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Ontology

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https://www.readbyqxmd.com/read/29786812/the-microrna-expression-profile-in-rat-lung-tissue-early-after-burn-injury
#1
Donghai Zhang, Yang Chang, Shaofang Han, Longlong Yang, Quan Hu, Yonghui Yu, Lingying Liu, Jiake Chai
BACKGROUND: Severe burn causes acute lung injury in many victims, but the related mechanisms have been barely investigated. microRNAs (miRNAs) important regulators in numerous physiological and pathophysiological process. However, the roles of miRNAs in burn lung injury are untested. METHODS: Six healthy male Sprague-Dawley rats were randomly assigned into burn and sham groups. Lung injury was evaluated by hematoxylin and eosin (HE) staining at 24 h after injury...
May 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#2
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785561/reptb-a-gene-ontology-based-drug-repurposing-approach-for-tuberculosis
#3
Anurag Passi, Neeraj Kumar Rajput, David J Wild, Anshu Bhardwaj
Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes...
May 21, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29785346/integrated-bioinformatic-changes-and-analysis-of-retina-with-time-in-diabetic-rats
#4
Zekai Cui, Qiaolang Zeng, Yonglong Guo, Shiwei Liu, Jiansu Chen
Diabetic retinopathy (DR) is the most common chronic complication of diabetes. It can cause impaired vision and even blindness. However, the pathological mechanism of DR is still unknown. In the present study, we use bioinformatic analysis to reveal the pathological changes of early DR in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database. To clarify the pathological mechanism of early DR, genes which were up-regulated (UP group) or down-regulated (DOWN group) over time were identified...
2018: PeerJ
https://www.readbyqxmd.com/read/29785181/on-using-a-mobile-application-to-support-teledermatology-a-case-study-in-an-underprivileged-area-in-colombia
#5
Juan Pablo Sáenz, Mónica Paola Novoa, Darío Correal, Bell Raj Eapen
Background: The use of mobile applications in dermatology to support remote diagnosis is gaining acceptance, particularly in rural areas, where dermatology services are commonly managed by healthcare personnel with no specialty training. Moreover, ontologies-sets of concepts that represent knowledge in a given domain-are increasingly being used to support medical diagnosis. A specific case is ONTODerm: an ontology to aid dermatological diagnosis. However, there is little information on the combined use of mobile applications and ontologies as support solutions in dermatology...
2018: International Journal of Telemedicine and Applications
https://www.readbyqxmd.com/read/29785177/characterization-of-new-microsatellite-markers-based-on-the-transcriptome-sequencing-of-clematis-finetiana
#6
Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye, Yongbao Shen
Background: Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the "Queen of the Vines". However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C...
2018: Hereditas
https://www.readbyqxmd.com/read/29785087/transcriptomic-impacts-of-rumen-epithelium-induced-by-butyrate-infusion-in-dairy-cattle-in-dry-period
#7
Ransom L Baldwin, Robert W Li, Yankai Jia, Cong-Jun Li
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function...
2018: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/29784931/reconstruction-of-the-diapsid-ancestral-genome-permits-chromosome-evolution-tracing-in-avian-and-non-avian-dinosaurs
#8
Rebecca E O'Connor, Michael N Romanov, Lucas G Kiazim, Paul M Barrett, Marta Farré, Joana Damas, Malcolm Ferguson-Smith, Nicole Valenzuela, Denis M Larkin, Darren K Griffin
Genomic organisation of extinct lineages can be inferred from extant chromosome-level genome assemblies. Here, we apply bioinformatic and molecular cytogenetic approaches to determine the genomic structure of the diapsid common ancestor. We then infer the events that likely occurred along this lineage from theropod dinosaurs through to modern birds. Our results suggest that most elements of a typical 'avian-like' karyotype (40 chromosome pairs, including 30 microchromosomes) were in place before the divergence of turtles from birds ~255 mya...
May 21, 2018: Nature Communications
https://www.readbyqxmd.com/read/29784930/comparative-mrna-and-mirna-expression-in-european-mouflon-ovis-musimon-and-sheep-ovis-aries-provides-novel-insights-into-the-genetic-mechanisms-for-female-reproductive-success
#9
Ji Yang, Xin Li, Yin-Hong Cao, Kisun Pokharel, Xiao-Ju Hu, Ze-Hui Chen, Song-Song Xu, Jaana Peippo, Mervi Honkatukia, Juha Kantanen, Meng-Hua Li
Prolific breeds of domestic sheep (Ovis aries) are important genetic resources due to their reproductive performance, which is characterized by multiple lambs per birth and out-of-season breeding. However, the lack of a comprehensive understanding of the genetic mechanisms underlying the important reproductive traits, particularly from the evolutionary genomics perspective, has impeded the efficient advancement of sheep breeding. Here, for the first time, by performing RNA-sequencing we built a de novo transcriptome assembly of ovarian and endometrial tissues in European mouflon (Ovis musimon) and performed an mRNA-miRNA integrated expression profiling analysis of the wild species and a highly prolific domestic sheep breed, the Finnsheep...
