bluuebunny/crossref_metadata_2025 huggingface dataset:
Significance of 1B and 2B domains in modulating elastic properties of lamin A
Authors: Bera Manindra , Ainavarapu Sri Rama Koti , Sengupta Kaushik
Published: June 2016

Nuclear lamins are type V intermediate filament proteins which form an elastic meshwork underlying the inner nuclear membrane. Lamins directly contribute to maintain the nuclear shape and elasticity. More than 400 mutations have been reported in lamin A that are involved in diseases known as laminopathies. These mutations are scattered mainly in the lamin rod domain along with some in its C-terminal domain. The contribution of the rod domain towards the elasticity of lamin A molecule was hitherto unknown. Here, we have elucidated the significance of the 1B and 2B domains of the rod in modulating the elastic behavior of lamin A by single-molecule force spectroscopy. In addition, we have also studied the network forming capacity of these domains and their corresponding viscoelastic behavior. We have shown that the 1B domain has the ability to form a lamin-like network and resists larger deformation. However at the single-molecular level, both the domains have comparable mechanical properties. The self-assembly of the 1B domain contributes to the elasticity of the lamin A network.
An Embodied Brain Model of the Human Foetus
Authors: Yamada Yasunori , Kanazawa Hoshinori , Iwasaki Sho , Tsukahara Yuki , Iwata Osuke , Yamada Shigehito , Kuniyoshi Yasuo
Published: June 2016

Cortical learning via sensorimotor experiences evoked by bodily movements begins as early as the foetal period. However, the learning mechanisms by which sensorimotor experiences guide cortical learning remain unknown owing to technical and ethical difficulties. To bridge this gap, we present an embodied brain model of a human foetus as a coupled brain-body-environment system by integrating anatomical/physiological data. Using this model, we show how intrauterine sensorimotor experiences related to bodily movements induce specific statistical regularities in somatosensory feedback that facilitate cortical learning of body representations and subsequent visual-somatosensory integration. We also show how extrauterine sensorimotor experiences affect these processes. Our embodied brain model can provide a novel computational approach to the mechanistic understanding of cortical learning based on sensorimotor experiences mediated by complex interactions between the body, environment and nervous system.
Estimating Potency in High-Throughput Screening Experiments by Maximizing the Rate of Change in Weighted Shannon Entropy
Authors: Shockley Keith R.
Published: June 2016

High-throughput in vitro screening experiments can be used to generate concentration-response data for large chemical libraries. It is often desirable to estimate the concentration needed to achieve a particular effect, or potency, for each chemical tested in an assay. Potency estimates can be used to directly compare chemical profiles and prioritize compounds for confirmation studies, or employed as input data for prediction modeling and association mapping. The concentration for half-maximal activity derived from the Hill equation model (i.e., AC50) is the most common potency measure applied in pharmacological research and toxicity testing. However, the AC50 parameter is subject to large uncertainty for many concentration-response relationships. In this study we introduce a new measure of potency based on a weighted Shannon entropy measure termed the weighted entropy score (WES). Our potency estimator (Point of Departure, PODWES) is defined as the concentration producing the maximum rate of change in weighted entropy along a concentration-response profile. This approach provides a new tool for potency estimation that does not depend on the assumption of monotonicity or any other pre-specified concentration-response relationship. PODWES estimates potency with greater precision and less bias compared to the conventional AC50 assessed across a range of simulated conditions.
Concurrent environmental stressors and jellyfish stings impair caged European sea bass (Dicentrarchus labrax) physiological performances
Authors: Bosch-Belmar Mar , Giomi Folco , Rinaldi Alessandro , Mandich Alberta , Fuentes Verónica , Mirto Simone , Sarà Gianluca , Piraino Stefano
Published: June 2016

The increasing frequency of jellyfish outbreaks in coastal areas has led to multiple ecological and socio-economic issues, including mass mortalities of farmed fish. We investigated the sensitivity of the European sea bass (Dicentrarchus labrax), a widely cultured fish in the Mediterranean Sea, to the combined stressors of temperature, hypoxia and stings from the jellyfish Pelagia noctiluca, through measurement of oxygen consumption rates (MO2), critical oxygen levels (PO2crit) and histological analysis of tissue damage. Higher levels of MO2, PO2crit and gill damage in treated fish demonstrated that the synergy of environmental and biotic stressors dramatically impair farmed fish metabolic performances and increase their health vulnerability. As a corollary, in the current scenario of ocean warming, these findings suggest that the combined effects of recurrent hypoxic events and jellyfish blooms in coastal areas might also threaten wild fish populations.
Shape-morphing composites with designed micro-architectures
Authors: Rodriguez Jennifer N. , Zhu Cheng , Duoss Eric B. , Wilson Thomas S. , Spadaccini Christopher M. , Lewicki James P.
Published: June 2016

