bluuebunny/crossref_metadata_2025 huggingface dataset:
Circular DNA elements of chromosomal origin are common in healthy human somatic tissue
Authors: Møller Henrik Devitt , Mohiyuddin Marghoob , Prada-Luengo Iñigo , Sailani M. Reza , Halling Jens Frey , Plomgaard Peter , Maretty Lasse , Hansen Anders Johannes , Snyder Michael P. , Pilegaard Henriette , Lam Hugo Y. K. , Regenberg Birgitte
Published: March 2018

The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal cells as a result of mutations. Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting ~100,000 unique eccDNA types from 16 million nuclei. Half of these structures carry genes or gene fragments and the majority are smaller than 25 kb. Transcription from eccDNAs suggests that eccDNAs reside in nuclei and recurrence of certain eccDNAs in several individuals implies DNA circularization hotspots. Gene-rich chromosomes contribute to more eccDNAs per megabase and the most transcribed protein-coding gene in muscle, TTN (titin), provides the most eccDNAs per gene. Thus, somatic genomes are rich in chromosome-derived eccDNAs that may influence phenotypes through altered gene copy numbers and transcription of full-length or truncated genes.
Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes
Authors: Yoshikawa Genki , Askora Ahmed , Blanc-Mathieu Romain , Kawasaki Takeru , Li Yanze , Nakano Miyako , Ogata Hiroyuki , Yamada Takashi
Published: March 2018

Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.
Constructing vesicle-based artificial cells with embedded living cells as organelle-like modules
Authors: Elani Yuval , Trantidou Tatiana , Wylie Douglas , Dekker Linda , Polizzi Karen , Law Robert V. , Ces Oscar
Published: March 2018

There is increasing interest in constructing artificial cells by functionalising lipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limited in comparison to their biological counterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger synthetic cell assembly. Using microfluidic technologies to construct such hybrid cellular bionic systems, we demonstrate that the vesicle host and the encapsulated cell operate in concert. The external architecture of the vesicle shields the cell from toxic surroundings, while the cell acts as a bioreactor module that processes encapsulated feedstock which is further processed by a synthetic enzymatic metabolism co-encapsulated in the vesicle.
Rapid histopathological imaging of skin and breast cancer surgical specimens using immersion microscopy with ultraviolet surface excitation
Authors: Yoshitake Tadayuki , Giacomelli Michael G. , Quintana Liza M. , Vardeh Hilde , Cahill Lucas C. , Faulkner-Jones Beverly E. , Connolly James L. , Do Daihung , Fujimoto James G.
Published: March 2018

Rapid histopathological evaluation of fresh, unfixed human tissue using optical sectioning microscopy would have applications to intraoperative surgical margin assessment. Microscopy with ultraviolet surface excitation (MUSE) is a low-cost optical sectioning technique using ultraviolet illumination which limits fluorescence excitation to the specimen surface. In this paper, we characterize MUSE using high incident angle, water immersion illumination to improve sectioning. Propidium iodide is used as a nuclear stain and eosin yellow as a counterstain. Histologic features of specimens using MUSE, nonlinear microscopy (NLM) and conventional hematoxylin and eosin (H&E) histology were evaluated by pathologists to assess potential application in Mohs surgery for skin cancer and lumpectomy for breast cancer. MUSE images of basal cell carcinoma showed high correspondence with frozen section H&E histology, suggesting that MUSE may be applicable to Mohs surgery. However, correspondence in breast tissue between MUSE and paraffin embedded H&E histology was limited due to the thicker optical sectioning in MUSE, suggesting that further development is needed for breast surgical applications. We further demonstrate that the transverse image resolution of MUSE is limited by the optical sectioning thickness and use co-registered NLM to quantify the improvement in MUSE optical sectioning from high incident angle water immersion illumination.
Identification and characterization of microRNAs in tree peony during chilling induced dormancy release by high-throughput sequencing
Authors: Zhang Yuxi , Wang Yanyan , Gao Xuekai , Liu Chunying , Gai Shupeng
Published: March 2018

Tree peony, one of the most valuable horticultural and medicinal plants in the world, has to go through winter to break dormancy. Growing studies from molecular aspects on dormancy release process have been reported, but inadequate study has been done on miRNA-guided regulation in tree peony. In this study, high-throughput sequencing was employed to identify and characterize miRNAs in three libraries (6 d, 18 d and 24 d chilling treatments). There were 7,122, 10,076 and 9,097 unique miRNA sequences belonging to 52, 87 and 68 miRNA families, respectively. A total of 32 conserved miRNAs and 17 putative novel miRNAs were identified during dormancy release. There were 771 unigenes as potential targets of 62 miRNA families. Total 112 known miRNAs were differentially expressed, of which 55 miRNAs were shared among three libraries and 28 miRNAs were only found in 18 d chilling duration library. The expression patterns of 15 conserved miRNAs were validated and classified into four types by RT-qPCR. Combining with our microarray data under same treatments, five miRNAs (miR156k, miR159a, miR167a, miR169a and miR172a) were inversely correlated to those of their target genes. Our results would provide new molecular basis about dormancy release in tree peony.
Computational Methods for Estimating Molecular System from Membrane Potential Recordings in Nerve Growth Cone
Authors: Yamada Tatsuya , Nishiyama Makoto , Oba Shigeyuki , Jimbo Henri Claver , Ikeda Kazushi , Ishii Shin , Hong Kyonsoo , Sakumura Yuichi
Published: March 2018

