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Gene Mapping

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https://www.readbyqxmd.com/read/28545128/common-variants-upstream-of-mlf1-at-3q25-and-within-cpz-at-4p16-associated-with-neuroblastoma
#1
Lee D McDaniel, Karina L Conkrite, Xiao Chang, Mario Capasso, Zalman Vaksman, Derek A Oldridge, Anna Zachariou, Millicent Horn, Maura Diamond, Cuiping Huo, Achille Iolascon, Hakon Hakonarson, Nazneen Rahman, Marcella Devoto, Sharon J Diskin
Neuroblastoma is a cancer of the developing sympathetic nervous system that most commonly presents in young children and accounts for approximately 12% of pediatric oncology deaths. Here, we report on a genome-wide association study (GWAS) in a discovery cohort or 2,101 cases and 4,202 controls of European ancestry. We identify two new association signals at 3q25 and 4p16 that replicated robustly in multiple independent cohorts comprising 1,163 cases and 4,396 controls (3q25: rs6441201 combined P = 1.2x10-11, Odds Ratio 1...
May 18, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28545025/oncogenic-mnk-signalling-regulates-the-metastasis-suppressor-ndrg1
#2
Shuye Tian, Xuemin Wang, Christopher G Proud
The protein N-myc down-regulated gene 1 (NDRG1) represses tumour metastasis. It is phosphorylated at several sites by serum and glucocorticoid-regulated kinase 1 (SGK1). Here we show that NDRG1 is also regulated by the oncogenic MAP kinase-interacting kinase (MNK) pathway, a target for cancer therapy.Inhibiting MNKs increases the expression of NDRG1 protein and mRNA in breast cancer cells. MNK inhibition also decreases the phosphorylation of NDRG1. Phosphorylation of NDRG1 is reduced in cells lacking MNK1, but not MNK2-knockout cells, indicating that NDRG1 phosphorylation is a specific target for MNK1...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544613/qtl-and-systems-genetics-analysis-of-mouse-grooming-and-behavioral-responses-to-novelty-in-an-open-field
#3
Anna Delprato, Marie-Paule Algéo, Brice Bonheur, Jason A Bubier, Lu Lu, Robert W Williams, Elissa J Chesler, Wim E Crusio
The open field is a classic test used to assess exploratory behavior, anxiety, and locomotor activity in rodents. Here we mapped quantitative trait loci (QTLs) underlying behaviors displayed in an open field, using a panel of 53 BXD recombinant inbred mouse strains with deep replication (10 per strain and sex). The use of these strains permits the integration and comparison of data obtained in different laboratories, and also offers the possibility to study trait covariance by exploiting powerful bioinformatics tools and resources...
May 24, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28544599/a-tumor-profile-in-patau-syndrome-trisomy-13
#4
Daniel Satgé, Motoi Nishi, Nicolas Sirvent, Michel Vekemans, Marie-Pierre Chenard, Ann Barnes
Individuals with trisomic conditions like Down syndrome and Edwards syndrome are prone to certain types of malignancy. However, for Patau syndrome (constitutional trisomy 13), which occurs in 1/10,000-1/20,000 live births, the tumor profile has not been well characterized. An awareness of susceptibility to malignancies can improve care of affected individuals, as well as further our understanding of the contribution of trisomy to carcinogenesis. Therefore, we conducted an extensive review of the literature; we found 17 malignancies reported in individuals with Patau syndrome...
May 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#5
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28543189/rapid-radiations-of-both-kiwifruit-hybrid-lineages-and-their-parents-shed-light-on-a-two-layer-mode-of-species-diversification
#6
Yifei Liu, Dawei Li, Qiong Zhang, Chi Song, Caihong Zhong, Xudong Zhang, Ying Wang, Xiaohong Yao, Zupeng Wang, Shaohua Zeng, Ying Wang, Yangtao Guo, Shuaibin Wang, Xinwei Li, Li Li, Chunyan Liu, Honour C McCann, Weiming He, Yan Niu, Min Chen, Liuwen Du, Junjie Gong, Paul M Datson, Elena Hilario, Hongwen Huang
Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting the patterns of phylogenetic networks for lineages that have undergone interspecific gene flow is challenging. Here we sequenced 25 taxa representing natural diversity in the genus Actinidia with an average mapping depth of 26× on the reference genome to reconstruct their reticulate history. We found evidence, including significant gene tree discordance, cytonuclear conflicts, and changes in genome-wide heterozygosity across taxa, collectively supporting extensive reticulation in the genus...
May 25, 2017: New Phytologist
https://www.readbyqxmd.com/read/28542722/a-homozygous-potentially-pathogenic-variant-in-the-paxbp1-gene-in-a-large-family-with-global-developmental-delay-and-myopathic-hypotonia
#7
Essa Alharby, Alia M Albalawi, Abdul Nasir, Sabri A Alhijji, Amer Mahmood, Khushnooda Ramzan, Firoz Abdusamad, Abdulkarim Aljohani, Osama Abdelsalam, Amr Eldardear, Sulman Basit
PAX binding protein 1 (PAXBP1) is an adaptor protein linking the transcription factor PAX3 and PAX7 to the histone methylation machinery. PAXBP1 is a nuclear protein and its high expression is known in brain cerebellar hemisphere and cerebellum. Moreover, it is also found in abundance in muscle precursor cells that are involved in myogenesis and skeletal muscles formation. Whole genome SNP genotyping and exome sequencing in a family with distinct syndrome of global developmental delay and hypotonia mapped the disease locus to the chromosome 21q22...
May 19, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28542649/evaluation-of-connectivity-map-discovered-celastrol-as-a-radiosensitizing-agent-in-a-murine-lung-carcinoma-model-feasibility-study-of-diffusion-weighted-magnetic-resonance-imaging
#8
Hong Young Jun, Tae-Hoon Kim, Jin Woo Choi, Young Hwan Lee, Kang Kyoo Lee, Kwon-Ha Yoon
This study was designed to identify potential radiosensitizing (RS) agents for combined radio- and chemotherapy in a murine model of human lung carcinoma, and to evaluate the in vivo effect of the RS agents using diffusion-weighted magnetic resonance imaging (DW-MRI). Radioresistance-associated genes in A549 and H460 cells were isolated on the basis of their gene expression profiles. Celastrol was selected as a candidate RS by using connectivity mapping, and its efficacy in lung cancer radiotherapy was tested...
2017: PloS One
https://www.readbyqxmd.com/read/28542579/transcriptomic-dissection-reveals-wide-spread-differential-expression-in-chickpea-during-early-time-points-of-fusarium-oxysporum-f-sp-ciceri-race-1-attack
#9
Sumanti Gupta, Anirban Bhar, Moniya Chatterjee, Amartya Ghosh, Sampa Das
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f...
2017: PloS One
https://www.readbyqxmd.com/read/28542571/quantitative-trait-loci-for-yield-and-grain-plumpness-relative-to-maturity-in-three-populations-of-barley-hordeum-vulgare-l-grown-in-a-low-rain-fall-environment
#10
Bulti Tesso Obsa, Jason Eglinton, Stewart Coventry, Timothy March, Maxime Guillaume, Thanh Phuoc Le, Matthew Hayden, Peter Langridge, Delphine Fleury
Identifying yield and grain plumpness QTL that are independent of developmental variation or phenology is of paramount importance for developing widely adapted and stable varieties through the application of marker assisted selection. The current study was designed to dissect the genetic basis of yield performance and grain plumpness in southern Australia using three doubled haploid (DH) populations developed from crosses between adapted parents that are similar in maturity and overall plant development. Three interconnected genetic populations, Commander x Fleet (CF), Commander x WI4304 (CW), and Fleet x WI4304 (FW) developed from crossing of Australian elite barley genotypes, were used to map QTL controlling yield and grain plumpness...
2017: PloS One
https://www.readbyqxmd.com/read/28542535/a-trichostatin-a-expression-signature-identified-by-tempo-seq-targeted-whole-transcriptome-profiling
#11
Joanne M Yeakley, Peter J Shepard, Diana E Goyena, Harper C VanSteenhouse, Joel D McComb, Bruce E Seligmann
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28542507/establishment-a-real-time-reverse-transcription-pcr-based-on-host-biomarkers-for-the-detection-of-the-subclinical-cases-of-mycobacterium-avium-subsp-paratuberculosis
#12
Hyun-Eui Park, Hong-Tae Park, Young Hoon Jung, Han Sang Yoo
Bovine paratuberculosis (PTB) is a chronic enteric inflammatory disease of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP) that causes large economic losses in the dairy industry. Spread of PTB is mainly provoked by a long subclinical stage during which MAP is shed into the environment with feces; accordingly, detection of subclinical animals is very important to its control. However, current diagnostic methods are not suitable for detection of subclinical animals. Therefore, the current study was conducted to develop a diagnostic method for analysis of the expression of genes of prognostic potential biomarker candidates in the whole blood of cattle naturally infected with MAP...
2017: PloS One
https://www.readbyqxmd.com/read/28542488/dissecting-the-old-mediterranean-durum-wheat-genetic-architecture-for-phenology-biomass-and-yield-formation-by-association-mapping-and-qtl-meta-analysis
#13
Jose Miguel Soriano, Marcos Malosetti, Martina Roselló, Mark Earl Sorrells, Conxita Royo
Association mapping was used to identify genome regions affecting yield formation, crop phenology and crop biomass in a collection of 172 durum wheat landraces representative of the genetic diversity of ancient local durum varieties from the Mediterranean Basin. The collection was genotyped with 1,149 DArT markers and phenotyped in Spanish northern and southern locations during three years. A total of 245 significant marker trait associations (MTAs) (P<0.01) were detected. Some of these associations confirmed previously identified quantitative trait loci (QTL) and/or candidate genes, and others are reported for the first time here...
2017: PloS One
https://www.readbyqxmd.com/read/28542451/mapping-genes-for-resistance-to-stripe-rust-in-spring-wheat-landrace-pi-480035
#14
Jinita Sthapit Kandel, Vandhana Krishnan, Derick Jiwan, Xianming Chen, Daniel Z Skinner, Deven R See
Stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikks. is an economically important disease of wheat (Triticum aestivum L.). Hexaploid spring wheat landrace PI 480035 was highly resistant to stripe rust in the field in Washington during 2011 and 2012. The objective of this research was to identify quantitative trait loci (QTL) for stripe rust resistance in PI 480035. A spring wheat, "Avocet Susceptible" (AvS), was crossed with PI 480035 to develop a biparental population of 110 recombinant inbred lines (RIL)...
2017: PloS One
https://www.readbyqxmd.com/read/28542427/fine-mapping-and-candidate-gene-analysis-of-qtac8-a-major-quantitative-trait-locus-controlling-tiller-angle-in-rice-oryza-sativa-l
#15
Jiwai He, Gaoneng Shao, Xiangjin Wei, Fenglin Huang, Zhonghua Sheng, Shaoqing Tang, Peisong Hu
Rice tiller angle is an important agronomic trait that contributes to crop production and plays a vital role in high yield breeding. In this study, a recombinant inbred line (RIL) population derived from the cross of a glabrous tropical japonica rice D50 and an indica rice HB277, was used to investigate quantitative trait loci (QTLs) controlling rice tiller angle. Two major QTLs, qTAC8 and qTAC9, were detected. While qTAC9 mapped with a previously identified gene (TAC1), using a BC2F2 population qTAC8 was mapped to a 16...
2017: PloS One
https://www.readbyqxmd.com/read/28542357/the-nrf2-transcription-factor-plays-a-dual-role-in-colorectal-cancer-a-systematic-review
#16
C Gonzalez-Donquiles, J Alonso-Molero, T Fernandez-Villa, L Vilorio-Marqués, A J Molina, V Martín
BACKGROUND: Colorectal cancer is one of the most common cancers worldwide, and is influenced by the interplay of various factors, including a very strong genetic component. For instance, incorrect mitochondrial biogenesis is correlated with increased risk of developing colorectal cancer. Thus, it is important to understand the consequences of changes in both the expression and the correct function of the transcription factors that regulate mitochondrial biogenesis, namely NRF2. OBJECTIVES: The main objective of this paper is to characterise the relationship between NRF2 and colorectal cancer by compiling data from an exhaustive literature search...
2017: PloS One
https://www.readbyqxmd.com/read/28542303/differential-dna-methylation-of-msi2-and-its-correlation-with-diabetic-traits
#17
Jae-Pil Jeon, In-Uk Koh, Nak-Hyun Choi, Bong-Jo Kim, Bok-Ghee Han, Suman Lee
Differential DNA methylation with hyperglycemia is significantly associated with Type 2 Diabetes (T2D). Longtime extended exposure to high blood glucose levels can affect the epigenetic signatures in all organs. However, the relevance of the differential DNA methylation changes with hyperglycemia in blood with pancreatic islets remains unclear. We investigated differential DNA methylation in relation to glucose homeostasis based on the Oral Glucose Tolerance Test (OGTT) in a population-based cohort. We found a total of 382 differential methylation sites from blood DNA in hyperglycemia and type 2 diabetes subgroups using a longitudinal and cross-sectional approach...
2017: PloS One
https://www.readbyqxmd.com/read/28541905/inferring-gene-species-assignments-in-the-presence-of-horizontal-gene-transfer
#18
Agnieszka Mykowiecka, Pawel Szczesny, Pawel Gorecki
BACKGROUND: Microbial communities from environmental samples show great diversity as bacteria quickly response to changes in their ecosystems. To assess the scenario of the actual changes, metagenomics experiments aimed at sequencing genomic DNA from such samples are performed. These new obtained sequences together with already known are used to infer phylogenetic trees assessing the taxonomic groups the species with these genes belong to. Here we propose the first approach to the gene-species assignment problem by using reconciliation with horizontal gene transfer...
May 24, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28541485/histologically-defined-intratumoral-sequencing-uncovers-evolutionary-cues-into-conserved-molecular-events-driving-gliomagenesis
#19
Antony Prabhu, Pravin Kesarwani, Shiva Kant, Stewart F Graham, Prakash Chinnaiyan
BACKGROUND: Glioblastoma represents an archetypal example of a heterogeneous malignancy. To understand the diverse molecular consequences of this complex tumor ecology, we analyzed RNA-seq data generated from commonly identified intra-tumoral structures in glioblastoma enriched using laser capture microdissection. METHODS: Raw gene-level fragments per kilobase of transcript per million reads mapped (FPKM) values and the associated clinical data were acquired from the publically available Ivy GAP database and analyzed using MetaboAnalyst (v...
May 25, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28541388/the-genome-sequence-of-sweet-cherry-prunus-avium-for-use-in-genomics-assisted-breeding
#20
Kenta Shirasawa, Kanji Isuzugawa, Mitsunobu Ikenaga, Yutaro Saito, Toshiya Yamamoto, Hideki Hirakawa, Sachiko Isobe
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing...
May 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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