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Structural Forms of the Human Amylase Locus and Their Relationships to Snps, Haplotypes, and Obesity
Structural Forms of the Human Amylase Locus and Their Relationships to SNPs, Haplotypes, and Obesity The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Usher, Christina Leigh. 2015. Structural Forms of the Human Amylase Locus and Their Relationships to SNPs, Haplotypes, and Obesity. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467224 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Structural forms of the human amylase locus and their relationships to SNPs, haplotypes, and obesity A dissertation presented by Christina Leigh Usher to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Genetics and Genomics Harvard University Cambridge, Massachusetts March 2015 © 2015 Christina Leigh Usher All rights reserved. Dissertation Advisor: Professor Steven McCarroll Christina Leigh Usher Structural forms of the human amylase locus and their relationships to SNPs, haplotypes, and obesity Abstract Hundreds of human genes reside in structurally complex loci that elude molecular analysis and assessment in genome-wide association studies (GWAS). One such locus contains the three different amylase genes (AMY2B, AMY2A, and AMY1) responsible for digesting starch into sugar. The copy number of AMY1 is reported to be the genome’s largest influence on obesity, yet has gone undetected in GWAS. -
Chromosome 1 (Human Genome/Inkae) A
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 4598-4602, May 1992 Medical Sciences Integration of gene maps: Chromosome 1 (human genome/inkae) A. COLLINS*, B. J. KEATSt, N. DRACOPOLIt, D. C. SHIELDS*, AND N. E. MORTON* *CRC Research Group in Genetic Epidemiology, Department of Child Health, University of Southampton, Southampton, S09 4XY, United Kingdom; tDepartment of Biometry and Genetics, Louisiana State University Center, 1901 Perdido Street, New Orleans, LA 70112; and tCenter for Cancer Research, Massachusetts Institute of Technology, 40 Ames Street, Cambridge, MA 02139 Contributed by N. E. Morton, February 10, 1992 ABSTRACT A composite map of 177 locI has been con- standard lod tables extracted from the literature. Multiple structed in two steps. The first combined pairwise logarithm- pairwise analysis of these data was performed by the MAP90 of-odds scores on 127 loci Into a comprehensive genetic map. computer program (6), which can estimate an errorfrequency Then this map was projected onto the physical map through e (7) and a mapping parameter p such that map distance w is cytogenetic assignments, and the small amount ofphysical data a function of 0, e and p (8). It also includes a bootstrap to was interpolated for an additional 50 loci each of which had optimize order and a stepwise elimination of weakly sup- been assigned to an interval of less than 10 megabases. The ported loci to identify a conservative set of reliably ordered resulting composite map is on the physical scale with a reso- (framework) markers. The genetic map was combined with lution of 1.5 megabases. -
Using Hominin Introgression to Trace Modern Human Dispersals PERSPECTIVE Jo~Ao C
PERSPECTIVE Using hominin introgression to trace modern human dispersals PERSPECTIVE Jo~ao C. Teixeiraa,1 and Alan Coopera,1 Edited by James F. O’Connell, University of Utah, Salt Lake City, UT, and approved June 17, 2019 (received for review March 26, 2019) The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic. human evolution | archaic introgression | anthropology | genetics As anatomically modern humans (AMHs) migrated out western Siberia (3, 4). Fig. 1 depicts these events, of Africa and around the rest of the world, they met and infers the migration routes of AMHs by following and interbred with multiple extinct hominin species savannah-like habitats predicted in paleoenvironmental (1). -
Characterization of Genomic Copy Number Variation in Mus Musculus Associated with the Germline of Inbred and Wild Mouse Populations, Normal Development, and Cancer
