Gene Expression Profiling of Human Oocytes Developed and Matured in Vivo Or in Vitro
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Comparative Mrna and Mirna Expression in European
Heredity (2019) 122:172–186 https://doi.org/10.1038/s41437-018-0090-1 ARTICLE Comparative mRNA and miRNA expression in European mouflon (Ovis musimon) and sheep (Ovis aries) provides novel insights into the genetic mechanisms for female reproductive success 1 1,2 1,2 3 1,2 1,2 1,2 Ji Yang ● Xin Li ● Yin-Hong Cao ● Kisun Pokharel ● Xiao-Ju Hu ● Ze-Hui Chen ● Song-Song Xu ● 3 3 3 1 Jaana Peippo ● Mervi Honkatukia ● Juha Kantanen ● Meng-Hua Li Received: 12 January 2018 / Revised: 20 March 2018 / Accepted: 18 April 2018 / Published online: 21 May 2018 © The Author(s) 2018. This article is published with open access Abstract Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis 1234567890();,: 1234567890();,: musimon) and performed an mRNA–miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep. We identified several novel genes with differentially expressed mRNAs (e.g., EREG, INHBA, SPP1, AMH, TDRD5, and ZP2) between the wild and domestic sheep, which are functionally involved in oocyte and follicle development and fertilization, and are significantly (adjusted P-value < 0.05) enriched in the Gene Ontology (GO) terms of various reproductive process, including the regulation of fertilization, oogenesis, ovarian follicle development, and sperm–egg recognition. -
Evaluation of SAS1B As an Immunotherapeutic Target for the Treatment of Cancer
Evaluation of SAS1B as an Immunotherapeutic Target for the Treatment of Cancer Kiley Anderson Knapp Barre, Vermont Bachelor of Science, University of New Hampshire, 2009 A Dissertation Presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Experimental Pathology University of Virginia May, 2018 ii Dedication I dedicate my work to daughter, Harper, my husband, Brook, and to my parents Kristin and Michael Gilbar and Thomas and Holly Anderson. My successes are owed in large part to my family; I sincerely thank them for their continued unconditional love and support. iii Acknowledgements Firstly, I offer thanks to my late mentor, Dr. John C. Herr (1948-2016), for the many lessons learned not only in science but also in leadership, perseverance, and expert- level gardening. For those of us working in Dr. Herr’s lab, his passion for and dedication to his research served as regular inspiration and motivation. His vision and expertise inspired this work and I am grateful to have had the opportunity to work with him. I also thank Dr. Timothy Bullock for serving as an exceptional mentor to me after Dr. Herr’s passing. I am grateful that despite his busy schedule, Dr. Bullock was regularly available and willing to offer guidance. Dr. Bullock went above and beyond with regard to intellectual support, research guidance, and invaluable assistance with manuscript and dissertation preparation for which I thank him. Dr. Eusebio Pires has also been a great mentor and friend of mine throughout this work and I am grateful to him for that. -
Testing for Ancient Selection Using Cross-Population Allele
Genetics: Early Online, published on November 23, 2015 as 10.1534/genetics.115.178095 1 1 Testing for ancient selection using cross-population allele 2 frequency differentiation 1, 3 Fernando Racimo ⇤ 4 1 Department of Integrative Biology, University of California, Berkeley, CA, USA 5 E-mail: [email protected] ⇤ 6 1 Abstract 7 Apowerfulwaytodetectselectioninapopulationisbymodelinglocalallelefrequencychangesina 8 particular region of the genome under scenarios of selection and neutrality, and finding which model is 9 most compatible with the data. Chen et al. [2010] developed a composite likelihood method called XP- 10 CLR that uses an outgroup population to detect departures from neutrality which could be compatible 11 with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive 12 to recent selection and may miss selective events that happened a long time ago. To overcome this, 13 we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three- 14 population tree. Our method - called 3P-CLR - outperforms XP-CLR when testing for selection that 15 occurred before two populations split from each other, and can distinguish between those events and 16 events that occurred specifically in each of the populations after the split. We applied our new test to 17 population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred 18 before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have 19 led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred 20 in East Asians, Europeans and the ancestors of both populations, after their split from Yoruba. -
Detecting Copy Number Variants from Whole-Exome
Magi et al. Genome Biology 2013, 14:R120 http://genomebiology.com/2013/14/10/R120 METHOD Open Access EXCAVATOR: detecting copy number variants from whole-exome sequencing data Alberto Magi1*†, Lorenzo Tattini1,2*†, Ingrid Cifola3, Romina D’Aurizio4, Matteo Benelli5, Eleonora Mangano3, Cristina Battaglia3,6, Elena Bonora7, Ants Kurg8, Marco Seri7, Pamela Magini7, Betti Giusti1, Giovanni Romeo7, Tommaso Pippucci7, Gianluca De Bellis3, Rosanna Abbate1 and Gian Franco Gensini1 Abstract We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/. Background 1000 Genomes Project and the Cancer Genome Atlas, Copy number variants (CNVs) are operationally defined but their computational complexity still limits the routine as 50 bp or larger DNA segments [1] that are present use of whole-genome sequencing to individual smaller at a variable copy number in comparison with a refer- projects. Whole-exome sequencing (WES), which is the ence genome. CNVs have been demonstrated to be one of sequencing of all the coding regions of a genome, is a very the main sources of genomic variation in humans [2-10] effective alternative to whole-genome sequencing and has and have been shown to participate in phenotypic vari- been successfully used to discover common and rare sin- ation and adaptation by disrupting genes and altering gle nucleotide variants (SNVs), small insertions/deletions gene dosage. -
Gene Expression Profiling of Human Oocytes Developed and Matured in Vivo Or in Vitro
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 879489, 20 pages http://dx.doi.org/10.1155/2013/879489 Review Article Gene Expression Profiling of Human Oocytes Developed and Matured In Vivo or In Vitro Irma Virant-Klun,1 Katja Knez,1 Tomaz Tomazevic,1 and Thomas Skutella2 1 Reproductive Unit, Department of Obstetrics and Gynecology, University Medical Centre Ljubljana, Slajmerjeva 3, 1000 Ljubljana, Slovenia 2 Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, 69120 Heidelberg, Germany Correspondence should be addressed to Irma Virant-Klun; [email protected] Received 30 September 2012; Revised 7 December 2012; Accepted 8 December 2012 Academic Editor: Xuan Jin Copyright © 2013 Irma Virant-Klun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The quality of the human oocyte determines the success of fertilization and affects the consequent embryo development, pregnancy and birth; it therefore serves as a basis for human reproduction and fertility. The possibility to evaluate oocyte quality in the in vitro fertilization programme is very limited. The only criterion which is commonly used to evaluate oocyte quality is its morphology. There is a mass of oocytes in the in vitro fertilization programme which are not fertilized in spite of normal morphology. In the past, several attempts focused on oocyte gene expression profiling by different approaches. The results elucidated groups of genes related to the human oocyte. It was confirmed that some factors, such as oocyte in vitro maturation, are detectable at the molecular level of human oocytes and their polar bodies in terms of gene expression profile. -
Testing for Ancient Selection Using Cross-Population Allele Frequency Differentiation
| INVESTIGATION Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation Fernando Racimo1 Department of Integrative Biology, University of California, Berkeley, California 94720 ABSTRACT A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called “3-population composite likelihood ratio” (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba.