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Molecular BioSystems

David Gnutt, Oliver Brylski, Eugen Edengeiser, Martina Havenith, Simon Ebbinghaus
Changes of the extracellular milieu could affect cellular crowding. To prevent detrimental effects, cells use adaptation mechanisms to react to such conditions. Using fluorescent crowding sensors, we show that the initial response to osmotic stress is fast but imperfect, while the slow response renders cells more tolerant to stress, particularly in the presence of osmolytes.
September 20, 2017: Molecular BioSystems
Arati B Deshmukh, Shakuntala Bai, Aarthy T, Rubina S Kazi, Reema Banarjee, Rajeshwari Rathore, Vijayakumar Mv, Thulasiram Hv, Manoj Kumar Bhat, Kulkarni Mj
Methylglyoxal (MG) is a highly reactive dicarbonyl known to be elevated under the hyperglycemic conditions of diabetes and is implicated in the development of diabetic complications. Therefore, the current study investigates the role of MG in exacerbating insulin resistance at the insulin signaling level, as well as its effect on the global proteomic level. By using insulin sensitive rat muscle cells (L6) and Chinese hamster ovary (CHO) cells stably expressing the insulin receptor (IR) and a glucose transporter fused with green fluorescent protein (GLUT4-GFP), we have observed that MG impairs insulin signaling, inhibits GLUT4 translocation and reduces glucose uptake...
September 19, 2017: Molecular BioSystems
G M Verkhivker
The overarching goal of delineating molecular principles underlying differentiation of the activation mechanisms in cyclin-dependent kinases (CDKs) is important for understanding regulatory divergences among closely related kinases which can be exploited in drug discovery of targeted and allosteric inhibitors. To systematically characterize dynamic, energetic and network signatures of the activation mechanisms, we combined atomistic simulations and elastic network modeling with the analysis of the residue interaction networks and rigidity decomposition of the CDK2-cyclin A and CDK4-cyclin D1/D3 complexes...
September 19, 2017: Molecular BioSystems
Liang Ding, Minghui Wang, Dongdong Sun, Ao Li
MicroRNAs (miRNAs), as a kind of important small endogenous single-stranded non-coding RNA, play critical roles in a large number of human diseases. However, the currently known experimental verifications of the disease-miRNA associations are still rare and experimental identification is time-consuming and labor-intensive. Accordingly, identifying potential disease-related miRNAs to help people understand the pathogenesis of complex diseases has become a hot topic. In this study, we take advantage of known disease-miRNA associations combined with a large number of experimentally validated miRNA-target associations, and further develop a novel disease-miRNA-target heterogeneous network for identifying disease-related miRNAs...
September 18, 2017: Molecular BioSystems
Aurelia A Williams, Lungile J Sitole, Debra Meyer
Chronic human immunodeficiency virus (HIV) infection, separately and in combination with highly active antiretroviral therapy (HAART) is closely associated with oxidative stress (OS). Most studies demonstrating redox imbalances in HIV-infected individuals have done so using conventional biochemical methodologies. The limited simultaneous detection of multiple OS markers within one sample is a major drawback of these methodologies and can be addressed through the use of metabonomics. HIV-metabonomic studies utilizing biofluids from HAART cohorts as the investigative source, are on the increase...
September 18, 2017: Molecular BioSystems
Ying Ge, Ya-Jun Zhou, Ke-Wu Yang, Yi-Lin Zhang, Yang Xiang, Yue-Juan Zhang
The emergence of antibiotic resistance caused by β-lactamases, including serine β-lactamases (SβLs) and metallo-β-lactamases (MβLs), is a global public health threat. L1, a B3 subclass MβL, hydrolyzes almost all of known β-lactam antibiotics. We report a simple and straightforward UV-Vis approach for real-time activity assays of β-lactamases inside living bacterial cells, and this method has been exemplified by choosing antibiotics, L1 enzyme, Escherichia coli expressing L1 (L1 E. coli), Escherichia coli expressing extended-spectrum β-lactamases (ESBL-E...
September 14, 2017: Molecular BioSystems
Wei Peng, Fei Ding
Chirality is a ubiquitous basic attribute of nature, which inseparably relates to the life activity of living organisms. However, enantiomeric differences have still failed to arouse enough attention during the biological evaluation and practical application of chiral substances, and this poses a large threat to human health. In the current study, we explore the enantioselective biorecognition of a chiral compound by an asymmetric biomolecule, and then decipher the molecular basis of such a biological phenomenon on the static and, in particular, the dynamic scale...
