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https://www.readbyqxmd.com/read/28813018/biophysical-and-computational-studies-of-the-vcci-vmip-ii-complex
#1
Anna F Nguyen, Nai-Wei Kuo, Laura J Showalter, Ricardo Ramos, Cynthia M Dupureur, Michael E Colvin, Patricia J LiWang
Certain viruses have the ability to subvert the mammalian immune response, including interference in the chemokine system. Poxviruses produce the chemokine binding protein vCCI (viral CC chemokine inhibitor; also called 35K), which tightly binds to CC chemokines. To facilitate the study of vCCI, we first provide a protocol to produce folded vCCI from Escherichia coli (E. coli.) It is shown here that vCCI binds with unusually high affinity to viral Macrophage Inflammatory Protein-II (vMIP-II), a chemokine analog produced by the virus, human herpesvirus 8 (HHV-8)...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812944/binding-forces-between-a-novel-schiff-base-palladium-ii-complex-and-two-carrier-proteins-human-serum-albumi-and%C3%AE-lactoglobulin
#2
Somaye Shahraki, Ali Heydari
Ligand binding studies on carrier proteins are crucial in determining the pharmacological properties of drug candidates. Here, a new palladium(II) complex was synthesized and characterized. The in vitro binding studies of this complexwith two carrier proteins, human serum albumin (HSA) and β-lactoglobulin (βLG) was investigated by employing biophysical techniques as well as computational modeling. The experimental results showed thatthe Pd(II) complex interacted with two carrier proteins with moderate binding affinity (Kb ~̴ 0...
August 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28809937/understanding-large-scale-long-term-larval-connectivity-patterns-the-case-of-the-northern-line-islands-in-the-central-pacific-ocean
#3
Lorenzo Mari, Luca Bonaventura, Andrea Storto, Paco Melià, Marino Gatto, Simona Masina, Renato Casagrandi
Protecting key hotspots of marine biodiversity is essential to maintain ecosystem services at large spatial scales. Protected areas serve not only as sources of propagules colonizing other habitats, but also as receptors, thus acting as protected nurseries. To quantify the geographical extent and the temporal persistence of ecological benefits resulting from protection, we investigate larval connectivity within a remote archipelago, characterized by a strong spatial gradient of human impact from pristine to heavily exploited: the Northern Line Islands (NLIs), including part of the Pacific Remote Islands Marine National Monument (PRI-MNM)...
2017: PloS One
https://www.readbyqxmd.com/read/28808316/habituation-based-synaptic-plasticity-and-organismic-learning-in-a-quantum-perovskite
#4
Fan Zuo, Priyadarshini Panda, Michele Kotiuga, Jiarui Li, Mingu Kang, Claudio Mazzoli, Hua Zhou, Andi Barbour, Stuart Wilkins, Badri Narayanan, Mathew Cherukara, Zhen Zhang, Subramanian K R S Sankaranarayanan, Riccardo Comin, Karin M Rabe, Kaushik Roy, Shriram Ramanathan
A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmental breathing studies...
August 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28808275/screening-drug-target-interactions-with-positive-unlabeled-learning
#5
Lihong Peng, Wen Zhu, Bo Liao, Yu Duan, Min Chen, Yi Chen, Jialiang Yang
Identifying drug-target interaction (DTI) candidates is crucial for drug repositioning. However, usually only positive DTIs are deposited in known databases, which challenges computational methods to predict novel DTIs due to the lack of negative samples. To overcome this dilemma, researchers usually randomly select negative samples from unlabeled drug-target pairs, which introduces a lot of false-positives. In this study, a negative sample extraction method named NDTISE is first developed to screen strong negative DTI examples based on positive-unlabeled learning...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28806076/structure-affinity-relationships-and-structure-kinetics-relationships-of-pyrido-2-1-f-purine-2-4-dione-derivatives-as-human-adenosine-a3-receptor-antagonists
#6
Lizi Xia, Wessel A C Burger, Jacobus P D van Veldhoven, Boaz J Kuiper, Tirsa T van Duijl, Eelke B Lenselink, Ellen Paasman, Laura H Heitman, Adriaan P IJzerman
We expanded on a series of pyrido[2,1-f]purine-2,4-dione derivatives as human adenosine A3 receptor (hA3R) antagonists to determine their kinetic profiles and affinities. Many compounds showed high affinities and a diverse range of kinetic profiles. We found hA3R antagonists with very short residence time at the receptor (RT of 2.2 min for 5) and much longer RTs (e.g. 376 min for 27, or 391 min for 31). Two representative antagonists (5 and 27) were tested in [(35)S]GTPγS binding assays, and their RTs appeared correlated to their (in)surmountable antagonism...
