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https://www.readbyqxmd.com/read/28943935/identification-of-key-genes-associated-with-the-effect-of-osmotic-stimuli-on-intervertebral-discs-using-microarray-analysis
#1
Guangxiao Ni, Guobin Liu, Kunlun Yu
The present study aimed to explore the effect of osmotic stimuli on intervertebral discs (IVDs) using microarray analysis. Gene expression dataset GSE1648 was downloaded from the Gene Expression Omnibus database. There were 11 IVD cell samples in this dataset, which included 4 hyperosmotic stimuli samples, 3 hypoosmotic stimuli samples and 4 isosmotic stimuli samples. The differentially expressed genes (DEGs) in hyperosmotic or hypoosmotic IVD cells (designated DEGs-hyper or DEGs-hypo) were identified, compared with isosmotic cells, using the limma package of R software...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28943325/lamin-like-proteins-negatively-regulate-plant-immunity-through-nac-with-transmembrane-motif1-like9-and-nonexpressor-of-pr-genes1-in-arabidopsis-thaliana
#2
Tongtong Guo, Xuegao Mao, Hui Zhang, Yu Zhang, Mengdi Fu, Zhenfei Sun, Peng Kuai, Yonggen Lou, Yuda Fang
Nuclear lamins are involved in multiple biological processes in metazoan cells. The CROWDED NUCLEI (CRWN) family proteins are considered as lamin-like candidates in Arabidopsis, however, the functions of these proteins are largely unknown. In this article, we show that crwn1 crwn2 double mutant displays an enhanced resistance against virulent bacterial pathogens, and both virulent bacteria and salicylic acid (SA) induce transcription of CRWN1 gene as well as proteasome-mediated degradation of CRWN1 protein...
September 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28942538/photoperiodism-dynamics-during-the-domestication-and-improvement-of-soybean
#3
REVIEW
Sheng-Rui Zhang, Huan Wang, Zhongyu Wang, Yao Ren, Lifang Niu, Jun Liu, Bin Liu
Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes...
September 21, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28939059/complex-integrated-analysis-of-lncrnas-mirnas-mrnas-in-oral-squamous-cell-carcinoma
#4
Simin Li, Xiujie Chen, Xiangqiong Liu, Yang Yu, Hongying Pan, Rainer Haak, Jana Schmidt, Dirk Ziebolz, Gerhard Schmalz
OBJECTIVES: This study aims to reveal regulatory network of lncRNAs-miRNAs-mRNAs in oral squamous cell carcinoma (OSCC) through gene expression data. MATERIAL AND METHODS: Differentially expressed lncRNAs, miRNAs and mRNAs (cut-off: False discovery rate (FDR)<0.05 and |fold change|>1.5) were unveiled by package edgeR of R. Cox regression analysis was performed to screen prognostic factors in OSCC related with overall survival (OS) and relapse-free survival (RFS)...
October 2017: Oral Oncology
https://www.readbyqxmd.com/read/28938158/directional-migration-in-esophageal-squamous-cell-carcinoma-escc-is-epigenetically-regulated-by-set-nuclear-oncogene-a-member-of-the-inhibitor-of-histone-acetyltransferase-complex
#5
Xiang Yuan, Xinshuai Wang, Bianli Gu, Yingjian Ma, Yiwen Liu, Man Sun, Jinyu Kong, Wei Sun, Huizhi Wang, Fuyou Zhou, Shegan Gao
Directional cell migration is of fundamental importance to a variety of biological events, including metastasis of malignant cells. Herein, we specifically investigated SET oncoprotein, a subunit of the recently identified inhibitor of acetyltransferases (INHAT) complex and identified its role in the establishment of front-rear cell polarity and directional migration in Esophageal Squamous Cell Carcinoma (ESCC). We further define the molecular circuits that govern these processes by showing that SET modulated DOCK7/RAC1 and cofilin signaling events...
