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Biased molecules

J Brand, P Ribeiro, N Néel, S Kirchner, J Kröger
Charge transport has been examined in junctions comprising the normal-metal tip of a low-temperature scanning tunneling microscope, the surface of a conventional superconductor, and adsorbed C_{60} molecules. The Bardeen-Cooper-Schrieffer energy gap gradually evolves into a zero-bias peak with decreasing electrode separation. The peak is assigned to the spectroscopic signature of Andreev reflection. The conductance due to Andreev reflection is determined by the atomic termination of the tip apex and the molecular adsorption orientation...
March 10, 2017: Physical Review Letters
Chunmei Li, Zhilong Yu, Yusi Fu, Yuhong Pang, Yanyi Huang
We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multi-fraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infers CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of reaction mix before amplification...
March 24, 2017: ACS Applied Materials & Interfaces
Jiang Liu, Dustin Yuan Chen, Xinning Luan, Kwing Tong, Fangchao Zhao, Chao Liu, Qibing Pei, Huaping Li
We report vertical, electrolyte-gated, red, green and blue phosphorescent small molecule organic light emitting diodes (OLED), in which light emission was modified by tuning the electron injection via electrochemical doping of the electron injection layer 4,4-bis(N-carbazolyl)-1,1-biphenyl (CBP) under the assistance of a polymer electrolyte. These devices comprise an electrolyte capacitor on top of a conventional OLED, with the interfacial contact between the electrolyte and electron injection layer CBP of OLEDs achieved through a porous cathode...
March 23, 2017: ACS Applied Materials & Interfaces
Aliasghar Sepehri, Troy D Loeffler, Bin Chen
A new method, called Jacobian-Gaussian scheme, has been developed to overcome the challenge of bending angle generation for linear and branched molecules in configurational-bias Monte Carlo. This method is simple, general, fast, and robust which can yield high acceptance rates. Since there are several bending angles in a branched point and their energies are coupled to each other, generating one trial that is acceptable for all energetic terms is a difficult problem. In order to reach reasonable acceptance rates, traditional methods either generate many trials uniformly or use prepared tables to generate trials according to the expected distribution...
March 15, 2017: Journal of Chemical Theory and Computation
Assaf Zaritsky, Uri Obolski, Zhuo Gan, Carlos R Reis, Zuzana Kadlecova, Yi Du, Sandra L Schmid, Gaudenz Danuser
Analysis of coupled variables is a core concept of cell biological inference, with co-localization of two molecules as a proxy for protein interaction being a ubiquitous example. However, external effectors may influence the observed co-localization independently from the local interaction of two proteins. Such global bias, although biologically meaningful, is often neglected when interpreting co-localization. Here, we describe DeBias, a computational method to quantify and decouple global bias from local interactions between variables by modeling the observed co-localization as the cumulative contribution of a global and a local component...
March 13, 2017: ELife
Jasvinder A Singh, Alomgir Hossain, Elizabeth Tanjong Ghogomu, Amy S Mudano, Lara J Maxwell, Rachelle Buchbinder, Maria Angeles Lopez-Olivo, Maria E Suarez-Almazor, Peter Tugwell, George A Wells
BACKGROUND: Biologic disease-modifying anti-rheumatic drugs (DMARDs: referred to as biologics) are effective in treating rheumatoid arthritis (RA), however there are few head-to-head comparison studies. Our systematic review, standard meta-analysis and network meta-analysis (NMA) updates the 2009 Cochrane overview, 'Biologics for rheumatoid arthritis (RA)' and adds new data. This review is focused on biologic or tofacitinib therapy in people with RA who had previously been treated unsuccessfully with biologics...
March 10, 2017: Cochrane Database of Systematic Reviews
Terry Kenakin
The availability of different functional pharmacological assays has revealed that agonists for receptors that are pleiotropically coupled to multiple signaling pathways in the cell can emphasize signals to some pathways over others, i.e. can be biased toward certain signals. This, in turn, opens the possibility that molecules can be made to emphasize favorable signals, de-emphasize harmful signals or selectively block the ability of the natural agonist to produce unfavorable signals. Areas covered: This paper discusses the mechanism of biased signaling, the possible therapeutic implications of this effect, methods to quantify and measure bias and the current literature describing the translation of biased measure in vitro to in vivo systems...
