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Functional genetics

Section edited by Federico Canzian

This section incorporates all aspects of the functional analysis of genes and genomes including but not limited to: sequence analysis and genotyping approaches to finding functional variation in genes and gene families, experimental studies of gene function, transcriptional regulation and gene expression.

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  1. Content type: Research article

    Eggshell quality is important for the poultry industry. During eggshell formation a mass of inorganic minerals is deposited. The Sodium Channel (SCNN1) gene family plays an essential role in cation transportat...

    Authors: Yan-Feng Fan, Zhuo-Cheng Hou, Guo-Qiang Yi, Gui-Yun Xu and Ning Yang

    Citation: BMC Genetics 2013 14:90

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  2. Content type: Research article

    Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging areas of research in animal genetics, particularly in livestock where few annotated ge...

    Authors: Bianca Moioli, Maria Carmela Scatà, Roberto Steri, Francesco Napolitano and Gennaro Catillo

    Citation: BMC Genetics 2013 14:76

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  3. Content type: Research article

    Collection of high-quality DNA is essential for molecular epidemiology studies. Methods have been evaluated for optimal DNA collection in studies of adults; however, DNA collection in young children poses addi...

    Authors: Jenny N Poynter, Julie A Ross, Anthony J Hooten, Erica Langer, Crystal Blommer and Logan G Spector

    Citation: BMC Genetics 2013 14:69

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  4. Content type: Research article

    The primary objective of this study is to identify novel copy number variations (CNVs) associated with familial ankylosing spondylitis (AS). A customized genome-wide microarray was designed to detect CNVs and ...

    Authors: Mohammed Uddin, Walter P Maksymowych, Robert Inman, Dafna Gladman, Alexandra Munn, Ramin Yazdani, Fawnda Pellett, Sean Hamilton, Darren D O’Rielly and Proton Rahman

    Citation: BMC Genetics 2013 14:67

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  5. Content type: Research article

    The Butyrophilin-like (BTNL) proteins are likely to play an important role in inflammation and immune response. Like the B7 protein family, many human and murine BTNL members have been shown to control T lymph...

    Authors: Johanna Aigner, Sergi Villatoro, Raquel Rabionet, Jaume Roquer, Jordi Jiménez-Conde, Eulàlia Martí and Xavier Estivill

    Citation: BMC Genetics 2013 14:61

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  6. Content type: Research article

    Vasa is a member of the DEAD-box protein family that plays an indispensable role in mammalian spermatogenesis, particularly during meiosis. Bovine vasa homology (Bvh) of Bos taurus has been reported, however, its...

    Authors: Hua Luo, Yang Zhou, Yingxia Li and Qifa Li

    Citation: BMC Genetics 2013 14:58

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  7. Content type: Research article

    Epidemiological studies indicate a substantial excess familial recurrence of non-syndromic Tetralogy of Fallot (TOF), implicating genetic factors that remain largely unknown. The Rho induced kinase 1 gene (ROC...

    Authors: Julian Palomino Doza, Ana Topf, Jamie Bentham, Shoumo Bhattacharya, Catherine Cosgrove, J David Brook, Javier Granados-Riveron, Frances A Bu’Lock, John O’Sullivan, A Graham Stuart, Jonathan Parsons, Caroline Relton, Judith Goodship, Deborah J Henderson and Bernard Keavney

    Citation: BMC Genetics 2013 14:57

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  8. Content type: Research article

    Certain mutations in the Deadend1 (Dnd1) gene are the most potent modifiers of testicular germ cell tumor (TGCT) susceptibility in mice and rats. In the 129 family of mice, the Dnd1 Ter ...

    Authors: Jennifer L Zechel, Stephanie K Doerner, Angela Lager, Paul J Tesar, Jason D Heaney and Joseph H Nadeau

    Citation: BMC Genetics 2013 14:54

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  9. Content type: Research article

    Skeletal muscle is one of the most important economic traits in agricultural animals, especially in pigs. In the modern pig industry, lean type pigs have undergone strong artificial selection for muscle growth...

    Authors: Jie Zhang, Chaowei Zhou, Jideng Ma, Lei Chen, Anan Jiang, Li Zhu, Surong Shuai, Jinyong Wang, Mingzhou Li and Xuewei Li

    Citation: BMC Genetics 2013 14:53

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  10. Content type: Research article

    Mice homozygous for the juvenile alopecia mutation (jal) display patches of hair loss that appear as soon as hair develops in the neonatal period and persist throughout life. Although a report initially describin...

