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https://www.readbyqxmd.com/read/30025407/identification-of-the-c-reactive-protein-interaction-network-using-a-bioinformatics-approach-provides-insights-into-the-molecular-pathogenesis-of-hepatocellular-carcinoma
#1
Sha She, Lingyu Jiang, Zhenfang Zhang, Min Yang, Huaidong Hu, Peng Hu, Yong Liao, Yixuan Yang, Hong Ren
BACKGROUND/AIMS: C reactive protein (CRP) levels are elevated in many diseases, including malignant tumors and cardiovascular disorders. In this study, the protein interaction network for CRP was evaluated to determine the importance of CRP and its interacting proteins in the molecular pathogenesis of hepatocellular carcinoma (HCC). METHODS: Isobaric tags for relative and absolute quantitation (iTRAQ) and mass spectrometry were used to identify CRP interacting proteins in SMMC7721 cells...
July 19, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/30025248/comparative-proteomic-analysis-of-escherichia-coli-o157-h7-following-ohmic-and-water-bath-heating-by-capillary-hplc-ms-ms
#2
Xiaojing Tian, Qianqian Yu, Wei Wu, Xingmin Li, Ruitong Dai
Escherichia coli O157:H7 is an important food-borne pathogenic microorganism that has been used as a model organism for studying microbial inactivation effects and inactivation mechanism in various sterilization technologies. The objective of this study was to investigate the effects of high voltage short time ohmic- (HVST), low voltage long time ohmic- (LVLT), and water bath- (WB) heating on inactivation and proteome changes of E. coli O157:H7 cells at the same endpoint temperature of 72 °C, and to analyze whether a non-thermal death effect existed in ohmic heating...
June 8, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/30025185/genome-based-identification-of-a-plant-associated-marine-bacterium-as-a-rich-natural-product-source
#3
Reiko Ueoka, Agneya Bhushan, Silke I Probst, Walter M Bray, R Scott Lokey, Roger G Linington, Jörn Piel
The large number of sequenced bacterial genomes provides the opportunity to bioinformatically identify rich natural product sources among previously neglected microbial groups. Testing this discovery strategy, unusually high biosynthetic potential was suggested for the Oceanospirillales member Gynuella sunshinyii, a Gram-negative marine bacterium from the rhizosphere of the halophilic plant Carex scabrifolia. Its genome contains numerous unusual biosynthetic gene clusters for diverse types of metabolites. Genome-guided isolation yielded representatives of four different natural product classes, of which only alteramide A was known...
July 19, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/30025119/microrna-profiling-in-glaucoma-eyes-with-varying-degrees-of-optic-neuropathy-by-using-next-generation-sequencing
#4
Yaoming Liu, Yang Chen, Yayi Wang, Xinyu Zhang, Kai Gao, Shida Chen, Xiulan Zhang
Purpose: To explore the microRNA (miRNA) profile and its putative role in glaucomatous optic neuropathy by using next-generation sequencing. Methods: Aqueous humor (AH) samples were collected from 19 primary open-angle glaucoma (POAG) eyes and 17 cataract eyes before surgery. Next-generation sequencing was performed for RNA samples extracted from 18 AH samples, and the bioinformatics approach was applied for samples with adequate clean data output. The other 18 samples were used for quantitative PCR validation of sequencing results...
June 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/30025106/the-proteomic-landscape-in-the-vitreous-of-patients-with-age-related-and-diabetic-retinal-disease
#5
Christian Schori, Christian Trachsel, Jonas Grossmann, Ioanna Zygoula, Daniel Barthelmes, Christian Grimm
Purpose: In contrast to neovascular AMD (nAMD), no treatment option exists for dry AMD. Hence, the identification of specific biomarkers is required to facilitate diagnosis and therapy of dry AMD. Methods: The proteome of 34 vitreous humor samples (dry AMD: n = 6; nAMD: n = 10; proliferative diabetic retinopathy [PDR]: n = 9; epiretinal membrane [ERM]: n = 9) was analyzed by liquid chromatography coupled mass spectrometry. Then, label-free relative quantification of dry AMD, nAMD, and PDR relative to ERM, which was defined as the reference group, was performed...