May 21, 2018: Heredity
https://www.readbyqxmd.com/read/29784595/comparative-proteome-analysis-of-the-capsule-from-patients-with-frozen-shoulder
#10
Yoshihiro Hagiwara, Masaru Mori, Kenji Kanazawa, Akira Ando, Yutaka Yabe, Masashi Koide, Takuya Sekiguchi, Nobuyuki Itaya, Masahiro Tsuchiya, Eiji Itoi
BACKGROUND: The etiology of frozen shoulder (FS) is unclear. Accordingly, this study used a label-free quantitative shotgun proteomic approach to elucidate the pathogenesis of FS based on protein expression levels. METHODS: Tissue samples from the rotator interval (RI), middle glenohumeral ligament (MGHL), and anterior-inferior glenohumeral ligament (IGHL) were collected from 12 FSs with severe stiffness and 7 shoulders with a rotator cuff tear (RCT) as controls...
May 18, 2018: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/29784049/identification-and-therapeutic-modulation-of-a-pro-inflammatory-subset-of-disease-associated-microglia-in-alzheimer-s-disease
#11
Srikant Rangaraju, Eric B Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M Duong, Michael W Pennington, James J Lah, Nicholas T Seyfried, Allan I Levey
BACKGROUND: Disease-associated-microglia (DAM) represent transcriptionally-distinct and neurodegeneration-specific microglial profiles with unclear significance in Alzheimer's disease (AD). An understanding of heterogeneity within DAM and their key regulators may guide pre-clinical experimentation and drug discovery. METHODS: Weighted co-expression network analysis (WGCNA) was applied to existing microglial transcriptomic datasets from neuroinflammatory and neurodegenerative disease mouse models to identify modules of highly co-expressed genes...
May 21, 2018: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/29781870/pregnancy-and-the-apoptotic-pathway-in-experimental-melanoma
#12
Anamaria S Facina, Gil Facina, Ismael D C Guerreiro da Silva, Silvana A A Corrêa, Sandra M Alexandre, Ângela F Logullo, Jorge K Hosomi, Mary U Nakamura
Pregnancy-associated melanoma is defined as melanoma diagnosed during pregnancy or within 1 year of delivery. The association of pregnancy with melanoma is well known, but its underlying molecular mechanisms of association are poorly understood. The aim was to assess the expression of apoptosis-related genes in melanoma tumors during pregnancy in an attempt to elucidate the molecular mechanisms underlying apoptosis-driven activation of melanoma cells in this period. Mice were allocated across two experimental groups (nonpregnant and pregnant) and implanted with the melanoma cell line BF16-F10...
May 17, 2018: Melanoma Research
https://www.readbyqxmd.com/read/29781033/microarray-analysis-of-circular-rna-expression-profiles-associated-with-gemcitabine-resistance-in-pancreatic-cancer-cells
#13
Chao Xu, Yue Yu, Fei Ding
Pancreatic cancer (PC) is one of the most malignant tumors of the digestive system due to its rapid progression, metastasis and resistance to chemotherapy. Gemcitabine (GEM) chemotherapy is the first‑choice treatment for advanced PC. However, the effect of GEM‑based chemotherapy on PC is limited due to the development of chemoresistance, and the molecular mechanisms underlying this resistance have yet to be investigated. Circular RNAs (circRNAs), which can function as microRNA sponges, have been found to be involved in the development of several types of cancer...
May 17, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29780284/up-regulation-of-ctd-2547g23-4-in-hepatocellular-carcinoma-tissues-and-its-prospective-molecular-regulatory-mechanism-a-novel-qrt-pcr-and-bioinformatics-analysis-study
#14
Dong-Yue Wen, Peng Lin, Hai-Wei Liang, Xia Yang, Hai-Yuan Li, Yun He, Hong Yang, Gang Chen
Background: Dysregulated expression of long non-coding RNAs (lncRNAs) has been reported in the pathogenesis and progression of multiple cancers, including hepatocellular carcinoma (HCC). LncRNA CTD-2547G23.4 is a novel lncRNA, and its role in HCC is still unknown. Here, we aimed to clarify the expression pattern and clinical value of CTD-2547G23.4 and to investigate the prospective regulatory mechanism via bioinformatics analysis in HCC. Methods: To identify differentially expressed lncRNAs in HCC, we downloaded RNA-Seq data for HCC and adjacent non-tumour tissues via The Cancer Genome Atlas (TCGA)...