    Authors: Francisco Ramirez, Aaron M Feliciano, Elisabeth B Adkins, Kevin M Child, Legairre A Radden II, Alexis Salas, Nelson Vila-Santana, José M Horák, Samantha R Hughes, Damek V Spacek and Thomas R King

    Citation: BMC Genetics 2013 14:40

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  11. Content type: Research article

    Anthracnose of lentil, caused by the hemibiotrophic fungal pathogen Colletotrichum truncatum is a serious threat to lentil production in western Canada. Colletotrichum truncatum employs a bi-phasic infection stra...

    Authors: Vijai Bhadauria, Kirstin E Bett, Tengsheng Zhou, Albert Vandenberg, Yangdou Wei and Sabine Banniza

    Citation: BMC Genetics 2013 14:31

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  12. Content type: Research article

    The discovery of TCF7L2 as a global type 2 diabetes (T2D) gene hassparked investigations to explore the clinical utility of its variants forguiding the development of new diagnostic and therapeutic strategies.How...

    Authors: Eric W Howard, Latonya F Been, Megan Lerner, Daniel Brackett, Stan Lightfoot, Elizabeth C Bullen and Dharambir K Sanghera

    Citation: BMC Genetics 2013 14:28

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  13. Content type: Research article

    Achromatopsia is an autosomal recessive disease characterized by the loss of cone photoreceptor function that results in day-blindness, total colorblindness, and decreased central visual acuity. The most commo...

    Authors: Connie Y Yeh, Orly Goldstein, Anna V Kukekova, Debbie Holley, Amy M Knollinger, Heather J Huson, Susan E Pearce-Kelling, Gregory M Acland and András M Komáromy

    Citation: BMC Genetics 2013 14:27

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  14. Content type: Research article

    MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Sequential cleavage of miRNA precursors results in a ~22 nucleotide duplex of which one strand, the mature miR...

    Authors: Monique Ohanian, David T Humphreys, Elizabeth Anderson, Thomas Preiss and Diane Fatkin

    Citation: BMC Genetics 2013 14:18

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  15. Content type: Research article

    Detecting mutations in disease genes by full gene sequence analysis is common in clinical diagnostic laboratories. Sanger dideoxy terminator sequencing allows for rapid development and implementation of sequen...

    Authors: Ephrem LH Chin, Cristina da Silva and Madhuri Hegde

    Citation: BMC Genetics 2013 14:6

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  16. Content type: Research article

    A genome wide association study for litter size in Norwegian White Sheep (NWS) was conducted using the recently developed ovine 50K SNP chip from Illumina. After genotyping 378 progeny tested artificial insemi...

    Authors: Dag I Våge, Maren Husdal, Matthew P Kent, Gunnar Klemetsdal and Inger A Boman

    Citation: BMC Genetics 2013 14:1

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  17. Content type: Research article

    The SNF3 gene in the yeast Saccharomyces cerevisiae encodes a low glucose sensor that regulates expression of an important subset of the hexose transporter (HXT) superfamily. Null mutations of snf3 result in a de...

    Authors: Kevin L Dietzel, Vidhya Ramakrishnan, Erin E Murphy and Linda F Bisson

    Citation: BMC Genetics 2012 13:107

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  18. Content type: Research article

    Our interests lie in determining the genes and genetic pathways that are important for establishing and maintaining maternal-fetal interactions during pregnancy. Mutation analysis targeted to a 34 Mb domain fl...

    Authors: Amy C Lossie, Chiao-Ling Lo, Katherine M Baumgarner, Melissa J Cramer, Joseph P Garner and Monica J Justice

    Citation: BMC Genetics 2012 13:106

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  19. Content type: Research article

    Beta-defensins (β-defensins) are innate immune peptides with evolutionary conservation across a wide range of species and has been suggested to play important roles in innate immune reactions against pathogens...

    Authors: Min-Kyeung Choi, Minh Thong Le, Dinh Truong Nguyen, Hojun Choi, Won Kim, Jin-Hoi Kim, Jungwan Chun, Jiyeon Hyeon, Kunho Seo and Chankyu Park

    Citation: BMC Genetics 2012 13:98

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  20. Content type: Research article

    WC1 co-receptors belong to the scavenger receptor cysteine-rich (SRCR) superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ γδ T cells. ...

