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Biased molecules

Thomas Kröber, Konstantinos Koussis, Martine Bourquin, Panagiota Tsitoura, Maria Konstantopoulou, Taiwo Sam Awolola, Francesca R Dani, Huili Qiao, Paolo Pelosi, Kostas Iatrou, Patrick M Guerin
There is increasing interest in the development of effective mosquito repellents of natural origin to reduce transmission of diseases such as malaria and yellow fever. To achieve this we have employed an in vitro competition assay involving odorant-binding proteins (OBPs) of the malaria mosquito, Anopheles gambiae, with a predominantly female expression bias to identify plant essential oils (EOs) containing bioactive compounds that target mosquito olfactory function. EOs and their fractions capable of binding to such OBPs displayed repellence against female mosquitoes in a laboratory repellence assay...
April 12, 2018: Insect Biochemistry and Molecular Biology
Jun Zhang, Lijun Ren, Xi Yang, Matthew White, James Greenhaw, Tashika Harris, Qiangen Wu, Matthew Bryant, Thomas Papoian, William Mattes, Qiang Shi
Of the 34 FDA approved oral small-molecule kinase inhibitors (KI), 23 (68%) have warnings for hepatotoxicity in product labeling. To better understand the mechanisms of KI hepatotoxicity and whether such effects can be predicted, we examined 34 KIs for cytotoxicity in primary rat and human hepatocytes. The hepatocytes were treated with KIs at ten concentrations normalized to maximal therapeutic blood levels (Cmax). At 5 and 24 h post treatment, lactate dehydrogenase or alanine aminotransferase leakage, caspase 3/7 activities and cellular adenosine triphosphate levels were measured...
April 12, 2018: Toxicology Letters
Gabriella Santagata, Salvatore Mallardo, Gabriella Fasulo, Paola Lavermicocca, Francesca Valerio, Mariaelena Di Biase, Michele Di Stasio, Mario Malinconico, Maria Grazia Volpe
In this paper, a novel and sustainable process for the fruit dehydration was described. Specifically, edible coatings based on pectin and honey were prepared and used as dehydrating and antimicrobial agents of cut fruit samples, in this way promoting the fruit preservation from irreversible deteriorative processes. Pectin-honey coating was tested on apple, cantaloupe melon, mango and pineapple. The analysis were performed also on uncoated dehydrated fruits (control). The coated fruit evidenced enhanced dehydration percentage, enriched polyphenol and vitamin C contents, improved antioxidant activity and volatile molecules profile...
August 30, 2018: Food Chemistry
Miao Zhang, Chonmanart Ngampeerapong, David Redin, Afshin Ahmadian, Ilya Sychugov, Jan Linnros
Large arrays of nanopores can be used for high throughput biomolecule translocation with applications towards size discrimination and sorting at the single-molecule level. In this paper, we propose to discriminate DNA length by the capture rate of the molecules to an array of relatively large nanopores (50 - 130 nm) by introducing a thermal gradient in front of the pores balancing the force from an external electric field. Nanopore arrays defined by photolithography were batch processed using standard silicon technology in combination with electrochemical etching...
April 12, 2018: ACS Nano
Andreas Spoerri, Despina Koletsi, Theodore Eliades
Background: External root resorption constitutes an adverse effect of orthodontic treatment. The aim of the present meta-analysis was to identify the effect of induced intrinsic/ hormone-like molecules such as prostaglandins, interleukins and others on external root resorption after orthodontic tooth movement in experimental animals Methods: An electronic database search of the literature was performed (Medline via PubMed, EMBASE, LILACS, and Open Gray). Search terms included root resorption, tooth movement and animal type...
2018: Frontiers in Physiology
J W Qu, X Q Lv, Z M Liu, Y Liao, P H Sun, B Wang, Z Tang
OBJECTIVE: To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval. METHODS: Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced...
