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Biased molecules

Wai Cheng Foong, Jacqueline J Ho, C Khai Loh, Vip Viprakasit
BACKGROUND: Non-transfusion dependent beta thalassaemia is a subset of inherited haemoglobin disorders characterised by reduced production of the beta globin chain of the haemoglobin molecule leading to anaemia of varying severity. Although blood transfusion is not a necessity for survival, it is required when episodes of chronic anaemia occur. This chronic anaemia can impair growth and affect quality of life. People with non-transfusion dependent beta thalassaemia suffer from iron overload due to their body's increased capability of absorbing iron from food sources...
October 18, 2016: Cochrane Database of Systematic Reviews
Gang Wu, Ah-Lim Tsai
Prostaglandin H synthase (PGHS) catalyzes the biosynthesis of PGG2 and PGH2, the precursor of all prostanoids, from arachidonic acid (AA). PGHS exhibits two enzymatic activities following a branched-chain radical mechanism: 1) a peroxidase activity (POX) which utilizes hydroperoxide through heme redox cycles to generate the critical Y385 tyrosyl radical for coupling both enzyme activities; 2) the cyclooxygenase (COX) activity which inserts two oxygen molecules into AA to generate endoperoxide/hydroperoxide PGG2 through a series of radical intermediates...
October 7, 2016: Protein and Peptide Letters
Philip J Wilson, Stephen L R Ellison
BACKGROUND: Digital PCR (dPCR) is a technique for estimating the concentration of a target nucleic acid by loading a sample into a large number of partitions, amplifying the target and using a fluorescent marker to identify which partitions contain the target. The standard analysis uses only the proportion of partitions containing target to estimate the concentration and depends on the assumption that the initial distribution of molecules in partitions is Poisson. In this paper we describe a way to extend such analysis using the quantification cycle (Cq) data that may also be available, but rather than assuming the Poisson distribution the more general Conway-Maxwell-Poisson distribution is used instead...
October 12, 2016: BMC Bioinformatics
M C R González, P Carro, L Vázquez, A H Creus
The morphology as well as the electric and electronic properties of aryl diazonium, in particular 4-nitrobenzene-diazonium (NBD), films on HOPG surfaces have been studied at the nanoscale level. By controlling the 2,2-diphenyl-1-picrylhydrazyl concentration during the NBD film growth, we have been able to control the thickness of the layer. The implications of NBD submonolayer adsorption on the electrical properties of this system have been analysed through Density Functional Theory (DFT) calculations, Atomic Force (AFM), Electric Force (EFM) and Kelvin Probe Force (KPFM) microscopies...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Matthew B O'Rourke, Matthew P Padula
PURPOSE: MALDI IMS is principally used for cancer diagnostics. In our own experience with publishing IMS data, we have been requested to modify our protocols with respect to the areas of the tissue that are imaged in order to comply with the wider literature. In light of this, we have determined that current methodologies lack effective controls and can potentially introduce bias by only imaging specific areas of the targeted tissue EXPERIMENTAL DESIGN: A previously imaged sample was selected and then cropped in different ways to show the potential effect of only imaging targeted areas...
October 11, 2016: Proteomics. Clinical Applications
Georg Kastlunger, Robert Stadler
ABSTRACT: The paper provides a comprehensive theoretical description of electron transport through transition metal complexes in single molecule junctions, where the main focus is on an analysis of the structural parameters responsible for bias-induced conductance switching as found in recent experiments, where an interpretation was provided by our simulations. The switching could be theoretically explained by a two-channel model combining coherent electron transport and electron hopping, where the underlying mechanism could be identified as a charging of the molecule in the junction made possible by the presence of a localized electronic state on the transition metal center...
2016: Monatshefte Für Chemie
Matthieu Koepf, Christopher Koenigsmann, Wendu Ding, Arunbah Batra, Christian F A Negre, Latha Venkataraman, Gary W Brudvig, Victor S Batista, Charles A Schmuttenmaer, Robert H Crabtree
The development of molecular components functioning as switches, rectifiers or amplifiers is a great challenge in molecular electronics. A desirable property of such components is functional robustness, meaning that the intrinsic functionality of components must be preserved regardless of the strategy used to integrate them into the final assemblies. Here, this issue is investigated for molecular diodes based on N-phenylbenzamide (NPBA) backbones. The transport properties of molecular junctions derived from NPBA are characterized while varying the nature of the functional groups interfacing the backbone and the gold electrodes required for break-junction measurements...