September 8, 2017: Molecular BioSystems
Taiyi Wang, Ming Lu, Qunqun Du, Xi Yao, Peng Zhang, Xiaonan Chen, Weiwei Xie, Zheng Li, Yuling Ma, Yan Zhu
Correction for 'An integrated anti-arrhythmic target network of a Chinese medicine compound, Wenxin Keli, revealed by combined machine learning and molecular pathway analysis' by Taiyi Wang et al., Mol. BioSyst., 2017, 13, 1018-1030.
September 8, 2017: Molecular BioSystems
Hao Li, Nalini Schaduangrat, Saw Simeon, Chanin Nantasenamat
Immune therapy is generally seen as the future of cancer treatment. The discovery of tumor-associated antigens and cytotoxic T lymphocyte epitope peptides spurned intensive research into effective peptide-based cancer vaccines. One of the major obstacles hindering the development of peptide-based cancer vaccines is the lack of humoral response induction. As of now, very limited work has been performed to identify epitope peptides capable of inducing both cellular and humoral anticancer responses. In addition, no research has been carried out to analyze the structure and properties of peptides responsible for such immunological activities...
September 7, 2017: Molecular BioSystems
Manohar C Dange, Hemangi S Bhonsle, Rashmi K Godbole, Shyam K More, Sanjay M Bane, Mahesh J Kulkarni, Rajiv D Kalraiya
Adhesive interactions between molecules on tumor cells and those on target organs play a key role in organ specific metastasis. Poly-N-acetyl-lactosamine (polyLacNAc) substituted N-oligosaccharides on melanoma cell surface glycoproteins promote lung specific metastasis via galectin-3 by facilitating their arrest and extravasation. This study reports the identification and characterization of galectin-3 interacting proteins using a combination of galectin-3 sepharose affinity and leucoagglutinating phytohemagglutinin (L-PHA) columns...
September 6, 2017: Molecular BioSystems
Ehsan Mohseni Fard, Behnam Bakhshi, Mohammad Farsi, Amin Mirshamsi Kakhki, Nava Nikpay, Mohammad Ali Ebrahimi, Mohsen Mardi, Ghasem Hosseini Salekdeh
MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. miRNA profiles of rice (Oryza sativa L. cv. IR64.) leaves in a partial root zone drying (PRD) system were analysed using a high-throughput sequencing approach to identify miRNAs associated with drought signalling. The treatments performed in this study were as follows: well-watered ("wet" roots, WW), wherein both halves of the pot were watered daily; drought ("dry" roots, DD), wherein water was withheld from both halves of the pot; and well-watered/drought ("wet" and "dry" roots, WD), wherein one half of each pot was watered daily, the same as in WW, and water was withheld from the other part, the same as in DD...
September 5, 2017: Molecular BioSystems
Kaveh Baghaei, Nazanin Hosseinkhan, Hamid Asadzadeh Aghdaei, M R Zali
According to GLOBOCAN 2012, the incidence and the mortality rate of colorectal, stomach and liver cancers are the highest among the total gastrointestinal (GI) cancers. Here we aimed to find the common genes and pathways that are simultaneously deregulated in these three malignancies using systems biology approaches. Here we conducted a differential expression analysis on high-quality gene expression datasets of gastric cancer (GC), colorectal cancer (CRC) and hepatocellular carcinoma (HCC). To address the inter gene correlations that were neglected in differential expression studies, we also applied differential co-expression analysis on the understudied datasets...
September 4, 2017: Molecular BioSystems
Weisha Liu, Shuyuan Wang, Shunheng Zhou, Feng Yang, Wei Jiang, Qingyuan Zhang, Lihong Wang
Cisplatin (CDDP)-based chemotherapy is a standard first-line therapy for ovarian cancer. However, drug resistance remains a major obstacle to its efficacy. Recently, increasing evidence suggested that the aberrant expression of microRNAs (miRNAs) may contribute to drug resistance. Here, we proposed a systems biology analysis strategy to identify the novel miRNAs potentially involved in CDDP resistance in human ovarian cancer cells. Firstly, we identified the candidate miRNAs associated with CDDP resistance using NCI-60 data...
