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Biological complex systems

Adity Bose, Priti Sengupta, Uttam Pal, Sanjib Senapati, Mohd Ahsan, Santanu Roy, Upasana Das, Kamalika Sen
Cyclodextrins have a wide range of applications in different areas of drug delivery and pharmaceutical industry due to their complexation ability and other versatile characteristics. Here we have studied the binding interactions of a small biologically important phenolic molecule, Thymol (Th), with both α and β cyclodextrins (CDs), which are well known drug delivery vehicles. Extent of encapsulation has been determined using several spectroscopic techniques. In fluorescence experiments, significant increase in fluorescence intensities have been discerned for both the CDs but there had been a much early saturation for αCD...
October 12, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Ying Shi, Yanjiao Pang, Ning Huang, Chaoqun Sun, Yadi Pan, Yuan Cheng, Yijuan Long, Huzhi Zheng
Dopamine (DA), a catecholamine neurotransmitter, is considered to be an important indicator for mental diseases detection in the clinic. In this study, a novel fluorescent sensing platform consisting of the ficin-H2 O2 -tyramine system for determining DA in cerebrospinal fluids (CSF) was established. The proposed method is based on the fact that ficin, a mimetic peroxidase, can catalyze H2 O2 decomposition into OH radicals, which can oxidize non-fluorescent tyramine into fluorescent dityramine. When DA was introduced, DA can compete with tyramine for OH and resulting in the oxidation reaction of tyramine inhibited along with the fluorescence intensity of the system decreased, which provides a unique strategy for fluorescence detection of DA...
October 16, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Ruijie K Zhang, Xiongyi Huang, Frances H Arnold
CH functionalization is an attractive strategy to construct and diversify molecules. Heme proteins, predominantly cytochromes P450, are responsible for an array of CH oxidations in biology. Recent work has coupled concepts from synthetic chemistry, computation, and natural product biosynthesis to engineer heme protein systems to deliver products with tailored oxidation patterns. Heme protein catalysis has been shown to go well beyond these native reactions and now accesses new-to-nature CH transformations, including CN and CC bond forming processes...
October 18, 2018: Current Opinion in Chemical Biology
Şükrü Barış Demiral, Dardo Tomasi, Joelle Sarlls, Hedok Lee, Corinde E Wiers, Amna Zehra, Tansha Srivastava, Kenneth Ke, Ehsan Shokri-Kojori, Clara R Freeman, Elsa Lindgren, Veronica Ramirez, Gregg Miller, Peter Bandettini, Silvina Horovitz, Gene-Jack Wang, Helene Benveniste, Nora D Volkow
The role of sleep in brain physiology is poorly understood. Recently rodent studies have shown that the glymphatic system clears waste products from brain more efficiently during sleep compared to wakefulness due to the expansion of the interstitial fluid space facilitating entry of cerebrospinal fluid (CSF) into the brain. Here, we studied water diffusivity in the brain during sleep and awake conditions, hypothesizing that an increase in water diffusivity during sleep would occur concomitantly with an expansion of CSF volume - an effect that we predicted based on preclinical findings would be most prominent in cerebellum...
October 17, 2018: NeuroImage
Inês L Martins, João Nunes, Catarina Charneira, Judit Morello, Sofia A Pereira, João P Telo, M Matilde Marques, Alexandra M M Antunes
Carbamazepine (CBZ) is one of the most widely used antiepileptic drugs by both adults and children. Despite its widespread use, CBZ is associated with central nervous system toxicity and severe hypersensitivity reactions, which raise concerns about its chronic use. While the precise mechanisms of CBZ-induced adverse events are still unclear, metabolic activation to the epoxide (CBZ-EP) has been thought to play a significant role. This work reports first-hand evidence that CBZ reacts readily with biologically relevant thiyl radicals with no need for bioactivation...
October 17, 2018: Free Radical Biology & Medicine
Hellen Franciane Gonçalves Barbosa, Éder Tadeu Gomes Cavalheiro
Influence of some reactional parameters as mol ratio (Schiff base:metal), solvent, temperature and reaction time were evaluated in order to improve the extension of complexation during the preparation of zinc complexes of biopolymeric Schiff base from chitosan and salicylaldehyde. Zinc(II) complex was used as a model system in order to improve the degree of complexation for further synthesis of different Schiff bases complexes from other aldehydes and metallic centers. The complexation yields for each synthesis were estimated on the basis of the zinc oxide formed after thermal degradation...