March 20, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/30024701/bioinformatic-analysis-of-differentially-expressed-genes-involved-in-the-hepatitis-b-virus-associated-acute-liver-failure
#6
Lv Yong, Bai Guang, Li Yan
BACKGROUND: The rarity of acute liver failure, along with its severity and heterogeneity, has resulted in a very limited evidence to understand of the molecular mechanism. To analyze the differentially expressed genes (DEGs) in the Hepatitis B Virus -Associated Acute Liver Failure and elucidate the biological significance of the DEGs. METHODS: Firstly, differentially expressed genes (DEGs) between seventeen HBV-associated acute liver failure liver samples and ten control normal liver samples were identified by R package...
April 2018: Acta Gastro-enterologica Belgica
https://www.readbyqxmd.com/read/30024615/mir-192-prevents-renal-tubulointerstitial-fibrosis-in-diabetic-nephropathy-by-targeting-egr1
#7
F Liu, Z-P Zhang, G-D Xin, L-H Guo, Q Jiang, Z-X Wang
OBJECTIVE: Diabetic nephropathy (DN), as the most common and serious diabetic microvascular complication, has become the first cause of end-stage renal disease (ESRD) in many countries and regions. However, the pathogenesis of renal fibrosis during the development of DN remains unknown. MATERIALS AND METHODS: The expression levels of miR-192 and early growth response factor 1 (Egr1) were determined by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and Western blotting in the renal tissues of Otsuka-Long-Evans-Tokushima-Fatty (OLETF) and Long-Evans-Tokushima-Otsuka (LETO) rats...
July 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/30024602/the-role-of-mir-144-gspt1-axis-in-gastric-cancer
#8
Q-G Tian, R-C Tian, Y Liu, A-Y Niu, J Zhang, W-F Gao
OBJECTIVE: To investigate the potential effects of miR-144/GSPT1 axis on the development of gastric cancer. PATIENTS AND METHODS: The expressions of GSPT1 (G1 to S Phase Transition 1) and miR-144 were detected in gastric cancer tissues and the adjacent normal tissues. We also explored the levels of GSPT1 and miR-144 in both normal gastric cell line (GES-1) and gastric cells (SGC7901). Luciferase assay was conducted to evaluate the interaction between miR-144 and GSPT1...
July 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/30024092/mircorna-1275-promotes-proliferation-invasion-and-migration-of-glioma-cells-via-serpine1
#9
Dong-Mei Wu, Shan Wang, Xin Wen, Xin-Rui Han, Yong-Jian Wang, Shao-Hua Fan, Zi-Feng Zhang, Qun Shan, Jun Lu, Yuan-Lin Zheng
This study was designed to explore the relationship between miR-1275 and SERPINE1 and its effects on glioma cell proliferation, migration, invasion and apoptosis. Differentially expressed miRNAs and mRNAs in glioma tissues were screened out by bioinformatic analysis. Dual-luciferase reporter gene assay was used to validate the targeted relationship between miR-1275 and SERPINE1. qRT-PCR was used to detect the expression of miR-1275 and SERPINE1 in glioma tissues. The expressions of SERPINE1 and p53 pathway-related proteins in glioma cells were detected by western blot...
July 19, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/30023140/secapr-a-bioinformatics-pipeline-for-the-rapid-and-user-friendly-processing-of-targeted-enriched-illumina-sequences-from-raw-reads-to-alignments
#10
Tobias Andermann, Ángela Cano, Alexander Zizka, Christine Bacon, Alexandre Antonelli
Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproducible way. To tackle these challenges we introduce the Sequence Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple sequence alignments for downstream phylogenetic and phylogeographic analyses...
