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Gene function prediction

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https://www.readbyqxmd.com/read/29045979/-changes-of-serum-krebs-von-den-lungen-6-levels-in-interstitial-lung-disease-associated-with-dermatomyositis-and-secondary-sj%C3%A3-gren-s-syndrome-a-case-report
#1
J F Yu, Y B Jin, J He, Y An, Z G Li
Interstitial lung diseases (ILDs) are a diverse group of pulmonary disorders characterized by various patterns of inflammation and fibrosis in the interstitium of the lung. The underlying pathogenesis of ILDs is complex and associated with multiple rheumatologic conditions, such as systemic sclerosis, rheumatoid arthritis, pollymyositis and dermatomyositis, Sjögren's syndrome, and systemic lupus erythematosus. As the disease progresses, excessive pulmonary fibrosis impairs alveolar gas exchange and damages pulmonary function...
October 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/29045649/understanding-evolutionary-impacts-of-seasonality-an-introduction-to-the-symposium
#2
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
October 16, 2017: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29045529/impact-of-genetic-variations-in-the-mapk-signaling-pathway-on-outcome-in-metastatic-colorectal-cancer-patients-treated-with-first-line-folfiri-and-bevacizumab-data-from-fire-3-and-tribe-trials
#3
M D Berger, S Stintzing, V Heinemann, D Yang, S Cao, Y Sunakawa, Y Ning, S Matsusaka, S Okazaki, Y Miyamoto, M Suenaga, M Schirripa, S Soni, W Zhang, A Falcone, F Loupakis, H-J Lenz
Background: The MAPK-interacting kinase 1 (MKNK1) is localized downstream of the RAS/RAF/ERK and the MAP3K1/MKK/p38 signaling pathway. Through phosphorylation MKNK1 regulates the function of eukaryotic translation initiation factor 4E, a key player in translational control, whose expression is often upregulated in metastatic colorectal cancer patients (mCRC). Preclinical data suggest that MKNK1 increases angiogenesis by upregulating angiogenic factors. We therefore hypothesize that variations in the MKNK1 gene predict outcome in mCRC patients treated with first-line FOLFIRI and bevacizumab (bev)...
August 2, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045509/the-antibody-drug-conjugate-target-landscape-across-a-broad-range-of-tumour-types
#4
K L Moek, D J A de Groot, E G E de Vries, R S N Fehrmann
Background: Antibody-drug conjugates (ADCs), consisting of an antibody designed against a specific target at the cell membrane linked with a cytotoxic agent, are an emerging class of therapeutics. Since ADC tumour cell targets do not have to be drivers of tumour growth, ADCs are potentially relevant for a wide range of tumours currently lacking clear oncogenic drivers. Therefore, we aimed to define the landscape of ADC targets in a broad range of tumours. Materials and methods: PubMed and ClinicalTrials...
September 25, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045400/analysis-of-temporal-transcription-expression-profiles-reveal-links-between-protein-function-and-developmental-stages-of-drosophila-melanogaster
#5
Cen Wan, Jonathan G Lees, Federico Minneci, Christine A Orengo, David T Jones
Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but struggle to provide useful annotations relating to biological process functions due to the limited power of sequence-based features in that functional domain. In this work, we systematically evaluate the predictive power of temporal transcription expression profiles for protein function prediction in Drosophila melanogaster. Our results show significantly better performance on predicting protein function when transcription expression profile-based features are integrated with sequence-derived features, compared with the sequence-derived features alone...