Shape memory polymers (SMPs) are attractive materials due to their unique mechanical properties, including high deformation capacity and shape recovery. SMPs are easier to process, lightweight, and inexpensive compared to their metallic counterparts, shape memory alloys. However, SMPs are limited to relatively small form factors due to their low recovery stresses. Lightweight, micro-architected composite SMPs may overcome these size limitations and offer the ability to combine functional properties (e.g., electrical conductivity) with shape memory behavior. Fabrication of 3D SMP thermoset structures via traditional manufacturing methods is challenging, especially for designs that are composed of multiple materials within porous microarchitectures designed for specific shape change strategies, e.g. sequential shape recovery. We report thermoset SMP composite inks containing some materials from renewable resources that can be 3D printed into complex, multi-material architectures that exhibit programmable shape changes with temperature and time. Through addition of fiber-based fillers, we demonstrate printing of electrically conductive SMPs where multiple shape states may induce functional changes in a device and that shape changes can be actuated via heating of printed composites. The ability of SMPs to recover their original shapes will be advantageous for a broad range of applications, including medical, aerospace, and robotic devices.
Longitudinal monitoring of immunoglobulin A glycosylation during pregnancy by simultaneous MALDI-FTICR-MS analysis of N- and O-glycopeptides
Authors: Bondt Albert , Nicolardi Simone , Jansen Bas C. , Stavenhagen Kathrin , Blank Dennis , Kammeijer Guinevere S. M. , Kozak Radoslaw P. , Fernandes Daryl L. , Hensbergen Paul J. , Hazes Johanna M. W. , van der Burgt Yuri E. M. , Dolhain Radboud J. E. M. , Wuhrer Manfred
Published: June 2016

Immunoglobulin A (IgA) is a glycoprotein of which altered glycosylation has been associated with several pathologies. Conventional methods for IgA N- and O-glycosylation analysis are tedious, thus limiting such analyses to small sample sizes. Here we present a high-throughput strategy for the simultaneous analysis of serum-derived IgA1 N- and O-glycopeptides using matrix-assisted laser/desorption ionisation Fourier transform ion cyclotron resonance (MALDI-FTICR) mass spectrometry (MS). Six non-fucosylated diantennary complex type glycoforms were detected on the Asn144-containing glycopeptide. Thirteen distinct glycoforms were identified for the Asn340-containing tailpiece glycopeptide, mainly of the diantennary complex type, and low amounts of triantennary glycoforms. Simultaneously with these N-glycopeptides, 53 compositional glycoforms of the hinge region O-glycopeptide were profiled in a single high resolution MALDI-FTICR spectrum. Since many pregnancy associated changes have been recognized for immunoglobulin G, we sought to demonstrate the clinical applicability of this method in a cohort of 29 pregnant women, from whom samples were collected at three time points during pregnancy and three time points after delivery. Pregnancy associated changes of N-glycan bisection were different for IgA1 as compared to IgG-Fc described earlier. We foresee further applications of the developed method for larger patient cohorts to study IgA N- and O-glycosylation changes in pathologies.
Disorganized cortical thickness covariance network in major depressive disorder implicated by aberrant hubs in large-scale networks
Authors: Wang Tao , Wang Kangcheng , Qu Hang , Zhou Jingjing , Li Qi , Deng Zhou , Du Xue , Lv Fajin , Ren Gaoping , Guo Jing , Qiu Jiang , Xie Peng
Published: June 2016

Major depressive disorder is associated with abnormal anatomical and functional connectivity, yet alterations in whole cortical thickness topology remain unknown. Here, we examined cortical thickness in medication-free adult depression patients (n = 76) and matched healthy controls (n = 116). Inter-regional correlation was performed to construct brain networks. By applying graph theory analysis, global (i.e., small-worldness) and regional (centrality) topology was compared between major depressive disorder patients and healthy controls. We found that in depression patients, topological organization of the cortical thickness network shifted towards randomness, and lower small-worldness was driven by a decreased clustering coefficient. Consistently, altered nodal centrality was identified in the isthmus of the cingulate cortex, insula, supra-marginal gyrus, middle temporal gyrus and inferior parietal gyrus, all of which are components within the default mode, salience and central executive networks. Disrupted nodes anchored in the default mode and executive networks were associated with depression severity. The brain systems involved sustain core symptoms in depression and implicate a structural basis for depression. Our results highlight the possibility that developmental and genetic factors are crucial to understand the neuropathology of depression.
Climate-driven C4 plant distributions in China: divergence in C4 taxa
Authors: Wang Renzhong , Ma Linna
Published: June 2016

There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale.
Gigahertz time-domain spectroscopy and imaging for non-destructive materials research and evaluation
Authors: Bulgarevich Dmitry S. , Shiwa Mitsuharu , Furuya Takashi , Tani Masahiko
Published: June 2016

By using optical sampling with repetition frequency modulation of pump/probe laser pulses on photoconductive emitter/detector antennas, the high-speed time/frequency domain gigahertz imaging is reported due to the absence of opto-mechanical delay line in this optical scheme. The clear contrast for a 3-cm wide metal plate, which was placed behind a 5-cm thick concrete block, was observed with a 1 × 1 mm image pixilation. On average, it took only ~0.75 s per pixel/waveform acquisition/assignment with a 675 ps time-domain window. This could become a valuable non-destructive evaluation technique in gigahertz spectral range with all benefits of time-domain spectroscopy.
A Thermochromic Superhydrophobic Surface
Authors: Cataldi Pietro , Bayer Ilker S. , Cingolani Roberto , Marras Sergio , Chellali Ryad , Athanassiou Athanassia
Published: June 2016

Highly enhanced solid-state thermochromism is observed in regioregular poly(3-hexylthiophene), P3HT, when deposited on a superhydrophobic polymer-SiO2 nanocomposite coating. The conformal P3HT coating on the nanocomposite surface does not alter or reduce superhydrophicity while maintaining its reversible enhanced thermochromism. The polymeric matrix of the superhydrophobic surface is comprised of a blend of poly(vinylidene fluoride-co-hexafluoropropylene) copolymer and an acrylic adhesive. Based on detailed X-ray diffraction measurements, this long-lasting, repeatable and hysteresis-free thermochromic effect is attributed to the enhancement of the Bragg peak associated with the d-spacing of interchain directional packing (100) which remains unaltered during several heating-cooling cycles. We propose that the superhydrophobic surface confines π–π interchain stacking in P3HT with uniform d-spacing into its nanostructured texture resulting in better packing and reduction in face-on orientation. The rapid response of the system to sudden temperature changes is also demonstrated by water droplet impact and bounce back on heated surfaces. This effect can be exploited for embedded thin film temperature sensors for metal coatings.
A humanized anti-DLL4 antibody promotes dysfunctional angiogenesis and inhibits breast tumor growth
Authors: Jia Xuelian , Wang Wenyi , Xu Zhuobin , Wang Shijing , Wang Tong , Wang Min , Wu Min
Published: June 2016