2018: Cancer Cell International
https://www.readbyqxmd.com/read/29779721/evaluation-of-an-ontology-based-system-for-computerized-cognitive-rehabilitation
#15
Anna Alloni, Silvana Quaglini, Silvia Panzarasa, Elena Sinforiani, Sara Bernini
OBJECTIVES: This paper describes the results of a randomized clinical trial about the effectiveness of a computerized rehabilitation treatment on a sample of 31 patients affected by Parkinson disease. METHODS: Computerized exercises were administered by the therapists to the intervention group (n = 17) through the CoRe tool, which automatically generates a big variety of exercises leveraging on a stimuli set (words, sounds and images) organized into a dedicated ontology...
July 2018: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/29777750/post-a-framework-for-set-based-association-analysis-in-high-dimensional-data
#16
Xueyuan Cao, E Olusegun George, Mingjuan Wang, Dale B Armstrong, Cheng Cheng, Susana Raimondi, Jeffrey E Rubnitz, James R Downing, Mondira Kundu, Stanley B Pounds
Evaluating the differential expression of a set of genes belonging to a common biological process or ontology has proven to be a very useful tool for biological discovery. However, existing gene-set association methods are limited to applications that evaluate differential expression across k⩾2 treatment groups or biological categories. This limitation precludes researchers from most effectively evaluating the association with other phenotypes that may be more clinically meaningful, such as quantitative variables or censored survival time variables...
May 16, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29776333/transcriptomic-analysis-of-genes-in-soybean-in-response-to-peronospora-manshurica-infection
#17
Hang Dong, Shuangfeng Shi, Chong Zhang, Sihui Zhu, Mei Li, Jie Tan, Yue Yu, Liping Lin, Shirong Jia, Xujing Wang, Yuanhua Wu, Yuhui Liu
BACKGROUND: Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. RESULTS: Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775750/the-effects-of-capn1-gene-inactivation-on-the-differential-expression-of-genes-in-skeletal-muscle
#18
William T Olive, Brittney N Keel, Amanda K Lindholm-Perry, Justyna Horodyska, Andrew P Foote
Protein turnover is required for muscle growth and regeneration and several proteolytic enzymes, including the calpains, degrade myofibrillar proteins during this process. In a previous experiment, phenotypic differences were observed between μ-calpain knockout (KO) and wild type (WT) mice, including nutrient accretion and fiber type differences. These changes were particularly evident as the animals aged. Thus, we utilized 18 mice (9 KO and 9 WT) to compare transcript abundance to identify differentially expressed genes (DEGs) at 52 wk of age...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29774872/a-signature-based-on-survival-related-genes-identifies-high-risk-glioblastomas-harboring-immunosuppressive-and-aggressive-ecm-characteristics
#19
Di Chen, Dikang Chen, Dongqing Cao, Jian Hu, Yu Yao
To seek survival-related genes in glioblastoma and establish a survival-gene signature for predicting prognoses of glioblastoma using public databases.
 Methods: Three independent glioma databases (GEO GSE53733, CGGA, TCGA) with whole genome expression data were included for analysis. Survival-related genes were obtained by comparing the long-term (>36 months) and short-term (<12 months) survivors in the database GSE53733. CGGA was used as the training set to develop the signature and TCGA was used as the validation set...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774170/liquid-biopsy-of-vitreous-reveals-an-abundant-vesicle-population-consistent-with-the-size-and-morphology-of-exosomes
#20
Yuanjun Zhao, Sarah R Weber, Joshua Lease, Mariano Russo, Christopher A Siedlecki, Li-Chong Xu, Han Chen, Weiwei Wang, Michael Ford, Rafael Simó, Jeffrey M Sundstrom
Purpose: To investigate the molecular components of the vitreous in order to better understand retinal physiology and disease. Methods: Vitreous was acquired from patients undergoing vitrectomy for macular hole and/or epiretinal membrane, postmortem donors, and C57BL/6J mice. Unbiased proteomic analysis was performed via electrospray ionization tandem mass spectrometry (MS/MS). Gene ontology analysis was performed and results were confirmed with transmission electron microscopy, atomic force microscopy, and nanoparticle tracking analysis (NTA)...
May 2018: Translational Vision Science & Technology
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