August 14, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28802824/highly-accurate-prediction-of-protein-self-interactions-by-incorporating-the-average-block-and-pssm-information-into-the-general-pseaac
#7
Jing-Xuan Zhai, Tian-Jie Cao, Ji-Yong An, Yong-Tao Bian
It is a challenging task for fundamental research whether proteins can interact with their partners. Protein self-interaction (SIP) is a special case of PPIs, which plays a key role in the regulation of cellular functions. Due to the limitations of experimental self-interaction identification, it is very important to develop an effective biological tool for predicting SIPs based on protein sequences. In the study, we developed a novel computational method called RVM-AB that combines the Relevance Vector Machine (RVM) model and Average Blocks (AB) for detecting SIPs from protein sequences...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28802032/deciphering-critical-amino-acid-residues-to-modify-and-enhance-the-binding-affinity-of-ankyrin-scaffold-specific-to-capsid-protein-of-human-immunodeficiency-virus-type-1
#8
Somphot Saoin, Tanchanok Wisitponchai, Kannaporn Intachai, Koollawat Chupradit, Sutpirat Moonmuang, Sawitree Nangola, Kuntida Kitidee, Kanda Fanhchaksai, Vannajan Sanghiran Lee, Saw-See Hong, Pierre Boulanger, Phimonphan Chuankhayan, Chun-Jung Chen, Chatchai Tayapiwatana
BACKGROUND: AnkGAG1D4 is an artificial ankyrin repeat protein which recognizes the capsid protein (CA) of the human immunodeficiency virus type 1 (HIV-1) and exhibits the intracellular antiviral activity on the viral assembly process. Improving the binding affinity of AnkGAG1D4 would potentially enhance the AnkGAG1D4-mediated antiviral activity. OBJECTIVE: To augment the affinity of AnkGAG1D4 scaffold towards its CA target, through computational predictions and experimental designs...
August 8, 2017: Asian Pacific Journal of Allergy and Immunology
https://www.readbyqxmd.com/read/28800346/how-should-a-virtual-agent-present-psychoeducation-influence-of-verbal-and-textual-presentation-on-adherence
#9
Myrthe L Tielman, Mark A Neerincx, Marieke van Meggelen, Ingmar Franken, Willem-Paul Brinkman
BACKGROUND AND OBJECTIVE: With the rise of autonomous e-mental health applications, virtual agents can play a major role in improving trustworthiness, therapy outcome and adherence. In these applications, it is important that patients adhere in the sense that they perform the tasks, but also that they adhere to the specific recommendations on how to do them well. One important construct in improving adherence is psychoeducation, information on the why and how of therapeutic interventions...
August 4, 2017: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/28799793/towards-quantitative-analysis-of-gene-regulation-by-enhancers
#10
Ekaterina V Nizovtseva, Stefjord Todolli, Wilma K Olson, Vasily M Studitsky
Enhancers are regulatory DNA sequences that can activate transcription over large distances. Recent studies have revealed the widespread role of distant activation in eukaryotic gene regulation and in the development of various human diseases, including cancer. Here we review recent progress in the field, focusing on new experimental and computational approaches that quantify the role of chromatin structure and dynamics during enhancer-promoter interactions in vitro and in vivo.
August 11, 2017: Epigenomics
https://www.readbyqxmd.com/read/28799651/thermal-mapping-on-male-genital-and-skin-tissues-of-laptop-thermal-sources-and-electromagnetic-interaction
#11
Mahdi Safari, Navid Mosleminiya, Ali Abdolali
Since the development of communication devices and expansion of their applications, there have been concerns about their harmful health effects. The main aim of this study was to investigate laptop thermal effects caused by exposure to electromagnetic fields and thermal sources simultaneously; propose a nondestructive, replicable process that is less expensive than clinical measurements; and to study the effects of positioning any new device near the human body in steady state conditions to ensure safety by U...
August 11, 2017: Bioelectromagnetics
https://www.readbyqxmd.com/read/28798412/a-time-varying-biased-random-walk-approach-to-human-growth
#12
Béla Suki, Urs Frey
Growth and development are dominated by gene-environment interactions. Many approaches have been proposed to model growth, but most are either descriptive or describe population level phenomena. We present a random walk-based growth model capable of predicting individual height, in which the growth increments are taken from time varying distributions mimicking the bursting behaviour of observed saltatory growth. We derive analytic equations and also develop a computational model of such growth that takes into account gene-environment interactions...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797090/imidazoquinoxaline-anticancer-derivatives-and-imiquimod-interact-with-tubulin-characterization-of-molecular-microtubule-inhibiting-mechanisms-in-correlation-with-cytotoxicity
#13
Alexis Courbet, Nicole Bec, Caroline Constant, Christian Larroque, Martine Pugniere, Safia El Messaoudi, Zahraa Zghaib, Sonia Khier, Carine Deleuze-Masquefa, Florence Gattacceca
Displaying a strong antiproliferative activity on a wide variety of cancer cells, EAPB0203 and EAPB0503 belong to the imidazo[1,2-a]quinoxalines family of imiquimod structural analogues. EAPB0503 has been shown to inhibit tubulin polymerization. The aim of the present study is to characterize the interaction of EAPB0203 and EAPB0503 with tubulin. We combine experimental approaches at the cellular and the molecular level both in vitro and in silico in order to evaluate the interaction of EAPB0203 and EAPB0503 with tubulin...