Blockage of Delta-like 4 (DLL4)-directed Notch signaling induces excessive tip cell formation and endothelial proliferation resulting in dysfunctional angiogenesis in tumors. MMGZ01, as a murine anti-human DLL4 monoclonal antibody, specifically binds to human DLL4 and blocks Notch pathway. Here, the structure of MMGZ01 variable fragment (Fv) was established and framework region (FR) residues which supported complementarily determining region (CDR) loop conformation were identified. Important residues interactions were also identified through docking MMGZ01 Fv with antigen epitope in DLL4. To humanize the murine antibody, we modified MMGZ01 Fv through CDR grafting and the reconstructed antibody (H3L2) maintained similar structure and binding affinity to parental MMGZ01 after back mutation of 12 canonical murine residues in the FRs. Meanwhile, H3L2 promoted human umbilical vein endothelial cell (HUVEC) proliferation through inhibiting DLL4-directed Notch pathway. Moreover, in MDA-MB-231-bearing nude mice, H3L2 induced dysfunctional angiogenesis and tumor cell apoptosis and showed superior anti-tumor activity. In conclusion, H3L2 is an ideal humanized antibody that inhibits tumor growth through targeting DLL4-Notch pathway and has attracting potentials for clinical applications.
FACS-sorted putative oogonial stem cells from the ovary are neither DDX4-positive nor germ cells
Authors: Zarate-Garcia Larissa , Lane Simon I. R. , Merriman Julie A. , Jones Keith T.
Published: June 2016

Whether the adult mammalian ovary contains oogonial stem cells (OSCs) is controversial. They have been isolated by a live-cell sorting method using the germ cell marker DDX4, which has previously been assumed to be cytoplasmic, not surface-bound. Furthermore their stem cell and germ cell characteristics remain disputed. Here we show that although OSC-like cells can be isolated from the ovary using an antibody to DDX4, there is no good in silico modelling to support the existence of a surface-bound DDX4. Furthermore these cells when isolated were not expressing DDX4 and did not initially possess germline identity. Despite these unremarkable beginnings, they acquired some pre-meiotic markers in culture, including DDX4, but critically never expressed oocyte-specific markers and furthermore were not immortal but died after a few months. Our results suggest that freshly isolated OSCs are not germ stem cells and are not being isolated by their DDX4 expression. However it may be that culture induces some pre-meiotic markers. In summary the present study offers weight to the dogma that the adult ovary is populated by a fixed number of oocytes and that adult de novo production is a rare or insignificant event.
Solute carrier 41A3 encodes for a mitochondrial Mg2+ efflux system
Authors: Mastrototaro Lucia , Smorodchenko Alina , Aschenbach Jörg R. , Kolisek Martin , Sponder Gerhard
Published: June 2016

The important role of magnesium (Mg2+) in normal cellular physiology requires flexible, yet tightly regulated, intracellular Mg2+ homeostasis (IMH). However, only little is known about Mg2+ transporters of subcellular compartments such as mitochondria, despite their obvious importance for the deposition and reposition of intracellular Mg2+ pools. In particular, knowledge about mechanisms responsible for extrusion of Mg2+ from mitochondria is lacking. Based on circumstantial evidence, two possible mechanisms of Mg2+ release from mitochondria were predicted: (1) Mg2+ efflux coupled to ATP translocation via the ATP-Mg/Pi carrier and (2) Mg2+ efflux via a H+/Mg2+ exchanger. Regardless, the identity of the H+-coupled Mg2+ efflux system is unknown. We demonstrate here that member A3 of solute carrier (SLC) family 41 is a mitochondrial Mg2+ efflux system. Mitochondria of HEK293 cells overexpressing SLC41A3 exhibit a 60% increase in the extrusion of Mg2+ compared with control cells. This efflux mechanism is Na+-dependent and temperature sensitive. Our data identify SLC41A3 as the first mammalian mitochondrial Mg2+ efflux system, which greatly enhances our understanding of intracellular Mg2+ homeostasis.
Translational and post-translational regulation of mouse cation transport regulator homolog 1
Authors: Nomura Yuki , Hirata Yoko , Kiuchi Kazutoshi , Oh-hashi Kentaro
Published: June 2016

Cation transport regulator homolog 1 (Chac1) is an endoplasmic reticulum (ER) stress inducible gene that has a function as a γ-glutamyl cyclotransferase involved in the degradation of glutathione. To characterize the translation and stability of Chac1, we found that the Kozak-like sequence present in the 5′ untranslated region (5′UTR) of the Chac1 mRNA was responsible for Chac1 translation. In addition, the short form (ΔChac1), which translated from the second ATG codon, was generated in the absence of the 5′UTR. The proteasome pathway predominantly participated in the stability of the Chac1 protein; however, its expression was remarkably up-regulated by co-transfection with ubiquitin genes. Using an immunoprecipitation assay, we revealed that ubiquitin molecule was directly conjugated to Chac1 and that mutated Chac1 with all lysine residues replaced by arginine was also ubiquitinated. Finally, we showed that WT Chac1 but not ΔChac1 reduced the intracellular level of glutathione. Taken together, our results suggest that the Chac1 protein expression is regulated in translational and post-translational fashion due to the Kozak-like sequence in the 5′UTR and the ubiquitin-mediated pathways. The bidirectional roles of ubiquitination in regulating Chac1 stabilization might give us a new insight into understanding the homeostasis of glutathione under pathophysiological conditions.
Inflated Sporopollenin Exine Capsules Obtained from Thin-Walled Pollen
Authors: Park Jae Hyeon , Seo Jeongeun , Jackman Joshua A. , Cho Nam-Joon
Published: June 2016

