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BMC Genomics

D S Fleming, J E Koltes, E R Fritz-Waters, M F Rothschild, C J Schmidt, C M Ashwell, M E Persia, J M Reecy, S J Lamont
BACKGROUND: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation...
October 19, 2016: BMC Genomics
Rama Raghavan, Stephen Hyter, Harsh B Pathak, Andrew K Godwin, Gottfried Konecny, Chen Wang, Ellen L Goode, Brooke L Fridley
BACKGROUND: Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer death among women in the United States (5 % of cancer deaths). The standard treatment for patients with advanced EOC is initial debulking surgery followed by carboplatin-paclitaxel combination chemotherapy. Unfortunately, with chemotherapy most patients relapse and die resulting in a five-year overall survival around 45 %. Thus, finding novel therapeutics for treating EOC is essential. Connectivity Mapping (CMAP) has been used widely in cancer drug discovery and generally has relied on cancer cell line gene expression and drug phenotype data...
October 19, 2016: BMC Genomics
William J Gammerdinger, Matthew A Conte, Jean-François Baroiller, Helena D'Cotta, Thomas D Kocher
BACKGROUND: Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation...
October 18, 2016: BMC Genomics
Jerôme Montfort, Aurelie Le Cam, Jean-Charles Gabillard, Pierre-Yves Rescan
BACKGROUND: Muscle fibre hyperplasia stops in most fish when they reach approximately 50 % of their maximum body length. However, new small-diameter muscle fibres can be produced de novo in aged fish after muscle injury. Given that virtually nothing is known regarding the transcriptional mechanisms that regulate regenerative myogenesis in adult fish, we explored the temporal changes in gene expression during trout muscle regeneration following mechanical crushing. Then, we compared the gene transcription profiles of regenerating muscle with the previously reported gene expression signature associated with muscle fibre hyperplasia...
October 18, 2016: BMC Genomics
Sebastian Hutchinson, Lucy Glover, David Horn
BACKGROUND: African trypanosomes cause lethal diseases in humans and animals and escape host immune attack by switching the expression of Variant Surface Glycoprotein (VSG) genes. The expressed VSGs are located at the ends of telomeric, polycistronic transcription units known as VSG expression sites (VSG-ESs). Each cell has many VSG-ESs but only one is transcribed in bloodstream-form parasites and all of them are inactive upon transmission to the insect vector mid-gut; a subset of monocistronic metacyclic VSG-ESs are then activated in the insect salivary gland...
October 18, 2016: BMC Genomics
Salma Jamal, Sukriti Goyal, Asheesh Shanker, Abhinav Grover
BACKGROUND: Alzheimer's disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheimer's is still unclear, however one of the other major factors involved in AD pathogenesis are the genetic factors and around 70 % risk of the disease is assumed to be due to the large number of genes involved. Although genetic association studies have revealed a number of potential AD susceptibility genes, there still exists a need for identification of unidentified AD-associated genes and therapeutic targets to have better understanding of the disease-causing mechanisms of Alzheimer's towards development of effective AD therapeutics...
October 18, 2016: BMC Genomics
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Florian Leplat, Pai Rosager Pedas, Søren Kjærsgaard Rasmussen, Søren Husted
No abstract text is available yet for this article.
October 18, 2016: BMC Genomics
Kentaro Mishima, Takeshi Fujiwara, Taiichi Iki, Katsushi Kuroda, Kana Yamashita, Miho Tamura, Yoshitake Fujisawa, Atsushi Watanabe
No abstract text is available yet for this article.
October 17, 2016: BMC Genomics
Samuel S Shepard, Sarah Meno, Justin Bahl, Malania M Wilson, John Barnes, Elizabeth Neuhaus
No abstract text is available yet for this article.
October 13, 2016: BMC Genomics
Yachun Su, Liping Xu, Zhuqing Wang, Qiong Peng, Yuting Yang, Yun Chen, Youxiong Que
BACKGROUND: Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the development of genome-assisted resistance breeding programs. Furthermore, the molecular basis of sugarcane response to S. scitamineum infection at the proteome level was incomplete and combining proteomic and transcriptional analysis has not yet been conducted...