2017: PloS One
https://www.readbyqxmd.com/read/28796787/the-quinic-acid-derivative-kz-41-prevents-glucose-induced-caspase-3-activation-in-retinal-endothelial-cells-through-an-igf-1-receptor-dependent-mechanism
#14
Hui He, Rebecca L Weir, Jordan J Toutounchian, Jayaprakash Pagadala, Jena J Steinle, Jerome Baudry, Duane D Miller, Charles R Yates
Retinal microaneurysms, an early disease manifestation of diabetic retinopathy, are associated with retinal endothelial cell (REC) death and macular edema. We previously demonstrated that a quinic acid (QA) analog, KZ-41, promoted REC survival by blunting stress-induced p38 MAPK activation. Herein, we sought to expand our understanding of the pro-survival signal transduction pathways actuated by KZ-41. Using human RECs exposed to high glucose (25 mM, 72 hours), we demonstrated that KZ-41 blocks caspase-3 activation by triggering phosphorylation of the PI3K regulatory subunit (p85; Tyr458) and its downstream target Akt (Ser473)...
2017: PloS One
https://www.readbyqxmd.com/read/28796781/embodied-conversational-agents-for-multimodal-automated-social-skills-training-in-people-with-autism-spectrum-disorders
#15
Hiroki Tanaka, Hideki Negoro, Hidemi Iwasaka, Satoshi Nakamura
Social skills training, performed by human trainers, is a well-established method for obtaining appropriate skills in social interaction. Previous work automated the process of social skills training by developing a dialogue system that teaches social communication skills through interaction with a computer avatar. Even though previous work that simulated social skills training only considered acoustic and linguistic information, human social skills trainers take into account visual and other non-verbal features...
2017: PloS One
https://www.readbyqxmd.com/read/28796622/w-fyd-a-wearable-fabric-based-display-for-haptic-multi-cue-delivery-and-tactile-augmented-reality
#16
Simone Fani, Simone Ciotti, Edoardo Battaglia, Alessandro Moscatelli, Matteo Bianchi
Despite the importance of softness, there is no evidence of wearable haptic systems able to deliver controllable softness cues. Here, we present the Wearable Fabric Yielding Display (W-FYD), a fabric-based display for multi-cue delivery that can be worn on user's finger and enables, for the first time, both active and passive softness exploration. It can also induce a sliding effect under the finger-pad. A given stiffness profile can be obtained by modulating the stretching state of the fabric through two motors...
August 7, 2017: IEEE Transactions on Haptics
https://www.readbyqxmd.com/read/28793925/perturbed-human-sub-networks-by-fusobacterium-nucleatum-candidate-virulence-proteins
#17
Andreas Zanzoni, Lionel Spinelli, Shérazade Braham, Christine Brun
BACKGROUND: Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. RESULTS: We devised a computational strategy to identify putative secreted F...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28793853/equine-skeletal-muscle-adaptations-to-exercise-and-training-evidence-of-differential-regulation-of-autophagosomal-and-mitochondrial-components
#18
Kenneth Bryan, Beatrice A McGivney, Gabriella Farries, Paul A McGettigan, Charlotte L McGivney, Katie F Gough, David E MacHugh, Lisa M Katz, Emmeline W Hill
BACKGROUND: A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exercise and again after an extended period of training...
August 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28792503/multi-scale-encoding-of-amino-acid-sequences-for-predicting-protein-interactions-using-gradient-boosting-decision-tree
#19
Chang Zhou, Hua Yu, Yijie Ding, Fei Guo, Xiu-Jun Gong
Nowadays a number of computational approaches have been developed to effectively and accurately predict protein interactions. However, most of these methods typically perform worse when other biological data sources (e.g., protein structure information, protein domains, or gene neighborhoods information) are not available. In the present work, we propose a method for predicting protein interactions making full use of physicochemical characteristics of amino acids. A protein sequence is encoded at multi-scale by seven properties, including their qualitative and quantitative descriptions, of amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28790884/the-effect-of-electroencephalogram-eeg-reference-choice-on-information-theoretic-measures-of-the-complexity-and-integration-of-eeg-signals
#20
Logan T Trujillo, Candice T Stanfield, Ruben D Vela
Converging evidence suggests that human cognition and behavior emerge from functional brain networks interacting on local and global scales. We investigated two information-theoretic measures of functional brain segregation and integration-interaction complexity C I (X), and integration I(X)-as applied to electroencephalographic (EEG) signals and how these measures are affected by choice of EEG reference. CI(X) is a statistical measure of the system entropy accounted for by interactions among its elements, whereas I(X) indexes the overall deviation from statistical independence of the individual elements of a system...
2017: Frontiers in Neuroscience
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