Read by QxMD icon Read

Network identification

Ronit Weisman
All organisms can respond to the availability of nutrients by regulating their metabolism, growth, and cell division. Central to the regulation of growth in response to nutrient availability is the target of rapamycin (TOR) signaling that is composed of two structurally distinct complexes: TOR complex 1 (TORC1) and TOR complex 2 (TORC2). The TOR genes were first identified in yeast as target of rapamycin, a natural product of a soil bacterium, which proved beneficial as an immunosuppressive and anticancer drug and is currently being tested for a handful of other pathological conditions including diabetes, neurodegeneration, and age-related diseases...
October 2016: Microbiology Spectrum
Jingjing Li, Jin Gao, Lei Han, Yinjie Zhang, Wen Guan, Liang Zhou, Yan Yu, Wei Han
Identifying interactions between ligands and transmembrane receptors is crucial for understanding the endocrine system. However, the present approaches for this purpose are still not capable of high-throughput screening. In this report, a membrane-anchored ligand and receptor yeast two-hybrid (MALAR-Y2H) system was established. In the method, an extracellular ligand is linked with an intracellular split-ubiquitin reporter system via a chimeric transmembrane structure. Meanwhile, the prey proteins of transmembrane receptors are fused to the other half of the split-ubiquitin reporter system...
October 20, 2016: Scientific Reports
Daniel V Guebel, Néstor V Torres
Motivation: In the brain of elderly-healthy individuals, the effects of sexual dimorphism and those due to normal aging appear overlapped. Discrimination of these two dimensions would powerfully contribute to a better understanding of the etiology of some neurodegenerative diseases, such as "sporadic" Alzheimer. Methods: Following a system biology approach, top-down and bottom-up strategies were combined. First, public transcriptome data corresponding to the transition from adulthood to the aging stage in normal, human hippocampus were analyzed through an optimized microarray post-processing (Q-GDEMAR method) together with a proper experimental design (full factorial analysis)...
2016: Frontiers in Aging Neuroscience
Yongbo Bao, Xiao Liu, Weiwei Zhang, Jianping Cao, Wei Li, Chenghua Li, Zhihua Lin
Clam, a filter-feeding lamellibranch mollusk, is capable to accumulate high levels of trace metals and has therefore become a model for investigation the mechanism of heavy metal toxification. In this study, the effects of cadmium were characterized in the gills of Tegillarca granosa during a 96-hour exposure course using integrated metabolomic and proteomic approaches. Neurotoxicity and disturbances in energy metabolism were implicated according to the metabolic responses after Cd exposure, and eventually affected the osmotic function of gill tissue...
October 20, 2016: Scientific Reports
Si Wu, Saleh Alseekh, Álvaro Cuadros-Inostroza, Corina M Fusari, Marek Mutwil, Rik Kooke, Joost B Keurentjes, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman
Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana...
October 2016: PLoS Genetics
Jimena Giudice, Zheng Xia, Wei Li, Thomas A Cooper
The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. We found that homozygous Celf1 knock-out neonates exhibited cardiac dysfunction not observed in older homozygous animals, although homozygous mice are smaller than wild type littermates throughout development...
October 19, 2016: Scientific Reports
Qiangfeng Wang, Huanxia Yang, Lingjiao Wu, Jian Yao, Xiaohua Meng, Han Jiang, Cheng Xiao, Fusheng Wu
BACKGROUND: In recent years, long non-coding RNAs (lncRNAs) have been shown to play a critical regulatory role in cancer biology. However, the contribution of lncRNAs to papillary thyroid cancer (PTC) remains largely unknown. METHODS: RNA sequencing and quantitative reverse transcription PCR (qRT-PCR) were used to detect and verify, respectively, changes to the transcriptomic profile in 12 PTC tissues compared to paired normal adjacent tissues. The statistical correlation between differentially expressed lncRNAs and clinicopathological characteristics was analysed, and potential lncRNA functions were predicted by examining annotations for the co-expressed mRNAs...