Biological cells express intracellular biomolecular information to the extracellular environment as various physical responses. We show a novel computational approach to estimate intracellular biomolecular pathways from growth cone electrophysiological responses. Previously, it was shown that cGMP signaling regulates membrane potential (MP) shifts that control the growth cone turning direction during neuronal development. We present here an integrated deterministic mathematical model and Bayesian reversed-engineering framework that enables estimation of the molecular signaling pathway from electrical recordings and considers both the system uncertainty and cell-to-cell variability. Our computational method selects the most plausible molecular pathway from multiple candidates while satisfying model simplicity and considering all possible parameter ranges. The model quantitatively reproduces MP shifts depending on cGMP levels and MP variability potential in different experimental conditions. Lastly, our model predicts that chloride channel inhibition by cGMP-dependent protein kinase (PKG) is essential in the core system for regulation of the MP shifts.
Real-time size modulation and synchronization of a microfluidic dropmaker with pulsed surface acoustic waves (SAW)
Authors: Schmid Lothar , Franke Thomas
Published: March 2018

We show that a microfluidic flow focusing drop maker can be synchronized to a surface acoustic waves (SAW) triggered by an external electric signal. In this way droplet rate and volume can be controlled over a wide range of values in real time. Using SAW, the drop formation rate of a regularly operating water in oil drop maker without SAW can be increased by acoustically enforcing the drop pinch-off and thereby reducing the volume. Drop makers of square cross-sections (w = h = 30 µm, with width w and height h) that produce large drops of length l = 10 w can be triggered to produce drops as short as l ~ 2w, approaching the geometical limit l = w without changing the flow rates. Unlike devices that adjust drop size by changing the flow rates the acoustic dropmaker has very short transients allowing to adjust the size of every single drop. This allows us to produce custom made emulsions with a defined size distribution as demonstrated here not only for a monodisperse emulsion but also for binary emulsions with drops of alternating size. Moreover, we show that the robustness and monodispersity of our devices is enhanced compared to purely flow driven drop makers in the absence of acoustic synchronization.
Application of a Genetic Risk Score to Racially Diverse Type 1 Diabetes Populations Demonstrates the Need for Diversity in Risk-Modeling
Authors: Perry Daniel J. , Wasserfall Clive H. , Oram Richard A. , Williams MacKenzie D. , Posgai Amanda , Muir Andrew B. , Haller Michael J. , Schatz Desmond A. , Wallet Mark A. , Mathews Clayton E. , Atkinson Mark A. , Brusko Todd M.
Published: March 2018

Prior studies identified HLA class-II and 57 additional loci as contributors to genetic susceptibility for type 1 diabetes (T1D). We hypothesized that race and/or ethnicity would be contextually important for evaluating genetic risk markers previously identified from Caucasian/European cohorts. We determined the capacity for a combined genetic risk score (GRS) to discriminate disease-risk subgroups in a racially and ethnically diverse cohort from the southeastern U.S. including 637 T1D patients, 46 at-risk relatives having two or more T1D-related autoantibodies (≥2AAb+), 790 first-degree relatives (≤1AAb+), 68 second-degree relatives (≤1 AAb+), and 405 controls. GRS was higher among Caucasian T1D and at-risk subjects versus ≤ 1AAb+ relatives or controls (P < 0.001). GRS receiver operating characteristic AUC (AUROC) for T1D versus controls was 0.86 (P < 0.001, specificity = 73.9%, sensitivity = 83.3%) among all Caucasian subjects and 0.90 for Hispanic Caucasians (P < 0.001, specificity = 86.5%, sensitivity = 84.4%). Age-at-diagnosis negatively correlated with GRS (P < 0.001) and associated with HLA-DR3/DR4 diplotype. Conversely, GRS was less robust (AUROC = 0.75) and did not correlate with age-of-diagnosis for African Americans. Our findings confirm GRS should be further used in Caucasian populations to assign T1D risk for clinical trials designed for biomarker identification and development of personalized treatment strategies. We also highlight the need to develop a GRS model that accommodates racial diversity.
Grain Yield, Starch Content and Activities of Key Enzymes of Waxy and Non-waxy Wheat (Triticum aestivum L.)
Authors: Zi Yan , Ding Jinfeng , Song Jianmin , Humphreys Gavin , Peng Yongxin , Li Chunyan , Zhu Xinkai , Guo Wenshan
Published: March 2018

Waxy wheat has unique end-use properties; however, its production is limited due mainly to its low grain yield compared with non-waxy wheat. In order to increase its grain yield, it is critical to understand the eco-physiological differences in grain filling between the waxy and non-waxy wheat. In this study, two waxy wheat and two non-waxy wheat cultivars were used to investigate the differences in starch-associated enzymes processes, sucrose and starch dynamics, yield components, and the final grain yield. The results indicated that the mean total grain starch and amylose content, the average 1000-kernel weight and grain yield of the waxy wheat were lower than those of the non-waxy wheat at maturity. The amylose content was significantly and positively correlated with the activity of GBSS (r = 0.80,p < 0.01). Significant positive correlation also exists among activities of AGPase, SSS, GBSS, and SBE, except for GBSS-SBE. In summary, our study has revealed that the reduced conversion of sucrose to starch in the late grain filling stage is the main cause for the low kernel weight and total starch accumulation of the waxy wheat. The reduced conversion also appears to be a factor contributing to the lower grain yield of the waxy wheat.
Fetal extracellular matrix nerve wraps locally improve peripheral nerve remodeling after complete transection and direct repair in rat
Authors: Ren Tanchen , Faust Anne , van der Merwe Yolandi , Xiao Bo , Johnson Scott , Kandakatla Apoorva , Gorantla Vijay S. , Badylak Stephen F. , Washington Kia M. , Steketee Michael B.
Published: March 2018