2018: PeerJ
https://www.readbyqxmd.com/read/30023002/irwnrlpi-integrating-random-walk-and-neighborhood-regularized-logistic-matrix-factorization-for-lncrna-protein-interaction-prediction
#11
Qi Zhao, Yue Zhang, Huan Hu, Guofei Ren, Wen Zhang, Hongsheng Liu
Long non-coding RNA (lncRNA) plays an important role in many important biological processes and has attracted widespread attention. Although the precise functions and mechanisms for most lncRNAs are still unknown, we are certain that lncRNAs usually perform their functions by interacting with the corresponding RNA- binding proteins. For example, lncRNA-protein interactions play an important role in post transcriptional gene regulation, such as splicing, translation, signaling, and advances in complex diseases...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/30022984/single-cell-rna-sequencing-of-rare-immune-cell-populations
#12
REVIEW
Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I Croucher, Tri Giang Phan
Single-cell RNA sequencing (scRNA-Seq) is transforming our ability to characterize cells, particularly rare cells that are often overlooked in bulk population analytical approaches. This has lead to the discovery of new cell types and cellular states that echo the underlying heterogeneity and plasticity in the immune system. Technologies for the capture, sequencing, and bioinformatic analysis of single cells are rapidly improving, and scRNA-Seq is now becoming much more accessible to non-specialized laboratories...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30022124/menthol-a-unique-urinary-volatile-compound-is-associated-with-chronic-inflammation-in-interstitial-cystitis
#13
Muhammad Shahid, Min Young Lee, Austin Yeon, Eunho Cho, Vikram Sairam, Luis Valdiviez, Sungyong You, Jayoung Kim
Chronic inflammation is a potential systemic risk factor for many bladder dysfunctions, including interstitial cystitis (IC). However, the underlying mechanism through which a healthy bladder protects itself from inflammatory triggers remains unknown. In this study, we identified odor compounds in urine obtained from IC patients and healthy controls. Using comprehensive solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (SPME-GC-TOF-MS) profiling and bioinformatics, we found that levels of urinary volatile metabolites, such as menthol, were significantly reduced in IC patients, compared to healthy controls...
July 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30021720/-mir-362-regulates-the-proliferation-and-apoptosis-of-porcine-immature-sertoli-cells-through-targeting-the-znf644-gene
#14
Mao Liang Ran, Lian Hua Dong, Bo Weng, Rong Cao, Fu Zhi Peng, Hu Gao, Hui Luo, Bin Chen
In testicular tissue, immature Sertoli cell proliferation ability determines the size of mature Sertoli cell populations, which further regulates the spermatogenesis in the adult male animals. Studies have demonstrated that microRNAs (miRNAs) participate in the regulation of the immature Sertoli cell proliferation and apoptosis, but the functions of most identified miRNAs remain unclear. In this study, based on previous RNA-seq results, we analyzed the regulatory role (s) of miR-362 in proliferation and apoptosis of porcine immature Sertoli cells...
July 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/30021719/-assessing-abundance-and-specificity-of-different-types-of-sgrna-targeting-mirna-precursors
#15
Hai Long Liu, Yang Shen, Yang Gao, Ling Zhou, Xiao Song Han, Chang Zhi Zhao, Gao Juan Yang, Yi Long Chen, Hui Yang, Sheng Song Xie
CRISPR/Cas technology enables efficient and specific editing the genome. Since different bacterial sources or artificially modified Cas9, as well as Cpf1 and other nucleases, recognize different PAMs (protospacer adjacent motifs), different gene editing nucleases may use different types of sgRNAs (small guide RNA). MicroRNAs (miRNAs) are a class of regulatory small non-coding RNAs. To determine whether specific targets for sgRNAs in miRNA precursor exit, the abundance and specificity of 11 different types of sgRNA targeting 28 645 miRNA precursors were analyzed in the present study using the CRISPR-offinder, a bioinformatics software developed in our own laboratory...
