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https://www.readbyqxmd.com/read/28938739/sequence-variants-of-khdrbs1-as-high-penetrance-susceptibility-risks-for-primary-ovarian-insufficiency-by-mis-regulating-mrna-alternative-splicing
#1
Binbin Wang, Lin Li, Ying Zhu, Wei Zhang, Xi Wang, Beili Chen, Tengyan Li, Hong Pan, Jing Wang, Kehkooi Kee, Yunxia Cao
STUDY QUESTION: Does a novel heterozygous KHDRBS1 variant, identified using whole-exome sequencing (WES) in two patients with primary ovarian insufficiency (POI) in a pedigree, cause defects in mRNA alternative splicing? SUMMARY ANSWER: The heterozygous variant of KHDRBS1 was confirmed to cause defects in alternative splicing of many genes involved in DNA replication and repair. WHAT IS KNOWN ALREADY: Studies in mice revealed that Khdrbs1 deficient females are subfertile, which manifests as delayed sexual maturity and significantly reduced numbers of secondary and pre-antral follicles...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938591/genistein-up-regulates-mir-20a-to-disrupt-spermatogenesis-via-targeting-limk1
#2
Hao Gu, Wei Wu, Beilei Yuan, Qiuqin Tang, Dan Guo, Yiqiu Chen, Yankai Xia, Lingqing Hu, Daozhen Chen, Jiahao Sha, Xinru Wang
Genistein (GEN) is one of the isoflavones that has effect on male reproduction. However, the underlying mechanism remains unknown. miRNAs are a type of small non-coding RNAs that play important roles in spermatogenesis. We measured the GEN levels and miR-17-92 cluster expression in infertile subjects and found that miR-17-92 might be involved in GEN induced abnormal spermatogenesis. To clarify, we fed adult ICR mice with different doses of GEN (0, 0.5, 5, 50 and 250 mg/kg/day) for 35 days to study the underlying mechanism...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938584/bmpr2-promotes-invasion-and-metastasis-via-the-rhoa-rock-limk2-pathway-in-human-osteosarcoma-cells
#3
Shidong Wang, Tingting Ren, Guangjun Jiao, Yi Huang, Xing Bao, Fan Zhang, Kuisheng Liu, Bingxin Zheng, Kunkun Sun, Wei Guo
Bone morphogenetic protein receptor 2 (BMPR2) has been identified in several types of cancer. However, its role in osteosarcoma is largely unknown. We systematically investigated the role of BMPR2 in osteosarcoma cell lines, human tissue samples and xenograft models. The relationship between BMPR2 expression and osteosarcoma patients' survival was investigated by bioinformatics and clinical data. Wound healing assay and transwell assay were used to detect the changes of cell migration and invasion ability after BMPR2 transfection...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938564/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#4
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938550/prognostic-value-of-dna-repair-genes-based-on-stratification-of-glioblastomas
#5
Sun Kun, Qiwen Duan, Gang Liu, Jing-Min Lu
Abnormal expression of DNA repair genes is frequently associated with cancerogenesis of many tumors, however, the role DNA repair genes play in the progression of glioblastoma remains unclear. In this study, taking advantage of large scale of RNA-seq data, as well as clinical data, the function and prognosis value of key DNA repair genes in glioblastoma were analyzed by systematically bioinformatic approaches. Clustering was performed to screen potentially abnormal DNA repair genes related to the prognosis of glioblastoma, followed by unsupervised clustering to identify molecular subtypes of glioblastomas...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938522/mir-539-inhibits-human-colorectal-cancer-progression-by-targeting-runx2
#6
Dacheng Wen, Songhe Li, Weidong Jiang, Jiaming Zhu, Jingjing Liu, Shutao Zhao
Emerging evidence has shown that microRNAs (miRNAs) such as miR-539 play critical roles in carcinogenesis and progression in many types of cancer, including human colorectal cancer (CRC). However, the roles and underlying mechanism of miR-539 in CRC have not been well identified. The aims of this study were, therefore, to investigate the regulatory role and potential mechanism of miR-539 in human CRC. Here, we show that miR-539 expression is downregulated in CRC tissues and cell lines. The expression level of miR-539 is inversely associated with advanced clinical stage and lymph node metastasis...
September 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28937906/protein-activation-in-periapical-reaction-to-iodoform-containing-root-canal-sealer
#7
Nili Tickotsky, Moti Moskovitz
OBJECTIVES: An association between root canal sealers and periapical lesions in primary dentition has been suggested, yet the chemical-protein interactions that may be involved in it have not been studied. The present study explored root sealer components' effect on periapical tissue proteins using bioinformatics tools. STUDY DESIGN: For each chemical component of Endoflas F.S. root sealing material we identified the known and predicted target proteins, using STITCH (search tool for interactions of chemicals http://stitch...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28937156/carsite-identifying-carbonylated-sites-of-human-proteins-based-on-a-one-sided-selection-resampling-method
#8
Yun Zuo, Cang-Zhi Jia
Protein carbonylation is one of the most important biomarkers of oxidative protein damage and such protein damage is linked to various diseases and aging. It is thus vital that carbonylation sites are identified accurately. In this study, CarSite, a novel bioinformatics tool, was established to identify carbonylation sites in human proteins. The one-sided selection (OSS) resampling method was used to establish balanced training datasets and this resampling method is demonstrated to perform better than a Monte Carlo resampling method via 10-fold cross-validation tests on the Jia dataset...
