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Tao Zhang, Jin Meng, Xinli Liu, Xutao Zhang, Xiaojun Peng, Zhongyi Cheng, Feng Zhang
ING5 belongs to the Inhibitor of Growth (ING) candidate tumor suppressor family. Previously, we have shown that ING5 inhibits invasiveness of lung cancer cells by downregulating EMT-inducing genes. However, the underlying mechanisms remain unclear. The aim of the study was to use integrated approach involving SILAC labeling and mass spectrometry-based quantitative proteomics to quantify dynamic changes of acetylation regulated by ING5 in lung cancer cells. Here, we have found that ING5 has a profound influence on protein lysine acetylation with 163 acetylation peptides on 122 proteins significantly upregulated and 100 acetylation peptides on 72 proteins downregulated by ING5 overexpression...
January 5, 2018: Oncotarget
Henry J Henderson, Balasubramanyam Karanam, Rajeev Samant, Komal Vig, Shree R Singh, Clayton Yates, Deepa Bedi
The molecular mechanisms involved in breast cancer progression and metastasis still remain unclear to date. It is a heterogeneous disease featuring several different phenotypes with consistently different biological characteristics. Neuroligins are neural cell adhesion molecules that have been implicated in heterotopic cell adhesion. In humans, alterations in neuroligin genes are implicated in autism and other cognitive diseases. Until recently, neuroligins have been shown to be abundantly expressed in blood vessels and also play a role implicated in the growth of glioma cells...
2017: PloS One
Hao Liu, Ping Zhou, Hong Lan, Jia Chen, Yu-Xiang Zhang
Notch signaling plays a key role in the development of pancreatic cancer. Among the four identified Notch receptors, Notch1 and Notch2 share the highest homology. Notch1 has been reported to be an oncogene but some reports indicate that Notch2, not Notch1, plays a key role in pancreatic carcinogenesis. As both are transcription factors, examination of their genomic binding sites might reveal interesting functional differences between them. Notch proteins do not have DNA-binding domain. In the canonical Notch signaling pathway, ligand binding induces the release and nuclear translocation of Notch receptor intracellular domains (NICDs), which then interact with the transcription factor CSL, resulting in subsequent activation of the canonical Notch target genes...
2017: Journal of Cancer
Terri D McBride, U Andrew, Nicko Ly, Julio G Soto
RNA sequencing of untreated and r-Moj-DM treated SK-Mel-28 cells was performed after 6 h, to begin unraveling the apoptotic pathway induced by r-Moj-DM. Bioinformatic analyses of RNA sequencing data yielded 40 genes that were differentially expressed. Nine genes were upregulated and 31 were downregulated. qRT-PCR was used to validate differential expression of 13 genes with known survival or apoptotic-inducing activities. Expression of BNiP3, IGFBP3, PTPSF, Prune 2, TGF-ß, and TXNIP were compared from cells treated with r-Moj-DN (a strong apoptotic inducer) or r-Moj-DA (a non-apoptotic inducer) for 1 h, 2 h, 4 h, and 6 h after treatment...
October 2016: Toxicon: Official Journal of the International Society on Toxinology
Kwangwoo Kim, So-Young Bang, Katsunori Ikari, Dae Hyun Yoo, Soo-Kyung Cho, Chan-Bum Choi, Yoon-Kyoung Sung, Tae-Hwan Kim, Jae-Bum Jun, Young Mo Kang, Chang-Hee Suh, Seung-Cheol Shim, Shin-Seok Lee, Jisoo Lee, Won Tae Chung, Seong-Kyu Kim, Jung-Yoon Choe, Shigeki Momohara, Atsuo Taniguchi, Hisashi Yamanaka, Swapan K Nath, Hye-Soon Lee, Sang-Cheol Bae
Considerable sharing of disease alleles among populations is well-characterized in autoimmune disorders (e.g., rheumatoid arthritis), but there are some exceptional loci showing heterogenic association among populations. Here we investigated genetic variants with distinct effects on the development of rheumatoid arthritis in Asian and European populations. Ancestry-related association heterogeneity was examined using Cochran's homogeneity tests for the disease association data from large Asian (n = 14,465; 9,299 discovery subjects and 5,166 validation subjects; 4 collections) and European (n = 45,790; 11 collections) rheumatoid arthritis case-control cohorts with Immunochip and genome-wide SNP array data...
June 8, 2016: Scientific Reports
Wei Peng, Jianxin Wang, Bihai Zhao, Lusheng Wang
Protein complexes play a significant role in understanding the underlying mechanism of most cellular functions. Recently, many researchers have explored computational methods to identify protein complexes from protein-protein interaction (PPI) networks. One group of researchers focus on detecting local dense subgraphs which correspond to protein complexes by considering local neighbors. The drawback of this kind of approach is that the global information of the networks is ignored. Some methods such as Markov Clustering algorithm (MCL), PageRank-Nibble are proposed to find protein complexes based on random walk technique which can exploit the global structure of networks...
