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Molecular BioSystems

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https://www.readbyqxmd.com/read/28232991/dna-condensation-in-live-e-coli-provides-evidence-for-transertion
#1
Anil K Gorle, Amy L Bottomley, Elizabeth J Harry, J Grant Collins, F Richard Keene, Clifford E Woodward
Condensation studies of chromosomal DNA in E. coli with a tetranuclear ruthenium complex are carried out and images obtained with wide-field fluorescence microscopy. Remarkably different condensate morphologies resulted, depending upon the treatment protocol. The occurrence of condensed nucleoid spirals in live bacteria provides evidence for the transertion hypothesis.
February 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28225105/elucidating-the-biosynthetic-pathways-of-volatile-organic-compounds-in-mycobacterium-tuberculosis-through-a-computational-approach
#2
Purva Bhatter, Karthik Raman, Vani Janakiraman
Microbial volatile organic compounds (VOCs) have gained prominence in the recent past for their potential use as disease markers. The discovery of microbial VOCs has benefited 'difficult to detect' diseases such as tuberculosis (TB). Few of the identified VOCs of Mycobacterium tuberculosis (Mtb) are currently being explored for their diagnostic potential. However, very little is known about the biosynthesis of these small lipophilic molecules. Here, we propose putative biosynthetic pathways in Mycobacterium tuberculosis for three VOCs, namely methyl nicotinate, methyl phenylacetate and methyl p-anisate, using computational approaches...
February 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28225098/urinary-metabolic-signatures-and-early-triage-of-acute-radiation-exposure-in-rat-model
#3
Mingxiao Zhao, Kim Kt Lau, Xian Zhou, Jianfang Wu, Jun Yang, Chang Wang
After a large-scale radiological accident, early-response biomarkers to assess radiation exposure over a broad dose range are not only the basis of rapid radiation triage, but are also the key to the rational use of limited medical resources and to the improvement of treatment efficiency. Because of its high throughput, rapid assays and minimally invasive sample collection, metabolomics has been applied to research into radiation exposure biomarkers in recent years. Due to the complexity of radiobiological effects, most of the potential biomarkers are both dose-dependent and time-dependent...
February 22, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28217795/understanding-the-microscopic-binding-mechanism-of-hydroxylated-and-sulfated-polybrominated-diphenyl-ethers-with-transthyretin-by-molecular-docking-molecular-dynamics-simulations-and-binding-free-energy-calculations
#4
Huiming Cao, Yuzhen Sun, Ling Wang, Chunyan Zhao, Jianjie Fu, Aiqian Zhang
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites...
February 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28207922/mass-spectrometry-for-the-discovery-of-biomarkers-of-sepsis
#5
REVIEW
Katelyn R Ludwig, Amanda B Hummon
Sepsis is a serious medical condition that occurs in 30% of patients in intensive care units (ICUs). Early detection of sepsis is key to prevent its progression to severe sepsis and septic shock, which can cause organ failure and death. Diagnostic criteria for sepsis are nonspecific and hinder a timely diagnosis in patients. Therefore, there is currently a large effort to detect biomarkers that can aid physicians in the diagnosis and prognosis of sepsis. Mass spectrometry is often the method of choice to detect metabolomic and proteomic changes that occur during sepsis progression...
February 16, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28197591/predicting-brain-network-changes-in-alzheimer-s-disease-with-link-prediction-algorithms
#6
Sadegh Sulaimany, Mohammad Khansari, Peyman Zarrineh, Madelaine Daianu, Neda Jahanshad, Paul M Thompson, Ali Masoudi-Nejad
Link prediction is a promising research area for modeling various types of networks and has mainly focused on predicting missing links. Link prediction methods may be valuable for describing brain connectivity, as it changes in Alzheimer's disease (AD) and its precursor, mild cognitive impairment (MCI). Here, we analyzed 3-tesla whole-brain diffusion-weighted images from 202 participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI) - 50 healthy controls, 72 with earlyMCI (eMCI) and 38 with lateMCI (lMCI) and 42 AD patients...
February 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28194469/phenylephrine-induced-cardiac-hypertrophy-is-attenuated-by-a-histone-acetylase-inhibitor-anacardic-acid-in-mice
#7
Chang Peng, Xiaomei Luo, Shuo Li, Huichao Sun
Cardiac hypertrophy is a complex process involving highly coordinated but tight regulation of multiple elements, such as in epigenetics, which make an important contribution to myocardium remodeling and cardiac hypertrophy. Epigenetic regulations, particularly histone acetylation, have been implicated in cardiac hypertrophy, however, the exact mechanism is still largely unknown. In the present study, we explored the potential attenuating effects of Chinese herbal extract anacardic acid on phenylephrine-induced cardiac hypertrophy and the underlying mechanism...