March 9, 2017: Expert Opinion on Drug Discovery
Hang Su, Ruijie Liu, Ming Chang, Jianhua Huang, Qingzhe Jin, Xingguo Wang
PURPOSE: The aim of the current meta-analysis was to investigate the effect of increasing dietary ALA intake on the blood concentration of inflammatory markers including tumor necrosis factor (TNF), interleukin 6 (IL-6), C-reactive protein (CRP), soluble intercellular adhesion molecule-1 (sICAM-1), and soluble vascular cell adhesion molecule-1 (sVCAM-1) in adults. METHODS: After a systemic search on PubMed, Embase, and Cochrane library and bibliographies of relevant articles, 25 randomized controlled trials that met the inclusion criteria were identified...
March 8, 2017: European Journal of Nutrition
Myra Grace Dela Peña-Ponce, Jennifer Rodriguez-Nieves, Janice Bernhardt, Ryan Tuck, Neelima Choudhary, Michael Mengual, Katie R Mollan, Michael G Hudgens, Sigal Peter-Wohl, Kristina De Paris
Most infant deaths occur in the first year of life. Yet, our knowledge of immune development during this period is scarce and derived from cord blood (CB) only. To more effectively combat pediatric diseases, a deeper understanding of the kinetics and the factors that regulate the maturation of immune functions in early life is needed. Increased disease susceptibility of infants is generally attributed to T helper 2-biased immune responses. The differentiation of CD4(+) T cells along a specific T helper cell lineage is dependent on the pathogen type, and on costimulatory and cytokine signals provided by antigen-presenting cells...
2017: Frontiers in Pediatrics
Josiane C S Mapplebeck, Simon Beggs, Michael W Salter
Microglia are dynamic immune cells with diverse roles in maintaining homeostasis of the central nervous system. Dysregulation of microglia has been critically implicated in the genesis of neuropathic pain. Peripheral nerve injury, a common cause of neuropathic pain, engages microglia-neuronal signalling which causes disinhibition and facilitated excitation of spinal nociceptive pathways. However, recent literature indicates that the role of microglia in neuropathic pain is sexually dimorphic, and that female pain processing appears to be independent of microglia, depending rather on T cells...
March 7, 2017: Molecular Brain
Ashley Page, Minkyung Kang, Alexander Armitstead, David Perry, Patrick R Unwin
A multifunctional dual-channel scanning probe nanopipet that enables simultaneous scanning ion conductance microscopy (SICM) and scanning electrochemical microscopy (SECM) measurements is demonstrated to have powerful new capabilities for spatially mapping the uptake of molecules of interest at living cells. One barrel of the probe is filled with electrolyte and the molecules of interest and is open to the bulk solution for both topographical feedback and local delivery to a target interface, while a solid carbon electrode in the other barrel measures the local concentration and flux of the delivered molecules...
March 7, 2017: Analytical Chemistry
Hua Hao, Ting Jia, Xiaohong Zheng, Zhi Zeng
The spin transition of spin crossover molecules induced by bias voltages from low spin to high spin was observed recently and several mechanisms were suggested to understand it. However, these mechanisms fail to explain the dependence of spin transitions on the bias polarity in experiments and thus may still be questionable. Based on a first-principles study, we propose that the bias-induced spin transition is triggered by a charging effect, namely, the filling of the lowest unoccupied molecular orbital of spin crossover molecules...
March 3, 2017: Physical Chemistry Chemical Physics: PCCP
Alessandro Genoni, Leonardo H R Dos Santos, Benjamin Meyer, Piero Macchi
The X-ray constrained wavefunction (XC-WF) method proposed by Jayatilaka [Jayatilaka & Grimwood (2001) ▸, Acta Cryst. A57, 76-86] has attracted much attention because it represents a possible third way of theoretically studying the electronic structure of atoms and molecules, combining features of the more popular wavefunction- and DFT-based approaches. In its original formulation, the XC-WF technique extracts statistically plausible wavefunctions from experimental X-ray diffraction data of molecular crystals...
March 1, 2017: IUCrJ
Daniel R Woldring, Patrick V Holec, Lawrence A Stern, Yang Du, Benjamin J Hackel
Engineered proteins provide clinically and industrially impactful molecules and utility within fundamental research, yet inefficiencies in discovering lead variants with new desired functionality, while maintaining stability, hinder progress. Improved function, which can result from a few strategic mutations, is fundamentally separate from discovering novel function, which often requires large leaps in sequence space. While a highly diverse combinatorial library covering immense sequence space would empower protein discovery, the ability to sample only a minor subset of sequence space and the typical destabilization of random mutations preclude this strategy...