    Authors: Chuang Chen, Carolyn TA Herzig, Leeson J Alexander, John W Keele, Tara G McDaneld, Janice C Telfer and Cynthia L Baldwin

    Citation: BMC Genetics 2012 13:86

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  21. Content type: Research article

    Waved with open eyelids 2 (woe2) is a novel autosomal recessive mouse mutation that arose spontaneously in our animal facility. Upon initial evaluation, mutant mice exhibited eyelids open at birth (EOB) and wavy ...

    Authors: Joseph Toonen, Lina Liang and Duska J Sidjanin

    Citation: BMC Genetics 2012 13:76

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  22. Content type: Research article

    DNA from buccal brush samples is being used for high-throughput analyses in a variety of applications, but the impact of sample type on genotyping success and downstream statistical analysis remains unclear. T...

    Authors: Jessica G Woo, Lisa J Martin, Lili Ding, W Mark Brown, Timothy D Howard, Carl D Langefeld, Charles J Moomaw, Mary Haverbusch, Guangyun Sun, Subba R Indugula, Hong Cheng, Ranjan Deka and Daniel Woo

    Citation: BMC Genetics 2012 13:75

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  23. Content type: Research article

    The Sialyl-Lewis X (Slex) is a well-known glycan structure involved in leukocyte homing and recruitment to inflammatory sites. SLex is well conserved among species and is mainly synthesized by FucT-VII in vertebr...

    Authors: Benoît Laporte, Daniel Petit, Dominique Rocha, Mekki Boussaha, Cécile Grohs, Abderrahman Maftah and Jean-Michel Petit

    Citation: BMC Genetics 2012 13:74

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  24. Content type: Research article

    Recent studies in human have highlighted the importance of the monocyte chemotactic proteins (MCP) in leukocyte trafficking and their effects in inflammatory processes, tumor progression, and HIV-1 infection. ...

    Authors: Wessel van der Loo, Sandra Afonso, Ana Lemos de Matos, Joana Abrantes and Pedro J Esteves

    Citation: BMC Genetics 2012 13:72

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  25. Content type: Research article

    The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymor...

    Authors: Marion T Ryan, Ruth M Hamill, Aisling M O’Halloran, Grace C Davey, Jean McBryan, Anne M Mullen, Chris McGee, Marina Gispert, Olwen I Southwood and Torres Sweeney

    Citation: BMC Genetics 2012 13:66

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  26. Content type: Research article

    Somatolactin alpha (SLa) is a fish-specific peptide hormone secreted from the pituitary. In medaka, SLa functions to darken the skin color and lack of SLa makes it pale. Transcription of SLa is enhanced or suppre...

    Authors: Yuko Sasano, Asami Yoshimura and Shoji Fukamachi

    Citation: BMC Genetics 2012 13:64

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  27. Content type: Research article

    Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to de...

    Authors: Maria Cecília Florisbal Damé, Gildenor Medeiros Xavier, José Paes Oliveira-Filho, Alexandre Secorun Borges, Henrique Nunes Oliveira, Franklin Riet-Correa and Ana Lucia Schild

    Citation: BMC Genetics 2012 13:62

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  28. Content type: Research article

    As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide c...

    Authors: Qiaoping Yuan, Zhifeng Zhou, Stephen G Lindell, J Dee Higley, Betsy Ferguson, Robert C Thompson, Juan F Lopez, Stephen J Suomi, Basel Baghal, Maggie Baker, Deborah C Mash, Christina S Barr and David Goldman

    Citation: BMC Genetics 2012 13:52

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  29. Content type: Research article

    Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three bo...

    Authors: María Pazos-Navarro, Mercedes Dabauza, Enrique Correal, Kelly Hanson, Natasha Teakle, Daniel Real and Matthew N Nelson

    Citation: BMC Genetics 2011 12:104

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  30. Content type: Research article

    Snake venom metalloproteinases (SVMPs) are widely distributed in snake venoms and are versatile toxins, targeting many important elements involved in hemostasis, such as basement membrane proteins, clotting pr...