In peripheral nerve (PN) injuries requiring surgical repair, as in PN transection, cellular and ECM remodeling at PN epineurial repair sites is hypothesized to reduce PN functional outcomes by slowing, misdirecting, or preventing axons from regrowing appropriately across the repair site. Herein this study reports on deriving and analyzing fetal porcine urinary bladder extracellular matrix (fUB-ECM) by vacuum assisted decellularization, fabricating fUBM-ECM nerve wraps, and testing fUB-ECM nerve wrap biocompatibility and bioactivity in a trigeminal, infraorbital nerve (ION) branch transection and direct end-to-end repair model in rat. FUB-ECM nerve wraps significantly improved epi- and endoneurial organization and increased both neovascularization and growth associated protein-43 (GAP-43) expression at PN repair sites, 28-days post surgery. However, the number of neurofilament positive axons, remyelination, and whisker-evoked response properties of ION axons were unaltered, indicating improved tissue remodeling per se does not predict axon regrowth, remyelination, and the return of mechanoreceptor cortical signaling. This study shows fUB-ECM nerve wraps are biocompatible, bioactive, and good experimental and potentially clinical devices for treating epineurial repairs. Moreover, this study highlights the value provided by precise, analytic models, like the ION repair model, in understanding how PN tissue remodeling relates to axonal regrowth, remyelination, and axonal response properties.
Different vasodilatation characteristics among the main cerebral arteries in fetuses with congenital heart defects
Authors: Peng Qinghai , Zeng Shi , Zhou Qichang , Deng Wen , Wang Tao , Tan Ya , Liu Yushan
Published: March 2018

To observe Doppler changes in the three main cerebral arteries in fetuses with congenital heart defects (CHDs). The pulsatility index (PI) values of the anterior cerebral artery (ACA), middle cerebral artery (MCA), and posterior cerebral artery (PCA) were prospectively compared in 78 CHD fetuses and 78 normal control fetuses. Correlations between the cerebral artery PIs and the neurodevelopment scores (psychomotor development index [PDI] and mental development index [MDI]) were assessed. The MCA-PI was decreased significantly in fetuses with hypoplastic left heart syndrome (HLHS). The ACA-PI was reduced significantly in fetuses with HLHS, fetuses with left-sided obstructive lesions (LSOLs) and fetuses with transposition of the great arteries. The PCA-PI was significantly smaller in fetuses with HLHS and fetuses with LSOLs. More fetuses presented signs of cerebral vasodilatation of the ACA than the MCA for certain types of CHD (P < 0.05). The ACA-PI was positively correlated with the PDI and MDI scores in fetuses with CHDs (r2 = 0.26, 0.20, P < 0.01). The MCA-PI was only positively correlated with the PDI scores (r2 = 0.15, P < 0.01). The ACA exhibited signs of vasodilatation more frequently and severely than the MCA. The ACA-PI appears to be more sensitive for predicting abnormal neurodevelopmental outcomes than the MCA-PI.
Reduced background autofluorescence for cell imaging using nanodiamonds and lanthanide chelates
Authors: Cordina Nicole M. , Sayyadi Nima , Parker Lindsay M. , Everest-Dass Arun , Brown Louise J. , Packer Nicolle H.
Published: March 2018

Bio-imaging is a key technique in tracking and monitoring important biological processes and fundamental biomolecular interactions, however the interference of background autofluorescence with targeted fluorophores is problematic for many bio-imaging applications. This study reports on two novel methods for reducing interference with cellular autofluorescence for bio-imaging. The first method uses fluorescent nanodiamonds (FNDs), containing nitrogen vacancy centers. FNDs emit at near-infrared wavelengths typically higher than most cellular autofluorescence; and when appropriately functionalized, can be used for background-free imaging of targeted biomolecules. The second method uses europium-chelating tags with long fluorescence lifetimes. These europium-chelating tags enhance background-free imaging due to the short fluorescent lifetimes of cellular autofluorescence. In this study, we used both methods to target E-selectin, a transmembrane glycoprotein that is activated by inflammation, to demonstrate background-free fluorescent staining in fixed endothelial cells. Our findings indicate that both FND and Europium based staining can improve fluorescent bio-imaging capabilities by reducing competition with cellular autofluorescence. 30 nm nanodiamonds coated with the E-selectin antibody was found to enable the most sensitive detective of E-selectin in inflamed cells, with a 40-fold increase in intensity detected.
The voltage-gated sodium channel EF-hands form an interaction with the III-IV linker that is disturbed by disease-causing mutations
Authors: Gardill Bernd R. , Rivera-Acevedo Ricardo E. , Tung Ching-Chieh , Okon Mark , McIntosh Lawrence P. , Van Petegem Filip
Published: March 2018