September 15, 2016: Nanoscale
Jennifer R Hiscock, Neil J Wells, Jayne A Ede, Philip A Gale, Mark R Sambrook
A series of neutral ditopic and negatively charged, monotopic host molecules have been evaluated for their ability to bind chloride and dihydrogen phosphate anions, and neutral organophosphorus species dimethyl methylphosphonate (DMMP), pinacolyl methylphosphonate (PMP) and the chemical warfare agent (CWA) pinacolyl methylphosphonofluoridate (GD, soman) in organic solvent via hydrogen bonding. Urea, thiourea and boronic acid groups are shown to bind anions and neutral guests through the formation of hydrogen bonds, with the urea and thiourea groups typically exhibiting higher affinity interactions...
October 12, 2016: Organic & Biomolecular Chemistry
Youhan Lee, Roberta Poloni, Jihan Kim
We propose a novel biased Widom insertion method that can efficiently compute the Henry coefficient, KH , of gas molecules inside porous materials exhibiting strong adsorption sites by employing purely DFT calculations. This is achieved by partitioning the simulation volume into strongly and weakly adsorbing regions and selectively biasing the Widom insertion moves into the former region. We show that only few thousands of single point energy calculations are necessary to achieve accurate statistics compared to many hundreds of thousands or millions of such calculations in conventional random insertions...
October 8, 2016: Journal of Computational Chemistry
Richard J Nichols, Simon J Higgins
It is now possible to reliably measure single molecule conductance in a wide variety of environments including organic liquids, ultrahigh vacuum, water, ionic liquids, and electrolytes. The most commonly used methods deploy scanning probe microscopes, mechanically formed break junctions, or lithographically formed nanogap contacts. Molecules are generally captured between a pair of facing electrodes, and the junction current response is measured as a function of bias voltage. Gating electrodes can also be added so that the electrostatic potential at the molecular bridge can be independently controlled by this third noncontacting electrode...
October 7, 2016: Accounts of Chemical Research
Do-Kyun Kwon, Su Jeong Lee, Jae-Min Myoung
In this work, vertically aligned zinc oxide (ZnO) nanorod (NR)-based flexible ultraviolet (UV) photodetectors were successfully fabricated on a polyimide (PI) substrate with a copper (Cu) nanowire (NW) electrode. To enhance the flexibility and sensing properties, the entangled networks of Cu NWs were applied to UV photodetectors as a flexible electrode. Here, Cu NWs have a high conductivity with a low cost compared to other metals to achieve a Schottky contact with ZnO NRs. Moreover, because of forming a network structure, the surface of the sensing material has a large contact area with oxygen molecules, resulting in a faster response time...
September 22, 2016: Nanoscale
Hao Ren, Guangping Zhang, Na Lin, Li Deng, Yi Luo, Fang Huang
We propose a high performance single molecule rectifier by sandwiching a deoxycytidine base pair between gold electrodes. The conductance of the single base pair junction can be controlled by its protonation status, with ON/OFF ratios between the protonated (pCC) and deprotonated (CC) junctions of 3-5 orders of magnitude. In the conducting pCC state, we observed a high rectification ratio of two orders of magnitude at bias voltage values around 0.1 V. This rectification ratio surpasses most of the theoretical designs for single molecular rectifiers, while the low working voltage implies significant energy efficiency...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
Qingling Wang, Ran Liu, Dong Xiang, Mingyu Sun, Zhikai Zhao, Lu Sun, Tingting Mei, Pengfei Wu, Haitao Liu, Xuefeng Guo, Zong-Liang Li, Takhee Lee
Utilizing individual atoms or molecules as functional units in electronic circuits meets the increasing technical demands for the miniaturization of traditional semiconductor devices. To be of technological interest, these functional devices should be high-yield, consume low amounts of energy, and operate at room temperature. In this study, we developed nanodevice called quantized conductance atomic switches (QCAS) that satisfies these requirements. The QCAS operates by applying a feedback-controlled voltage to a nano-constriction within a stretched nanowire...