    Authors: Ana M Moura-da-Silva, Maria Stella Furlan, Maria Cristina Caporrino, Kathleen F Grego, José Antonio Portes-Junior, Patrícia B Clissa, Richard H Valente and Geraldo S Magalhães

    Citation: BMC Genetics 2011 12:94

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  31. Content type: Research article

    Hypohidrotic ectodermal dysplasia (HED) is a congenital disorder characterized by sparse hair, oligodontia, and inability to sweat. It is caused by mutations in any of three Eda pathway genes: ectodysplasin (Eda)...

    Authors: Takashi Kuramoto, Mayuko Yokoe, Ryoko Hashimoto, Hiroshi Hiai and Tadao Serikawa

    Citation: BMC Genetics 2011 12:91

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  32. Content type: Research article

    Genes in the major histocompatibility complex (MHC) have a critical role in both the innate and adaptive immune responses because of their involvement in presenting foreign peptides to T cells. However, the na...

    Authors: Min Du, Song-lin Chen, Yan-hong Liu, Yang Liu and Jing-feng Yang

    Citation: BMC Genetics 2011 12:78

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  33. Content type: Research article

    Plasmodium falciparum malaria remains a leading cause of morbidity and mortality among African children. Innate immunity provides the first line of defence against P. falciparum infections, particularly in young ...

    Authors: John M Ong'echa, Evans O Raballah, Prakasha M Kempaiah, Samuel B Anyona, Tom Were, Gregory C Davenport, Stephen Konah, John M Vulule, Collins Ouma, James B Hittner and Douglas J Perkins

    Citation: BMC Genetics 2011 12:69

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  34. Content type: Research article

    Temperature adaptation is one of the most important determinants of distribution and population size of organisms in nature. Recently, quantitative trait loci (QTL) mapping and gene expression profiling approa...

    Authors: Kazuo H Takahashi, Yasukazu Okada and Kouhei Teramura

    Citation: BMC Genetics 2011 12:57

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  35. Content type: Research article

    Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized de novo in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanism...

    Authors: Hilde Sundvold, Hanna Helgeland, Matthew Baranski, Stig W Omholt and Dag Inge Våge

    Citation: BMC Genetics 2011 12:52

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  36. Content type: Research article

    The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci re...

    Authors: Øivind Andersen, Maria Cristina De Rosa, Davide Pirolli, Ave Tooming-Klunderud, Petra E Petersen and Carl André

    Citation: BMC Genetics 2011 12:51

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  37. Content type: Research article

    Arachidonic acid (AA) is a long-chain omega-6 polyunsaturated fatty acid (PUFA) synthesized from the precursor dihomo-gamma-linolenic acid (DGLA) that plays a vital role in immunity and inflammation. Variants ...

    Authors: Rasika A Mathias, Susan Sergeant, Ingo Ruczinski, Dara G Torgerson, Christina E Hugenschmidt, Meghan Kubala, Dhananjay Vaidya, Bhoom Suktitipat, Julie T Ziegler, Priscilla Ivester, Douglas Case, Lisa R Yanek, Barry I Freedman, Megan E Rudock, Kathleen C Barnes, Carl D Langefeld…

    Citation: BMC Genetics 2011 12:50

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  38. Content type: Research article

    Numerous immune-mediated diseases have been associated with the class I and II HLA genes located within the major histocompatibility complex (MHC) consisting of highly polymorphic alleles encoded by the HLA-A,...

    Authors: Xinyi Cindy Zhang, Shuying Sue Li, Hongwei Wang, John A Hansen and Lue Ping Zhao

    Citation: BMC Genetics 2011 12:39

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  39. Content type: Research article

    The monocyte chemoattractant protein 1 (MCP-1) is involved in the recruitment of lymphocytes and monocytes and their migration to sites of injury and cellular immune reactions. In a Ghanaian tuberculosis (TB) ...

    Authors: Christopher D Intemann, Thorsten Thye, Birgit Förster, Ellis Owusu-Dabo, John Gyapong, Rolf D Horstmann and Christian G Meyer

    Citation: BMC Genetics 2011 12:34

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  40. Content type: Database

    The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural vari...

    Authors: Ram Vinay Pandey, Robert Kofler, Pablo Orozco-terWengel, Viola Nolte and Christian Schlötterer

    Citation: BMC Genetics 2011 12:27

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