Sporopollenin is a physically robust and chemically resilient biopolymer that comprises the outermost layer of pollen walls and is the first line of defense against harsh environmental conditions. The unique physicochemical properties of sporopollenin increasingly motivate the extraction of sporopollenin exine capsules (SECs) from pollen walls as a renewable source of organic microcapsules for encapsulation applications. Despite the wide range of different pollen species with varying sizes and wall thicknesses, faithful extraction of pollen-mimetic SECs has been limited to thick-walled pollen capsules with rigid mechanical properties. There is an unmet need to develop methods for producing SECs from thin-walled pollen capsules which constitute a large fraction of all pollen species and have attractive materials properties such as greater aerosol dispersion. Herein, we report the first successful extraction of inflated SEC microcapsules from a thin-walled pollen species (Zea mays), thereby overcoming traditional challenges with mechanical stability and loss of microstructure. Morphological and compositional characterization of the SECs obtained by the newly developed extraction protocol confirms successful protein removal along with preservation of nanoscale architectural features. Looking forward, there is excellent potential to apply similar strategies across a wide range of unexplored thin-walled pollen species.
In vivo Monitoring of Serotonin by Nanomaterial Functionalized Acupuncture Needle
Authors: Li Yu-Tao , Tang Li-Na , Ning Yong , Shu Qing , Liang Feng-Xia , Wang Hua , Zhang Guo-Jun
Published: June 2016

Acupuncture treatment is amazing but controversial. Up to now, the mechanism of treating diseases by acupuncture and moxibustion is still unclear, especially the occurrence of the molecular events in local acupoints. Herein, we report an extremely stable microsensor by modifying carbon nanotube (CNT) to the tip surface of acupuncture needle and applying this CNT-modified acupuncture needle for real time monitoring of serotonin (5-HT)in vivo. To stabilize CNT modification on the needle tip surface, poly(3,4-ethylenedioxythiophene)(PEDOT) was employed as glue water to stick CNT on the needle. The detection limit of the CNT-modified needle was found to be approximately 50 nM and 78 nM in the PBS and the cell medium, respectively. In addition, the needle showed good selectivity to some inflammatory mediators and some electroactive molecules. For the first time, the CNT-modified needle could be directly probed into rat body for real time monitoring of 5-HTin vivo, showing a great potential for better understanding the mechanism of acupuncture treatment.
Characterisation of light responses in the retina of mice lacking principle components of rod, cone and melanopsin phototransduction signalling pathways
Authors: Hughes Steven , Rodgers Jessica , Hickey Doron , Foster Russell G. , Peirson Stuart N. , Hankins Mark W.
Published: June 2016

Gnat−/−, Cnga3−/−, Opn4−/− triple knockout (TKO) mice lack essential components of phototransduction signalling pathways present in rods, cones and photosensitive retinal ganglion cells (pRGCs) and are therefore expected to lack all sensitivity to light. However, a number of studies have shown that light responses persist in these mice. In this study we use multielectrode array (MEA) recordings and light-induced c-fos expression to further characterise the light responses of the TKO retina. Small, but robust electroretinogram type responses are routinely detected during MEA recordings, with properties consistent with rod driven responses. Furthermore, a distinctive pattern of light-induced c-fos expression is evident in the TKO retina, with c-fos expression largely restricted to a small subset of amacrine cells that express disabled-1 (Dab1) but lack expression of glycine transporter-1 (GlyT-1). Collectively these data are consistent with the persistence of a novel light sensing pathway in the TKO retina that originates in rod photoreceptors, potentially a rare subset of rods with distinct functional properties and which is propagated to an atypical subtype of AII amacrine cells. Furthermore, the minimal responses observed following UV light stimulation suggest only a limited role for the non-visual opsin OPN5 in driving excitatory light responses within the mouse retina.
Electronic structure and electron-phonon coupling in TiH2
Authors: Shanavas K. V. , Lindsay L. , Parker D. S.
Published: June 2016

Calculations using first principles methods and strong coupling theory are carried out to understand the electronic structure and superconductivity in cubic and tetragonal TiH2. A large electronic density of states at the Fermi level in the cubic phase arises from Ti-t2g states and leads to a structural instability towards tetragonal distortion at low temperatures. However, constraining the in-plane lattice constants diminishes the energy gain associated with the tetragonal distortion, allowing the cubic phase to be stable at low temperatures. Calculated phonon dispersions show decoupled acoustic and optic modes arising from Ti and H vibrations, respectively and frequencies of optic modes to be rather high. The cubic phase has a large electron-phonon coupling parameter λ and critical temperature of several K. Contribution of the hydrogen sublattice to λ is found to be small in this material, which we understand from strong coupling theory to be due to the small H-s DOS at the Fermi level and high energy of hydrogen modes at the tetrahedral sites.
CRACM3 regulates the stability of non-excitable exocytotic vesicle fusion pores in a Ca2+-independent manner via molecular interaction with syntaxin4
Authors: Liu Shuang , Sahid Muhammad Novrizal Abdi , Takemasa Erika , Kiyoi Takeshi , Kuno Miyuki , Oshima Yusuke , Maeyama Kazutaka
Published: June 2016