March 9, 2017: Biochemistry
Adam Price, Jaishree Garhyan, Cynthia Gibas
High-throughput sequencing is subject to sequence dependent bias, which must be accounted for if researchers are to make precise measurements and draw accurate conclusions from their data. A widely studied source of bias in sequencing is the GC content bias, in which levels of GC content in a genomic region effect the number of reads produced during sequencing. Although some research has been performed on methods to correct for GC bias, there has been little effort to understand the underlying mechanism. The availability of sequencing protocols that target the specific location of structure in nucleic acid molecules enables us to investigate the underlying molecular origin of observed GC bias in sequencing...
2017: PloS One
Sheh-Yi Sheu, Yu-Cheng Liu, Dah-Yen Yang
Cooperativity is important in controlling the biological functions of allosteric proteins. Understanding the detailed mechanisms of cooperativity and allosteric regulation in such proteins is essential to understanding their function; however, the mechanism by which allosteric proteins undergo conformational transitions to aid the ligand escape process and its relevance to interfacial water molecules is not well understood. Here, we perform molecular dynamics simulations to examine these issues in Scapharca dimeric hemoglobin...
February 28, 2017: Physical Chemistry Chemical Physics: PCCP
Amin Morteza Najarian, Richard L McCreery
Carbon-based molecular junctions consisting of aromatic oligomers between conducting sp(2) hybridized carbon electrodes exhibit structure-dependent current densities (J) when the molecular layer thickness (d) exceeds ∼5 nm. All four of the molecular structures examined exhibit an unusual, nonlinear ln J vs bias voltage (V) dependence which is not expected for conventional coherent tunneling or activated hopping mechanisms. All molecules exhibit a weak temperature dependence, with J increasing typically by a factor of 2 over the range of 200-440 K...
March 1, 2017: ACS Nano
Peter Bretscher, Alexandre Corthay, Colin C Anderson, Zlatko Dembic, Calliopi Havele, Zoltan A Nagy, Inger Øynebråten
We discussed different proposals for how the nature of the Th1/Th2 phenotype of an immune response is determined, and favored one, the Threshold Hypothesis, as plausible and so useful as the basis for further discussions. The activation of a target CD4 T cell can be facilitated by helper CD4 T cells when the CD4 T cells interact via an antigen-presenting cell (APC). The Threshold Hypothesis states that tentative and robust antigen-mediated CD4 T cell cooperation results in the target CD4 T cell respectively giving rise, upon activation, to Th1 and Th2 cells...
February 25, 2017: Scandinavian Journal of Immunology
Walter Bottje, Byung-Whi Kong, Antonio Reverter, Ashley J Waardenberg, Kentu Lassiter, Nicholas J Hudson
BACKGROUND: We contrast the pectoralis muscle transcriptomes of broilers selected from within a single genetic line expressing divergent feed efficiency (FE) in an effort to improve our understanding of the mechanistic basis of FE. RESULTS: Application of a virtual muscle model to gene expression data pointed to a coordinated reduction in slow twitch muscle isoforms of the contractile apparatus (MYH15, TPM3, MYOZ2, TNNI1, MYL2, MYOM3, CSRP3, TNNT2), consistent with diminishment in associated slow machinery (myoglobin and phospholamban) in the high FE animals...
February 24, 2017: BMC Systems Biology
Dominic Devost, Rory Sleno, Darlaine Petrin, Alice Zhang, Yuji Shinjo, Rakan Okde, Junken Aoki, Asuka Inoue, Terence E Hebert
Here, we report the design and use of GPCR-based biosensors to monitor ligand-mediated conformational changes in receptors in intact cells. These biosensors use Bioluminescence Resonance Energy Transfer (BRET) with Renilla luciferase (RlucII) as an energy donor, placed at the distal end of the receptor C-tail and the small fluorescent molecule FlAsH, as an energy acceptor, its binding site inserted at different positions throughout the intracellular loops and carboxy-terminal tail of the angiotensin II type I receptor (AT1R)...
February 17, 2017: Journal of Biological Chemistry
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