Voltage-gated sodium channels (NaV) are responsible for the rapid depolarization of many excitable cells. They readily inactivate, a process where currents diminish after milliseconds of channel opening. They are also targets for a multitude of disease-causing mutations, many of which have been shown to affect inactivation. A cluster of disease mutations, linked to Long-QT and Brugada syndromes, is located in a C-terminal EF-hand like domain of NaV1.5, the predominant cardiac sodium channel isoform. Previous studies have suggested interactions with the III-IV linker, a cytosolic element directly involved in inactivation. Here we validate and map the interaction interface using isothermal titration calorimetry (ITC) and NMR spectroscopy. We investigated the impact of various disease mutations on the stability of the domain, and found that mutations that cause misfolding of the EF-hand domain result in hyperpolarizing shifts in the steady-state inactivation curve. Conversely, mutations in the III-IV linker that disrupt the interaction with the EF-hand domain also result in large hyperpolarization shifts, supporting the interaction between both elements in intact channels. Disrupting the interaction also causes large late currents, pointing to a dual role of the interaction in reducing the population of channels entering inactivation and in stabilizing the inactivated state.
Defects in Quantum Computers
Authors: Gardas Bartłomiej , Dziarmaga Jacek , Zurek Wojciech H. , Zwolak Michael
Published: March 2018

The shift of interest from general purpose quantum computers to adiabatic quantum computing or quantum annealing calls for a broadly applicable and easy to implement test to assess how quantum or adiabatic is a specific hardware. Here we propose such a test based on an exactly solvable many body system–the quantum Ising chain in transverse field–and implement it on the D-Wave machine. An ideal adiabatic quench of the quantum Ising chain should lead to an ordered broken symmetry ground state with all spins aligned in the same direction. An actual quench can be imperfect due to decoherence, noise, flaws in the implemented Hamiltonian, or simply too fast to be adiabatic. Imperfections result in topological defects: Spins change orientation, kinks punctuating ordered sections of the chain. The number of such defects quantifies the extent by which the quantum computer misses the ground state, and is, therefore, imperfect.
Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A
Authors: Shahid Muhammad , Gull Nicole , Yeon Austin , Cho Eunho , Bae Jooeun , Yoon Hyun Seok , You Sungyong , Yoon Hana , Kim Minjung , Berman Benjamin P. , Kim Jayoung
Published: March 2018

Interstitial cystitis (IC) is a chronic urinary tract disease that is characterized by unpleasant sensations, such as persistent pelvic pain, in the absence of infection or other identifiable causes. We previously performed comprehensive metabolomics profiling of urine samples from IC patients using nuclear magnetic resonance and gas-chromatography/mass spectrometry and found that urinary α-oxoglutarate (α-OG), was significantly elevated. α-OG, a tricarboxylic acid (TCA) cycle intermediate, reportedly functions to suppress the proliferation of immortalized normal human bladder epithelial cells. Here, we identified AT-rich interactive domain 1 A (ARID1A), a key chromatin remodeler, as being hypomethylated and upregulated by α-OG treatment. This was done through EPIC DNA methylation profiling and subsequent biochemical approaches, including quantitative RT-PCR and western blot analyses. Furthermore, we found that α-OG almost completely suppresses ten-eleven translocation (TET) activity, but does not affect DNA methyltransferase (DNMT) activity. Altogether, our studies reveal the potential role of α-OG in epigenetic remodeling through its effects on ARID1A and TET expression in the bladder. This may provide a new possible therapeutic strategy in treating IC.
Microcirculatory Disorders and Protective Role of Xuebijing in Severe Heat Stroke
Authors: Jin Hui , Chen Yi , Ding Chengjia , Lin Youping , Chen Yulan , Jiang Dongxin , Su Lei
Published: March 2018

This study was conducted to explore underlying mechanism of microcirculation dysfunction and protectiverole of Xuebijing in heat stroke. Forty rats were divided into: control, vehicle + heat stress (HS), superoxide dismutase (SOD) + HS, and Xuebijing + HS groups. Rats in heat stress groups were subjected to continuous heat stress in infant incubator 1 h after tail vein injection of the tested compound and spinotrapezius preparation. Velocity of blood flow through micro-vessels and vascular diameter were detected in real time. Another 27 rats were divided into: vehicle, SOD, and Xuebijing groups, then further divided into three subgroups each: control, Tcore = 38 °C, Tcore = 41 °C. Rats were sacrificed, and spinotrapezius single-cell suspensions were prepared for detecting SOD and reactive oxygen species (ROS). The results showed that heat stress decreased SOD activity, increased ROS levels, and reduced the blood flow rate. Xuebijing increased SOD activity, decreased ROS levels and exhibited a protective effect in terms of blood flow rate but was less protective than SOD. The survival time in Xuebijing + HS group was longer than that in vehicle group but shorter than that in SOD + HS group. The results suggested Xuebijing could decrease ROS levels and have protective effects in severe heat stroke.
Mechanical Vibration Influences the Perception of Electrovibration
Authors: Ryu Semin , Pyo Dongbum , Lim Soo-Chul , Kwon Dong-Soo
Published: March 2018

