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https://www.readbyqxmd.com/read/29149761/crizotinib-achieves-long-lasting-disease-control-in-advanced-papillary-renal-cell-carcinoma-type-1-patients-with-met-mutations-or-amplification-eortc-90101-create-trial
#1
Patrick Schöffski, Agnieszka Wozniak, Bernard Escudier, Piotr Rutkowski, Alan Anthoney, Sebastian Bauer, Jozef Sufliarsky, Carla van Herpen, Lars H Lindner, Viktor Grünwald, Branko Zakotnik, Evelyne Lerut, Maria Debiec-Rychter, Sandrine Marréaud, Michela Lia, Tiana Raveloarivahy, Sandra Collette, Laurence Albiges
PURPOSE: Papillary renal-cell carcinoma type 1 (PRCC1) is associated with MET gene alterations. Our phase II trial prospectively assessed the efficacy and safety of crizotinib in patients with advanced/metastatic PRCC1 with or without MET mutations (MET+ and MET-). EXPERIMENTAL DESIGN: Eligible patients with reference pathology-confirmed PRCC1 received 250 mg oral crizotinib twice daily. Patients were attributed to MET+/MET- sub-cohorts by the sequencing of exons 16-19 of the MET gene in tumour tissue...
November 14, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29149730/divergence-of-insulin-superfamily-ligands-receptors-and-igf-binding-proteins-in-marine-versus-freshwater-stickleback-evidence-of-selection-in-known-and-novel-genes
#2
Tim Pellissier, Hend Al Nafea, Sara V Good
Three-spine stickleback (Gasterosteus aculeatus) is a teleost model for understanding genetic, physiological and morphological changes accompanying freshwater (FW) adaptation. There is growing evidence that the insulin superfamily plays important roles in traits involved in marine and FW adaptation. We performed a candidate gene analysis to look for evidence of selection on 33 insulin superfamily ligand-receptor genes and insulin-like growth factor binding proteins (Igfbp's) in stickleback. Using genotype data from 11 marine and 10 FW populations, we calculated the number of SNPs per site in regulatory and intronic regions, the number of synonymous and nonsynonymous mutations in coding regions, Wright's fixation index (Fst), and performed t-tests to identify SNPs with divergent genotype frequencies between marine/FW versus Atlantic/Pacific populations...
November 10, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29149504/mybl1-rearrangements-and-myb-amplification-in-breast-adenoid-cystic-carcinomas-lacking-the-myb-nfib-fusion-gene
#3
Jisun Kim, Felipe C Geyer, Luciano G Martelotto, Charlotte K Y Ng, Raymond S Lim, Pier Selenica, Anqi Li, Fresia Pareja, Nicola Fusco, Marcia Edelweiss, Rahul Kumar, Rodrigo Gularte-Merida, Andre N Forbes, Ekta Khurana, Odette Mariani, Sunil Badve, Anne Vincent-Salomon, Larry Norton, Jorge S Reis-Filho, Britta Weigelt
Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer (TNBC), has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression...
November 17, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29149195/age-of-heart-disease-presentation-and-dysmorphic-nuclei-in-patients-with-lmna-mutations
#4
Jason Q Core, Mehrsa Mehrabi, Zachery R Robinson, Alexander R Ochs, Linda A McCarthy, Michael V Zaragoza, Anna Grosberg
Nuclear shape defects are a distinguishing characteristic in laminopathies, cancers, and other pathologies. Correlating these defects to the symptoms, mechanisms, and progression of disease requires unbiased, quantitative, and high-throughput means of quantifying nuclear morphology. To accomplish this, we developed a method of automatically segmenting fluorescently stained nuclei in 2D microscopy images and then classifying them as normal or dysmorphic based on three geometric features of the nucleus using a package of Matlab codes...