October 12, 2016: BMC Genomics
Weiwei Li, Ming Chen, Erhui Wang, Liqin Hu, Malcolm J Hawkesford, Li Zhong, Zhu Chen, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Changhong Guo, Youzhi Ma
BACKGROUND: Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants...
October 12, 2016: BMC Genomics
Ni Ai, Haoyang Cai, Caius Solovan, Michael Baudis
BACKGROUND: DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly...
October 12, 2016: BMC Genomics
Rachel S Leisso, Nigel E Gapper, James P Mattheis, Nathanael L Sullivan, Christopher B Watkins, James J Giovannoni, Robert J Schaffer, Jason W Johnston, Ines Hanrahan, Maarten L A T M Hertog, Bart M Nicolaï, David R Rudell
BACKGROUND: 'Honeycrisp' is an apple cultivar that is susceptible to soft scald, a chilling injury expressed as necrotic patches on the peel. Improved understanding of metabolism associated with the disorder would improve our understanding of soft scald and contribute to developing more effective management strategies for apple storage. It was expected that specific gene expression and specific metabolite levels in the peel would be linked with soft scald risk at harvest and/or specific time points during cold storage...
October 12, 2016: BMC Genomics
M Constanza Mannino, Máximo Rivarola, Alejandra C Scannapieco, Sergio González, Marisa Farber, Jorge L Cladera, Silvia B Lanzavecchia
BACKGROUND: Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories and successfully used worldwide. A peculiar biological aspect of Hymenoptera is its haplo-diploid life cycle, where females (diploid) develop from fertilized eggs and males (haploid) from unfertilized eggs. Diploid males were described in many species and recently evidenced in D. longicaudata by mean of inbreeding studies...
October 12, 2016: BMC Genomics
Da-Long Guo, Fei-Fei Xi, Yi-He Yu, Xiao-Yu Zhang, Guo-Hai Zhang, Gan-Yuan Zhong
BACKGROUND: Early ripening is an important desirable attribute for fruit crops. 'Kyoho' is a popular table grape cultivar in many Asian countries. 'Fengzao' is a bud mutant of 'Kyoho' and ripens nearly 30 days earlier than 'Kyoho'. To identify genes controlling early fruit development and ripening in 'Fengzao', RNA-Seq profiles of the two cultivars were compared at 8 different berry developmental stages in both berry peel and flesh tissues. METHODS: RNA-Seq profiling of berry development between 'Kyoho' and 'Fenzhao' were obtained using the Illumina HiSeq system and analyzed using various statistical methods...
October 12, 2016: BMC Genomics
Thanh Van Nguyen, Daniel Wibberg, Kai Battenberg, Jochen Blom, Brian Vanden Heuvel, Alison M Berry, Jörn Kalinowski, Katharina Pawlowski
BACKGROUND: The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents...
October 12, 2016: BMC Genomics
Meng Lin, Dadong Zhang, Shubing Liu, Guorong Zhang, Jianming Yu, Allan K Fritz, Guihua Bai
BACKGROUND: Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS (TaPHS1) and 4A have been cloned. METHODS: To determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U...
October 12, 2016: BMC Genomics
Sheng Xu, Yumei Jiang, Ning Wang, Bing Xia, Yilong Jiang, Xiaodan Li, Zhengzhi Zhang, Yikui Li, Ren Wang
BACKGROUND: Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer's disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing...
October 10, 2016: BMC Genomics
Sudeep Kumar, Hyun Joo Lee, Hee-Sae Park, Keesook Lee
BACKGROUND: Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talking with different kinases and playing a role in cellular signaling. However, only a few Rab proteins have been found to have a role in male germ cell development. The most notable functions of this process are performed by numerous testis-specific and/or germ cell-specific genes...
October 10, 2016: BMC Genomics
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