April 18, 2018: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
Luana S Pedroza, Pedro Brandimarte, Alexandre Reily Rocha, M-V Fernández-Serra
Understanding the local structure of water at the interfaces of metallic electrodes is a key issue in aqueous-based electrochemistry. Nevertheless a realistic simulation of such a setup is challenging, particularly when the electrodes are maintained at different potentials. To correctly compute the effect of an external bias potential applied to truly semi-infinite surfaces, we combine Density Functional Theory (DFT) and Non-Equilibrium Green's Function (NEGF) methods. This framework allows for the out-of-equilibrium calculation of forces and dynamics, and directly correlates to the chemical potential of the electrodes, which is introduced experimentally...
January 7, 2018: Chemical Science
Rafael G Almeida, Simon Pan, Katy L H Cole, Jill M Williamson, Jason J Early, Tim Czopka, Anna Klingseisen, Jonah R Chan, David A Lyons
The correct targeting of myelin is essential for nervous system formation and function. Oligodendrocytes in the CNS myelinate some axons, but not others, and do not myelinate structures including cell bodies and dendrites [1]. Recent studies indicate that extrinsic signals, such as neuronal activity [2, 3] and cell adhesion molecules [4], can bias myelination toward some axons and away from cell bodies and dendrites, indicating that, in vivo, neuronal and axonal cues regulate myelin targeting. In vitro, however, oligodendrocytes have an intrinsic propensity to myelinate [5-7] and can promiscuously wrap inert synthetic structures resembling neuronal processes [8, 9] or cell bodies [4]...
March 31, 2018: Current Biology: CB
Hideaki Takahashi, Hiroyuki Kambe, Akihiro Morita
It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential...
April 7, 2018: Journal of Chemical Physics
Joshua Chan Mun Wei, Zicheng Zhao, Shuai Cheng Li, Yen Kaow Ng
DNA fingerprinting, also known as DNA profiling, serves as a standard procedure in forensics to identify a person by the short tandem repeat (STR) loci in their DNA. By comparing the STR loci between DNA samples, practitioners can calculate a probability of match to identity the contributors of a DNA mixture. Most existing methods are based on 13 core STR loci which were identified by the Federal Bureau of Investigation (FBI). Analyses based on these loci of DNA mixture for forensic purposes are highly variable in procedures, and suffer from subjectivity as well as bias in complex mixture interpretation...
March 28, 2018: Computational Biology and Chemistry
Dennis J Milanowski, Naoya Oku, Laura K Cartner, Heidi R Bokesch, R Thomas Williamson, Josep Saurí, Yizhou Liu, Kirill A Blinov, Yuanqing Ding, Xing-Cong Li, Daneel Ferreira, Larry A Walker, Shabana Khan, Michael T Davies-Coleman, James A Kelley, James B McMahon, Gary E Martin, Kirk R Gustafson
Ambiguities and errors in the structural assignment of organic molecules hinder both drug discovery and total synthesis efforts. Newly described NMR experimental approaches can provide valuable structural details and a complementary means of structure verification. The caulamidines are trihalogenated alkaloids from a marine bryozoan with an unprecedented structural scaffold. Their unique carbon and nitrogen framework was deduced by conventional NMR methods supplemented by new experiments that define 2-bond heteronuclear connectivities, reveal very long-range connectivity data, or visualize the35,37 Cl isotopic effect on chlorinated carbons...
January 14, 2018: Chemical Science
Jessica C Kling, Margaret A Jordan, Lauren A Pitt, Jana Meiners, Thao Thanh-Tran, Le Son Tran, Tam T K Nguyen, Deepak Mittal, Rehan Villani, Raymond J Steptoe, Kiarash Khosrotehrani, Stuart P Berzins, Alan G Baxter, Dale I Godfrey, Antje Blumenthal
Natural killer T (NKT) cells are prominent innate-like lymphocytes in the liver with critical roles in immune responses during infection, cancer, and autoimmunity. Interferon gamma (IFN-γ) and IL-4 are key cytokines rapidly produced by NKT cells upon recognition of glycolipid antigens presented by antigen-presenting cells (APCs). It has previously been reported that the transcriptional coactivator β-catenin regulates NKT cell differentiation and functionally biases NKT cell responses toward IL-4, at the expense of IFN-γ production...