September 1, 2017: Molecular BioSystems
Habib Motieghader, Morteza Kouhsar, Ali Najafi, Balal Sadeghi, Ali Masoudi-Nejad
Biomarker detection is one of the most important and challenging problems in cancer studies. Recently, non-coding RNA based biomarkers such as miRNA expression levels have been used for early diagnosis of many cancer types. In this study, a systems biology approach was used to detect novel miRNA based biomarkers for CRC diagnosis in early stages. The mRNA expression data from three CRC stages (Low-grade Intraepithelial Neoplasia (LIN), High-grade Intraepithelial Neoplasia (HIN) and Adenocarcinoma) were used to reconstruct co-expression networks...
September 1, 2017: Molecular BioSystems
Nazam Khan, Rajender Kumar, Shakti Chauhan, Umar Farooq
Plasmodium falciparum erythrocyte membrane protein-1 (Pfemp-1), a variant adhesion molecule, can act as a key component of immunity against malaria. In the current selection of malaria vaccines, no efficient vaccines are available that can be employed for its proper treatment. Unfortunately, resistance to post-infection treatments is increasing and therefore there is a pressing need to develop an efficient vaccine. Peptide-based vaccines can be effective tools against malaria but HLA restriction is a major hindrance which can be conquered by using promiscuous peptides...
August 31, 2017: Molecular BioSystems
Xu Shang, Wenting Chu, Xiakun Chu, Chuanbo Liu, Liufang Xu, Jin Wang
The intrinsically disordered protein (IDP) Chz.core, which is the interaction core of Chz1, shows binding preference to histone variant H2A.z. Although there are several studies on the binding process of Chz.core, the detailed coupled binding-folding processes are still elusive. In this study, we explored the coupled binding-folding mechanism and the effect of flexibility by continuously monitoring the flexibility degree of Chz.core. We applied an all-atom structure-based model (SBM), which takes advantage of providing both backbone and sidechain information about the conformational changes of Chz...
August 23, 2017: Molecular BioSystems
Yi-Le Zhang, Zhao-Feng Han
The recognition and association between the Ca(2+)/calmodulin-activated protein kinase II-α (CaMKIIα) and the multi-PDZ domain protein 1 (MUPP1) plays an important role in the sperm acrosome reaction and human fertilization. Previously, we have demonstrated that the MUPP1 PDZ11 domain is the primary binding partner of the CaMKIIα C-terminal tail, which can be targeted by a rationally designed sia peptide with nanomolar affinity. Here, we further introduced an orthogonal noncovalent interaction (ONI) system between a native hydrogen bond and a designed halogen bond across the complex interface of the PDZ11 domain with the sia [Asn-1Phe] peptide mutant, where the halogen bond was formed by substituting the o-hydrogen atom of the benzene ring of the peptide Phe-1 residue with a halogen atom (F, Cl, Br or I)...
August 23, 2017: Molecular BioSystems
Qianqian Wang, Fei Lu, Rongfeng Lan
Overcoming chemoresistance will prevent cancer relapse and contribute to clinical chemotherapy. In order to explore the underlying mechanism of chemoresistance, we firstly incubated cancer cells with a combination of cisplatin + paclitaxel (C + P) or cisplatin + paclitaxel + docetaxel (C + P + D) to mimic the treatment of cancer therapy in the laboratory. We found that polyploidy is a recurring strategy that cells adopt in response to cisplatin-based treatments. RNA-sequencing was performed to identify differentially expressed genes (DEGs) that may contribute to drug resistance...
August 21, 2017: Molecular BioSystems
Jianing Xi, Minghui Wang, Ao Li
The accumulating availability of next-generation sequencing data offers an opportunity to pinpoint driver genes that are causally implicated in oncogenesis through computational models. Despite previous efforts made regarding this challenging problem, there is still room for improvement in the driver gene identification accuracy. In this paper, we propose a novel integrated approach called IntDriver for prioritizing driver genes. Based on a matrix factorization framework, IntDriver can effectively incorporate functional information from both the interaction network and Gene Ontology similarity, and detect driver genes mutated in different sets of patients at the same time...
August 21, 2017: Molecular BioSystems
Shuhong Guan, Jun Zhou
Lung fibrosis is a progressive and often fatal lung disease characterized by fibroblast proliferation and excessive deposition of extracellular matrix in the lungs. The chemokine receptor CXCR7 has been shown to control cell adhesion, migration and proliferation by regulating the epithelial-to-mesenchymal transition (EMT), but the role of CXCR7 in regulating the endothelial-to-mesenchymal transition (EndMT) and lung fibrosis remains largely unclear. In this study, we investigated the interrelation of CXCR7 and TGF-β, a crucial player in lung fibrogenesis...
August 18, 2017: Molecular BioSystems
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