2017: PloS One
https://www.readbyqxmd.com/read/29148086/novel-gene-fusion-of-prcc-mitf-defines-a-new-member-of-mit-family-translocation-renal-cell-carcinoma-clinicopathologic-analysis-and-detection-of-the-gene-fusion-by-rna-sequencing-and-fish
#5
Qiu-Yuan Xia, Xiao-Tong Wang, Sheng-Bing Ye, Xuan Wang, Rui Li, Shan-Shan Shi, Ru Fang, Ru-Song Zhang, Heng-Hui Ma, Zhen-Feng Lu, Qin Shen, Wei Bao, Xiao-Jun Zhou, Qiu Rao
AIMS: MITF, TFE3, TFEB and TFEC belong to the same microphthalmia-associated transcription factor family (MiT). Two transcription factors in this family have been identified in two unusual types of renal cell carcinoma (RCC): Xp11 translocation RCC harboring TFE3 gene fusions and t(6;11) RCC harboring a MALAT1-TFEB gene fusion. The 2016 World Health Organization classification of renal neoplasia grouped these two neoplasms together under the category of MiT family translocation RCC. RCCs associated with the other two MiT family members, MITF and TFEC, have rarely been reported...
November 17, 2017: Histopathology
https://www.readbyqxmd.com/read/29147684/c-207c-g-mutation-in-sepiapterin-reductase-causes-autosomal-dominant-dopa-responsive-dystonia
#6
Ali S Shalash, Thomas W Rösler, Stefanie H Müller, Mohamed Salama, Günther Deuschl, Ulrich Müller, Thomas Opladen, Britt-Sabina Petersen, Andre Franke, Franziska Hopfner, Gregor Kuhlenbäumer, Günter U Höglinger
Objective: To elucidate the genetic cause of an Egyptian family with dopa-responsive dystonia (DRD), a childhood-onset dystonia, responding therapeutically to levodopa, which is caused by mutations in various genes. Methods: Rare variants in all coding exons of GCH1 were excluded by Sanger sequencing. Exome sequencing was applied for 1 unaffected and 2 affected family members. To investigate the functional consequences of detected genetic variants, urinary sepiapterin concentrations were determined by high-performance liquid chromatography...
December 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/29147619/the-jak2v617f-and-calr-exon-9-mutations-are-shared-immunogenic-neoantigens-in-hematological-malignancy
#7
Morten Orebo Holmström, Hans Carl Hasselbalch, Mads Hald Andersen
Approximately 90% of patients with the hematological malignancies termed the chronic myeloproliferative neoplasms harbor either the JAK2V617F-mutation or CALR exon 9 mutation. Both of these are recognized by T-cells, which make the mutations ideal targets for cancer immune therapy as they are shared antigens.
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29147026/leveraging-genome-characteristics-to-improve-gene-discovery-for-putamen-subcortical-brain-structure
#8
Chi-Hua Chen, Yunpeng Wang, Min-Tzu Lo, Andrew Schork, Chun-Chieh Fan, Dominic Holland, Karolina Kauppi, Olav B Smeland, Srdjan Djurovic, Nilotpal Sanyal, Derrek P Hibar, Paul M Thompson, Wesley K Thompson, Ole A Andreassen, Anders M Dale
Discovering genetic variants associated with human brain structures is an on-going effort. The ENIGMA consortium conducted genome-wide association studies (GWAS) with standard multi-study analytical methodology and identified several significant single nucleotide polymorphisms (SNPs). Here we employ a novel analytical approach that incorporates functional genome annotations (e.g., exon or 5'UTR), total linkage disequilibrium (LD) scores and heterozygosity to construct enrichment scores for improved identification of relevant SNPs...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146882/physiological-srsf2-p95h-expression-causes-impaired-hematopoietic-stem-cell-functions-and-aberrant-rna-splicing-in-mice
#9
Ayana Kon, Satoshi Yamazaki, Yasuhito Nannya, Keisuke Kataoka, Yasunori Ota, Masahiro Marshall Nakagawa, Kenichi Yoshida, Yusuke Shiozawa, Maiko Morita, Tetsuichi Yoshizato, Masashi Sanada, Manabu Nakayama, Haruhiko Koseki, Hiromitsu Nakauchi, Seishi Ogawa
Splicing factor (SF) mutations are characteristic of myelodysplastic syndromes (MDS) and related myeloid neoplasms and implicated in their pathogenesis, but their roles in the development of MDS have not fully been elucidated. Here, we investigated the consequence of mutant Srsf2 expression using newly generated Vav1-Cre-mediated conditional knock-in mice. Mice carrying a heterozygous Srsf2 P95H mutation showed significantly reduced numbers of hematopoietic stem and progenitor cells (HSPCs) and differentiation defects both in the steady-state condition and transplant settings...