September 19, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28934501/model-based-design-of-rna-hybridization-networks-implemented-in-living-cells
#6
Guillermo Rodrigo, Satya Prakash, Shensi Shen, Eszter Majer, José-Antonio Daròs, Alfonso Jaramillo
Synthetic gene circuits allow the behavior of living cells to be reprogrammed, and non-coding small RNAs (sRNAs) are increasingly being used as programmable regulators of gene expression. However, sRNAs (natural or synthetic) are generally used to regulate single target genes, while complex dynamic behaviors would require networks of sRNAs regulating each other. Here, we report a strategy for implementing such networks that exploits hybridization reactions carried out exclusively by multifaceted sRNAs that are both targets of and triggers for other sRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934252/three-way-interaction-model-to-trace-the-mechanisms-involved-in-alzheimer-s-disease-transgenic-mice
#7
Nasibeh Khayer, Sayed-Amir Marashi, Mehdi Mirzaie, Fatemeh Goshadrou
Alzheimer's disease (AD) is the most common cause for dementia in human. Currently, more than 46 million people in the world suffer from AD and it is estimated that by 2050 this number increases to more than 131 million. AD is considered as a complex disease. Therefore, understanding the mechanism of AD is a universal challenge. Nowadays, a huge number of disease-related high-throughput "omics" datasets are freely available. Such datasets contain valuable information about disease-related pathways and their corresponding gene interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28931651/region-specific-rna-m-6-a-methylation-represents-a-new-layer-of-control-in-the-gene-regulatory-network-in-the-mouse-brain
#8
Mengqi Chang, Hongyi Lv, Weilong Zhang, Chunhui Ma, Xue He, Shunli Zhao, Zhi-Wei Zhang, Yi-Xin Zeng, Shuhui Song, Yamei Niu, Wei-Min Tong
N(6)-methyladenosine (m(6)A) is the most abundant epitranscriptomic mark found on mRNA and has important roles in various physiological processes. Despite the relatively high m(6)A levels in the brain, its potential functions in the brain remain largely unexplored. We performed a transcriptome-wide methylation analysis using the mouse brain to depict its region-specific methylation profile. RNA methylation levels in mouse cerebellum are generally higher than those in the cerebral cortex. Heterogeneity of RNA methylation exists across different brain regions and different types of neural cells including the mRNAs to be methylated, their methylation levels and methylation site selection...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28931004/the-logic-of-the-floral-transition-reverse-engineering-the-switch-controlling-the-identity-of-lateral-organs
#9
Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman
Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the question of whether alternative networks could produce the same set of observed results. This issue has been addressed here through a survey of the published intercellular distribution of expressed regulatory genes and techniques both developed and applied to Boolean network models...
September 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28930614/inter-species-functional-interactome-of-nuclear-steroid-receptors-r1
#10
Styliani A Geronikolou, Athanasia Pavlopoulou, Christina Kanaka-Gantenbein, George Chrousos
Steroids exert their actions by binding to the glucocorticoid, mineralocorticoid, androgen, estrogen and progesterone classes of receptors. Despite an exponential increase in our knowledge of steroid receptors, their interactions with other molecules, subcellular location and functions still need further elucidation. To unravel the mechanism(s) of action of the steroid hormones, as well as the function of their cognate nuclear receptors, an interaction network was created (henceforth referred to as "R1 Interactome")- illustrating that robust interactions have been preserved in rodents, frog, zebra fish and drosophila...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#11
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28929029/association-of-rs1801157-single-nucleotide-polymorphism-of-cxcl12-gene-in-breast-cancer-in-pakistan-and-in-silico-expression-analysis-of-cxcl12-cxcr4-associated-biological-regulatory-network
#12
Samra Khalid, Rumeza Hanif
BACKGROUND: C-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and tumorigenesis. The single nucleotide polymorphism (SNP) rs1801157 of CXCL12 gene has been found to be associated with higher risk of BC. METHODS: Our study focuses on the genotypic and allelic distribution of SNP (rs1801157; G/A) in Pakistani population as well as its association with the clinico-pathological features...
2017: PeerJ
https://www.readbyqxmd.com/read/28928947/puzzles-in-modern-biology-v-why-are-genomes-overwired
#13
Steven A Frank
Many factors affect eukaryotic gene expression. Transcription factors, histone codes, DNA folding, and noncoding RNA modulate expression. Those factors interact in large, broadly connected regulatory control networks. An engineer following classical principles of control theory would design a simpler regulatory network. Why are genomes overwired? Neutrality or enhanced robustness may lead to the accumulation of additional factors that complicate network architecture. Dynamics progresses like a ratchet. New factors get added...