October 17, 2018: International Journal of Biological Macromolecules
Dragan Milenkovic, Wim Vanden Berghe, Christine Morand, Sylvain Claude, Annette van de Sandt, Simone Gorressen, Laurent-Emmanuel Monfoulet, Chandra S Chirumamilla, Ken Declerck, Katarzyna Szarc Vel Szic, Maija Lahtela-Kakkonen, Clarissa Gerhauser, Marc W Merx, Malte Kelm
Although vasculo-protective effects of flavan-3-ols are widely accepted today, their impact on endothelial cell functions and molecular mechanisms of action involved is not completely understood. The aim of this study was to characterize the potential endothelium-protective effects of circulating epicatechin metabolites and to define underlying mechanisms of action by an integrated systems biology approach. Reduced leukocyte rolling over vascular endothelium was observed following epicatechin supplementation in a mouse model of inflammation...
October 19, 2018: Scientific Reports
Anil P S Ori, Merel H M Bot, Remco T Molenhuis, Loes M Olde Loohuis, Roel A Ophoff
BACKGROUND: Common psychiatric disorders are characterized by complex disease architectures with many small genetic effects that contribute and complicate biological understanding of their etiology. There is therefore a pressing need for in vitro experimental systems that allow for interrogation of polygenic psychiatric disease risk to study the underlying biological mechanisms. METHODS: We have developed an analytical framework that integrates genome-wide disease risk from genome-wide association studies with longitudinal in vitro gene expression profiles of human neuronal differentiation...
September 6, 2018: Biological Psychiatry
Pawel Krzeminski, Maria Concetta Tomei, Popi Karaolia, Alette Langenhoff, C Marisa R Almeida, Ewa Felis, Fanny Gritten, Henrik Rasmus Andersen, Telma Fernandes, Celia M Manaia, Luigi Rizzo, Despo Fatta-Kassinos
Contaminants of emerging concern (CEC) discharged in effluents of wastewater treatment plants (WWTPs), not specifically designed for their removal, pose serious hazards to human health and ecosystems. Their impact is of particular relevance to wastewater disposal and re-use in agricultural settings due to CEC uptake and accumulation in food crops and consequent diffusion into the food-chain. This is the reason why the chemical CEC discussed in this review have been selected considering, besides recalcitrance, frequency of detection and entity of potential hazards, their relevance for crop uptake...
January 15, 2019: Science of the Total Environment
Tao Yun, Jionggang Hua, Weicheng Ye, Bin Yu, Zheng Ni, Liu Chen, Cun Zhang
Duck reovirus (DRV), a member of the genus Orthoreovirus in the family Reoviridae, was first isolated from Muscovy ducks. The disease associated with DRV causes great economic losses to the duck industry. However, the responses of duck (Cairna moschata) to the classical/novel DRV (C/NDRV) infections are largely unknown. To reveal the relationship of pathogenesis and immune response, the proteomes of duck spleen cells under the control and C/NDRV infections were compared. In total, 5986 proteins were identified, of which 5389 proteins were quantified...
October 16, 2018: Journal of Proteomics
Yuxiang Chen, M Lisa Phipps, James H Werner, Saumen Chakraborty, Jennifer S Martinez
Metal nanoclusters containing a few to several hundred atoms with sizes ranging from sub-nanometer to ∼2 nm occupy an intermediate size regime that bridges larger plasmonic nanoparticles and smaller metal complexes. With strong quantum confinement, metal nanoclusters exhibit molecule-like properties. This Account focuses on noble metal nanoclusters that are synthesized within a single stranded DNA template. Compared to other ligand protected metal nanoclusters, DNA-templated metal nanoclusters manifest intriguing physical and chemical properties that are heavily influenced by the design of DNA templates...
October 19, 2018: Accounts of Chemical Research
Jie Gu, Sha Song, Huiying Han, Hongxia Xu, Gao Fan, Chen'ao Qian, Yingchun Qiu, Wenqi Zhou, Wenzhuo Zhuang, Bingzong Li
Treatment failure remains a main challenge in the management of high-risk multiple myeloma (MM) even with the expanding repertoire of new drugs. Combinatorial therapy is considered an encouraging strategy that can overcome the compensatory mechanisms and undesirable off-target effects that limit the benefits of many prospective agents. Preliminary results of a current phase I trial have indicated that the new BET bromodomain inhibitor OTX015 has favorable activity and tolerability. However, OTX015 is not efficacious enough as a monotherapy...