Recently, various methods using, simultaneously, two types of tactile feedback have been proposed to emulate a real object. However, the possible masking effect when providing two types of tactile feedback has been scarcely reported. In this study, we investigated the masking effect caused by mechanical vibration on the perception of electrovibration. The absolute and difference thresholds of the electrovibration were measured according to the presence/absence, frequency, and intensity of the mechanical vibration. The absolute threshold of electrovibration tended to increase in the form of a ramp function, as the intensity of the masking stimulus (mechanical vibration) increased. Particularly, the masking effect was more remarkable when the frequency of both the target and the masking stimulus was the same (up to 13 dB increase with 25 dB SL masker). Furthermore, the difference in the threshold (average of 1.21 dB) did not significantly change due to the masking stimulus, when the sensation level intensity of the target stimulus was within the section following the Weber’s law. The results further indicated that electrovibration contributes to the activation of slowly adapting afferents as well. This investigation will provide important guidelines for the design of haptic interface that employs multiple types of tactile feedback.
Correction: Corrigendum: Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing
Authors: Stanurova Jana , Neureiter Anika , Hiber Michaela , de Oliveira Kessler Hannah , Stolp Kristin , Goetzke Roman , Klein Diana , Bankfalvi Agnes , Klump Hannes , Steenpass Laura
Published: March 2018

Scientific Reports 6: Article number: 30792; published online: 03 August 2016; updated: 08 March 2018 This Article contains typographical errors. In the Results section, “We reprogrammed primary dermal fibroblasts isolated from a female patient with AS harboring a three-base pair deletion in exon 4 of the UBE3A gene (accession NM_130838)11, and from a normal healthy control person.
DNA Recognition by Parallel Triplex Formation
Authors: Fox Keith R. , Brown Tom , Rusling David A.
Published: March 2018

Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA-recognition agents that bind within the duplex major groove by forming Hoogsteen hydrogen bonds with exposed groups on the base pairs, generating a triple-helical, or triplex, structure. The unique recognition properties of these molecules have been exploited in such diverse areas as gene-targeting, diagnostics and bionanotechnology. However, the applications of TFOs containing natural nucleotides is somewhat restricted by their low affinity and slow association kinetics at physiological pH, as well as a requirement for oligopurine–oligopyrimidine duplex target sequences. In recent years these limitations have been overcome by using TFOs incorporating novel base, sugar and backbone modifications, and triplex formation at mixed sequence duplex targets with high affinity at physiological pH is now achievable. This review will discuss the structural properties and solution requirements of DNA triplexes, with reference to state-of-the-art of modifications used to improve the DNA-recognition properties of TFOs.
Thermal Denaturation of Drug–DNA Complexes
Authors: Chaires Jonathan B.
Published: March 2018

Thermal denaturation studies provide a simple and unambiguous demonstration of drug binding to DNA. Small molecules that bind preferentially to the DNA duplex stabilize the structure and elevate its melting temperature (Tm). Apart from a simple qualitative demonstration of binding to DNA, melting studies can be analysed to obtain quantitative information about the binding interaction. One purpose of this chapter is to illustrate the utility of such methods in the quantitative analysis of drug–DNA melting curves to obtain thermodynamic data. A powerful high-throughput screening method for the discovery of nucleic acid binders, differential scanning fluorometry (DSF), will be described.
Computer Simulations of Drug–DNA Interactions: A Personal Journey
Authors: Gago Federico
Published: March 2018

This chapter updates much of what was contained in the first edition and includes new material on more tetrahydroisoquinoline antibiotics related to trabectedin, investigating the details of bis-adduct formation with Mitomycin C and a novel study entitled “melting DNA on the computer”. Throughout the emphasis is firmly rooted in computer simulations ‘in silico’ aimed at furnishing evidence of their relevance to experimental studies.
Structural Studies of DNA-binding Metal Complexes of Therapeutic Importance
Authors: Cardin Christine J. , Hall James P.
Published: March 2018

Ruthenium polypyridyl complexes are of interest for their possible applications as cellular probes, in anticancer therapeutics and, most recently, for their antibacterial properties. For many years there was no crystallographic evidence showing how any of these complexes bound to duplex or higher-order DNA, but since 2011 a series of structural studies have shown aspects of sequence, enantiomeric, substituent and structural specificity. The principal binding mode to duplex DNA of complexes typified by [Ru(phen)2dppz]2+ (where dppz=dipyridophenazene) is by angled (canted) intercalation from the minor groove, with a distinct symmetric binding mode so far only known for lambda enantiomers at the TA/TA steps. Kinking (semi-intercalation) has also been characterised, so far only at CC/GG steps, e.g. for phen ligands within these complexes. Delta enantiomers are capable of mismatch recognition, so far structurally characterised for the A–A mismatch. This binding mode, insertion, is characterised by the flipping out of the adenine, with the base stacking on the ancillary ligand of the complex. For binding to higher-order DNA, sequences with loops, such as the unimolecular G-quadruplex, have so far resisted attempts at crystallisation, although an NMR structure of a diruthenium complex has been reported.
Sequence-selective Interactions of Actinomycin D with DNA: Discovery of a Thermodynamic Switch
Authors: Hudson Jason S. , Lucius Aaron , Waring Michael J. , Graves David E.
Published: March 2018