October 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29044988/age-associated-microrna-expression-in-human-peripheral-blood-is-associated-with-all-cause-mortality-and-age-related-traits
#6
Tianxiao Huan, George Chen, Chunyu Liu, Anindya Bhattacharya, Jian Rong, Brian H Chen, Sudha Seshadri, Kahraman Tanriverdi, Jane E Freedman, Martin G Larson, Joanne M Murabito, Daniel Levy
Recent studies provide evidence of correlations of DNA methylation and expression of protein-coding genes with human aging. The relations of microRNA expression with age and age-related clinical outcomes have not been characterized thoroughly. We explored associations of age with whole-blood microRNA expression in 5221 adults and identified 127 microRNAs that were differentially expressed by age at P < 3.3 × 10(-4) (Bonferroni-corrected). Most microRNAs were underexpressed in older individuals. Integrative analysis of microRNA and mRNA expression revealed changes in age-associated mRNA expression possibly driven by age-associated microRNAs in pathways that involve RNA processing, translation, and immune function...
October 17, 2017: Aging Cell
https://www.readbyqxmd.com/read/29044507/tieg-and-estrogen-modulate-sost-expression-in-the-murine-skeleton
#7
Malayannan Subramaniam, Kevin S Pitel, Elizabeth S Bruinsma, David G Monroe, John R Hawse
TIEG knockout (KO) mice exhibit a female-specific osteopenic phenotype and altered expression of TIEG in humans is associated with osteoporosis. Gene expression profiling studies identified sclerostin as one of the most highly up-regulated transcripts in the long bones of TIEG KO mice relative to WT littermates suggesting that TIEG may regulate SOST expression. TIEG was shown to substantially suppress SOST promoter activity and the regulatory elements through which TIEG functions were identified using promoter deletion and chromatin immunoprecipitation assays...
October 16, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29044504/a-low-frequency-haplotype-spanning-slx4-fancp-constitutes-a-new-risk-locus-for-early-onset-breast-cancer-60-years-and-is-associated-with-reduced-dna-repair-capacity
#8
Harald Surowy, Dominic Varga, Barbara Burwinkel, Frederik Marmé, Christof Sohn, Manuel Luedeke, Antje Rinckleb, Christiane Maier, Helmut Deissler, Meta Volcic, Lisa Wiesmüller, Annette Hasenburg, Maximilian Klar, Josef Hoegel, Walther Vogel
Only a fraction of breast cancer (BC) cases can be yet explained by mutations in genes or genomic variants discovered in linkage, genome-wide association and sequencing studies. The known genes entailing medium or high risk for BC are strongly enriched for a function in DNA double strand repair. Thus, aiming at identifying low frequency variants conferring an intermediate risk, we here investigated 17 variants (MAF: 0.01-0.1) in 10 candidate genes involved in DNA repair or cell cycle control. In an exploration cohort of 437 cases and 1189 controls we show the variant rs3810813 in the SLX4/FANCP gene to be significantly associated with both BC (≤60 years; OR=2...
October 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29044474/exome-sequencing-identifies-a-novel-nonsense-mutation-of-myo6-as-the-cause-of-deafness-in-a-brazilian-family
#9
Juliana Sampaio-Silva, Ana Carla Batissoco, Rafaela Jesus-Santos, Osório Abath-Neto, Luciano Cesar Scarpelli, Patricia Yoshie Nishimura, Layla Testa Galindo, Ricardo Ferreira Bento, Jeanne Oiticica, Karina Lezirovitz
We investigated 313 unrelated subjects who presented with hearing loss to identify the novel genetic causes of this condition in Brazil. Causative GJB2/GJB6 mutations were found in 12.7% of the patients. Among the familial cases (100/313), four were selected for exome sequencing. In one case, two novel heterozygous variants were found and were predicted to be pathogenic based on bioinformatics tools, that is, p.Ser906* (MYO6) and p.Arg42Cys (GJB3). We confirmed that this nonsense MYO6 mutation segregated with deafness in this family...