Ca2+ release-activated calcium channel 3 (CRACM3) is a unique member of the CRAC family of Ca2+-selective channels. In a non-excitable exocytosis model, we found that the extracellular L3 domain and the cytoplasmic C-terminus of CRACM3 interacted in an activity-dependent manner with the N-peptide of syntaxin4, a soluble N-ethylmaleimide-sensitive factor attachment receptor protein. Our biochemical, electrophysiological and single-vesicle studies showed that knockdown of CRACM3 suppressed functional exocytosis by decreasing the open time of the vesicle fusion pore without affecting Ca2+ influx, the activity-dependent membrane capacitance (Cm) change, and the total number of fusion events. Conversely, overexpressing CRACM3 significantly impaired cell exocytosis independent of Ca2+, led to an impaired Cm change, decreased the number of fusion events, and prolonged the dwell time of the fusion pore. CRACM3 changes the stability of the vesicle fusion pore in a manner consistent with the altered molecular expression. Our findings imply that CRACM3 plays a greater role in exocytosis than simply acting as a compensatory subunit of a Ca2+ channel.
Real-time microstructure imaging by Laue microdiffraction: A sample application in laser 3D printed Ni-based superalloys
Authors: Zhou Guangni , Zhu Wenxin , Shen Hao , Li Yao , Zhang Anfeng , Tamura Nobumichi , Chen Kai
Published: June 2016

Synchrotron-based Laue microdiffraction has been widely applied to characterize the local crystal structure, orientation, and defects of inhomogeneous polycrystalline solids by raster scanning them under a micro/nano focused polychromatic X-ray probe. In a typical experiment, a large number of Laue diffraction patterns are collected, requiring novel data reduction and analysis approaches, especially for researchers who do not have access to fast parallel computing capabilities. In this article, a novel approach is developed by plotting the distributions of the average recorded intensity and the average filtered intensity of the Laue patterns. Visualization of the characteristic microstructural features is realized in real time during data collection. As an example, this method is applied to image key features such as microcracks, carbides, heat affected zone, and dendrites in a laser assisted 3D printed Ni-based superalloy, at a speed much faster than data collection. Such analytical approach remains valid for a wide range of crystalline solids, and therefore extends the application range of the Laue microdiffraction technique to problems where real-time decision-making during experiment is crucial (for instance time-resolved non-reversible experiments).
Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes
Authors: Webb Chiu-Ho T. , Nguyen Dang , Myszka Marie , Lupták Andrej
Published: June 2016

Self-cleaving ribozymes fold into intricate structures, which orient active site groups into catalytically competent conformations. Most ribozyme families have distinct catalytic cores stabilized by tertiary interactions between domains peripheral to those cores. We show that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring two helical segments, P1 and P2, into proximity – a “pinch” that results in rate acceleration by almost three orders of magnitude. Kinetic analysis of ribozymes with systematically altered length and stability of the peripheral domain revealed that about one third of its free energy of formation is used to lower an activation energy barrier, likely related to a rate-limiting conformational change leading to the pre-catalytic state. These findings provide a quantitative view of enzyme regulation by peripheral domains and may shed light on the energetics of allosteric regulation.
Interaction of tRNA with MEK2 in pancreatic cancer cells
Authors: Wang Xiaoyun , Chow Christina R. , Ebine Kazumi , Lee Jiyoung , Rosner Marsha R. , Pan Tao , Munshi Hidayatullah G.
Published: June 2016

Although the translational function of tRNA has long been established, extra translational functions of tRNA are still being discovered. We previously developed a computational method to systematically predict new tRNA-protein complexes and experimentally validated six candidate proteins, including the mitogen-activated protein kinase kinase 2 (MEK2), that interact with tRNA in HEK293T cells. However, consequences of the interaction between tRNA and these proteins remain to be elucidated. Here we tested the consequence of the interaction between tRNA and MEK2 in pancreatic cancer cell lines. We also generated disease and drug resistance-derived MEK2 mutants (Q60P, P128Q, S154F, E207K) to evaluate the function of the tRNA-MEK2 interaction. Our results demonstrate that tRNA interacts with the wild-type and mutant MEK2 in pancreatic cancer cells; furthermore, the MEK2 inhibitor U0126 significantly reduces the tRNA-MEK2 interaction. In addition, tRNA affects the catalytic activity of the wild type and mutant MEK2 proteins in different ways. Overall, our findings demonstrate the interaction of tRNA with MEK2 in pancreatic cancer cells and suggest that tRNA may impact MEK2 activity in cancer cells.
Structure–mechanical property correlations of hydrogel forming β-sheet peptides
Authors: De Leon Rodriguez Luis M. , Hemar Yacine , Cornish Jillian , Brimble Margaret A.
Published: June 2016

This review discusses about β-sheet peptide structure at the molecular level and the bulk mechanical properties of the corresponding hydrogels.
Enhanced biogas production from wheat straw with the application of synergistic microbial consortium pretreatment
Authors: Zhong Chao , Wang Chunming , Wang Fengxue , Jia Honghua , Wei Ping , Zhao Yin
Published: June 2016

Pretreatment of lignocellulosic biomass by using synergistic microbial consortium is an efficient way to promote biomass utilization efficiency.
Bodipy recognizes polyaromatic hydrocarbons via C–H⋯F type weak H-bonding
Authors: Chaudhuri Tandrima , Shivran Neelam , Mula Soumyaditya , Karmakar Animesh , Chattopadhyay Soumi , Chattopadhyay Subrata , Bandyopadhyay Debasis
Published: June 2016