The interactions of actinomycin D with DNA serve as a paradigm for DNA base sequence selectivity through its demonstrated preference for binding to the d(GpC) step. Using the photoreactive 7-azido-actinomycin D, we have demonstrated that actinomycin D binding to DNA is more promiscuous than previously reported, with additional strong binding to ‘atypical’ sequences such as d(GpG) and d(GpGpG) steps. Similarly, our laboratory has demonstrated that the 5′-flanking base adjacent to the d(GpC) intercalation site plays a significant role in directing the thermodynamic mechanism associated with complex formation. Isothermal titration calorimetry (ITC) and UV–visible spectroscopy have been used to discern thermodynamic and kinetic properties associated with complex formation. These studies reveal significant thermodynamic and kinetic changes resulting from single-base modification to the 5′-flanking base. Historically, the interactions of actinomycin with native DNAs have been characterized as an entropy-driven process with observed binding enthalpies of approximately 0 to −1 kcal mol−1. The interaction of actinomycin D with the -TGCA- duplex is characterized by a high binding affinity and large favourable binding entropy. However, substitution of the 5′-T to 5′-C results in complex formation that is characterised by a large favourable binding enthalpy (−7 kcal mol−1). Hence, subtle changes to the DNA intercalation sequence or bases adjacent to the intercalation step results in significant changes in the thermodynamic binding mechanism for the ligand.
Evidence of homo-FRET in quantum dot–dye heterostructured assembly
Authors: Saha Samyabrata , Majhi Debashis , Bhattacharyya Kalishankar , Preeyanka Naupada , Datta Ayan , Sarkar Moloy
Published: March 2018

Evidence of homo-FRET in inorganic–organic hybrid hetero-structured assembly is demonstrated
Mechanistic insights into two-photon-driven photocatalysis in organic synthesis
Authors: Marchini Marianna , Gualandi Andrea , Mengozzi Luca , Franchi Paola , Lucarini Marco , Cozzi Pier Giorgio , Balzani Vincenzo , Ceroni Paola
Published: March 2018

Is two-photon catalysis better than one-photon? The sequential absorption of two photons enables the production of highly reducing or oxidizing species. The short lifetime of the excited states and the photostability of the photocatalyst pose significant limitations to this approach.
Lycopene crystalloids exhibit singlet exciton fission in tomatoes
Authors: Llansola-Portoles M. J. , Redeckas K. , Streckaité S. , Ilioaia C. , Pascal A. A. , Telfer A. , Vengris M. , Valkunas L. , Robert B.
Published: March 2018

Transient absorption studies conducted onin vitrolycopene aggregates, as well as on lycopene crystalloids inside tomato chromoplasts, reveal the appearance of a long-lived excited state, which we unambiguously identified as lycopene triplet generated by singlet exciton fission.
Molecular engineering of polymeric carbon nitride: advancing applications from photocatalysis to biosensing and more
Authors: Zhou Zhixin , Zhang Yuye , Shen Yanfei , Liu Songqin , Zhang Yuanjian
Published: March 2018

Different designs and constructions of molecular structures of carbon nitride for emerging applications, such as biosensing, are discussed.
One-step synthesis of MnS/MoS2/C through the calcination and sulfurization of a bi-metal–organic framework for a high-performance supercapacitor and its photocurrent investigation
Authors: Yan Zhi Shuo , Long Ji Ying , Zhou Qing Feng , Gong Yun , Lin Jian Hua
Published: March 2018

Using a bi-metallic Mn/Mo-MOF as a precursor, a MnS/MoS2/C hybrid material was synthesized with a high specific capacitance of 1162 F g−1 at 0.5 A g−1 in 2 M KOH solution due to the synergetic effects of the individual components and their exposed active sites.
A structurally versatile nickel phosphite acting as a robust bifunctional electrocatalyst for overall water splitting
Authors: Menezes Prashanth W. , Panda Chakadola , Loos Stefan , Bunschei-Bruns Florian , Walter Carsten , Schwarze Michael , Deng Xiaohui , Dau Holger , Driess Matthias
Published: March 2018

The mechanistically distinct and synergistic role of phosphite anions in hydrogen evolution and nickel cations in oxygen evolution have been uncovered for active and durable overall water splitting catalysis in nickel phosphite.
Supported metal nanoparticles with tailored catalytic properties through sol-immobilisation: applications for the hydrogenation of nitrophenols
Authors: Rogers Scott M. , Catlow C. Richard A. , Gianolio Diego , Wells Peter P. , Dimitratos Nikolaos
Published: March 2018

Nanoparticle property control, and excellent catalytic capabilities, has been demonstrated using Pd/TiO2prepared by sol-immobilisation with solvent and temperature control.
A droplet energy harvesting and actuation system for self-powered digital microfluidics
Authors: Chen Guijun , Liu Xiaohua , Li Sufen , Dong Ming , Jiang Dongyue
Published: March 2018

This study presents an interesting phenomenon: using the triboelectrification of a sliding droplet to actuate another droplet by the EWOD effect.
Designing model imino bifunctional chelators for radiopharmaceuticals –in vitroantitumor activity, photoluminescence and structural analysis
Authors: Brink Alice , Kroon Robin E. , Visser Hendrik G. , van Rensburg Constance E. J. , Roodt Andreas
Published: March 2018

Designed bifunctional chelators for the radionuclides of188/186Re or99mTc. Structure, DFT calculations, antitumor and imaging properties are described.
The effect of the catalyst and the type of ionic liquid on the hydrosilylation process under batch and continuous reaction conditions
Authors: Jankowska-Wajda M. , Kukawka R. , Smiglak M. , Maciejewski H.
Published: March 2018

We present a simplified method for performing the hydrosilylation reaction in a heterogeneous catalytic system with the use of ionic liquids and microreactor systems.
Synthesis of novel series of 7,7′-(substituted methylene)bis-imidazo[1,2-b]pyrazoles via an acid catalyzed one-pot three-component reaction
Authors: Driowya Mohsine , Allouchi Hassan , Gally José Manuel , Bonnet Pascal , Guillaumet Gérald
Published: March 2018