November 16, 2017: Blood
https://www.readbyqxmd.com/read/29146871/postcatalytic-spliceosome-structure-reveals-mechanism-of-3-splice-site-selection
#10
Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Christine M Norman, Andrew J Newman, Kiyoshi Nagai
Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. After the branching reaction protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146870/structure-of-the-yeast-spliceosomal-postcatalytic-p-complex
#11
Shiheng Liu, Xueni Li, Lingdi Zhang, Jiansen Jiang, Ryan C Hill, Yanxiang Cui, Kirk C Hansen, Z Hong Zhou, Rui Zhao
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B(act), C, C*, and ILS complexes revealed mechanisms of 5' splice site (ss) recognition, branching, and intron release, but lacked information on 3' ss recognition, exon ligation and release. Here, we report a cryoEM structure of the postcatalytic P complex at 3.3Å resolution, revealing that 3' ss is mainly recognized through non-Watson-Crick basepairing with the 5' ss and branch point. Furthermore, an unidentified protein becomes stably associated with the P complex, securing the 3' exon and potentially regulating Prp22 activity...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146476/mutation-screening-of-the-glis3-gene-in-a-cohort-of-592-chinese-patients-with-congenital-hypothyroidism
#12
Chunyun Fu, Shiyu Luo, Xigui Long, Yingfeng Li, Shangyang She, Xuehua Hu, Meizhen Mo, Zhanghong Wang, Yuhua Chen, Chun He, Jiasun Su, Yue Zhang, Fei Lin, Bobo Xie, Qifei Li, Shaoke Chen
OBJECTIVES: Defects in the human GLI-similar 3 (GLIS3) gene are reported to be a rare cause of congenital hypothyroidism (CH) and neonatal diabetes. The aim of this study was to examine the prevalence of GLIS3 mutation among CH patients in the Guangxi Zhuang Autonomous Region of China and to define the relationships between GLIS3 genotypes and clinical phenotypes. METHODS: Blood samples were collected from 592 patients with CH in Guangxi Zhuang Autonomous Region, China, and genomic DNA was extracted from peripheral blood leukocytes...
November 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29145422/missense-mutation-at-cldn8-associated-with-a-high-plasma-interferon-gamma-inducible-protein-10-level-in-methadone-maintained-patients-with-urine-test-positive-for-morphine
#13
Tung-Hsia Liu, Ren-Hua Chung, Sheng-Chang Wang, Chiu-Ping Fang, Hsiao-Hui Tsou, Chia-Lung Shih, Hsiang-Wei Kuo, Yun Wang, Yu-Li Liu
We previously reported a high plasma chemokine interferon gamma-inducible protein 10 (IP-10) level and prolonged electrocardiography QT-interval in methadone maintenance treatment (MMT) patients with HIV or HCV infection. The purpose of this study was to evaluate the genetic association of high plasma IP-10 level in the MMT patients. The gene-based and pathway-based association analyses were conducted using a genome-wide association study dataset in 344 MMT patients for identifying genes and pathways associated with plasma IP-10 level...
2017: PloS One
https://www.readbyqxmd.com/read/29145060/familial-cerebral-cavernous-malformation-report-of-a-novel-krit1-mutation-in-a-portuguese-family
#14
Inês Rosário Marques, Francisco Antunes, Nadine Ferreira, Miguel Grunho
Cerebral cavernous malformations (CCMs) are vascular malformations which may occur in familial forms which have autosomal dominant inheritance. Mutations have been identified in three genes: KRIT1, MGC4607 and PDCD10. We have documented a novel mutation on KRIT1 gene, and the second to be reported in a Portuguese family. This mutation consists in a two nucleotide insertion (c.947_948insAC) within the exon 10, resulting in premature protein termination (p.Leu317Argfs*2). These findings will hopefully contribute to a better clinical, imaging and genetic characterisation of this disease, particularly while trying to identify the factors that influence its treatment and prognosis...