January 2015: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Luoqiang Lin, Dan Liu, Hongyan Liang, Li Xue, Changlei Su, Ming Liu
Breast cancer is the most common cancer in women around the world. However, the molecular mechanisms underlying breast cancer pathogenesis are only partially understood. Here, in this study, we found that miR-1228 was up-regulated in breast cancer cell lines and tissues. Ectopic expression of miR-1228 mimics leads to promoted cell growth, invasion and migration. Using bioinfomatic analysis and 3'UTR luciferase reporter assay, we determined SCAI can be directly targeted by miR-1228, which can down-regulate endogenous SCAI protein level...
2015: International Journal of Clinical and Experimental Pathology
Pei Shen, Hong Zhang, Zhaoliang Su, Shengjun Wang, Huaxi Xu
Tumor necrosis factor α-induced protein 8 (TNFAIP8)-like protein 1 (TIPE1) was a member of TNFAIP8 family. Previous studies have shown that TIPE1 could induce apoptosis in hepatocellular carcinoma. In this study, we attempted to predict its potential structure. Bioinformatic analysis of TIPE1 was performed to predict its potential structure using the bioinfomatic web services or softwares. The results showed that the amino acid sequences of TIPE1 were well conserved in mammals. No signal peptide and no transmembrane domain existed in human TIPE1...
2015: PloS One
Yang Wang, Zhi-Hao Chen, Chun Yin, Jian-Hua Ma, Di-Jie Li, Fan Zhao, Yu-Long Sun, Li-Fang Hu, Peng Shang, Ai-Rong Qian
The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling...
2015: PloS One
Y Takahashi, P Sheridan, A Niida, G Sawada, R Uchi, H Mizuno, J Kurashige, K Sugimachi, S Sasaki, Y Shimada, K Hase, M Kusunoki, S Kudo, M Watanabe, K Yamada, K Sugihara, H Yamamoto, A Suzuki, Y Doki, S Miyano, M Mori, K Mimori
BACKGROUND: The MYC oncogene has long been established as a central driver in many types of human cancers including colorectal cancer. However, the realization of MYC-targeting therapies remains elusive; as a result, synthetic lethal therapeutic approaches are alternatively being explored. A synthetic lethal therapeutic approach aims to kill MYC-driven tumors by targeting a certain co-regulator on the MYC pathway. PATIENTS AND METHODS: We analyzed copy number and expression profiles from 130 colorectal cancer tumors together with publicly available datasets to identify co-regulators on the MYC pathway...
May 2015: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Luming Zheng, Xukui Zhang, Feng Yang, Jian Zhu, Peng Zhou, Fang Yu, Lei Hou, Lei Xiao, Qingqing He, Baocheng Wang
Breast cancer is the most common cancer in women around the world. However, the molecular mechanisms underlying breast cancer pathogenesis are only partially understood. Here, in this study, we found that P2X7R was up-regulated and miR-216b was down-regulated in breast cancer cell lines and tissues. Using bioinformatic analysis and 3'UTR luciferase reporter assay, we determined P2X7R can be directly targeted by miR-216b, which can down-regulate endogenous P2X7R mRNA and protein levels. Ectopic expression of miR-216b mimics leads to inhibited cell growth and apoptosis, while blocking expression of the miR-216b results in increased cell proliferation...
September 12, 2014: Biochemical and Biophysical Research Communications
Molong Li, Sanna Vattulainen, Joonas Aho, Marc Orcholski, Vanessa Rojas, Ke Yuan, Mikko Helenius, Pekka Taimen, Samuel Myllykangas, Vinicio De Jesus Perez, Juha W Koskenvuo, Tero-Pekka Alastalo
Occlusive vasculopathy with intimal hyperplasia and plexogenic arteriopathy are severe histopathological changes characteristic of pulmonary arterial hypertension (PAH). Although a phenotypic switch in pulmonary endothelial cells (ECs) has been suggested to play a critical role in the formation of occlusive lesions, the pathobiology of this process is poorly understood. The goal of this study was to identify novel molecular mechanisms associated with EC dysfunction and PAH-associated bone morphogenetic protein receptor 2 (BMPR2) deficiency during PAH pathogenesis...