Polycyclic aromatic hydrocarbons (PAHs) demonstrated unusual weak C–H⋯F type H-bonding interaction with meso-substituted Bodipy dyes (1–3) in ethanol medium.
Investigating non-specific binding to chemically engineered sensor surfaces using liposomes as models
Authors: Fenzl C. , Genslein C. , Domonkos C. , Edwards K. A. , Hirsch T. , Baeumner A. J.
Published: June 2016

Clever surface engineering strategies lead to the minimization of non-specific binding of liposomes to sensor substrates.
Electrocatalytic monitoring of peptidic proton-wires
Authors: Dorčák V. , Kabeláč M. , Kroutil O. , Bednářová K. , Vacek J.
Published: June 2016

The transfer of protons or proton donor/acceptor abilities is an important phenomenon in many biomolecular systems.
An electrochemical biosensor for rapid detection of E. coli O157:H7 with highly efficient bi-functional glucose oxidase-polydopamine nanocomposites and Prussian blue modified screen-printed interdigitated electrodes
Authors: Xu Meng , Wang Ronghui , Li Yanbin
Published: June 2016

An electrochemical biosensor was developed based on the bifunctional ABs/GOxext/AuNPs/MBs-GOx@PDA magnetic PMNCs that can rapidly and sensitively detect E. coli O157:H7.
A ratiometric two-photon fluorescent probe for fluoride ion imaging in living cells and zebrafish
Authors: Hu Wei , Zeng Lingyu , Wang Yanying , Liu Zhihong , Ye Xiaoxue , Li Chunya
Published: June 2016

Using 6-hydroxyl-quinoline-2-benzothiazole as a two-photon fluorophore and tert-butyldiphenylsilyl as a recognition domain, a ratiometric two-photon fluorescent probe was developed for fluoride ion (F−) determination. Two-photon microscopic imaging of F− in living HeLa Cells and zebrafish was also achieved.
Potentiometric sensing of aqueous phosphate by competition assays using ion-exchanger doped-polymeric membrane electrodes as transducers
Authors: Li Long , Shang Guoliang , Qin Wei
Published: June 2016

Using Zn2+–BPMP or Cu2+–BPMP as a receptor and o-mercaptophenol as an indicator, potentiometric sensing of aqueous phosphate by competition assays was achieved.
Simultaneous analysis of tocopherols, tocotrienols, phospholipids, γ-oryzanols and β-carotene in rice by ultra-high performance liquid chromatography coupled to a linear ion trap-orbitrap mass spectrometer
Authors: Zhu Li , Yang Shitian , Li Gongke , Zhang Xieguang , Yang Jun , Lai Xiaofang , Yang Guowu
Published: June 2016

An UHPLC-LTQ-Orbitrap MS method was developed for the simultaneous analysis of tocopherols, tocotrienols, phospholipids, γ-oryzanols and β-carotene in rice.
A rapid quantitative 1H NMR analysis of kinsenoside and other bioactive principles from Anoectochilus formosanus
Authors: Hsieh Li-Ying , Chan Hsiu-Hui , Hung Hsin-Yi , Kuo Chao-Lin , Wu Jin-Bin , Sun I-Wen , Kuo Ping-Chung , Wu Tian-Shung
Published: June 2016

1H NMR spectra of samples 1–9 (A–I).
Molecularly imprinted polymer-based solid phase extraction combined high performance liquid chromatography for determination of fluoroquinolones in milk
Authors: Wang Geng Nan , Yang Kun , Liu Hui Zhi , Feng Meng Xiao , Wang Jian Ping
Published: June 2016

Molecularly imprinted polymer based solid phase extraction combined high performance liquid chromatography to determine fluoroquinolone drugs in milk.
Response surface methodology based on central composite design as a chemometric tool for optimizing dispersive liquid–liquid microextraction for determining ultra-trace amounts of zinc in oil and water samples
Authors: Khazaeli Elaheh , Haddadi Hedayat , Zargar Behrooz , Hatamie Amir
Published: June 2016

The reliable and rapid dispersive liquid–liquid microextraction method for extraction of ultra-trace Zn2+ levels.
A novel ratiometric fluorescent immunoassay for human α-fetoprotein based on carbon nanodot-doped silica nanoparticles and FITC
Authors: Wu Yuanyuan , Wei Peng , Pengpumkiat Sumate , Schumacher Emily A. , Remcho Vincent T.
Published: June 2016

Non-toxic, fluorescent carbon nanodot labels are employed as novel ratiometric immunosensors for α-fetoprotein (AFP), a liver cancer biomarker. The assay generates a broad linear range, a low detection limit, and can be adapted to a variety of immunoassay targets.
A molecular beacon-based DNA switch for reversible pH sensing in vesicles and live cells
Authors: Narayanaswamy Nagarjun , Nair Raji R. , Suseela Y. V. , Saini Deepak Kumar , Govindaraju T.
Published: June 2016

The DNA switch based on a molecular beacon (closed state) to A-motif (open state) structural transformation is developed as an efficient and reversible pH sensor in synthetic vesicles and live cells.
J-aggregation of a sulfur-substituted naphthalenediimide (NDI) with remarkably bright fluorescence
Authors: Kar Haridas , Ghosh Suhrit
Published: June 2016

This communication reveals the H-bonding driven supramolecular assembly of a sulfur-substituted naphthalenediimide leading to the formation of very strong (Tg > 90 °C) organogel in aliphatic hydrocarbons.
Imaging and therapeutic applications of zinc(ii)-dipicolylamine molecular probes for anionic biomembranes
Authors: Rice Douglas R. , Clear Kasey J. , Smith Bradley D.
Published: June 2016