September 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28936982/optimization-and-quality-control-of-genome-wide-hi-c-library-preparation
#9
Xiang-Yuan Zhang, Chao He, Bing-Yu Ye, De-Jian Xie, Ming-Lei Shi, Yan Zhang, Wen-Long Shen, Ping Li, Zhi-Hu Zhao
Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28936555/resveratrol-suppresses-melanoma-by-inhibiting-nf-%C3%AE%C2%BAb-mir-221-and-inducing-tfg-expression
#10
Fangfang Wu, Liying Cui
Resveratrol (Res) is a natural compound with anti-cancer effects. The goal of this study is to evaluate the suppression of Res in melanoma and investigate its relationship with miRNAs during this process. The in vitro and in vivo anti-cancer abilities of Res were evaluated using cellular assays and animal model. Two melanoma cell lines (A375 and MV3) were used for both in vitro assay and in vivo experiments. qRT-PCR and Western blot were used to detect the changes in gene expressions and protein levels. Dual-luciferase reporter assay and bioinformatic tools were used to further confirm the protein binding and activation of targeted genes...
September 21, 2017: Archives of Dermatological Research
https://www.readbyqxmd.com/read/28936142/bioinformatics-approach-a-powerful-tool-for-microrna-research
#11
EDITORIAL
Zafar Rasheed
No abstract text is available yet for this article.
July 2017: International Journal of Health Sciences
https://www.readbyqxmd.com/read/28935987/toward-the-identification-of-a-type-i-toxin-antitoxin-system-in-the-plasmid-dna-of-dairy-lactobacillus-rhamnosus
#12
Claudia Folli, Alessia Levante, Riccardo Percudani, Davide Amidani, Stefania Bottazzi, Alberto Ferrari, Claudio Rivetti, Erasmo Neviani, Camilla Lazzi
Plasmids carry genes that give bacteria beneficial traits and allow them to survive in competitive environments. In many cases, they also harbor toxin-antitoxin (TA) systems necessary for plasmid maintenance. TA systems are generally characterized by a stable "toxin", a protein or peptide capable of killing the cell upon plasmid loss and by an unstable "antitoxin", a protein or a non-coding RNA that inhibits toxin activity. Here we report data toward the identification of a RNA-regulated TA system in the plasmid DNA of L...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935959/the-crystal-structure-of-the-regulatory-domain-of-the-human-sodium-driven-chloride-bicarbonate-exchanger
#13
Carolina M Alvadia, Theis Sommer, Kaare Bjerregaard-Andersen, Helle Hasager Damkier, Michele Montrasio, Christian Aalkjaer, J Preben Morth
The sodium-driven chloride/bicarbonate exchanger (NDCBE) is essential for maintaining homeostatic pH in neurons. The crystal structure at 2.8 Å resolution of the regulatory N-terminal domain of human NDCBE represents the first crystal structure of an electroneutral sodium-bicarbonate cotransporter. The crystal structure forms an equivalent dimeric interface as observed for the cytoplasmic domain of Band 3, and thus establishes that the consensus motif VTVLP is the key minimal dimerization motif. The VTVLP motif is highly conserved and likely to be the physiologically relevant interface for all other members of the SLC4 family...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935842/the-paralogs-to-the-c-terminal-domain-of-the-cyanobacterial-ocp-are-carotenoid-donors-to-hcps
#14
Fernando Muzzopappa, Adjélé Wilson, Vinosa Yogarajah, Sandrine Cot, François Perreau, Cédric Montigny, Céline Bourcier de Carbon, Diana Kirilovsky
The photoactive Orange Carotenoid Protein photoprotects cyanobacteria cells by quenching singlet oxygen and excess excitation energy. Its N-terminal domain (NTD) is the active part of the protein and the C-terminal domain (CTD) regulates the activity. Recently, the characteristics of a family of soluble carotenoid-binding proteins (Helical Carotenoid Proteins or HCPs), paralogs of NTD-OCP, were described. Bioinformatics studies also revealed the existence of genes coding for homologs of CTD. Here, we show that the latter genes encode carotenoid proteins (CTDHs)...
