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https://www.readbyqxmd.com/read/27922692/mir-195-inhibits-the-proliferation-and-migration-of-chondrocytes-by-targeting-git1
#1
Yang-Lin Gu, Xiao-Xu Rong, Li-Ting Wen, Guo-Xing Zhu, Ming-Quan Qian
Previous studies have demonstrated that G-protein coupled receptor kinase interacting protein-1 (GIT1) and microRNAs (miRNAs) serve an important role in chondrocyte proliferation and migration. However, a limited number of studies conducted thus far have investigated the association between GIT1 and miRNAs. In the present study, putative miR‑195 binding sites in the GIT1 3'‑untranslated region were identified using common bioinformatic algorithms (miRanda, TargetScan, miRBase and miRWalk), and it was demonstrated that they may be involved in regulating GIT1 expression...
December 5, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27922681/cxcr4-promotes-cisplatin-resistance-of-non-small-cell-lung-cancer-in-a-cyp1b1-dependent-manner
#2
Songping Xie, Zhenbo Tu, Jie Xiong, Ganjun Kang, Lina Zhao, Weidong Hu, Haiyan Tan, Kingsley Miyanda Tembo, Qianshan Ding, Xinzhou Deng, Jie Huang, Qiuping Zhang
Chemoresistance is the main cause of treatment failure and high mortality in advanced lung cancer. Cisplatin, an important chemotherapeutic agent for lung cancer, has been observed to show enormously reduced chemotherapeutic efficacy owing to the development of chemoresistance. CXCR4, a stromal-derived-factor-1 specific chemokine receptor, is highly expressed in non-small cell lung cancer (NSCLC) tissues and participates in cancer progression by regulating cell growth, apoptosis or invasion. In this study, we therefore investigated whether CXCR4 plays a role in the cisplatin associated resistance in NSCLC...
December 2, 2016: Oncology Reports
https://www.readbyqxmd.com/read/27922680/identification-of-key-genes-induced-by-platelet-rich-plasma-in-human-dermal-papilla-cells-using-bioinformatics-methods
#3
Haiyan Shen, Hanxiao Cheng, Haihua Chen, Jufang Zhang
Dermal papilla cells (DPCs) are located at the base of hair follicles, and are known to induce hair follicle regeneration. Platelet-rich plasma (PRP) functions in hair follicle regeneration. To investigate the influence of PRP on DPCs, the present study analyzed RNA‑seq data of human hair dermal papilla cells (HHDPCs) that were treated or untreated by PRP. The data included in the RNA‑seq were from two normal and two treated HHDPC samples. Following identification by Cuffdiff software, differentially expressed genes (DEGs) underwent enrichment analyses, and protein-protein interaction networks were constructed using Cytoscape software...
December 6, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27922111/mir-365-targets-%C3%AE-arrestin-2-to-reverse-morphine-tolerance-in-rats
#4
Jian Wang, Wei Xu, Tao Zhong, Zongbin Song, Yu Zou, Zhuofeng Ding, Qulian Guo, Xinzhong Dong, Wangyuan Zou
Morphine tolerance is a challenging clinical problem that limits its clinical application in pain treatment. Non-coding microRNAs (miRNAs) modulate gene expression in a post transcriptional manner, and their dysregulation causes various diseases. However, the significance of miRNAs in morphine tolerance is still poorly understood. In the present study, we hypothesized that microRNA-365 (miR-365) is a key functional small RNA that reverses morphine tolerance through regulation of β-arrestin 2 in rats. Here, microarray analysis and quantitative real-time PCR showed that miR-365 was robustly decreased in the spinal cord after chronic morphine administration...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922074/resistance-gene-identification-from-larimichthys-crocea-with-machine-learning-techniques
#5
Yinyin Cai, Zhijun Liao, Ying Ju, Juan Liu, Yong Mao, Xiangrong Liu
The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921404/genome-wide-profiling-of-genetic-variation-in-agrobacterium-transformed-rice-plants
#6
Wen-Xu Li, San-Ling Wu, Yan-Hua Liu, Gu-Lei Jin, Hai-Jun Zhao, Long-Jiang Fan, Qing-Yao Shu
Agrobacterium-mediated transformation has been widely used in producing transgenic plants, and was recently used to generate "transgene-clean" targeted genomic modifications coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Although tremendous variation in morphological and agronomic traits, such as plant height, seed fertility, and grain size, was observed in transgenic plants, the underlying mechanisms are not yet well understood, and the types and frequency of genetic variation in transformed plants have not been fully disclosed...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27921077/data-of-the-interacting-protein-networks-and-nucleotide-metabolism-pathways-related-to-ndk-and-nt5
#7
Dan Zhang, Wen Ma, Yu He, Gu He, Peng Zhang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
The data presented in this article are related to the research article entitled "Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis" (Ma et al., 2016) [1]. Nucleoside diphosphate kinase (NDK) and 5'-nucleotidase (NT5) are two proteins related to bacterial growth. Here, a bioinformatics analysis was presented to explore NDK and NT5-invovled in the interacting protein network and purine metabolism.