July 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/30021643/discovery-and-validation-of-autosomal-dominant-alzheimer-s-disease-mutations
#16
Simon Hsu, Brian A Gordon, Russ Hornbeck, Joanne B Norton, Denise Levitch, Adia Louden, Ellen Ziegemeier, Robert Laforce, Jasmeer Chhatwal, Gregory S Day, Eric McDade, John C Morris, Anne M Fagan, Tammie L S Benzinger, Alison M Goate, Carlos Cruchaga, Randall J Bateman, Celeste M Karch
BACKGROUND: Alzheimer's disease (AD) is a neurodegenerative disease that is clinically characterized by progressive cognitive decline. Mutations in amyloid-β precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) are the pathogenic cause of autosomal dominant AD (ADAD). However, polymorphisms also exist within these genes. METHODS: In order to distinguish polymorphisms from pathogenic mutations, the DIAN Expanded Registry has implemented an algorithm for determining ADAD pathogenicity using available information from multiple domains, including genetic, bioinformatic, clinical, imaging, and biofluid measures and in vitro analyses...
July 18, 2018: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/30021600/downregulation-of-mir-133a-3p-promotes-prostate-cancer-bone-metastasis-via-activating-pi3k-akt-signaling
#17
Yubo Tang, Jincheng Pan, Shuai Huang, Xinsheng Peng, Xuenong Zou, Yongxiang Luo, Dong Ren, Xin Zhang, Ronggang Li, Peiheng He, Qingde Wa
BACKGROUND: Bone metastasis is a leading cause of morbidity and mortality in advanced prostate cancer (PCa). Downexpression of miR-133a-3p has been found to contribute to the progression, recurrence and distant metastasis in PCa. However, clinical significance of miR-133a-3p in bone metastasis of PCa, and the biological role of miR-133a-3p and its molecular mechanisms underlying bone metastasis of PCa remain unclear. METHODS: miR-133a-3p expression was evaluated in 245 clinical PCa tissues by real-time PCR...
July 18, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/30021530/de-novo-profile-generation-based-on-sequence-context-specificity-with-the-long-short-term-memory-network
#18
Kazunori D Yamada, Kengo Kinoshita
BACKGROUND: Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Amino acid sequence profiles are widely used for bioinformatics studies, such as sequence similarity searches, multiple alignments, and evolutionary analyses. Currently, many biological sequences are becoming available, and the rapidly increasing amount of sequence data emphasizes the importance of scalable generators of amino acid sequence profiles...
July 18, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/30021381/microrna-519d-3p-inhibits-cell-proliferation-and-migration-by-targeting-troap-in-colorectal-cancer
#19
Xiaoyong Ye, Huizeng Lv
Increasing evidence suggests that miR-519d-3p functions as tumor suppressor in several tumors, including breast cancer. However, its biological role in the development of colorectal cancer (CRC) still remains unclear. In this study, we found that miR-519d-3p expression level was remarkably down-regulated in CRC tissues samples and cell lines when compared to adjacent normal tissues and cell line by using qRT-PCR detection. Lower miR-519d-3p expression was significantly correlated with TNM stage, tumor size and lymph node metastasis...
September 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/30021359/lncrna-meg3-enhances-131-i-sensitivity-in-thyroid-carcinoma-via-sponging-mir-182
#20
Yang Liu, Peiru Yue, Tao Zhou, Fengzhen Zhang, Huixiang Wang, Xiaoqi Chen
BACKGROUND: Long non-coding RNA (LncRNA) MEG3 has been demonstrated as a tumor suppressor in various cancers, including thyroid carcinoma (TC). However, the detail functions and possible mechanisms of MEG3 in 131 I resistance of TC remain to be uncovered. METHODS: qRT-PCR was performed for the detection of MEG3 and miR-182 levels. 131 I-resistant TC cells were constructed by continuous exposure to stepwise increased concentrations of 131 I. Western blot assay was used to measure the protein expressions of γ-H2 AX and H2 AX...
September 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
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