bluuebunny/crossref_metadata_2025 huggingface dataset:
Nodal marginal zone B cells in mice: a novel subset with dormant self-reactivity
Authors: Palm Anna-Karin E. , Friedrich Heike C. , Kleinau Sandra
Published: June 2016

Marginal zone (MZ) B cells, representing a distinct subset of innate-like B cells, mount rapid T-independent responses to blood-borne antigens. They express low-affinity polyreactive antigen receptors that recognize both foreign and self-structures. The spleen is considered the exclusive site for murine MZ B cells. However, we have here identified B cells with a MZ B-cell phenotype in the subcapsular sinuses of mouse lymph nodes. The nodal MZ (nMZ) B cells display high levels of IgM, costimulators and TLRs, and are represented by naïve and memory cells. The frequency of nMZ B cells is about 1–6% of nodal B cells depending on mouse strain, with higher numbers in older mice and a trend of increased numbers in females. There is a significant expansion of nMZ B cells following immunization with an autoantigen, but not after likewise immunization with a control protein or with the adjuvant alone. The nMZ B cells secrete autoantibodies upon activation and can efficiently present autoantigen to cognate T cells in vitro, inducing T-cell proliferation. The existence of self-reactive MZ B cells in lymph nodes may be a source of autoantigen-presenting cells that in an unfortunate environment may activate T cells leading to autoimmunity.
Stimulus-Dependent Inhibitor of Apoptosis Protein Expression Prolongs the Duration of B Cell Signalling
Authors: Shinohara Hisaaki , Inoue Kentaro , Yumoto Noriko , Nagashima Takeshi , Okada-Hatakeyama Mariko
Published: June 2016

Different dynamic behaviours of signalling activity can induce distinct biological responses in a variety of cells. However, the molecular mechanisms that determine the dynamics of kinase activities in immune cells are not well understood. In this study, we showed that the duration of both IκB kinase (IKK) and extracellular signal-regulated kinase (ERK) activities in B cell receptor (BCR)- and CD40-signalling pathways in B cells were regulated by transcriptional feedback loops. We conducted a time-course transcriptome analysis after BCR or CD40 stimulation and identified the following four candidate genes as feedback regulators for IKK and ERK: inhibitor of apoptosis protein (IAP), TNF alpha-induced protein 3, dual-specificity phosphatase 5 and sprouty homolog 2. Quantitative experiments and mathematical modelling suggested that IAP inhibition shortened the duration of IKK and ERK activity following both BCR and CD40 pathway stimulation, indicating a positive role for IAP in B cell signalling. Furthermore, transient kinase activities induced by IAP blockage reduced the levels of delayed expression genes. Together, our findings suggest that IKK and ERK activity durations can be fine-tuned by the coordinated regulation of positive and negative transcriptional feedback and that these network properties determine the biological output of B cells.
Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Authors: Fonville Natalie C. , Velmurugan Karthik Raja , Tae Hongseok , Vaksman Zalman , McIver Lauren J. , Garner Harold R.
Published: June 2016

The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA.
Highly selective and sensitive phosphate anion sensors based on AlGaN/GaN high electron mobility transistors functionalized by ion imprinted polymer
Authors: Jia Xiuling , Chen Dunjun , Bin Liu , Lu Hai , Zhang Rong , Zheng Youdou
Published: June 2016

A novel ion-imprinted electrochemical sensor based on AlGaN/GaN high electron mobility transistors (HEMTs) was developed to detect trace amounts of phosphate anion. This sensor combined the advantages of the ion sensitivity of AlGaN/GaN HEMTs and specific recognition of ion imprinted polymers. The current response showed that the fabricated sensor is highly sensitive and selective to phosphate anions. The current change exhibited approximate linear dependence for phosphate concentration from 0.02 mg L−1 to 2 mg L−1, the sensitivity and detection limit of the sensor is 3.191 μA/mg L−1 and 1.97 μg L−1, respectively. The results indicated that this AlGaN/GaN HEMT-based electrochemical sensor has the potential applications on phosphate anion detection.
Stable and null current hysteresis perovskite solar cells based nitrogen doped graphene oxide nanoribbons hole transport layer
Authors: Kim Jeongmo , Mat Teridi Mohd Asri , Mohd Yusoff Abd. Rashid bin , Jang Jin
Published: June 2016

Perovskite solar cells are becoming one of the leading technologies to reduce our dependency on traditional power sources. However, the frequently used component poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) has several shortcomings, such as an easily corroded indium-tin-oxide (ITO) interface at elevated temperatures and induced electrical inhomogeneity. Herein, we propose solution-processed nitrogen-doped graphene oxide nanoribbons (NGONRs) as a hole transport layer (HTL) in perovskite solar cells, replacing the conducting polymer PEDOT:PSS. The conversion efficiency of NGONR-based perovskite solar cells has outperformed a control device constructed using PEDOT:PSS. Moreover, our proposed NGONR-based devices also demonstrate a negligible current hysteresis along with improved stability. This work provides an effective route for substituting PEDOT:PSS as the effective HTL.
Nanoscale mapping of intrinsic defects in single-layer graphene using tip-enhanced Raman spectroscopy
Authors: Su Weitao , Kumar Naresh , Dai Ning , Roy Debdulal
Published: June 2016

