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Network biology

Jianjun Niu, Yong Lin, Pingguo Liu, Yiwen Yu, Chenghao Su, Xiaomin Wang
Long non-coding RNAs are involved with development and progression of cancer, and the advance of microarray technology allows the researchers to investigate the complete expression profile of lncRNA in various kinds of sample. We enrolled 5 male primary HCC cases with chronic HBV infection and the HCC and normal tissues have been obtained during the resection surgery. After total RNA extraction, the lncRNA microarray analysis was conducted to determine the lncRNA and mRNA expression signals. 612 lncRNAs and 1,064 mRNAs were significantly up-regulated in HCC tissue while 656 lncRNAs and 1,532 mRNAs were down-regulated in HCC tissues...
October 18, 2016: Oncotarget
Olivier Taboureau, Karine Audouze
During the past decades, many epidemiological, toxicological and biological studies have been performed to assess the role of environmental chemicals as potential toxicants for diverse human disorders. However, the relationships between diseases based on chemical exposure have been rarely studied by computational biology. We developed a human environmental disease network (EDN) to explore and suggest novel disease-disease and chemical-disease relationships. The presented scored EDN model is built upon the integration on systems biology and chemical toxicology using chemical contaminants information and their disease relationships from the reported TDDB database...
October 21, 2016: ALTEX
Feifei Xiao, Guoshuai Cai, Heping Zhang
In early 2015, the debate of blue-black and white-gold color perception from "the dress" became an overnight internet phenomenon. According to the vote from the online social network Twitter, more people observed white-gold colors than those who observed blue-black colors. Biological explanations have been proposed by neurologist and other scientists, most of which mainly focus on the bias of color perception from visual cortex assuming different illuminants as backgrounds. The goal of this study was to investigate the genetic reason that might be underlying this phenomenon...
2016: PloS One
Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
Emanuele Mauri, Alessandro Sacchetti, Filippo Rossi
The use of polymers as biomaterials has provided significant advantages in therapeutic applications. In particular, the possibility to modify and functionalize polymer chains with compounds that are able to improve biocompatibility, mechanical properties, or cell viability allows the design of novel materials to meet new challenges in the biomedical field. With the polymer functionalization strategies, click chemistry is a powerful tool to improve cell-compatibility and drug delivery properties of polymeric devices...
October 7, 2016: Journal of Visualized Experiments: JoVE
Navadon Khunlertgit, Byung-Jun Yoon
BACKGROUND: Discovering robust markers for cancer prognosis based on gene expression data is an important yet challenging problem in translational bioinformatics. By integrating additional information in biological pathways or a protein-protein interaction (PPI) network, we can find better biomarkers that lead to more accurate and reproducible prognostic predictions. In fact, recent studies have shown that, "modular markers," that integrate multiple genes with potential interactions can improve disease classification and also provide better understanding of the disease mechanisms...
October 6, 2016: BMC Bioinformatics
Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon
BACKGROUND: Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. RESULTS: In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks...
October 6, 2016: BMC Bioinformatics
Sang-Ho Kwon, Sekyung Oh, Marisa Nacke, Keith E Mostov, Joshua H Lipschutz
Exosomes, 40-150 nm extracellular vesicles, transport biological macromolecules that mediate intercellular communications. While exosomes are known to originate from maturation of endosomes into multivesicular endosomes (MVEs; also known as multivesicular bodies, MVBs) with subsequent fusion of the MVEs with the plasma membrane, it remains unclear how cargos are selected for exosomal release. Using an inducible expression system for the exosome cargo protein GPRC5B and following its trafficking trajectory, we show here that newly synthesized GPRC5B protein accumulates in the Golgi complex prior to its release into exosomes...
October 20, 2016: Journal of Biological Chemistry
Terezinha M Souza, Linda Rieswijk, Twan van den Beucken, Jos Kleinjans, Danyel Jennen
Chemical carcinogenesis, albeit complex, often relies on modulation of transcription through activation or repression of key transcription factors. While analyzing extensive networks may hinder the biological interpretation, one may focus on dynamic network motifs, among which persistent feed-forward loops (FFLs) are known to chronically influence transcriptional programming. Here, to investigate the relevance a FFL-oriented approach in depth, we have focused on aflatoxin B1-induced transcriptomic alterations during distinct states of exposure (daily administration during 5 days followed by a non-exposed period) of human hepatocytes, by exploring known interactions in human transcription...
October 17, 2016: Toxicology
Yajie Hu, Jie Song, Longding Liu, Jing Li, Beibei Tang, Jingjing Wang, Xiaolong Zhang, Ying Zhang, Lichun Wang, Yun Liao, Zhanlong He, Qihan Li
Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the predominant pathogens of hand, foot, and mouth disease (HFMD). Although these viruses exhibit genetic homology, the clinical manifestations caused by the two viruses have some discrepancies. In addition, the underlying mechanisms leading to these differences remain unclear. microRNAs (miRNAs) participate in numerous biological or pathological processes, including host responses to viral infections. Here, we focused on differences in miRNA expression patterns in rhesus monkey peripheral blood mononuclear cells (PBMCs) infected with EV71 and CA16 at various time points using high-throughput sequencing...
October 17, 2016: International Journal of Biochemistry & Cell Biology
Xue Jiang, Lichun Feng, Baoqiang Dai, Liping Li, Weiwei Lu
INTRODUCTION: Nasopharyngeal carcinoma is the most common cancer originating from the nasopharynx. OBJECTIVE: To study the mechanisms of nasopharyngeal carcinoma, we analyzed GSE12452 microarray data. METHODS: GSE12452 was downloaded from the Gene Expression Omnibus database and included 31 nasopharyngeal carcinoma samples and 10 normal nasopharyngeal tissue samples. The differentially expressed genes were screened by ANOVA in the PGS package...