October 5, 2016: ACS Nano
Bijoyita Roy, Westley J Friesen, Yuki Tomizawa, John D Leszyk, Jin Zhuo, Briana Johnson, Jumana Dakka, Christopher R Trotta, Xiaojiao Xue, Venkateshwar Mutyam, Kim M Keeling, James A Mobley, Steven M Rowe, David M Bedwell, Ellen M Welch, Allan Jacobson
A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in control, ataluren-treated, and aminoglycoside-treated cells...
October 4, 2016: Proceedings of the National Academy of Sciences of the United States of America
Ting Song, Ziqian Wang, Fangling Ji, Yingang Feng, Yudan Fan, Gaobo Chai, Xiangqian Li, Zhiqiang Li, Zhichao Zhang
By means of limited proteolysis assay, three-dimensional NMR, X-ray crystallography and alanine mutations, a dynamic region at the Q221R222N223 motif in the Bcl-2 homology 3 (BH3) domain of Mcl-1 has been identified as a conformational switch which controls Mcl-1 ubiquitination. Noxa(BH3) binding biases the QRN motif toward a helical conformation, thus leading to an enhanced in vitro ubiquitination of Mcl-1. In contrast, Bim(BH3) binding biases the QRN motif toward a nonhelical conformation, thus leading to the inhibition of ubiquitination...
October 4, 2016: Angewandte Chemie
R Frisenda, H S J van der Zant
We have investigated charge transport in single-molecule junctions using gold nanoelectrodes at room and cryogenic (10 K) temperatures. A statistical analysis of the low-bias conductance, measured during the stretching of the molecular junctions, shows that the most probable single-molecule conductance is insensitive to the temperature as expected for off-resonant coherent transport. Low-temperature current-voltage measurements show that these junction conformations have a smooth tunnelinglike shape. While separating the electrodes further we find that, in about one-fourth of the cases, the junction switches in an abrupt way to a configuration with I-V characteristics exhibiting a gap around zero bias and resonances at finite bias...
September 16, 2016: Physical Review Letters
Qian Yang, Xingyu Lin, Bin Su
An ideal molecular filtration membranes should be highly permeable and selective, thus desiring the membranes to be ultrathin, be highly porous, and consists of small and uniform pores or channels. In this work, we report the molecular filtration by free-standing ultrathin silica nanochannel membranes (SNMs) using a U-shaped cell and spectrophotometric detection, focusing on the quantitative evaluation of permeability and selectivity of SNMs. Thanks to the ultrasmall channel size, namely, ∼2-3 nm, and the negatively charged channel surface arising from the deprotonation of silanol groups, the SNM displayed excellent size and charge selectivity for molecular filtration...
October 7, 2016: Analytical Chemistry
Celine Prakash, Arndt Von Haeseler
RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain fragments in RNA-seq library preparation and sequencing. To investigate the expected coverage obtained from fragmentation, we develop a simple fragmentation model that is independent of bias from the experimental method and is not specific to the transcript sequence...
September 23, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Jian Yin, Niel M Henriksen, David R Slochower, Michael R Shirts, Michael W Chiu, David L Mobley, Michael K Gilson
The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein-ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods...
September 22, 2016: Journal of Computer-aided Molecular Design
Yunqing Tang, Johnny Hendriks, Thomas Gensch, Luru Dai, Junbai Li
Single molecule localization microscopy (SMLM) is on its way to become a mainstream imaging technique in the life sciences. However, analysis of SMLM data is biased by user provided subjective parameters required by the analysis software. To remove this human bias we introduce here the Auto-Bayes method that executes the analysis of SMLM data automatically. We demonstrate the success of the method using the photoelectron count of an emitter as selection characteristic. Moreover, the principle can be used for any characteristic that is bimodally distributed with respect to false and true emitters...
2016: Scientific Reports
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