November 10, 2017: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/29144405/genomic-analysis-of-the-asmt-gene-family-in-solanum-lycopersicum
#15
Weicheng Liu, Dake Zhao, Chunfang Zheng, Chen Chen, Xin Peng, Yuan Cheng, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29144233/a-high-resolution-mrna-expression-time-course-of-embryonic-development-in-zebrafish
#16
Richard J White, John E Collins, Ian M Sealy, Neha Wali, Christopher M Dooley, Zsofia Digby, Derek L Stemple, Daniel N Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J Enright, Elisabeth M Busch-Nentwich
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation...
November 16, 2017: ELife
https://www.readbyqxmd.com/read/29144210/a-new-allele-of-the-kappa-casein-gene-in-local-zebu-cattle-breeds
#17
Tauseef Ahmad, Ashwin Atkulwar, Sameera Farah, Vijendra Singh, Mumtaz Baig
Local zebu cattle breeds in Indian villages are crossbred with exotic breeds at an unprecedented rate without utilising the full potential of genomic technologies. In addition to agriculture produce, livestock, particularly cattle, constitute a vital source of livelihood for farmers in India. Age-old agricultural practices, errant monsoon, and frequent crop failures have resulted in Maharashtra having the highest number of farmer suicides in the country. Local cattle breeds are considered low-yield breeds and thus are primarily used as beasts of burden...
November 16, 2017: Journal of Dairy Research
https://www.readbyqxmd.com/read/29144179/effects-of-active-immunization-against-akirin2-on-muscle-fiber-type-composition-in-pigs
#18
Xiaoling Chen, Yafei Guo, Gang Jia, Hua Zhao, Guangmang Liu, Zhiqing Huang
The objective of this study was to investigate effects of active immunization against Akirin2 on muscle fiber-type composition in pigs. Here we showed that the titer of Akirin2 antibody in pigs immunized with porcine Akirin2 (pAkirin2) was significantly increased. Active immunization against pAkirin2 decreased succinic dehydrogenase and malate dehydrogenase activities and increased lactate dehydrogenase activity in the longissimus dorsi muscle of pigs. Active immunization against pAkirin2 significantly decreased MyHC I and MyHC IIa mRNA expressions and MyHC I protein expression and increased mRNA expressions of MyHC IIb as well as protein expressions of MyHC IIb and fast-MyHC...
November 16, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/29143945/one-evidence-of-cocaine-and-amphetamine-regulated-transcript-cart-has-the-bidirectional-effects-on-appetite-in-siberian-sturgeon-acipenser-baerii
#19
Xin Zhang, Yundi Gao, Ni Tang, Jinwen Qi, Yuanbing Wu, Jin Hao, Shuyao Wang, Defang Chen, Zhiqiong Li
Cocaine- and amphetamine-regulated transcript (CART), discovered in 1995, with various biological functions, has received much attention recently due to its role in the regulation of appetite in mammals. However, the function of CART on the appetite control in fish species is still not very clear. In this study, Siberian sturgeon (Acipenser baerii Brandt) cart gene was cloned for the first time, and the cart mRNA levels in 11 feeding-related tissues was investigated. The Siberian sturgeon cart gene sequence was 1459 base pairs (bp), including a 3'-terminal untranslated region (3'-UTR) of 39 bp, a 5'-terminal untranslated region (5'-UTR) of 52 bp, and an open reading frame (ORF) of 348 bp encoding 115 amino acids...
November 16, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/29143605/impact-of-the-7-bp-deletion-in-hvga20ox2-gene-on-agronomic-important-traits-in-barley-hordeum-vulgare-l
#20
Serafima Teplyakova, Marina Lebedeva, Nadezhda Ivanova, Valentina Horeva, Nina Voytsutskaya, Olga Kovaleva, Elena Potokina
BACKGROUND: Alike to Reduced height-1 (Rht-1) genes in wheat and the semi dwarfing (sd-1) gene in rice, the sdw1/denso locus involved in the metabolism of the GA, was designated as the 'Green Revolution' gene in barley. The recent molecular characterization of the candidate gene HvGA20ox2 for sdw1/denso locus allows to estimate the impact of the functional polymorphism of this gene on the variation of agronomically important traits in barley. RESULTS: We investigated the effect of the 7-bp deletion in exon 1 of HvGA20ox2 gene (sdw1...
November 14, 2017: BMC Plant Biology
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