October 19, 2016: Thyroid: Official Journal of the American Thyroid Association
B Li, J Liu, Y Y Zhang, P Q Wang, Y N Yu, R X Kang, H L Wu, X X Zhang, Z Wang, Y Y Wang
Module-based methods have made much progress in deconstructing biological networks. However, it is a great challenge to quantitatively compare the topological structural variations of modules (allosteric modules [AMs]) under different situations. A total of 23, 42, and 15 coexpression modules were identified in baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) in a global anti-ischemic mice network, respectively. Then, we integrated the methods of module-based consensus ratio (MCR) and modified Zsummary module statistic to validate 12 BA, 22 JA, and 8 UA on-modules based on comparing with vehicle...
October 19, 2016: CPT: Pharmacometrics & Systems Pharmacology
Zhanzhan Xu, Yu Zhou, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Ovarian cancer is the first leading cause of mortality in gynecological malignancies. To identify key genes and microRNAs in ovarian cancer, mRNA microarray dataset GSE36668, GSE18520, GSE14407 and microRNA dataset GSE47841 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and microRNAs (DEMs) were obtained using GEO2R. Functional and pathway enrichment analysis were performed for DEGs using DAVID database. Protein-protein interaction (PPI) network was established by STRING and visualized by Cytoscape...
November 2016: Medical Oncology
Zhi Chen, Hao Wu, Guohua Wang, Ye Feng
BACKGROUND: This study was aimed to explore the molecular mechanisms of hypertensive nephropathy (HTN). METHODS: Gene expression profile of GSE37460, which based on 27 healthy living donor samples (HTN group) and 15 hypertensive nephropathy samples (control group), were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between two groups were identified. STRING database was used to reveal protein-protein interaction (PPI) network of DEGs, followed by the functional enrichment analysis of the PPI network...
October 18, 2016: BMC Nephrology
Salma Jamal, Sukriti Goyal, Asheesh Shanker, Abhinav Grover
BACKGROUND: Alzheimer's disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheimer's is still unclear, however one of the other major factors involved in AD pathogenesis are the genetic factors and around 70 % risk of the disease is assumed to be due to the large number of genes involved. Although genetic association studies have revealed a number of potential AD susceptibility genes, there still exists a need for identification of unidentified AD-associated genes and therapeutic targets to have better understanding of the disease-causing mechanisms of Alzheimer's towards development of effective AD therapeutics...
October 18, 2016: BMC Genomics
Jessica A Castillo, Clinton W Epps, Mackenzie R Jeffress, Chris Ray, Thomas J Rodhouse, Donelle Schwalm
Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Salvatore De Cosmo, Francesca Viazzi, Antonio Pacilli, Carlo Giorda, Antonio Ceriello, Sandro Gentile, Giuseppina Russo, Maria C Rossi, Antonio Nicolucci, Pietro Guida, Roberto Pontremoli
: The identification of clinical predictors for the development of chronic kidney disease is a critical issue in the management of patients with type 2 diabetes mellitus.We evaluated 27,029 patients with type 2 diabetes mellitus and estimated glomerular filtration rate (eGFR) ≥60 mL/min/1.73 m and normoalbuminuria from the database of the Italian Association of Clinical Diabetologists network. Primary outcomes were eGFR <60 mL/min/1.73 m and normoalbuminuria; albuminuria and eGFR ≥60 mL/min/1...
July 2016: Medicine (Baltimore)
Shazia Nafis, Kalaiarasan Ponnusamy, Mohammad Husain, R K Brojen Singh, Rameshwar N K Bamezai
An experimentally validated set of apoptosis-regulatory proteins was subjected to network analysis, depicting a scale-free hierarchical fractal network. The power-law distribution of the various topological properties of the network revealed the fractal nature of the network, a signature of self-organization of the network where the network maintained the democratic constitution of nodes at various levels and showed the absence of the centrality-lethality control system. Even though network breakdown under the absence of the centrality-lethality rule of hub removal did not happen, the change in the topological properties of the network could be observed...