Synthetic ZnDPA receptors are used for molecular imaging of disease and targeted therapeutics.
[Ni(OH)3W6O18(OCH2)3CCH2OH]4−: the first tris-functionalized Anderson-type heteropolytungstate
Authors: Gumerova Nadiia I. , Roller Alexander , Rompel Annette
Published: June 2016

Na2[TMA]2[Ni(OH)3W6O18(OCH2)3CCH2OH]·9H2O represents the first covalent tris-functionalized Anderson-type heteropolytungstate and was characterized by single-crystal X-ray diffraction, electrospray ionization mass spectrometry, TGA and IR spectroscopy.
Cross-triggered and cascaded recycling amplification for ultrasensitive electrochemical sensing of the mutant human p53 gene
Authors: Yang Cuiyun , Dou Baoting , Yang Jianmei , Yuan Ruo , Xiang Yun
Published: June 2016

Cross-triggered and cascaded recycling amplification enables the highly sensitive electrochemical detection of the mutant p53 gene in human serum.
Core electron excitations in U4+: modelling of the nd105f2→ nd95f3transitions with n = 3, 4 and 5 by ligand field tools and density functional theory
Authors: Ramanantoanina Harry , Kuri Goutam , Daul Claude , Bertsch Johannes
Published: June 2016

A theoretical model of the core d-electron excitations in uranium compounds is accomplished with the LFDFT code.
Excitation dependent Raman studies of self-seeded grown InN nanoparticles with different carrier concentration
Authors: Madapu Kishore K. , Polaki S. R. , Dhara Sandip
Published: June 2016

High quality InN nanoparticles with varying carrier concentration are grown via self-seeded catalytic approach for understanding its optical phonon structure.
Why are some cyano-based ionic liquids better glucose solvents than water?
Authors: Batista Marta L. S. , Passos Helena , Henriques Bruno J. M. , Maginn Edward J. , Pinho Simão P. , Freire Mara G. , Gomes José R. B. , Coutinho João A. P.
Published: June 2016

Among different classes of ionic liquids (ILs), those with cyano-based anions have been of special interest due to their low viscosity and enhanced solvation ability for a large variety of compounds.
Shape-dependent photocatalytic hydrogen evolution activity over a Pt nanoparticle coupled g-C3N4 photocatalyst
Authors: Cao Shaowen , Jiang Jing , Zhu Bicheng , Yu Jiaguo
Published: June 2016

A Pt decorated g-C3N4 photocatalyst exhibits remarkable shape-dependent photocatalytic hydrogen evolution activity.
Glycerol inhibits the primary pathways and transforms the secondary pathway of insulin aggregation
Authors: Saha Shivnetra , Deep Shashank
Published: June 2016

Aggregation of insulin initiated from the monomeric form proceedsviathe secondary pathway of fragmentation.
An NMR study on the mechanisms of freezing and melting of water confined in spherically mesoporous silicas SBA-16
Authors: Miyatou Tatsuya , Ohashi Ryutaro , Ida Tomonori , Kittaka Shigeharu , Mizuno Motohiro
Published: June 2016

Thermodynamic and dynamic properties of water confined in mesoporous silica glass SBA-16 were investigated by DSC and 1,2H NMR spectroscopy and 2H NMR spin–lattice relaxation time as a function of pore size.
Dipole correlation effects on the local field and the effective dielectric constant in composite dielectrics containing high-k inclusions
Authors: Allahyarov Elshad , Löwen Hartmut , Zhu Lei
Published: June 2016

Mixing dielectric polymers with high permittivity (high-k) inclusions can boost their actuation and energy storage properties.
Molecular self-healing mechanisms between C60-fullerene and anthracene unveiled by Raman and two-dimensional correlation spectroscopy
Authors: Geitner R. , Kötteritzsch J. , Siegmann M. , Fritzsch R. , Bocklitz T. W. , Hager M. D. , Schubert U. S. , Gräfe S. , Dietzek B. , Schmitt M. , Popp J.
Published: June 2016

C60-fullerene–anthracene self-healing copolymers were studied by time-, temperature- and concentration-dependent FT-Raman spectroscopy and advanced 2D correlation analysis.
Simplifying metal-‘ate’ chemistry: formation and comprehensive characterisation of a homo-metallic amido lithiate complex
Authors: Greer Jamie A. , Blair Victoria L. , Thompson Christopher D. , Andrews Philip C.
Published: June 2016

This manuscript describes the first comprehensive characterisation of a simple homo-metallic amido lithate complex, the crystals of which arise from treatment of N-allyl-1-naphthylamine with BuLi and TMEDA.
Temperature dependent structures and properties of Bi0.5Na0.5TiO3-based lead free piezoelectric composite
Authors: Zhang Ji , Sun Lei , Geng Xiao-Yu , Zhang Bin-Bin , Yuan Guo-Liang , Zhang Shan-Tao
Published: June 2016

The thermal depolarization of Bi0.5Na0.5TiO3-BaTiO3 is deferred by introducing ZnO to construct composite, the detailed crystal structures of unpoled and poled composites were comparatively investigated.
Optical vs. chemical driving for molecular machines
Authors: Astumian R. D.
Published: June 2016

Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy sourcevs.the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium. Applying the constraints of microscopic reversibility assures that a coarse grained model is consistent with an underlying model for motion on a single time-independent potential energy surface. In contrast, light-driven processes, and processes driven by external modulation of the thermodynamic parameters of a system cannot in general be described in terms of motion on a single time-independent potential energy surface, and the rate constants are not constrained by microscopic reversibility. The results presented here call into question the value of the so-called power stroke model as an explanation of the function of autonomous chemically-driven molecular machines such as are commonly found in biology.
Drinking pattern of wine and effects on human health: why should we drink moderately and with meals?
Authors: Boban Mladen , Stockley Creina , Teissedre Pierre-Louis , Restani Patrizia , Fradera Ursula , Stein-Hammer Claudia , Ruf Jean-Claude
Published: June 2016