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 4-18-2019 2:00 PM Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer Maja Milojevic The University of Western Ontario Supervisor Hill, Kathleen A. The University of Western Ontario Graduate Program in Biology A thesis submitted in partial fulfillment of the equirr ements for the degree in Doctor of Philosophy © Maja Milojevic 2019 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Genetics and Genomics Commons Recommended Citation Milojevic, Maja, "Characterization of genomic copy number variation in Mus musculus associated with the germline of inbred and wild mouse populations, normal development, and cancer" (2019). Electronic Thesis and Dissertation Repository. 6146. https://ir.lib.uwo.ca/etd/6146 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract Mus musculus is a human commensal species and an important model of human development and disease with a need for approaches to determine the contribution of copy number variants (CNVs) to genetic variation in laboratory and wild mice, and arising with normal mouse development and disease. Here, the Mouse Diversity Genotyping array (MDGA)-approach to CNV detection is developed to characterize CNV differences between laboratory and wild mice, between multiple normal tissues of the same mouse, and between primary mammary gland tumours and metastatic lung tissue. -
The Wily and Courageous Red Fox: Behavioural Analysis of a Mesopredator at Resource Points Shared by an Apex Predator
animals Article The Wily and Courageous Red Fox: Behavioural Analysis of a Mesopredator at Resource Points Shared by an Apex Predator Eamonn Wooster *, Arian D. Wallach and Daniel Ramp Centre for Compassionate Conservation, University of Technology Sydney, P.O. Box 123, Ultimo, New South Wales 2007, Australia; [email protected] (A.D.W.); [email protected] (D.R.) * Correspondence: [email protected] Received: 21 September 2019; Accepted: 31 October 2019; Published: 4 November 2019 Simple Summary: The red fox is one of the Earth’s most widespread mammalian predators. Human globalisation has further expanded its range, so that today they are found on most continents. Despite their abundance, knowledge of fox behaviour remains limited. Most studies have observed foxes either in captivity or in their native range where both they and their predators are killed by humans. We conducted a behavioural study on foxes outside of their native range in Australia, at a unique location where all wildlife are protected. We developed an ethogram to explore fox behaviour at resource points shared with a potentially deadly apex predator, the dingo. We were surprised to find that foxes were in a confident state more often than in a cautious state, even leaving territorial markings over those of dingoes. One possible explanation for the confidence of foxes is that the social stability of both foxes and dingoes makes their world more predictable. Abstract: The red fox (Vulpes vulpes) is a widespread and ecologically significant terrestrial mesopredator, that has expanded its range with human globalisation. Despite this, we know relatively little about their behaviour under the wide range of ecological conditions they experience, particularly how they navigate the risk of encounters with apex predators. -
Maize Nested Introgression Library Provides Evidence for the Involvement of 2 Liguleless1 in Resistance to Northern Leaf Blight 3
bioRxiv preprint doi: https://doi.org/10.1101/818518; this version posted October 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Maize nested introgression library provides evidence for the involvement of 2 liguleless1 in resistance to northern leaf blight 3 4 Judith M. Kolkmana, Josh Strableb, Kate Harlineb, Dallas E. Kroonc,1, Tyr Wiesner-Hanksd,2, 5 Peter J. Bradburyc, and Rebecca J. Nelsona,d 6 a School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, 7 NY 14853, USA. 8 b School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY 14853, USA. 9 c US Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853, USA 10 d School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, 11 USA. 12 1 Present address: DuPont de Nemours, Inc., Experimental Station, 200 Powder Mill Road, Wilmington, DE 19083, 13 USA 14 2 Present address: PepsiCo, 4295 Tenderfoot Rd., Rhinelander WI, 54501, USA 15 3 To whom correspondence should be addressed. Email: [email protected] 16 Keywords 17 Zea mays, Setosphaeria turcica, near-isogenic lines, liguleless1 18 Author contributions: 19 J.M.K., R.J.N., and J.S. designed research 20 J.M.K. performed research 21 J.M.K., P.B., J.S., D.K., K.H., and T.W-H. contributed new reagents/analytic tools 22 J.M.K., K.H., D.K. analyzed data 23 JMK, RJN wrote the paper 24 1 bioRxiv preprint doi: https://doi.org/10.1101/818518; this version posted October 24, 2019. -
Dingo [Western Australia]