September 26, 2016: Brazilian Journal of Otorhinolaryngology
Mario Encinar, Santiago Casado, Alicia Calzado-Martín, P Natale, Álvaro San Paulo, Montserrat Calleja, Marisela Vélez, Francisco Monroy, Iván López-Montero
Erythrocyte membranes have been particularly useful as a model for studies of membrane structure and mechanics. Native erythroid membranes can be electroformed as giant unilamellar vesicles (eGUVs). In the presence of ATP, the erythroid membrane proteins of eGUVs rearrange into protein networks at the microscale. Here, we present a detailed nanomechanical study of individual protein microfilaments forming the protein networks of eGUVs when spread on supporting surfaces. Using Peak Force tapping Atomic Force Microscopy (PF-AFM) in liquid environment we have obtained the mechanical maps of the composite lipid-protein networks supported on solid surface...
October 13, 2016: Colloids and Surfaces. B, Biointerfaces
Patricia O'Campo, Rhonda BeLue, Heidi Borenstein, Maxine Reed-Vance, Robin Gaines Lanzi, Peter Schafer, Loretta Jones, Richard Woolord
The inclusion of biomarkers in studies of stress and health outcomes is of growing interest, including for community-based participatory research (CBPR) studies. Yet the perspectives of participants and communities have been infrequently consulted to inform the biomarker collection process. The objective of this paper is to describe the process and outcomes of using CBPR in framing biomarker collection in a study of allostatic load in a maternal and child health population. Through analysis of focus group data, we identify aspects of CBPR that facilitate increased community trust and endorsement related to collecting biological samples, and also provide a community perspective that is often overlooked in the literature...
2016: Journal of Health Care for the Poor and Underserved
Laiyuan Wang, Zhiyong Wang, Jinyi Lin, Jie Yang, Linghai Xie, Mingdong Yi, Wen Li, Haifeng Ling, Changjin Ou, Wei Huang
Most simulations of neuroplasticity in memristors, which are potentially used to develop artificial synapses, are confined to the basic biological Hebbian rules. However, the simplex rules potentially can induce excessive excitation/inhibition, even collapse of neural activities, because they neglect the properties of long-term homeostasis involved in the frameworks of realistic neural networks. Here, we develop organic CuPc-based memristors of which excitatory and inhibitory conductivities can implement both Hebbian rules and homeostatic plasticity, complementary to Hebbian patterns and conductive to the long-term homeostasis...
October 20, 2016: Scientific Reports
Anup Arumughan, Yvette Roske, Carolin Barth, Laura Lleras Forero, Kenny Bravo-Rodriguez, Alexandra Redel, Simona Kostova, Erik McShane, Robert Opitz, Katja Faelber, Kirstin Rau, Thorsten Mielke, Oliver Daumke, Matthias Selbach, Elsa Sanchez-Garcia, Oliver Rocks, Daniela Panáková, Udo Heinemann, Erich E Wanker
Interaction mapping is a powerful strategy to elucidate the biological function of protein assemblies and their regulators. Here, we report the generation of a quantitative interaction network, directly linking 14 human proteins to the AAA+ ATPase p97, an essential hexameric protein with multiple cellular functions. We show that the high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers. High-resolution structural and biochemical studies indicate that an extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers...
October 20, 2016: Nature Communications
Feng Zhang, Bo Yang, Kailiang Zhang, Mei-Ling Hou, Xue-Chun Lu, Yu-Xin Li
Amifostine (AMF), 2-(3-Aminopropyl) aminoethyl phosphorothioate is a broad-spectrum cytoprotective agent used to treat nuclear radiation and chemical weapon injuries. Recently, amifostine has been shown to have a profound biological influence on tumor cells. In order to examine the effects and mechanisms underlying the effects of amifostine on human acute megakaryocytic leukemia, we evaluated the efficacy of amifostine against Dami cells and observed a cell cycle arrest in G2 /M phase. Amifostine treatment also induced cell apoptosis of Dami cells which corresponds to formal studies...
October 19, 2016: Chemical Biology & Drug Design
Dogyeong Ha, Jisoo Hong, Heungjoo Shin, Taesung Kim
Micro-/nanofabrication-based lab-on-a-chip (LOC) technologies have recently been substantially advanced and have become widely used in various inter-/multidisciplinary research fields, including biological, (bio-)chemical, and biomedical fields. However, such hybrid-scale LOC devices are typically fabricated using microfabrication and nanofabrication processes in series, resulting in increased cost and time and low throughput issues. In this review, after briefly introducing the conventional micro-/nanofabrication technologies, we focus on unconventional micro-/nanofabrication technologies that allow us to produce either in situ micro-/nanoscale structures or master molds for additional replication processes to easily and conveniently create novel LOC devices with micro- or nanofluidic channel networks...
October 20, 2016: Lab on a Chip
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
Kevin A McGoff, Xin Guo, Anastasia Deckard, Christina M Kelliher, Adam R Leman, Lauren J Francey, John B Hogenesch, Steven B Haase, John L Harer
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle...
October 19, 2016: Genome Biology
Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors (TFs), cellular growth factors and microRNAs. A subsystem's gene expression may be controlled by its internal regulatory factors, exclusively, or by external subsystems, or by both. It is thus useful to distinguish the degree to which a subsystem is regulated internally or externally-e.g., how non-conserved, species-specific TFs affect the expression of conserved, cross-species genes during evolution...
October 2016: PLoS Computational Biology
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