An efficient and rapid synthesis of new series of N-alkyl-2-aryl-5H-imidazo[1,2-b]pyrazoles has been achieved in high yields through a three-component reaction of 3-amino-4-substituted pyrazoles, aromatic aldehydes and isocyanides mediated by acid catalysts.
Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products
Authors: Janata J. , Kamenik Z. , Gazak R. , Kadlcik S. , Najmanova L.
Published: March 2018

This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.
Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide
Authors: Mizuta R. , Devos J. M. , Webster J. , Ling W. L. , Narayanan T. , Round A. , Munnur D. , Mossou E. , Farahat A. A. , Boykin D. W. , Wilson W. D. , Neidle S. , Schweins R. , Rannou P. , Haertlein M. , Forsyth V. T. , Mitchell E. P.
Published: March 2018

We describe the preparation of a novel self-assembling supramolecular nanotube system.
Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides
Authors: Nici F. , Oliviero G. , Falanga A. P. , D'Errico S. , Marzano M. , Musumeci D. , Montesarchio D. , Noppen S. , Pannecouque C. , Piccialli G. , Borbone N.
Published: March 2018

The synthesis of a new dimeric G-quadruplex-based DNA aptamer endowed with anti-HIV activity is reported.
One-pot synthesis of diverseN,N′-disubstituted guanidines fromN-chlorophthalimide, isocyanides and aminesvia N-phthaloyl-guanidines
Authors: Demjén András , Angyal Anikó , Wölfling János , Puskás László G. , Kanizsai Iván
Published: March 2018

A sequential one-pot approach towardsN,N′-disubstituted guanidines fromN-chlorophthalimide, isocyanides and amines is reported.
Engineering the porosity and acidity of H-Beta zeolite by dealumination for the production of 2-ethylanthraquinone via 2-(4′-ethylbenzoyl)benzoic acid dehydration
Authors: Liu J. X. , He N. , Liu C. Y. , Wang G. R. , Xin Q. , Guo H. C.
Published: March 2018

Mild HNO3 treated nano-sized H-Beta zeolite showed outstanding catalytic activity, selectivity and reusability, compared with a commercial oleum catalyst.
Hydration and ion association of La3+ and Eu3+ salts in aqueous solution
Authors: Friesen Sergej , Krickl Sebastian , Luger Magdalena , Nazet Andreas , Hefter Glenn , Buchner Richard
Published: March 2018

Lanthanide ions affect water out to the third shell and form double solvent-separated and solvent-shared ion pairs.
A combined crossed molecular beams and computational study on the formation of distinct resonantly stabilized C5H3radicalsviachemically activated C5H4and C6H6intermediates
Authors: Thomas Aaron M. , Lucas Michael , Zhao Long , Liddiard Jerid , Kaiser Ralf I. , Mebel Alexander M.
Published: March 2018

In a single-collision environment dicarbon reacts with 1-butyne to form resonantly stabilized C5H3radical products.
Anisotropic vacancy-mediated phonon mode softening in Sm and Gd doped ceria
Authors: Jung Dong-Hyuk , Lee Ji-Hwan , Kilic Mehmet Emin , Soon Aloysius
Published: March 2018

The structural, vibrational, and diffusion properties of different ceria-based systems (including oxygen vacancies and rare-earth dopants (Sm or Gd)) have been examined using both first-principles density-functional theory calculations and finite-temperature molecular dynamics simulations.
Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM
Authors: Fritz Matthew , Quinn Caitlin M. , Wang Mingzhang , Hou Guangjin , Lu Xingyu , Koharudin Leonardus M. I. , Struppe Jochem , Case David A. , Polenova Tatyana , Gronenborn Angela M.
Published: March 2018

Experimental-NMR and calculated-QM/MM13Cαand15NHchemical-shift tensors are presented for microcrystalline OAA; factors determining the calculation accuracy are discussed.
Mechanism of ionic-liquid-based acidic aqueous biphasic system formation
Authors: Schaeffer Nicolas , Passos Helena , Gras Matthieu , Mogilireddy Vijetha , Leal João P. , Pérez-Sánchez Germán , Gomes José R. B. , Billard Isabelle , Papaiconomou Nicolas , Coutinho João A. P.
Published: March 2018

This work represents a major contribution to the understanding of ionic liquid-based acidic aqueous biphasic system formation and application.
Computational mechanistic study of Ru-catalyzed CO2 reduction by pinacolborane revealing the σ–π coupling mechanism for CO2 decarbonylation
Authors: Huang Fang , Wang Qiong , Guo Jiandong , Wen Mingwei , Wang Zhi-Xiang
Published: March 2018

A σ–π coupling mechanism for CO2 decarbonylation has been revealed in a Ru-catalyzed system by DFT study.
Salen-indium/triarylborane triads: synthesis and ratiometric emission-colour changes by fluoride ion binding
Authors: Kwak Sang Woo , Kwon Hyoshik , Lee Ji Hye , Hwang Hyonseok , Kim Min , Chung Yongseog , Kim Youngjo , Lee Kang Mun , Park Myung Hwan
Published: March 2018

Two salen-In triads bearing aryl borane units were prepared and these showed ratiometric ‘color-change’ response in PL spectra upon fluoride binding to the borane moiety.
Plasmon-enhanced triplet–triplet annihilation upconversion of post-modified polymeric acceptors
Authors: Westbrook Emily G. , Zhang Peng
Published: March 2018