September 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28935819/identification-of-truncated-form-of-nosp-as-a-transcription-factor-to-regulate-the-biosynthesis-of-nosiheptide
#15
Xuri Wu, Liang Jin, Hong Zhang, Ruinian Tong, Min Ma, Yijun Chen
Nosiheptide (NOS), a typical member of the thiopeptides, possesses strong activities against multidrug-resistant, gram-positive bacterial pathogens. Similar to other thiopeptides, the biosynthetic pathway of NOS belongs to a ribosomally synthesized and posttranslationally modified peptide system. Bioinformatics analysis of the NOS gene cluster suggests that nosP gene encodes a homologous protein of Streptomyces antibiotic regulatory protein (SARP) family. In the present study, the actual initiation codon of nosP was identified by comparison of potential initiation codons GUG and AUG...
September 21, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28935764/ubiquitin-recognition-of-bap1-understanding-its-enzymatic-function
#16
Pranita Hanpude, Sushmita Bhattacharya, Abhishek Kumar Singh, Tushar Kanti Maiti
BRCA1 associated protein 1 (BAP1) is a nuclear localizing UCH, having tumor suppressor activity and is widely involved in many crucial cellular processes. BAP1 has garnered attention for its links with cancer, however, the molecular mechanism in the regulation of cancer by BAP1 has not been established. Among the four UCHs, only BAP1 and UCHL5 are able to hydrolyze small and large ubiquitin adducts but UCHL5 hydrolyzes only when it is present in the PA700 complex of the proteasome. The ability of BAP1 to cleave large ubiquitin derivatives is because of its relatively longer active-site crossover loop than other UCHs...
September 21, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28935704/the-splicing-co-factor-barricade-tat-sf1-is-required-for-cell-cycle-and-lineage-progression-in-drosophila-neural-stem-cells
#17
Monika K Abramczuk, Thomas R Burkard, Vivien Rolland, Victoria Steinmann, Peter Duchek, Yanrui Jiang, Sebastian Wissel, Heinrich Reichert, Juergen A Knoblich
Stem cells need to balance self-renewal and differentiation for correct tissue development and homeostasis. Defects in this balance can lead to developmental defects or tumor formation. In recent years, mRNA splicing has emerged as one important mechanism regulating cell fate decisions. Here we address the role of the evolutionary conserved splicing co-factor Barricade (Barc)/Tat-SF1/CUS2 in Drosophila neural stem cell (neuroblast) lineage formation. We show that Barc is required for the generation of neurons during Drosophila brain development by ensuring correct neural progenitor proliferation and differentiation...
September 21, 2017: Development
https://www.readbyqxmd.com/read/28934732/long-noncoding-rna-cir-promotes-chondrocyte-extracellular-matrix-degradation-in-osteoarthritis-by-acting-as-a-sponge-for-mir-27b
#18
Yu-Fei Li, Shu-Hua Li, Yong Liu, Ya-Tong Luo
BACKGROUND/AIMS: Osteoarthritis (OA) is a degenerative joint disease characterized by articular cartilage degradation. The degradation of the extracellular matrix (ECM) of chondrocyte is closely associated with the destruction of joints in OA patients. lncRNAs are non-coding segments of RNA that possess important regulatory functions at the cellular level and in a variety of pathophysiological processes. The present study was conducted to investigate whether lncRNA-CIR regulated the expression of MMP13 as a sponge of miR-27 in OA...
September 21, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28934692/identification-of-key-genes-and-pathways-and-therapeutic-agents-in-cadmium-treated-liver-cells-a-bioinformatics-study
#19
Liang Zhang, Yi Huang, Zhen Yu, Mengmeng Shao, Yunbo Luo, Yi Zhu
Evidence indicates that Cadmium (Cd) can accumulate in liver, which results in acute or chronic cell damage with unclear complex mechanisms. Thus, we aimed to explore the possible molecules and pathways by using bioinformatics methods Consequently, two datasets (GSE8865 and GSE31286) were retrieved and the differentially expressed genes (DEGs) were screened out. The intersection of the DEGs included seven up-regulated and forty-three down-regulated genes, which were mainly enriched in biological cell proliferation items, and were enriched in several metabolism-related pathways...
September 14, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28934514/new-bioinformatics-based-discrimination-formulas-for-differentiation-of-thalassemia-traits-from-iron-deficiency-anemia
#20
Abdul Hafeez Kandhro, Watshara Shoombuatong, Virapong Prachayasittikul, Pornlada Nuchnoi
Thalassemia traits (TTs) and iron deficiency anemia (IDA) are the most common disorders of hypochromic microcytic anemia (HMA). The present study aimed to differentiate TTs from IDA by analyzing discrimination formulas and provides comprehensive data of hemoglobin disorders prevalent in Pakistan. Among 12 published discrimination formulas, 6 formulas-MI, EF, G&K, RDWI, R, and HHI-were the most reliable to discriminate TTs from IDA. The failure cutoff values were improved by the random forest (RF) decision-tree approach...
August 1, 2017: Laboratory Medicine
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