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Molecular BioSystems

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https://www.readbyqxmd.com/read/28524204/correction-metabolomic-profiling-and-biochemical-evaluation-of-the-follicular-fluid-of-endometriosis-patients
#1
Marianna Santonastaso, Alessia Pucciarelli, Susan Costantini, Francesca Caprio, Angela Sorice, Francesca Capone, Antonella Natella, Patrizia Iardino, Nicola Colacurci, Emilio Chiosi
Correction for 'Metabolomic profiling and biochemical evaluation of the follicular fluid of endometriosis patients' by Marianna Santonastaso et al., Mol. BioSyst., 2017, DOI: 10.1039/c7mb00181a.
May 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28497156/tumor-suppressors-microrna-302d-and-microrna-16-inhibit-human-glioblastoma-multiforme-by-targeting-nf-%C3%AE%C2%BAb-and-fgf2
#2
Feng Wang, Lijun Yang, Jianping Sun, Jun Zheng, Lin Shi, Gengshen Zhang, Na Cui
Glioblastoma multiforme (GBM) is a highly malignant cancer in the brain with a median survival time of approximately one year. However, the mechanisms underlying GBM development and occurrence are poorly understood. Recently, miRNAs were reported to play important roles in GBM. We performed microRNA profiling by comparing the human GBM cell line T98G and control cell line HCN1A. MicroRNA assays, PCR and Western blot analysis were performed to detect the expressions of microRNAs, mRNAs and proteins of target genes, respectively...
May 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28488707/emergent-properties-of-extracellular-vesicles-a-holistic-approach-to-decode-the-complexity-of-intercellular-communication-networks
#3
REVIEW
Yong Song Gho, Changjin Lee
Shedding of nano-sized bilayered extracellular vesicles and extracellular vesicle-mediated intercellular communication are evolutionarily conserved biological processes. Communication between cells and the environment is an essential process in living organisms and dysregulation of intercellular communication leads to various diseases. Thus, systematic studies on extracellular vesicles, also known as exosomes, microvesicles, and outer membrane vesicles, are critical for a deeper understanding of intercellular communication networks that are crucial for decoding the exact causes of various difficult-to-cure diseases...
May 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28485748/genespider-gene-regulatory-network-inference-benchmarking-with-controlled-network-and-data-properties
#4
Andreas Tjärnberg, Daniel C Morgan, Matthew Studham, Torbjörn E M Nordling, Erik L L Sonnhammer
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method. We present GeneSPIDER - a Matlab package for tuning, running, and evaluating inference algorithms that allows independent control of network and data properties to enable data-driven benchmarking. GeneSPIDER is uniquely suited to address this question by first extracting salient properties from the experimental data and then generating simulated networks and data that closely match these properties...
May 9, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28485414/systematic-comparison-of-the-response-properties-of-protein-and-rna-mediated-gene-regulatory-motifs
#5
Bharat Ravi Iyengar, Beena Pillai, K V Venkatesh, Chetan J Gadgil
We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters...
May 9, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28480928/differential-flap-dynamics-in-l-d-transpeptidase2-from-mycobacterium-tuberculosis-revealed-by-molecular-dynamics
#6
Zeynab Fakhar, Thavendran Govender, Glenn E M Maguire, Gyanu Lamichhane, Ross C Walker, Hendrik G Kruger, Bahareh Honarparvar
Despite the advances in tuberculosis treatment, TB is still one the most deadly infectious diseases and remains a major global health quandary. Mycobacterium tuberculosis (Mtb) is the only known mycobacterium with a high content of 3→3 crosslinks in the biosynthesis of peptidoglycan, which is negligible in most bacterial species. An Mtb lacking LdtMt2 leads to alteration of the colony morphology and loss of virulence which makes this enzyme an attractive target. Regardless of the vital role of LdtMt2 for cell wall survival, the impact of ligand binding on the dynamics of the β-hairpin flap is still unknown...
May 8, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28475193/metabolomic-profiling-and-biochemical-evaluation-of-the-follicular-fluid-of-endometriosis-patients
#7
Santonastaso Marianna, Pucciarelli Alessia, Costantini Susan, Caprio Francesca, Sorice Angela, Capone Francesca, Natella Antonella, Iardino Patrizia, Colacurci Nicola, Chiosi Emilio
Diseases are complex systems that can be studied through the integration of data derived from different disciplines to obtain a global and reliable picture of the biological phenomenon under investigation. Based on the recent observations that the metabolomics profiling of follicular fluids reflects the ovarian microenvironment of women and that endometriosis represents an example of complex diseases, clearly diagnosed by laparoscopy, we thought that the follicular fluids of endometriosis patients can represent a study model to evaluate the possibility of integrating data obtained by different approaches...