October 17, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/29044218/wax-ester-synthase-diacylglycerol-acyltransferase-isoenzymes-play-a-pivotal-role-in-wax-ester-biosynthesis-in-euglena-gracilis
#10
Takuya Tomiyama, Kaeko Kurihara, Takahisa Ogawa, Takanori Maruta, Takumi Ogawa, Daisaku Ohta, Yoshihiro Sawa, Takahiro Ishikawa
Wax ester fermentation is a unique energy gaining pathway for a unicellular phytoflagellated protozoan, Euglena gracilis, to survive under anaerobiosis. Wax esters produced in E. gracilis are composed of saturated fatty acids and alcohols, which are the major constituents of myristic acid and myristyl alcohol. Thus, wax esters can be promising alternative biofuels. Here, we report the identification and characterization of wax ester synthase/diacylglycerol acyltrasferase (WSD) isoenzymes as the terminal enzymes of wax ester production in E...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29044159/global-identification-classification-and-expression-analysis-of-mapkkk-genes-functional-characterization-of-mdraf5-reveals-evolution-and-drought-responsive-profile-in-apple
#11
Meihong Sun, Yang Xu, Jinguang Huang, Zesheng Jiang, Huairui Shu, Huasen Wang, Shizhong Zhang
Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal components of Mitogen-activated protein kinase (MAPK) cascades, which play a significant role in many biological processes. Although genome-wide analysis of MAPKKKs has been conducted in many species, extant results in apple are scarce. In this study, a total of 72 putative MdMAPKKKs in Raf-like group, 11 in ZIK-like group and 37 in MEEK were identified in apple firstly. Predicted MdMAPKKKs were located in 17 chromosomes with diverse densities, and there was a high-level of conservation in and among the evolutionary groups...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043564/the-ucp2-866g-a-polymorphism-could-be-considered-as-a-genetic-marker-of-different-functional-prognosis-in-ischemic-stroke-after-recanalization
#12
I Díaz-Maroto Cicuéndez, E Fernández-Díaz, J García-García, J Jordán, I Fernández-Cadenas, J Montaner, G Serrano-Heras, T Segura
Recent studies based on experimental animal models of stroke have suggested that uncoupling protein 2 (UCP2), an inner mitochondrial membrane protein that is thought to regulate energy metabolism and reduce reactive oxygen species generation, provides protection against reperfusion damage. We aimed to investigate whether -866G/A polymorphism in the promoter of the UCP2 gene, which enhances its transcriptional activity, is associated with functional prognosis in patients with embolic ischemic stroke after early recanalization...
October 17, 2017: Neuromolecular Medicine
https://www.readbyqxmd.com/read/29043485/nitrate-assimilation-pathway-nap-role-of-structural-nit-and-transporter-ntr1-genes-in-fusarium-oxysporum-f-sp-lycopersici-growth-and-pathogenicity
#13
Lucia Gomez-Gil, Jesus Camara Almiron, Patricia Lizett Rodriguez Carrillo, Cindy Nayely Olivares Medina, Gustavo Bravo Ruiz, Pamela Romo Rodriguez, Alma Rosa Corrales Escobosa, Felix Gutierrez Corona, M Isabel Roncero
The tomato pathogen Fusarium oxysporum f.sp. lycopersici possesses the capability to use nitrate as the only nitrogen source under aerobic and anaerobic conditions and to activate virulence-related functions when cultivated in the presence of nitrate, but not in ammonium. The genome of F. oxysporum f.sp. lycopersici encodes three paralogs nitrate reductase (NR) genes (nit1, nit2 and nit3) and one predicted ortholog of the Aspergillus nidulans high-affinity nitrate/nitrite transporters NtrA and NtrB, named ntr1...
October 17, 2017: Current Genetics
https://www.readbyqxmd.com/read/29043106/sediment-microbial-taxonomic-and-functional-diversity-in-a-natural-salinity-gradient-challenge-remane-s-species-minimum-concept
#14
Christina Pavloudi, Jon B Kristoffersen, Anastasis Oulas, Marleen De Troch, Christos Arvanitidis
Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's...