February 14, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28194462/designing-an-efficient-multi-epitope-oral-vaccine-against-helicobacter-pylori-using-immunoinformatics-and-structural-vaccinology-approaches
#8
Navid Nezafat, Mahboobeh Eslami, Manica Negahdaripour, Mohammad Reza Rahbar, Younes Ghasemi
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and "CTGKSC" peptide motif that target epithelial microfold cells (M cells) to enhance vaccine uptake from the gut barrier...
February 14, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28181620/effect-of-flexible-linker-length-on-the-activity-of-fusion-protein-4-coumaroyl-coa-ligase-stilbene-synthase
#9
Huili Guo, Yadong Yang, Feiyan Xue, Hong Zhang, Tiran Huang, Wenbin Liu, Huan Liu, Fenqiang Zhang, Mingfeng Yang, Chunmei Liu, Heshu Lu, Yansheng Zhang, Lanqing Ma
In order to elucidate the effect of flexible linker length on the catalytic efficiency of fusion proteins, two short flexible peptide linkers of various lengths were fused between Arabidopsis thaliana 4-coumaroyl-CoA ligase (4CL) and Polygonum cuspidatum stilbene synthase (STS) to generate fusion proteins 4CL-(GSG)n-STS (n ≤ 5) and 4CL-(GGGGS)n-STS (n ≤ 4). The fusion proteins were expressed in both Escherichia coli and Saccharomyces cerevisiae, and their bioactivities were tested in vitro and in vivo using purified proteins and engineered strains, respectively...
February 9, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28170013/non-active-site-mutations-disturb-the-loop-dynamics-dimerization-viral-budding-and-egress-of-vp40-of-the-ebola-virus
#10
Marissa Balmith, Mahmoud E S Soliman
The first account of the dynamic features of the loop region of VP40 of the Ebola virus (EboV) using accelerated molecular dynamics (aMD) simulations is reported herein. Due to its major role in the Ebola life cycle, VP40 is considered a promising therapeutic target. The available experimental data on the N-terminal domain (NTD) loop indicates that mutations K127A, T129A and N130A demonstrate an unrecognized role for NTD-plasma membrane (PM) interaction for efficient VP40-PM localization, oligomerization, matrix assembly and egress...
February 7, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28145541/gene-essentiality-prediction-based-on-fractal-features-and-machine-learning
#11
Yongming Yu, Licai Yang, Zhiping Liu, Chuansheng Zhu
Essential genes are required for the viability of an organism. Accurate and rapid identification of new essential genes is of substantial theoretical interest to synthetic biology and has practical applications in biomedicine. Fractals provide facilitated access to genetic structure analysis on a different scale. In this study, machine learning-based methods using solely fractal features are presented and the problem of predicting essential genes in bacterial genomes is evaluated. Six fractal features were investigated to learn the parameters of five supervised classification methods for the binary classification task...
February 1, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28128835/identification-of-novel-inhibitors-of-the-translationally-controlled-tumor-protein-tctp-insights-from-molecular-dynamics
#12
Rakesh Kumar, Ranjana Maurya, Shweta Saran
The translationally controlled tumor protein (TCTP) is a highly conserved multifunctional protein, preferentially expressed in mitotically active tissues and is a potential biomarker and a therapeutic target for lung cancers. An understanding of the biology of this molecule and model systems for the screening of drugs is still awaited. In the absence of complete crystal structure, NMR structures as templates were used for homology modeling and MD optimization of both Dictyostelium discoideum and human TCTPs, which was followed by pocket-site prediction, ligand screening and docking...
January 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28128379/regulation-of-lipids-is-central-to-replicative-senescence
#13
Darleny Y Lizardo, Yen-Lung Lin, Omer Gokcumen, G Ekin Atilla-Gokcumen
Cellular replicative senescence, a state of permanent cell-cycle arrest, has been linked to organismal aging, tissue repair and tumorigenesis. In this study, we comparatively investigated the global lipid profiles and mRNA content of proliferating and senescent-state BJ fibroblasts. We found that both expression levels of lipid-regulating genes and the abundance of specific lipid families, are actively regulated. We further found that 19 specific polyunsaturated triacylglycerol species constituted the most prominent changes in lipid composition during replicative senescence...
January 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28127595/small-rna-sequencing-revealed-dysregulated-pirnas-in-alzheimer-s-disease-and-their-probable-role-in-pathogenesis
#14
Jyoti Roy, Arijita Sarkar, Sibun Parida, Zhumur Ghosh, Bibekanand Mallick
PIWI-interacting RNAs (piRNAs), ∼23-36 nucleotide-long small non-coding RNAs, earlier believed to be germline-specific, have now been identified in somatic cells including neural cells. However, piRNAs have not yet been studied in the human brain (HB) and Alzheimer's disease (AD)-affected brain. In this study, by next-generation small RNA sequencing, 564 and 451 piRNAs were identified in the HB and AD-affected brain respectively. The majority of the neuronal piRNAs have intronic origin wherein primary piRNAs are mostly from the negative strand...