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27920952/a-methodology-for-the-design-of-experiments-in-computational-intelligence-with-multiple-regression-models
#8
Carlos Fernandez-Lozano, Marcos Gestal, Cristian R Munteanu, Julian Dorado, Alejandro Pazos
The design of experiments and the validation of the results achieved with them are vital in any research study. This paper focuses on the use of different Machine Learning approaches for regression tasks in the field of Computational Intelligence and especially on a correct comparison between the different results provided for different methods, as those techniques are complex systems that require further study to be fully understood. A methodology commonly accepted in Computational intelligence is implemented in an R package called RRegrs...
2016: PeerJ
https://www.readbyqxmd.com/read/27920753/neuroproteomics-and-systems-biology-approach-to-identify-temporal-biomarker-changes-post-experimental-traumatic-brain-injury-in-rats
#9
Firas H Kobeissy, Joy D Guingab-Cagmat, Zhiqun Zhang, Ahmed Moghieb, Olena Y Glushakova, Stefania Mondello, Angela M Boutté, John Anagli, Richard Rubenstein, Hisham Bahmad, Amy K Wagner, Ronald L Hayes, Kevin K W Wang
Traumatic brain injury (TBI) represents a critical health problem of which diagnosis, management, and treatment remain challenging. TBI is a contributing factor in approximately one-third of all injury-related deaths in the United States. The Centers for Disease Control and Prevention estimate that 1.7 million people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#10
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27920295/a-novel-transcriptional-regulator-related-to-thiamine-phosphate-synthase-controls-thiamine-metabolism-genes-in-archaea
#11
Dmitry A Rodionov, Semen A Leyn, Xiaoqing Li, Irina A Rodionova
: Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamin biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages from the Crenarchaeota phylum, as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain that is similar to the archaeal thiamin phosphate synthase ThiN...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27920156/nf%C3%AE%C2%BAb-induced-periostin-activates-integrin-%C3%AE-3-signaling-to-promote-renal-injury-in-gn
#12
Niki Prakoura, Panagiotis Kavvadas, Raphaёl Kormann, Jean-Claude Dussaule, Christos E Chadjichristos, Christos Chatziantoniou
De novo expression in the kidney of periostin, a protein involved in odontogenesis and osteogenesis, has been suggested as a biomarker of renal disease. In this study, we investigated the mechanism(s) of induction and the role of periostin in renal disease. Using a combination of bioinformatics, reporter assay, and chromatin immunoprecipitation analyses, we found that NFκB and other proinflammatory transcription factors induce periostin expression in vitro and that binding of these factors on the periostin promoter is enriched in glomeruli during experimental GN...
December 5, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27919802/integrative-view-of-2-oxoglutarate-fe-ii-dependent-oxygenase-diversity-and-functions-in-bacteria
#13
Baolei Jia, Xiaomeng Jia, Kyung Hyun Kim, Che Ok Jeon
BACKGROUND: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites. METHODS: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27918674/mir-224-affects-mammary-epithelial-cell-apoptosis-and-triglyceride-production-by-downregulating-acadm-and-aldh2-genes
#14
Binglei Shen, Qiqi Pan, Yuwei Yang, Yan Gao, Xin Liu, Wei Li, Yunsheng Han, Xue Yuan, Yongli Qu, Zhihui Zhao
MicroRNAs (miRNAs) are small noncoding RNA molecules that involve in various biological functions by regulating the expressions of target genes. In recent years, many researchers have demonstrated that miR-224 played an important role in regulating lipid metabolism. Therefore, in this study, the target genes of miR-224 were verified and the regulatory role of miR-224 was confirmed in lipid metabolism. In this study, bioinformatics methods were used for primarily predicting the target gene of miR-224 and dual-luciferase reporter system was used for further verify the relationship between miR-224 and its target gene...