2017: PeerJ
https://www.readbyqxmd.com/read/29042983/microrna-17-downregulates-expression-of-the-pten-gene-to-promote-the-occurrence-and-development-of-adenomyosis
#15
Haiyan Hu, Huijuan Li, Yuanli He
The aim of the current study was to evaluate the expression of microRNA (miR)-17 in the endometrial tissues of patients with adenomyosis (AM) and determine its biological function in the occurrence and development of the disease. A total of 45 fresh endometrial tissues of AM patients and 32 normal endometrial tissues were collected from healthy controls. The expression of miR-17 was evaluated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The miR-17-targeting gene phosphatase and tensin homolog (PTEN) was predicted using bioinformatics and its expression was evaluated with RT-qPCR and western blot analysis...
October 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29042795/significant-association-of-the-exo1-rs851797-polymorphism-with-clinical-outcome-of-ovarian-cancer
#16
Tingyan Shi, Rong Jiang, Pan Wang, Yuan Xu, Sheng Yin, Xi Cheng, Rongyu Zang
BACKGROUND: Exonuclease 1 (EXO1), one of DNA mismatch repair pathway genes, functions in maintaining genomic stability and affects tumor progression. We hypothesized that genetic variations in EXO1 may predict clinical outcomes in epithelial ovarian cancer (EOC). METHODS: In this cohort study with 1,030 consecutive EOC patients, we genotyped four potentially functional polymorphisms in EXO1 by the Taqman assay and evaluated their associations with patients' survival...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29041960/substantial-contribution-of-genetic-variation-in-the-expression-of-transcription-factors-to-phenotypic-variation-revealed-by-erd-gwas
#17
Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J Scanlon, Dan Nettleton, Patrick S Schnable
BACKGROUND: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes...
October 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/29041935/a-long-non-coding-rna-hottip-expression-is-associated-with-disease-progression-and-predicts-outcome-in-small-cell-lung-cancer-patients
#18
Yanqin Sun, Yuanyuan Zhou, Yifeng Bai, Qiongyao Wang, Jiarong Bao, Yingshan Luo, Ying Guo, Linlang Guo
BACKGROUND: Despite progress in treatment of small cell lung cancer (SCLC), the biology of the tumor still remains poorly understood. Recently, we globally investigated the contributions of lncRNA in SCLC with a special focus on sponge regulatory network. Here we report lncRNA HOTTIP, which is specifically amplified in SCLC, is associated with SCLC proliferation and poor prognosis of patients. METHODS: RT-qPCR was used to investigate the expression of HOTTIP in SCLC tissues and cell lines...
October 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29039586/a-single-nucleotide-polymorphism-located-in-microrna-499a-causes-loss-of-function-resulting-in-increased-expression-of-osbpl1a-and-reduced-serum-hdl-level
#19
Li-Bo Chen, Hai-Kuo Zheng, Lei Zhang, Zhe An, Xin-Peng Wang, Rui-Ting Shan, Wen-Qi Zhang
Atherosclerosis is the main pathological process that induces CVD (cardiovascular diseases), and the objective of our study was explore whether miR‑499a rs3746444 polymorphism was associated with the HDL level, one of the risk factors of atherosclerosis. Online public miRNA database was utilized to predict the miR‑499a target, and luciferase assay was conducted to confirm that miR‑499a targeted osbpl1a, then western blot analysis and real-time PCR were performed to verify miRNA-mRNA regulatory relationship between miR‑499a and osbpl1a...
October 9, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29039523/analysis-of-men1-c-482g-a-p-gly161asp-mutation-in-a-pedigree-with-familial-multiple-endocrine-neoplasia-type-1
#20
Yuanyuan Luo, Yongxiang Sun, Xiaofan Zhu, Xialian Li
Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder characterized by the development of neuroendocrine tumors, which in turn are caused by mutations in the MEN1 gene. In the present study, a case of a 46‑year‑old woman who was clinically diagnosed with MEN1 based on the presence of prolactinoma and bilateral parathyroid adenoma was reported. The patient's serum prolactin (PRL) levels were successfully controlled via bromocriptine therapy, and the serum levels of calcium and intact parathyroid hormone (PTH) reduced one day following parathyroidectomy...
October 10, 2017: Molecular Medicine Reports
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