Plasmonic enhancement of TTA-UC is demonstrated on an easily adaptable polymer platform containing silver nanoparticles and various covalently attached chromophores.
Facile reactions of gold(i) complexes with tri(tert-butyl)azadiboriridine
Authors: Shang Rong , Saito Souta , Jimenez-Halla J. Oscar C. , Yamamoto Yohsuke
Published: March 2018

Direct structural evidence for group 11 metal-mediated B–B bond activation from tri(tert-butyl)azadiboriridine (1) and AuCl(L) complexes.
Interactions of Schiff base compounds and their coordination complexes with the drug cisplatin
Authors: Magyari József , Barta Holló Berta , Vojinović-Ješić Ljiljana S. , Radanović Mirjana M. , Armaković Stevan , Armaković Sanja J. , Molnár Joseph , Kincses Annamária , Gajdács Márió , Spengler Gabriella , Mészáros Szécsényi Katalin
Published: March 2018

There is a complex interplay between the structural and other physicochemical properties of new compounds and the molecules in living organisms.
Synthesis, characterization and determination of absolute structures of palladium complexes of novel chiral acyclic tellurated Schiff base ligands
Authors: Rajegowda H. R. , Kumar P. Raghavendra , Hosamani Amar , Butcher R. J.
Published: March 2018

Enantiomerically pure chiral hybrid organotellurium ligands and their asymmetric palladium complexes have been synthesized and characterized.
Direct synthesis of 2-methylpyridines via I2-triggered [3 + 2 + 1] annulation of aryl methyl ketoxime acetates with triethylamine as the carbon source
Authors: Gao Qinghe , Yan Huijuan , Wu Manman , Sun Jiajia , Yan Xiqing , Wu Anxin
Published: March 2018

I2-Triggered reductive generation of iminyl radicals for the synthesis of 2-methylpyridines by employing triethylamine as the carbon source.
Direct synthesis of poly(benzoxazine imide) from an ortho-benzoxazine: its thermal conversion to highly cross-linked polybenzoxazole and blending with poly(4-vinylphenol)
Authors: El-Mahdy Ahmed F. M. , Kuo Shiao-Wei
Published: March 2018

A facile one-pot synthesis of a poly(benzoxazine imide), NDOPoda Bz, was prepared without the need for either the preparation of an amino-functionalized benzoxazine or subsequent thermal treatment.
Silicone/Ag@SiO2core–shell nanocomposite as a self-cleaning antifouling coating material
Authors: Selim Mohamed S. , Yang Hui , Wang Feng Q. , Li Xue , Huang Yong , Fatthallah Nesreen A.
Published: March 2018

The effects of Ag@SiO2core–shell nanofiller dispersion and micro-nano binary structure on the fouling release of silicone paints were studied. An ultrahydrophobic PDMS/Ag@SiO2core–shell nanocomposite was prepared as an antifouling coating material.
Autophoretic motion in three dimensions
Authors: Lisicki Maciej , Reigh Shang Yik , Lauga Eric
Published: March 2018

We explore theoretically the three-dimensional phoretic motion of a sphere covered with an arbitrary chemical activity and mobility patterns.
Microenvironment construction of strontium–calcium-based biomaterials for bone tissue regeneration: the equilibrium effect of calcium to strontium
Authors: Xie Huixu , Gu Zhipeng , He Yan , Xu Jia , Xu Chun , Li Longjiang , Ye Qingsong
Published: March 2018

Strontium-doped calcium phosphate-based biomaterials have gained increased recognition due to their beneficial effects on bone formation.
Achieving long-term zero-thermal-quenching with the assistance of carriers from deep traps
Authors: Fan Xiaotong , Chen Wenbo , Xin Shuangyu , Liu Zhichao , Zhou Min , Yu Xue , Zhou Dacheng , Xu Xuhui , Qiu Jianbei
Published: March 2018

Achieving long-term zero-thermal-quenching in a Sr3SiO5:Eu2+,Tm3+-based wLED.
Strain sensing characteristics of 3D‐printed conductive plastics
Authors: McGhee J.R. , Sinclair M. , Southee D.J. , Wijayantha K.G.U.
Published: March 2018

Three types of commercially available conductive three‐dimensional (3D) printing filament are electrically characterised for use in 3D‐printed functional devices. The three plastics were carbon dispersed acrylonitrile butadiene styrene, carbon dispersed polylactic acid (PLA) and graphene dispersed PLA. The method of 3D printing used was material extrusion and prints were made in both single and dual extrusion modes. The plastics were found to be piezoresistive, enabling them to be characterised as strain sensors. The electrical characteristics of these materials enabled the measurement of strain using low cost, readily available prototyping equipment and minimising the requirement for dedicated instrumentation components (e.g. Wheatstone bridges). Increasing the thickness of the plastics improved conductivity. However, this also decreased the reliability and reproducibility of strain sensor data due to a complex internal 3D structure. The recommendation for reliable use in prototyping and manufacturing is to print tracking under 0.8 mm thickness, thus producing resistance measurements that are predictable and follow a linear regression up to R2 = 0.9991. A dual extruded 3D print was fabricated as a final demonstration. A force sensing resistor interface was created. The final demonstration uses a PIC18F45K20 microcontroller to process sensor inputs, outputting to an alphanumeric LCD.