2018: Frontiers in Immunology
Kah Meng Yam, Na Guo, Chun Zhang
Building electronic devices on top of two dimensional (2D) materials has become one of most interesting topics recently in nanoelectronics. Finding high-performance 2D electrode materials is one central issue in 2D nanoelectronics. In current study, based on first principles calculations, we compare the electronic and transport properties of two nanoscale devices. One device consists of two single-atom-thick planar Cu2Si electrodes and a nickel-phthalocyanine (NiPc) molecule in middle. The other one is made of often-used graphene electrodes and a NiPc molecule...
April 3, 2018: Nanotechnology
Orly B Tarun, Christof Hannesschläger, Peter Pohl, Sylvie Roke
Biological membranes are highly dynamic and complex lipid bilayers, responsible for the fate of living cells. To achieve this function, the hydrating environment is crucial. However, membrane imaging typically neglects water, focusing on the insertion of probes, resonant responses of lipids, or the hydrophobic core. Owing to a recent improvement of second-harmonic (SH) imaging throughput by three orders of magnitude, we show here that we can use SH microscopy to follow membrane hydration of freestanding lipid bilayers on millisecond time scales...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
Vern L Schramm, Steven D Schwartz
A complete understanding of enzyme catalysis requires knowledge of transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the fsec lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experi- mental approach to transition state structure and a method to obtain transition state analogues...
April 2, 2018: Biochemistry
Sarah N Innes-Gold, Ian L Morgan, Omar A Saleh
Single-molecule measurements of polymer elasticity are powerful, direct probes of both biomolecular structure and principles of polymer physics. Recent work has revealed low-force regimes in which biopolymer elasticity is understood through blob-based scaling models. However, the small tensions required to observe these regimes have the potential to create measurement biases, particularly due to the increased interactions of the polymer chain with tethering surfaces. Here, we examine one experimentally observed bias, in which fluctuation-based estimates of elasticity report an unexpectedly low chain compliance...
March 28, 2018: Journal of Chemical Physics
Linfeng Zhang, Han Wang, Weinan E
A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function...
March 28, 2018: Journal of Chemical Physics
Pankaj Kumar Singh, Om Silakari
O-heterocycles have been explored since long in the field of medicinal chemistry but they have not yet been given their due significance and are usually shunned out in comparison to N-heterocycles. Designing of bioactive molecules for almost every pathophysiological condition is primarily focused on designing novel N-heterocycles. The basic reasons for this bias are the ease of synthesis and possible mimicking of physiological molecules by N-heterocycles. But considering only this criteria never provides any breakthrough molecule for any disease condition, rather risk of toxicity/side effects are increased with such molecules...
March 30, 2018: ChemMedChem
Sukrit Silas, Nimit Jain, Michael Stadler, Becky Xu Hua Fu, Antonio Sánchez-Amat, Andrew Z Fire, Joshua Arribere
Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation and strand-specific sequencing of small RNA pools from bacteria that can be multiplexed to accommodate multiple biological samples in a single experiment. Small RNAs are isolated by polyacrylamide gel electrophoresis and treated with T4 polynucleotide kinase. This allows for 3' adapter ligation to CRISPR RNAs, which don't have pre-existing 3'-OH ends...
February 20, 2018: Bio-protocol
Chuan Shi, Shalom Goldberg, Tricia Lin, Vadim Y Dudkin, Wayne C Widdison, Luke Harris, Sharon D Wilhelm, Yazen Jmeian, Darryl Davis, Karyn O'Neil, Naidong Weng, Wenying Jian
Bioanalysis of antibody-drug conjugates (ADCs) is challenging due to the complex, heterogeneous nature of their structures and their complicated catabolism. To fully describe the pharmacokinetics (PK) of an ADC, several analytes are commonly quantified, including total antibody, conjugate, and payload. Among them, conjugate is the most challenging to measure because it requires detection of both small and large molecules as one entity. Existing approaches to quantify the conjugated species of ADCs involve a ligand binding assay (LBA) for conjugated antibody or hybrid LBA/liquid chromatography-tandem mass spectrometry (LC-MS/MS) for quantitation of conjugated drug...
March 28, 2018: Analytical Chemistry
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