Pedigree ,Female ,Generic health relevance ,Biotechnology ,Developmental Biology - Abstract
Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these “cold regions” are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants.
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- 2014
50. The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse
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Cheryl N. Miller, R. Balfour Sartor, Allison Ryan, Sur Herrera Paredes, Thomas H. Kawula, Maureen A. Bower, James J. Crowley, Randal J. Nonneman, Andrew P. Morgan, Corey R. Quackenbush, Patrick F. Sullivan, Molly A. Bogue, Scott Yourstone, and Ian M. Carroll
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Olanzapine ,Molecular biology ,Psychopharmacology ,medicine.medical_treatment ,Inbred Strains ,lcsh:Medicine ,Gut flora ,Pharmacology ,Weight Gain ,Benzodiazepines ,Mice ,Sequencing techniques ,Mathematical and Statistical Techniques ,Medicine and Health Sciences ,DNA sequencing ,lcsh:Science ,Multidisciplinary ,biology ,Ecology ,Gastrointestinal Microbiome ,Animal Models ,Antimicrobial ,3. Good health ,Female ,medicine.symptom ,Transcriptome Analysis ,medicine.drug ,Antipsychotic Agents ,Research Article ,Next-Generation Sequencing ,medicine.medical_specialty ,Mouse Models ,Research and Analysis Methods ,Microbiology ,Microbial Ecology ,Multivariate Data Analysis ,Model Organisms ,Internal medicine ,Mental Health and Psychiatry ,medicine ,Animals ,Microbiome ,Antipsychotic ,Biology and life sciences ,lcsh:R ,Computational Biology ,biology.organism_classification ,Genome Analysis ,Commensalism ,Species Interactions ,Endocrinology ,Molecular biology techniques ,lcsh:Q ,Weight gain ,Drug metabolism - Abstract
The second-generation antipsychotic olanzapine is effective in reducing psychotic symptoms but can cause extreme weight gain in human patients. We investigated the role of the gut microbiota in this adverse drug effect using a mouse model. First, we used germ-free C57BL/6J mice to demonstrate that gut bacteria are necessary and sufficient for weight gain caused by oral delivery of olanzapine. Second, we surveyed fecal microbiota before, during, and after treatment and found that olanzapine potentiated a shift towards an “obesogenic” bacterial profile. Finally, we demonstrated that olanzapine has antimicrobial activity in vitro against resident enteric bacterial strains. These results collectively provide strong evidence for a mechanism underlying olanzapine-induced weight gain in mouse and a hypothesis for clinical translation in human patients.
- Published
- 2014
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