2017: F1000Research
https://www.readbyqxmd.com/read/28928941/computational-design-of-molecular-motors-as-nanocircuits-in-leishmaniasis
#14
Dipali Kosey, Shailza Singh
Cutaneous leishmaniasis is the most common form of lesihmaniasis, caused by Leishmania major and is spread by the bite of a sandfly .This species infects the macrophages and dendritic cells Due to multi-drug resistance, there is a need for a new therapeutic technique. Recently, a novel molecular motor of Leishmania, Myosin XXI, was classified and characterized. In addition, the drug resistance in this organism has been linked with the overexpression of ABC transporters. Systems biology aims to study the simulation and modeling of natural biological systems whereas synthetic biology deals with building novel and artificial biological parts and devices  Together they have contributed enormously to drug discovery, vaccine design and development, infectious disease detection and diagnostics...
2017: F1000Research
https://www.readbyqxmd.com/read/28927264/comparative-interactomes-of-vrk1-and-vrk3-with-their-distinct-roles-in-the-cell-cycle-of-liver-cancer
#15
Namgyu Lee, Dae-Kyum Kim, Seung Hyun Han, Hye Guk Ryu, Sung Jin Park, Kyong-Tai Kim, Kwan Yong Choi
Vaccinia-related kinase 1 (VRK1) and VRK3 are members of the VRK family of serine/threonine kinases and are principally localized in the nucleus. Despite the crucial roles of VRK1/ VRK3 in physiology and disease, the molecular and functional interactions of VRK1/VRK3 are poorly understood. Here, we identified over 200 unreported VRK1/VRK3-interacting candidate proteins by affinity purification and LC-MS/MS. The networks of VRK1 and VRK3 interactomes were found to be associated with important biological processes such as the cell cycle, DNA repair, chromatin assembly, and RNA processing...
August 31, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28919364/forward-and-reverse-genetics-approaches-to-uncover-metabolic-aging-pathways-in-caenorhabditis-elegans
#16
REVIEW
Arwen W Gao, Jelmi Uit de Bos, Mark G Sterken, Jan E Kammenga, Reuben L Smith, Riekelt H Houtkooper
The biological mechanisms of aging have been studied in depth and prominent findings in this field promote the development of new therapies for age-associated disorders. Various model organisms are used for research on aging; among these, the nematode Caenorhabditis elegans has been widely used and has provided valuable knowledge in determining the regulatory mechanisms driving the aging process. Many genes involved in lifespan regulation are associated with metabolic pathways and are influenced by genetic and environmental factors...
September 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28919164/integrated-analysis-of-microrna-and-gene-expression-profiles-reveals-a-functional-regulatory-module-associated-with-liver-fibrosis
#17
Wei Chen, Wenshan Zhao, Aiting Yang, Anjian Xu, Huan Wang, Min Cong, Tianhui Liu, Ping Wang, Hong You
BACKGROUND: Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation have important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS: The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28916800/alternative-splicing-complexity-contributes-to-genetic-improvement-of-drought-resistance-in-the-rice-maintainer-huhan2b
#18
Haibin Wei, Qiaojun Lou, Kai Xu, Ming Yan, Hui Xia, Xiaosong Ma, Xinqiao Yu, Lijun Luo
Water-saving and drought-resistantce rice (WDR) breeding practices have greatly increased grain yield and drought resistance. To study the genetic basis of adaptation to drought, transcriptome sequences from the WDR maintainer line HuHan2B and the recurrent parent HanFengB were analyzed for alternative splicing (AS) complexity. Intron retention, the dominant AS type, accounted for 42% of the observed AS events. Differential expression analysis revealed transcripts were preferentially expressed in different varieties and conditions...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912490/the-interdependent-network-of-gene-regulation-and-metabolism-is-robust-where-it-needs-to-be
#19
David F Klosik, Anne Grimbs, Stefan Bornholdt, Marc-Thorsten Hütt
Despite being highly interdependent, the major biochemical networks of the living cell-the networks of interacting genes and of metabolic reactions, respectively-have been approached mostly as separate systems so far. Recently, a framework for interdependent networks has emerged in the context of statistical physics. In a first quantitative application of this framework to systems biology, here we study the interdependent network of gene regulation and metabolism for the model organism Escherichia coli in terms of a biologically motivated percolation model...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28904337/toxoplasma-modulates-signature-pathways-of-human-epilepsy-neurodegeneration-cancer
#20
Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima McLeod
One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a comprehensive systems analysis of the infected brain: We identified susceptibility genes for congenital toxoplasmosis in our cohort of infected humans and found these genes are expressed in human brain...
September 13, 2017: Scientific Reports
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