Epidemiological studies examining the effects of alcoholic beverages on human health may be unclear if they do not take into account drinking pattern parameters such as beverage type, regular moderateversusbinge drinking and drinking with meals.
Impact of engineered lignin composition on biomass recalcitrance and ionic liquid pretreatment efficiency
Authors: Shi Jian , Pattathil Sivakumar , Parthasarathi Ramakrishnan , Anderson Nickolas A. , Kim Jeong Im , Venketachalam Sivasankari , Hahn Michael G. , Chapple Clint , Simmons Blake A. , Singh Seema
Published: June 2016

Impact of engineered lignin composition on biomass recalcitrance.
Molecular and genetic inflammation networks in major human diseases
Authors: Zhao Yongzhong , Forst Christian V. , Sayegh Camil E. , Wang I-Ming , Yang Xia , Zhang Bin
Published: June 2016

Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions.
Thioether functionalised gallium and indium alkoxides in materials synthesis
Authors: Biegger Felix , Rameshan Christoph , Opitz Alexander K. , Noll Julian , Haunold Thomas , Lang Heinrich , Barth Sven
Published: June 2016

Thermolysis of thioether functionalised metal alkoxides leads to the incorporation of sulphides in materials synthesized by CVD and hot-injection method.
Interplay between hydrophobicity and basicity toward the catalytic activity of isoreticular MOF organocatalysts
Authors: Abedi Sedigheh , Azhdari Tehrani Alireza , Ghasempour Hosein , Morsali Ali
Published: June 2016

Four MOF catalysts showing different hydrophobic characters around the basic reaction center showed subtle substrate selectivity in aldol-type condensation reaction.
Facile hydrothermal synthesis of Tb2(MoO4)3:Eu3+ phosphors: controllable microstructures, tunable emission colors, and the energy transfer mechanism
Authors: Yang Jun , Zhou Lei , Yuan Li , Zhou Xianju , Hu Bin , Zhang Xinlei , Hu Shanshan
Published: June 2016

Microsphere-like Tb2(MoO4)3 structures have been successfully synthesized by a facile hydrothermal method with the subsequent calcination treatment.
Role of solvent in the phosphatase activity of a dinuclear nickel(ii) complex of a Schiff base ligand: mechanistic interpretation by DFT studies
Authors: Sanyal Ria , Zhang Xuepeng , Chakraborty Prateeti , Giri Sanjib , Chattopadhyay Shyamal Kumar , Zhao Cunyuan , Das Debasis
Published: June 2016

A biomimetic metallohydrolase has been synthesized and its catalytic mechanism and the related solvent effect were elucidated using theoretical modeling.
Straight chain D–A copolymers based on thienothiophene and benzothiadiazole for efficient polymer field effect transistors and photovoltaic cells
Authors: Li Yuxiang , Lee Tack Ho , Park Song Yi , Uddin Mohammad Afsar , Kim Taehyo , Hwang Sungu , Kim Jin Young , Woo Han Young
Published: June 2016

Fine modulation of chain linearity suggests an effective way to control interchain ordering for specific application in polymer solar cells or field effect transistors.
Hollow anatase TiO2 nanoparticles with excellent catalytic activity for dichloromethane combustion
Authors: Huang Haifeng , Zhang Xixiong , Jiang Xiaojia , Dou Kang , Ni Zhiyi , Lu Hanfeng
Published: June 2016

Hollow anatase TiO2 nanoparticles around 11.4 nm in size were prepared by a CTAB-assisted hydrothermal method. The catalyst showed high catalytic activity for dichloromethane (DCM) combustion with 90% DCM conversion at 201 °C.
Preparation of reduced graphene oxide/Co3O4 composites and sensing performance to toluene at low temperature
Authors: Bai Shouli , Du Long , Sun Jianhua , Luo Ruixian , Li Dianqing , Chen Aifan , Liu Chung-Chiun
Published: June 2016

The rGO/Co3O4 composite not only exhibits the high response to 5 ppm toluene but also displays excellent selectivity to some of VOCs.
Cuprous oxide/titanium dioxide nanotube-array with coaxial heterogeneous structure synthesized by multiple-cycle chemical adsorption plus reduction method
Authors: Zhu Wen , Chong Baohe , Qin Ke , Guan Li , Hou Xianghui , Chen George Z.
Published: June 2016

We report the formation and characterization of Cu2O/TiO2 nanotube-array coaxial heterogeneous structure, which is supposed to have potential applications in photo-induced water decomposition and organic pollutant degradation.
Hydroxyapatite doped CeO2 nanoparticles: impact on biocompatibility and dye adsorption properties
Authors: Chaudhary Savita , Sharma Priyanka , Renu Renu , Kumar Rajeev
Published: June 2016

The toxicity imparted by the commercialized use of nanoparticles in environmental remediation has become a big concern.
Rapid on-site detection of paraquat in biologic fluids by iodide-facilitated pinhole shell-isolated nanoparticle-enhanced Raman spectroscopy
Authors: Zhu Yingjie , Wu Jianfeng , Gao Haiyue , Liu Guokun , Tian Zhongqun , Feng Jianlin , Guo Lei , Xie Jianwei
Published: June 2016

We report a sensitive iodide-facilitated SERS method on paraquat without any tedious pretreatment in biologic fluids, ​which clinical diagnosis prefers.