June 2014: American Journal of Respiratory Cell and Molecular Biology
Xiangpeng Chen, Xiaojuan Tan, Jing Li, Yu Jin, Liming Gong, Mei Hong, Yonglin Shi, Shuangli Zhu, Baomin Zhang, Shuang Zhang, Yong Zhang, Naiying Mao, Wenbo Xu
Coxsackievirus A16 (CVA16) is responsible for nearly 50% of all the confirmed hand, foot, and mouth disease (HFMD) cases in mainland China, sometimes it could also cause severe complications, and even death. To clarify the genetic characteristics and the epidemic patterns of CVA16 in mainland China, comprehensive bioinfomatics analyses were performed by using 35 CVA16 whole genome sequences from 1998 to 2011, 593 complete CVA16 VP1 sequences from 1981 to 2011, and prototype strains of human enterovirus species A (EV-A)...
2013: PloS One
Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch
MOTIVATION: For biological pathways, it is common to measure a gene expression time series after various knockdowns of genes that are putatively involved in the process of interest. These interventional time-resolved data are most suitable for the elucidation of dynamic causal relationships in signaling networks. Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network. RESULTS: In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks...
February 1, 2014: Bioinformatics
Alex J McCarthy, Jodi A Lindsay
Staphylococcus aureus is a major human pathogen, and is targeted by the host innate immune system. In response, S. aureus genomes encode dozens of secreted proteins that inhibit complement, chemotaxis and neutrophil activation resulting in successful evasion of innate immune responses. These proteins include immune evasion cluster proteins (IEC; Chp, Sak, Scn), staphylococcal superantigen-like proteins (SSLs), phenol soluble modulins (PSMs) and several leukocidins. Biochemical studies have indicated that genetic variants of these proteins can have unique functions...
October 2013: Infection, Genetics and Evolution
Lucia Banci, Ivano Bertini
In this chapter we aim at underlining the complexity of the interactions between living systems and inorganic elements. Attempts are made to move this field towards an "omics" approach through bioinfomatics and information technology. The metallome can be defined as the ensemble of all the biomolecules in a system which bind a given metal ion or an inorganic element at broad, or are affected by that element. A number of subsets of a metallome can then be defined based on the nature of the biomolecules interacting with the metal ions and the inorganic elements in general...
2013: Metal Ions in Life Sciences
Filipe de Carvalho Victoria, Clauber Mateus Priebe Bervald, Luciano Carlos da Maia, Rogerio Oliveira de Sousa, Olivier Panaud, Antônio Costa de Oliveira
Iron is involved in many metabolic processes, such as respiration and photosynthesis, and therefore an essential element for plant development. Comparative analysis of gene copies between crops and lower plant groups can shed light on the evolution of genes important to iron homeostasis. A phylogenetic analysis of five metal homeostasis gene families (NAS, NRAMP, YSL, FRO, and IRT) selected in monocots, dicots, gymnosperms, and bryophytes was performed. The homologous genes were found using known iron homeostasis gene sequences of Oryza sativa, Arabidopsis thaliana, and Physcomitrella patens as queries...
December 2012: Genome Génome / Conseil National de Recherches Canada
Paul N Ulrich, Veronica Jimenez, Miyoung Park, Vicente P Martins, James Atwood, Kristen Moles, Dalis Collins, Peter Rohloff, Rick Tarleton, Silvia N J Moreno, Ron Orlando, Roberto Docampo
Contractile vacuole complexes are critical components of cell volume regulation and have been shown to have other functional roles in several free-living protists. However, very little is known about the functions of the contractile vacuole complex of the parasite Trypanosoma cruzi, the etiologic agent of Chagas disease, other than a role in osmoregulation. Identification of the protein composition of these organelles is important for understanding their physiological roles. We applied a combined proteomic and bioinfomatic approach to identify proteins localized to the contractile vacuole...
2011: PloS One
Tobias C Walther, Jesper V Olsen, Matthias Mann
Comprehensive analysis of yeast as a model system requires to reliably determine its composition. Systematic approaches to globally determine the abundance of RNAs have existed for more than a decade and measurements of mRNAs are widely used as proxies for detecting changes in protein abundance. In contrast, methodologies to globally quantitate proteins are only recently becoming available. Such experiments are essential as proteins mediate the majority of biological processes and their abundance does not always correlate well with changes in gene expression...
2010: Methods in Enzymology
Benjamin Kormeier, Klaus Hippe, Thoralf Töpel, Ralf Hofestädt
One of the major challenges in bioinfomatics is to integrate and manage data from different sources as well as experimental microarray data and present them in a user-friendly format. Therefore, we present CardioVINEdb, a data warehouse approach developed to interact with and explore life science data. The data warehouse architecture provides a platform independent web interface that can be used with any common web browser. A monitor component controls and updates the data from the different sources to guarantee up-todateness...
2010: Journal of Integrative Bioinformatics
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