October 19, 2018: Molecular Pharmaceutics
Pei Chen, Ely Chen, Luonan Chen, Xianghong Jasmine Zhou, Rui Liu
The seasonal outbreaks of influenza infection cause globally respiratory illness, or even death in all age groups. Given early-warning signals preceding the influenza outbreak, timely intervention such as vaccination and isolation management effectively decrease the morbidity. However, it is usually a difficult task to achieve the real-time prediction of influenza outbreak due to its complexity intertwining both biological systems and social systems. By exploring rich dynamical and high-dimensional information, our dynamic network marker/biomarker (DNM/DNB) method opens a new way to identify the tipping point prior to the catastrophic transition into an influenza pandemics...
October 19, 2018: Journal of Cellular and Molecular Medicine
Somsankar Dasgupta, Swapan K Ray
Sphingolipids are enriched in the Central Nervous System (CNS) and display multiple biological functions. They participate in tissue development, cell recognition and adhesion, and act as receptors for toxins. During myelination, a variety of interactive molecules such as myelin basic protein, myelin associated glycoprotein, phospholipids, cholesterol, sphingolipids, etc., participate in a complex fashion. Precise roles of some sphingolipids in myelination still remain unexplored. Our investigation delineated participation of several sphingolipids in myelination during rat brain development as well as in human brain demyelination during pathogenesis of Multiple Sclerosis (MS)...
December 2017: Journal of Neurology and Psychology
Joshua D Wofford, Naimah Bolaji, Nathaniel Dziuba, F Wayne Outten, Paul A Lindahl
Iron is critical for virtually all organisms, yet major questions remain regarding the systems' level understanding of iron in whole cells. Here, we obtained Mössbauer and EPR spectra of Escherichia coli cells prepared under different nutrient iron concentrations, carbon sources, growth phases, and O2 concentrations to better understand their global iron content. We investigated wild-type cells and those lacking Fur, FtnA, Bfr, and Dps proteins. The coarse-grain iron content of exponentially growing cells consisted of iron-sulfur clusters, variable amounts of nonheme high-spin FeII species, and an unassigned residual quadrupole doublet...
October 18, 2018: Journal of Biological Chemistry
Songhee H Kim, Melissa Vieira, Jae Youn Shim, Hongyoung Choi, Hye Yoon Park
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules...
October 19, 2018: RNA Biology
Zachary Boswell, Michael P Latham
Nuclear Magnetic Resonance (NMR) spectroscopy is particularly adept at site-specifically monitoring dynamic processes in proteins, such as protein folding, domain movements, ligand binding, and side chain rotations. By coupling the favorable spectroscopic properties of highly dynamic side chain methyl groups with Transverse Relaxation Optimized SpectroscopY (TROSY), it is now possible to routinely study such dynamic processes in large molecular weight proteins and complexes approaching 1 MDa. In this perspective, we describe many elegant methyl-based NMR experiments that probe slow (second) to fast (picosecond) dynamics in large systems...
October 18, 2018: Biochemistry
Mahla Poudineh, Zongjie Wang, Mahmoud Labib, Moloud Ahmadi, Libing Zhang, Jagotamoy Das, Sharif Ahmed, Stephane Angers, Shana O Kelley
Cell morphology and geometry affect cellular processes such as stem cell differentiation, suggesting that these parameters serve as fundamental regulators of biological processes within the cell. Hierarchical architectures featuring micro- and nanotopographical features therefore offer programmable systems for stem cell differentiation. However, a limited number of studies have explored the effects of hierarchical architectures due to the complexity of fabricating systems with rationally tunable micro- and nanostructuring...
October 18, 2018: Nano Letters
Somayeh Bakhteh, Alireza Ghaffari-Hadigheh, Nader Chaparzadeh
Identification of master regulatory genes is one of the primary challenges in systems biology. The minimum dominating set problem is a powerful paradigm in analyzing such complex networks. In these models, genes stand as nodes and their interactions are assumed as edges. Here, members of a minimal dominating set could be regarded as master genes. As finitely many minimum dominating sets may exist in a network, it is difficult to identify which one represents the most appropriate set of master genes. In this paper, we develop a weighted gene regulatory network problem with two objectives as a version of the dominating set problem...
October 12, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Melissa L D Rayner, Simão Laranjeira, Rachael E Evans, Rebecca J Shipley, Jess Healy, James B Phillips
Peripheral nerve injuries (PNI) have a high prevalence and can be debilitating, resulting in life-long loss or disturbance in end-organ function, which compromises quality of life for patients. Current therapies use microsurgical approaches but there is the potential for enhancing recovery through other therapeutic modalities such as; cell-based conduits, gene therapy and small molecules. A number of molecular targets and drugs which have the potential to improve nerve regeneration have been identified, however, there are challenges associated with moving therapies toward clinical translation...
October 17, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
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