May 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28474020/characterization-of-the-structure-dynamics-and-allosteric-pathways-of-human-npp1-in-its-free-form-and-substrate-bound-complex-from-molecular-modeling
#8
Xavier Barbeau, Patrick Mathieu, Jean-François Paquin, Patrick Lagüe
The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of ATP into AMP and diphosphate. NPP1 is a promising drug target as it plays a role in several disorders. In the present work, we report the 3D structure modeling and extensive molecular dynamics simulations of NPP1-h, both in its free and ATP-bound forms. We identified the key residues involved in the binding of the ATP and the binding modes...
May 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28470277/characterizing-the-structure-function-relationship-reveals-the-mode-of-action-of-a-novel-antimicrobial-peptide-p1-from-jumper-ant-myrmecia-pilosula
#9
Tien-Sheng Tseng, Keng-Chang Tsai, Chinpan Chen
Microbial infections of antibiotic-resistant strains cause serious diseases and have a significant impact on public health worldwide, so novel antimicrobial drugs are urgently needed. Insect venoms, a rich source of bioactive components containing antimicrobial peptides (AMPs), are attractive candidates for new therapeutic agents against microbes. Recently, a novel peptide, P1, identified from the venom of the Australian jumper ant Myrmecia pilosula, showed potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, but its structure-function relationship is unknown...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28470264/reconstruction-and-analysis-of-the-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-reveal-functional-lncrnas-in-rheumatoid-arthritis
#10
Hui Jiang, Rong Ma, Shubiao Zou, Yongzhong Wang, Zhuqing Li, Weiping Li
Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28470244/a-novel-computational-model-based-on-super-disease-and-mirna-for-potential-mirna-disease-association-prediction
#11
Xing Chen, Zhi-Chao Jiang, Di Xie, De-Shuang Huang, Qi Zhao, Gui-Ying Yan, Zhu-Hong You
In recent years, more and more studies have indicated that microRNAs (miRNAs) play critical roles in various complex human diseases and could be regarded as important biomarkers for cancer detection in early stages. Developing computational models to predict potential miRNA-disease associations has become a research hotspot for significant reduction of experimental time and cost. Considering the various disadvantages of previous computational models, we proposed a novel computational model based on super-disease and miRNA for potential miRNA-disease association prediction (SDMMDA) to predict potential miRNA-disease associations by integrating known associations, disease semantic similarity, miRNA functional similarity, and Gaussian interaction profile kernel similarity for diseases and miRNAs...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28466892/the-multi-output-incoherent-feedforward-loop-constituted-by-the-transcriptional-regulators-lasr-and-rsal-confers-robustness-to-a-subset-of-quorum-sensing-genes-in-pseudomonas-aeruginosa
#12
Roslen Bondí, Francesca Longo, Marco Messina, Francesca D'Angelo, Paolo Visca, Livia Leoni, Giordano Rampioni
Quorum sensing (QS) is an intercellular communication system which controls virulence-related phenotypes in the human pathogen Pseudomonas aeruginosa. LasR is the QS receptor protein which responds to the signal molecule N-(3-oxododecanoyl)homoserine lactone (3OC12-HSL) and promotes signal production by increasing the transcription of the 3OC12-HSL synthase gene, lasI. LasR also activates the expression of other genes, including rsaL, coding for the RsaL protein which acts as a transcriptional repressor of lasI...
May 3, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28463380/metabolic-profiling-of-asthma-in-mice-and-the-interventional-effects-of-spa-using-liquid-chromatography-and-q-tof-mass-spectrometry
#13
Li Su, Lei Shi, Jian Liu, Lifei Huang, Yi Huang, Xiaomeng Nie
Asthma is a chronic inflammatory lung disease that leads to 250 000 deaths annually. There is a need to better understand asthma by identifying new pathogenic molecules. We conducted a liquid-chromatography time-of-flight mass spectrometry (LC-Q-TOF-MS)-based metabolomics study to test for asthma and investigate the interventional mechanisms of surfactant protein A (SPA) in OVA-induced asthma mice. The results revealed that asthma disturbed 32 metabolites in 9 metabolic pathways. After SPA treatment, the metabolomics profile found in asthma was significantly reversed, shifting much closer to that of the control group, indicating that SPA has therapeutic effects against asthma...