October 18, 2016: Molecular BioSystems
Langdong Chen, Diya Lv, Dongyao Wang, Xiaofei Chen, Zhenyu Zhu, Yan Cao, Yifeng Chai
Herbal medicines have long been widely used in the treatment of various complex diseases in China. However, the active constituents and therapeutic mechanisms of many herbal medicines remain undefined. Therefore, the identification of the active components and target proteins in these herbal medicines is a formidable task in herbal medicine research. In this study, we proposed a strategy, which integrates network pharmacology with biomedical analysis and surface plasmon resonance (SPR) to predict the active ingredients and potential targets of herbal medicine Sophora flavescens or Kushen in Chinese, and evaluate its anti-fibrosis activity...
October 18, 2016: Molecular BioSystems
Hjalte C R Sass, Rehannah Borup, Mikkel Alanin, Finn Cilius Nielsen, Per Cayé-Thomasen
The objective of this study was to determine global gene expression in relation to Vestibular schwannomas (VS) growth rate and to identify signal transduction pathways and functional molecular networks associated with growth. Repeated magnetic resonance imaging (MRI) prior to surgery determined tumor growth rate. Following tissue sampling during surgery, mRNA was extracted from 16 sporadic VS. Double stranded cDNA was synthesized from the mRNA and used as template for in vitro transcription reaction to synthesize biotin-labeled antisense cRNA, which was hybridized to Affymetrix HG-U133A arrays and analyzed by dChip software...
October 17, 2016: Journal of Neuro-oncology
Kaname Uno, Katsunori Iijima, Yasuhiko Abe, Tomoyuki Koike, Yasushi Takahashi, Nobuyuki Ara, Tooru Shimosegawa
PURPOSE: Endoscopic diagnosis of gastric cancer (GC) that emerges after eradication of Helicobacter pylori may be affected by unique morphological changes. Using comprehensive endoscopic imaging, which can reveal biological alterations in gastric mucosa after eradication, previous studies demonstrated that Congo red chromoendoscopy (CRE) might clearly show an acid non-secretory area (ANA) with malignant potential, while autofluorescence imaging (AFI) without drug injection or dyeing may achieve early detection or prediction of GC...
September 2016: Journal of Gastric Cancer
Vincenza Granata, Roberta Fusco, Alfonso Reginelli, Luca Roberto, Francesco Granata, Daniela Rega, Antonio Rotondo, Roberto Grassi, Francesco Izzo, Antonella Petrillo
Anal cancer is uncommon neoplasm with an incidence of 2 new cases per 100,000 per year in the USA, accounting approximately 0.4 % of all tumors and 2.5 % of gastrointestinal malignancies. An early detection of the anal cancer is crucial for the patient management, whereas the diagnosis at an early stage allows conservative management with sphincter sparing, on the contrary a delays in diagnosis might lead to an advance cancer stage at presentation with worst survival. According to National Comprehensive Cancer Network (NCCN) Anal Carcinoma guidelines the patients should be subjected to a careful clinical examination, including a digital rectal examination (DRE), an anoscopic examination, and palpation of inguinal nodes...
2016: Infectious Agents and Cancer
Hao Li, Jizong Zhao, Wen Wang, Lu Zhang, Qing Lan, Jiangfei Wang, Yong Cao, Jizong Zhao
BACKGROUND: Intracranial aneurysm (IA) is a cerebrovascular disorder characterized by an abnormally bulged artery in the brain and subarachnoid hemorrhage caused by IA rupture with a high ratio of fatality and morbidity. However, the genetic etiology of IA remains largely unknown. MATERIALS AND METHODS: A dysregulated lncRNA-associated competing endogenous RNA (ceRNA) network was constructed by utilizing sample-matched microRNA (miRNA), long non-coding RNA (lncRNA) and mRNA expression profiles in 12 saccular IA samples and paired control arteries...
October 14, 2016: World Neurosurgery
Yolande F M Ramos, Ingrid Meulenbelt
PURPOSE OF REVIEW: The purpose of this review is to provide an update of recent advances in the established role of different layers of epigenetic control mechanism that are used by joint cells to ensure tissue homeostasis and cope with changing microenvironment (e.g. ageing or disease). RECENT FINDINGS: New studies have further strengthened the evidence that joint tissue cells highly dependent on epigenetic control mechanisms, such as methylation at CpG-sites, noncoding RNAs and histone modifications to assure phenotypic plasticity and respective tissue homeostasis...
October 5, 2016: Current Opinion in Rheumatology
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"