Non-gap TERS with a contrast of 8.5 enables TERS mapping of graphene's intrinsic defect with a spatial resolution of 20 nm.
A low recombination rate indolizine sensitizer for dye-sensitized solar cells
Authors: Huckaba Aron J. , Yella Aswani , Brogdon Phillip , Scott Murphy J. , Nazeeruddin Mohammad Khaja , Grätzel Michael , Delcamp Jared H.
Published: June 2016

A novel indolizine donor for DSC use with an extended absorption spectrum shows good voltages and enhanced short circuit current.
N-Heterocyclic carbene-mediated redox condensation of alcohols
Authors: Kato Terumasa , Matsuoka Shin-ichi , Suzuki Masato
Published: June 2016

N-Heterocyclic carbenes (NHCs) with a variety of oxidants promote the Mitsunobu-type coupling reactions of alcohols with phenols, carboxylic acids, and phthalimide.
Correction: From FOX-7 to H-FOX to insensitive energetic materials with hypergolic properties
Authors: Dharavath Srinivas , Mitchell Lauren A. , Parrish Damon A. , Shreeve Jean'ne M.
Published: June 2016

Correction for ‘From FOX-7 to H-FOX to insensitive energetic materials with hypergolic properties’ by Dharavath Srinivas et al., Chem. Commun., 2016, 52, 7668–7671.
How surface reparation prevents catalytic oxidation of carbon monoxide on atomic gold at defective magnesium oxide surfaces
Authors: Töpfer Kai , Tremblay Jean Christophe
Published: June 2016

First principles simulations of CO and O2 on a single gold atom deposited at defective magnesium oxide surfaces reveal that surface reparation prevents catalytic oxidation by insertion of either molecular or atomic oxygen inside the defect.
Rovibrational energy levels of the F−(H2O) and F−(D2O) complexes
Authors: Sarka János , Lauvergnat David , Brites Vincent , Császár Attila G. , Léonard Celine
Published: June 2016

A new accurate 6D PES is determined obtained from CCSD(T)-F12 calculations including two dissociation channels (HF + OH− and F− + H2O). A novel way is developed to use complex coordinates in variational nuclear motion computations. The rovibrational energies of F−(H2O) (the complete set up to 3700 cm−1) and F−(D2O) have been computed. The tunneling splittings describing the two complexes are obtained.
The effect of the zeolite pore size on the Lewis acid strength of extra-framework cations
Authors: Thang Ho Viet , Frolich Karel , Shamzhy Mariya , Eliášová Pavla , Rubeš Miroslav , Čejka Jiří , Bulánek Roman , Nachtigall Petr
Published: June 2016

The Lewis acid strength of Li+sites in Li-exchanged zeolites depends on the diameter of the pores.
Thermopower measurements in molecular junctions
Authors: Rincón-García Laura , Evangeli Charalambos , Rubio-Bollinger Gabino , Agraït Nicolás
Published: June 2016

The measurement of thermopower in molecular junctions offers complementary information to conductance measurements and is becoming essential for the understanding of transport processes at the nanoscale.
Cobalt-bis(imino)pyridine complexes as catalysts for hydroalumination–isomerisation of internal olefins
Authors: Weliange Nandita M. , McGuinness David S. , Gardiner Michael G. , Patel Jim
Published: June 2016

The hydroalumination–isomerisation of α- and internal olefins catalysed by bis(imino)pyridine cobalt complexes is investigated.
Dual-drug loaded nanoformulation with a galactosamine homing moiety for liver-targeted anticancer therapy
Authors: Muhammad Nafees , Wang Xiaoyong , Wang Kun , Zhu Chengcheng , Zhu Zhenzhu , Jiao Yang , Guo Zijian
Published: June 2016

A platinum(iv) complex was prepared as a prodrug of cisplatin and co-loaded with α-tocopheryl succinate into the galactosamine-modified PLGA nanoparticle for combinational chemotherapy of liver cancer.
On-line monitoring of organic matter concentrations and character in drinking water treatment systems using fluorescence spectroscopy
Authors: Shutova Y. , Baker A. , Bridgeman J. , Henderson R. K.
Published: June 2016

There is a need for a rapid and robust method of organic matter (OM) monitoring during drinking water treatment.
Large scale flow visualization and anemometry applied to lab-on-a-chip models of porous media
Authors: Paiola Johan , Auradou Harold , Bodiguel Hugues
Published: June 2016