Farmnote 133/2000 : Dingo [Western Australia] Dingo Farmnote 133/2000 By Peter Thomson, Vertebrate Pest Research Section, Forrestfield The dingo or wild dog (Canis familiaris dingo) is found across most of Western Australia. It is subject to management programs in grazing areas because of its predation of livestock. Name 'Dingo' was the name recorded in the early days of European settlement in New South Wales for the 'dogs' belonging to the local Aborigines. 'Warrigal' is one of the central Australian Aboriginal names for the dingo. Although the dingo was classified in the same species as the domestic dog (Canis familiaris), it was probably never exposed to the processes of artificial selection that eventually produced the modern domestic dog. A suggested change in scientific name to Canis lupus dingo reflects the origin of dingoes from wolves (Canis lupus) and the separation of dingoes from domestic dogs. Farmnote 133/2000 : Dingo [Western Australia] Origin The dingo is a primitive dog that evolved from the Indian or Pallid wolf and became widespread throughout southern Asia between 6000 and 10,000 years ago. It is now believed that dingoes were introduced into Australia about 4000 years ago by Asian seafarers, rather than during an Aboriginal migration. Description Dingoes are anatomically very similar to domestic dogs with which they are able to interbreed. They are usually sandy red or ginger in colour, with white feet and a white tail tip. White dingoes and black and tan individuals are also found. Patchy colouration or brindling is a sign of hybridisation with domestic dogs. Occurrence Dingoes are found through much of the state. -
Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School July 2017 Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Pathology Commons Scholar Commons Citation Mohamed, Mai, "Role of Amylase in Ovarian Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6907 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Role of Amylase in Ovarian Cancer by Mai Mohamed A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida Major Professor: Patricia Kruk, Ph.D. Paula C. Bickford, Ph.D. Meera Nanjundan, Ph.D. Marzenna Wiranowska, Ph.D. Lauri Wright, Ph.D. Date of Approval: June 29, 2017 Keywords: ovarian cancer, amylase, computational analyses, glycocalyx, cellular invasion Copyright © 2017, Mai Mohamed Dedication This dissertation is dedicated to my parents, Ahmed and Fatma, who have always stressed the importance of education, and, throughout my education, have been my strongest source of encouragement and support. They always believed in me and I am eternally grateful to them. I would also like to thank my brothers, Mohamed and Hussien, and my sister, Mariam. I would also like to thank my husband, Ahmed. -
Title: the Genomic Consequences of Hybridization Authors
Title: The genomic consequences of hybridization Authors: Benjamin M Moran1,2*+, Cheyenne Payne1,2*+, Quinn Langdon1, Daniel L Powell1,2, Yaniv Brandvain3, Molly Schumer1,2,4+ Affiliations: 1Department of Biology, Stanford University, Stanford, CA, USA 2Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, Mexico 3Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA 4Hanna H. Gray Fellow, Howard Hughes Medical Institute, Stanford, CA, USA *Contributed equally to this work +Correspondence: [email protected], [email protected], [email protected] Abstract In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We discuss what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization. Introduction Recent evidence has shown that hybridization between species is common. Hybridization is widespread across the tree of life, spanning both ancient and recent timescales and a broad range of divergence levels between taxa [1–10]. This appreciation of the prevalence of hybridization has renewed interest among researchers in understanding its consequences. -
Reintroducing the Dingo: the Risk of Dingo Predation to Threatened Vertebrates of Western New South Wales
CSIRO PUBLISHING Wildlife Research http://dx.doi.org/10.1071/WR11128 Reintroducing the dingo: the risk of dingo predation to threatened vertebrates of western New South Wales B. L. Allen A,C and P. J. S. Fleming B AThe University of Queensland, School of Animal Studies, Gatton, Qld 4343, Australia. BVertebrate Pest Research Unit, NSW Department of Primary Industries, Orange Agricultural Institute, Forest Road, Orange, NSW 2800, Australia. CCorresponding author. Present address: Vertebrate Pest Research Unit, NSW Department of Primary Industries, Sulfide Street, Broken Hill, NSW 2880, Australia. Email: [email protected] Abstract Context. The reintroduction of dingoes into sheep-grazing areas south-east of the dingo barrier fence has been suggested as a mechanism to suppress fox and feral-cat impacts. Using the Western Division of New South Wales as