May 2, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28463369/the-impact-of-thr91-mutation-on-c-src-resistance-to-um-164-molecular-dynamics-study-revealed-a-new-opportunity-for-drug-design
#14
Umar Ndagi, Ndumiso N Mhlongo, Mahmoud E Soliman
The emergence of a drug resistant non-receptor tyrosine kinase (c-Src) in triple-negative breast cancer (TNBC) remains a prime concern in relation to the burden of TNBC among people living with breast cancer and drug development. Thr91 mutation was found to induce a complete loss of protein conformation required for drug fitness. Herein, we provide the first account of the molecular impact of the Thr91 mutation on c-Src resistance to experimental drug UM-164 using various computational approaches, namely molecular dynamics simulation, principal component analysis (PCA), dynamic cross-correlation matrices (DCCM) analysis, hydrogen bond occupancy, thermodynamics calculation, ligand-residue interaction and residue interaction networks (RINs)...
May 2, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28453010/effect-of-nucleobase-change-on-cytosine-deamination-through-dna-photo-cross-linking-reaction-via-3-cyanovinylcarbazole-nucleoside
#15
Siddhant Sethi, Minako Ooe, Takashi Sakamoto, Kenzo Fujimoto
Photo-chemical deamination of cytosine using 3-cyanovinylcarbazole nucleoside ((CNV)K) mediated photo-cross-linking is a technique for site-directed mutagenesis. Using this technique in vivo requires the elimination of a high-temperature incubation step; instead, incubation should be carried out under physiological conditions. To improve the reactivity of (CNV)K mediated photo-cross-link induced deamination of cytosine under physiological conditions, an evaluation of base pairing in cytosine was carried out with respect to its deamination...
April 28, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28443890/the-characteristic-landscape-of-lncrnas-classified-by-rbp-lncrna-interactions-across-10-cancers
#16
Qiang Zhang, Yunzhen Wei, Zichuang Yan, Cheng Wu, Zhiqiang Chang, Yinling Zhu, Kun Li, Yan Xu
RNA-binding proteins (RBPs) are key regulators of gene expression. Some long non-coding RNAs (lncRNAs) affect gene expression by interacting with RBPs. However, whether this influences the biological characteristics of lncRNAs in diseases still remains unknown. Here, we classify lncRNAs into two categories, using the interaction information between lncRNAs and RBPs: the lncRNAs that interact with RBPs (Rlncs) and the lncRNAs that do not interact with RBPs (NRlncs). Then we systematically analyze the basic attributes and functions of the two categories of lncRNAs across 10 cancers...
April 26, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#17
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28429027/a-metabolomic-study-on-high-risk-stroke-patients-determines-low-levels-of-serum-lysine-metabolites-a-retrospective-cohort-study
#18
Yeseung Lee, Adnan Khan, Seri Hong, Sun Ha Jee, Youngja H Park
Identifying changes in serum metabolites during cerebral ischemia is an important approach for early diagnosis of thrombotic stroke. Herein, we highlight novel biomarkers for early diagnosis of patients at high risk of thrombotic stroke using high resolution metabolomics (HRM). In this retrospective cohort study, serum samples obtained from patients at risk of thrombotic stroke (n  =  62) and non-risk individuals (n  =  348) were tested using HRM, coupled with LC-MS/MS, to discriminate between metabolic profiles of control and stroke risk patients...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28429008/anticancer-effects-of-novel-resveratrol-analogues-on-human-ovarian-cancer-cells
#19
Daniele Vergara, Stefania De Domenico, Andrea Tinelli, Eleonora Stanca, Loretta L Del Mercato, Anna M Giudetti, Pasquale Simeone, Nicola Guazzelli, Marco Lessi, Chiara Manzini, Angelo Santino, Fabio Bellina, Michele Maffia
Resveratrol, a naturally occurring phytoalexin, has long been known to play an important regulatory role in key functions in cell physiology. This multifunctional role of resveratrol is explained by its ability to interact with several targets of various cell pathways. In the recent past, synthetic chemical modifications have been made in an attempt to enhance the biological effects of resveratrol, including its anti-cancer properties. In this study, we investigated the molecular mechanisms of action of novel trans-restricted analogues of resveratrol in which the C-C double bond of the natural derivative has been replaced by diaryl-substituted imidazole analogues...
April 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28428989/generation-and-characterization-of-the-blood-transcriptome-of-macaca-thibetana-and-comparative-analysis-with-m-mulatta
#20
Peng Li, Lianming Du, Wujiao Li, Zhenxin Fan, Daiwen Zeng, Hui Chen, Liang Zhou, Yong Yi, Na Yang, Kefeng Dou, Bisong Yue, Jing Li
Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published. The Tibetan macaque (Macaca thibetana) is commonly considered to be an endemic species to China and an important animal in biomedical research in the present day. In the present study, we report the de novo assembly and characterization of the blood transcriptome of the Tibetan macaque from three individuals, and we also sequenced the blood transcriptome of the rhesus macaque (Macaca mulatta) for comparison...
April 21, 2017: Molecular BioSystems
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