December 5, 2016: DNA and Cell Biology
https://www.readbyqxmd.com/read/27918592/microrna-497-induces-apoptosis-and-suppresses-proliferation-via-the-bcl-2-bax-caspase9-caspase3-pathway-and-cyclin-d2-protein-in-huvecs
#15
Ridong Wu, Shi Tang, Mian Wang, Xiangdong Xu, Chen Yao, Shenming Wang
INTRODUCTION: MicroRNAs play crucial roles in various types of diseases. However, to date, no information about the role of miR-497 in the development of atherosclerosis has been reported. This study investigated the possible role of miR-497 in vascular endothelial cell injury during the early stage of atherosclerosis. MATERIALS AND METHODS: The expression level of miR-497 in human umbilical vein endothelial cells (HUVECs) exposed to ox-LDL was detected using qRT-PCR...
2016: PloS One
https://www.readbyqxmd.com/read/27918472/a-review-of-computational-methods-for-finding-non-coding-rna-genes
#16
REVIEW
Qaisar Abbas, Syed Mansoor Raza, Azizuddin Ahmed Biyabani, Muhammad Arfan Jaffar
Finding non-coding RNA (ncRNA) genes has emerged over the past few years as a cutting-edge trend in bioinformatics. There are numerous computational intelligence (CI) challenges in the annotation and interpretation of ncRNAs because it requires a domain-related expert knowledge in CI techniques. Moreover, there are many classes predicted yet not experimentally verified by researchers. Recently, researchers have applied many CI methods to predict the classes of ncRNAs. However, the diverse CI approaches lack a definitive classification framework to take advantage of past studies...
December 3, 2016: Genes
https://www.readbyqxmd.com/read/27918247/type-iv-effector-proteins-involved-in-the-sinorhizobium-medicago-symbiosis
#17
Matthew S Nelson, Chan Lan Chun, Michael Jay Sadowsky
In this study, we investigated genetic elements of the type IV secretion system (T4SS) found in Sinorhizobium and the role they play in symbiosis. Sinorhizobium meliloti and S. medicae each contain a putative T4SS, similar to that used by Agrobacterium tumefaciens during pathogenesis. The Cre reporter assay for translocation (CRAfT) system was used to validate potential effector proteins. Both S. meliloti and S. medicae contained the effector protein TfeA, which was translocated into the host plant. Sequence analysis revealed the presence of a nod box, involved in transcriptional activation of symbiosis-related genes, upstream of the transcriptional regulator (virG) in the Sinorhizobium T4SS...
December 5, 2016: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/27918077/type-2-diabetes-inhibited-human-mesenchymal-stem-cells-angiogenic-response-by-over-activity-of-the-autophagic-pathway
#18
Aysa Rezabakhsh, Omid Cheraghi, Alireza Nourazarian, Mehdi Hassanpour, Masoumeh Kazemi, Shahrooz Ghaderi, Esmaeil Faraji, Reza Rahbarghazi, Çığır Biray Avci, Bakiye Goker Bagca, Alireza Garjani
The current study aimed to address the impact of serum from type 2 diabetes patients on the angiogenic properties of human bone marrow mesenchymal stem cells and its relationship to autophagy signaling. Human primary stem cells were enriched and incubated with serum from diabetic and normal subjects for 7 days. Compared to data from the control group, diabetic serum was found to induce a higher cellular death rate (p < 0.001) and apoptotic changes (p < 0.01). We also showed that diabetic condition significantly abolished angiogenesis tube formation on Matrigel substrate, decreased cell chemotaxis (p < 0...
December 5, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27917953/the-core-subunit-of-a-chromatin-remodeling-complex-zmchb101-plays-essential-roles-in-maize-growth-and-development
#19
Xiaoming Yu, Lili Jiang, Rui Wu, Xinchao Meng, Ai Zhang, Ning Li, Qiong Xia, Xin Qi, Jinsong Pang, Zheng-Yi Xu, Bao Liu
ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917895/small-molecules-increase-direct-neural-conversion-of-human-fibroblasts
#20
Ulrich Pfisterer, Fredrik Ek, Stefan Lang, Shamit Soneji, Roger Olsson, Malin Parmar
The generation of human induced neurons (hiNs) via exogenous delivery of neural transcription factors represents a novel technique to obtain disease and patient specific neurons. These cells have the potential to be used for disease modeling, diagnostics and drug screening, and also to be further developed for brain repair. In the present study, we utilized hiNs to develop an unbiased screening assay for small molecules that increase the conversion efficiency. Using this assay, we screened 307 compounds from five annotated libraries and identified six compounds that were very potent in potentiating the reprogramming process...
December 5, 2016: Scientific Reports
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