a case study, Dickman et al. (2009) recently assessed the risk of fox and cat predation to extant threatened species and concluded that reintroducing dingoes into the area would have positive effects for most of the threatened vertebrates there, aiding their recovery through trophic cascade effects. However, they did not formally assess the risk of dingo predation to the same threatened species. Aims. To assess the risk of dingo predation to the extant and locally extinct threatened vertebrates of western New South Wales using methods amenable to comparison with Dickman et al. (2009). Methods. The predation-risk assessment method used in Dickman et al. (2009) for foxes and cats was applied here to dingoes, with minor modification to accommodate the dietary differences of dingoes. This method is based on six independent biological attributes, primarily reflective of potential vulnerability characteristics of the prey. -
This Is the Authors' Post-Print PDF Version
This is the authors’ post-print PDF version of the paper ‘Wild dogs and village dogs in New Guinea: Were they different?’ which was published in Australian Mammalogy. Citation details for the published version are: Dwyer, P. D. and M. Minnegal (2016) Wild dogs and village dogs in New Guinea: Were they different? Australian Mammalogy 38(1): 1-11. DOI: 10.1071/AM15011 WILD DOGS AND VILLAGE DOGS IN NEW GUINEA: WERE THEY DIFFERENT? PETER D. DWYER and MONICA MINNEGAL Recent accounts of wild-living dogs in New Guinea argue that these animals qualify as an “evolutionarily significant unit” that is distinct from village dogs, have been and remain genetically isolated from village dogs and merit taxonomic recognition at, at least, subspecific level. These accounts have paid little attention to reports concerning village dogs. This paper reviews some of those reports, summarizes observations from the interior lowlands of Western Province and concludes that: (1) at the time of European colonization, wild- living dogs and most, if not all, village dogs of New Guinea comprised a single though heterogeneous gene pool; (2) eventual resolution of the phylogenetic relationships of New Guinea wild-living dogs will apply equally to all or most of the earliest New Guinea village-based dogs; and (3) there remain places where the local village-based population of domestic dogs continues to be dominated by individuals whose genetic inheritance can be traced to pre- colonization canid forebears. At this time, there is no firm basis from which to assign a unique Linnaean name to dogs that live as wild animals at high altitudes of New Guinea. -
Lntrogression and Its Consequences in Plants Loren H
Botany Publication and Papers Botany 1993 lntrogression and Its Consequences in Plants Loren H. Rieseberg Rancho Santa Ana Botanic Garden Jonathan F. Wendel Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/bot_pubs Part of the Botany Commons, Evolution Commons, and the Plant Breeding and Genetics Commons Recommended Citation Rieseberg, Loren H. and Wendel, Jonathan F., "lntrogression and Its Consequences in Plants" (1993). Botany Publication and Papers. 8. http://lib.dr.iastate.edu/bot_pubs/8 This Book Chapter is brought to you for free and open access by the Botany at Iowa State University Digital Repository. It has been accepted for inclusion in Botany Publication and Papers by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. lntrogression and Its Consequences in Plants Abstract The or le of introgression in plant evolution has been the subject of considerable discussion since the publication of Anderson's influential monograph, Introgressive Hybridization (Anderson, 1949). Anderson promoted the view, since widely held by botanists, that interspecific transfer of genes is a potent evolutionary force. He suggested that "the raw material for evolution brought about by introgression must greatly exceed the new genes produced directly by mutation" ( 1949, p. 102) and reasoned, as have many subsequent authors, that the resulting increases in genetic diversity and number of genetic combinations promote the development or acquisition of novel adaptations (Anderson, 1949, 1953; Stebbins, 1959; Rattenbury, 1962; Lewontin and Birch, 1966; Raven, 1976; Grant, 1981 ). In contrast to this "adaptationist" perspective, others have accorded little ve olutionary significance to introgression, suggesting instead that it should be considered a primarily local phenomenon with only transient effects, a kind of"evolutionary noise" (Barber and Jackson, 1957; Randolph et al., 1967; Wagner, 1969, 1970; Hardin, 1975).