January 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28124051/solid-support-resins-and-affinity-purification-mass-spectrometry
#15
REVIEW
Spencer Havis, Wilna J Moree, Sujina Mali, Steven J Bark
Co-affinity purification-mass spectrometry (CoAP-MS) is a primary technology for elucidating the protein-protein interactions that form the basis of all biological processes. A critical component of CoAP-MS is the affinity purification (AP) of the bait protein, usually by immobilization of an antibody to a solid-phase resin. This Minireview discusses common resins, reagents, tagging methods, and their consideration for successful AP of tagged proteins. We discuss our experiences with different solid supports, their impact in AP experiments, and propose areas where chemistry can advance this important technology...
January 26, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28112328/super-rluc8-sfv-a-new-luciferase-labeled-probe-for-detection-of-human-cd4-cells
#16
A Safavi, R Emamzadeh, M Nazari, M Ehsani, S H Zarkesh-Esfahani, S Rahgozar
The human immunodeficiency virus (HIV) destroys CD4+ lymphocytes and monitoring these cells is one of the best techniques for studying HIV infection. In the present study a novel bioluminescent probe, super RLuc8-sFv, is developed in order to detect human CD4+ cells by fusion of an anti-human CD4 sFv to the C-terminus of super RLuc8. The results indicate that the probe can bind to CD4+ cells via its sFv domain; also it emits visible light through its signalling domain. Super RLuc8-sFv provides a new gateway for detection of human CD4+ cells using luminometric-based assays and may reduce the difficulties involved in, and the cost of, HIV-related diagnostic tests...
January 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28112326/crosstalk-between-the-nucleolus-and-the-dna-damage-response
#17
REVIEW
L M Ogawa, S J Baserga
Nucleolar function and the cellular response to DNA damage have long been studied as distinct disciplines. New research and a new appreciation for proteins holding multiple functional roles, however, is beginning to change the way we think about the crosstalk among distinct cellular processes. Here, we focus on the crosstalk between the DNA damage response and the nucleolus, including a comprehensive review of the literature that reveals a role for conventional DNA repair proteins in ribosome biogenesis, and conversely, ribosome biogenesis proteins in DNA repair...
January 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28112324/inference-of-cancer-mechanisms-through-computational-systems-analysis
#18
Zhen Qi, Eberhard O Voit
Large amounts of metabolomics data have been accumulated to study metabolic alterations in cancer that allow cancer cells to synthesize molecular materials necessary for cell growth and proliferation. Although metabolic reprogramming in cancer was discovered almost a century ago, the underlying biochemical mechanisms are still unclear. We show that metabolomics data can be used to infer likely biochemical mechanisms associated with cancer. The proposed inference method is data-driven and quite generic; its efficacy is demonstrated by the analysis of changes in purine metabolism of human renal cell carcinoma...
January 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28112313/soluble-epoxide-hydrolase-inhibitors-might-prevent-ischemic-arrhythmias-via-microrna-1-repression-in-primary-neonatal-mouse-ventricular-myocytes
#19
Qiong Liu, Xuan Zhao, Ran Peng, Mi Wang, Wang Zhao, Ya-Jun Gui, Cai-Xiu Liao, Dan-Yan Xu
Ischemic arrhythmias are the main causes of sudden cardiac death. It has been reported that soluble epoxide hydrolase inhibitors (sEHis) could prevent arrhythmias; however, the underlying molecular mechanisms remain unclear. In recent years, the proarrhythmic role of microRNA-1 (miR-1) has been investigated. This study aimed to elucidate whether sEHis prevented ischemic arrhythmias by suppressing miR-1. The primary neonatal mouse ventricular myocyte model of miR-1 overexpression was established by incubating with agonist microONTM mmu-miR-1a-3p agomir (DAEDstain(TM) Dye) (agomiR-1)...
January 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28102871/correction-elucidating-time-dependent-changes-in-the-urinary-metabolome-of-renal-transplant-patients-by-a-combined-1-h-nmr-and-gc-ms-approach
#20
Kienana Muhrez, Lydie Nadal-Desbarats, Jean-Michel Halimi, Binta Dieme, Matthias Büchler, Patrick Emond, Hélène Blasco, Chantal Le Guellec
Correction for 'Elucidating time-dependent changes in the urinary metabolome of renal transplant patients by a combined (1)H NMR and GC-MS approach' by Kienana Muhrez et al., Mol. BioSyst., 2015, 11, 2493-2510.
January 19, 2017: Molecular BioSystems
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