The following is a report on an experimental technique that allows one to quantify and map the velocity field with very high resolution and simple equipment in large 2D devices.
A DFT study on NHC-catalyzed intramolecular aldehyde–ketone crossed-benzoin reaction: mechanism, regioselectivity, stereoselectivity, and role of NHC
Authors: Zhang Wei , Wang Yang , Wei Donghui , Tang Mingsheng , Zhu Xinju
Published: June 2016

A computational study on NHC-catalyzed intramolecular aldehyde–ketone crossed-benzoin reaction has been performed using a DFT method.
Designed synthesis of well-defined titania/iron(iii) acetylacetonate nanohybrids with magnetic/luminescent properties
Authors: Shiba Kota , Kataoka Takuya , Okuda Mitsuhiro , Blanco-Canosa Santiago , Tagaya Motohiro
Published: June 2016

Synthesis and magnetic/luminescent properties of well-defined titania/octadecylamine/iron(iii) acetylacetonate hybrid functional particles were demonstrated.
Photoinduced energy and charge transfer in a bis(triphenylamine)–BODIPY–C60artificial photosynthetic system
Authors: Liu Jian-Yong , Hou Xue-Ni , Tian Ye , Jiang Lizhi , Deng Shuiquan , Röder Beate , Ermilov Eugeny A.
Published: June 2016

The bis(triphenylamine)–BODIPY–C60artificial photosynthetic system has been prepared and studied for its photoinduced transfer processes in polar and nonpolar solvents using various steady-state and time-resolved spectroscopic techniques.
Fabrication of modified bismaleimide resins by hyperbranched phenyl polysiloxane and improvement of their thermal conductivities
Authors: Gu Junwei , Liang Chaobo , Dang Jing , Meng Xudong , Tang Lin , Li Yang , Zhang Qiuyu
Published: June 2016

Synthetic terminal amine group hyperbranched phenyl polysiloxane (NH2-HBPSi) is introduced into a bismaleimide/diallylbisphenol A (BMI/DABA) prepolymer to fabricate NH2-HBPSi/BMI/DABA resins.
Double cyclization of O-acylated hydroxyamides generates 1,6-dioxa-3,9-diazaspiro[4.4]nonanes a new class of oxy-oxazolidinones
Authors: Nazarian Zohreh , Forsyth Craig
Published: June 2016

This work explains preparation of a new class of heterocyclic compounds namely 1,6-dioxa-3,9-diazaspiro[4.4]nonanes triggered by the cyclization of acyloxy amides and their subsequent spirocyclization to generate densely functionalized 3-azaspirocyclic orthoamide compounds.
Self-assembled structures of polyhedral gold nanocrystals: shape-directive arrangement and structure-dependent plasmonic enhanced characteristics
Authors: Liu Yanting , Zhou Jun , Zhou Lu , Yue-Bun Pun Edwin , Jiang Tao , Petti Lucia , Mormile Pasquale
Published: June 2016

Self-assembly structures of different types of polyhedral nanocrystals through drop casting method and their plasmonic enhancement characteristics and SERS performances due to the nano-antenna effect.
Understanding the anatase–rutile phase junction in charge separation and transfer in a TiO2 electrode for photoelectrochemical water splitting
Authors: Li Ailong , Wang Zhiliang , Yin Heng , Wang Shengyang , Yan Pengli , Huang Baokun , Wang Xiuli , Li Rengui , Zong Xu , Han Hongxian , Li Can
Published: June 2016

The key to phase junctions for efficient charge separation is to consider both the phase alignment and interface structure.
Direct quantitative identification of the “surface trans-effect”
Authors: Deimel Peter S. , Bababrik Reda M. , Wang Bin , Blowey Phil J. , Rochford Luke A. , Thakur Pardeep K. , Lee Tien-Lin , Bocquet Marie-Laure , Barth Johannes V. , Woodruff D. Phil , Duncan David A. , Allegretti Francesco
Published: June 2016

Quantification of the surfacetrans-effect: delocalised surface, rather than atomic, electrons acting as if a ligand in a traditionaltrans-effect.
Asymmetric [4 + 2] annulation of 5H-thiazol-4-ones with a chiral dipeptide-based Brønsted base catalyst
Authors: Zhu Bo , Qiu Shuai , Li Jiangtao , Coote Michelle L. , Lee Richmond , Jiang Zhiyong
Published: June 2016

We have developed a new family of dipeptide-based multifunctional Brønsted base organocatalysts capable of the asymmetric [4 + 2] annulation of 5H-thiazol-4-ones with electron-deficient alkenes.
In situ growth of porphyrinic metal–organic framework nanocrystals on graphene nanoribbons for the electrocatalytic oxidation of nitrite
Authors: Kung Chung-Wei , Li Yan-Sheng , Lee Min-Han , Wang Shan-Yu , Chiang Wei-Hung , Ho Kuo-Chuan
Published: June 2016

A nanocomposite of MOF-525 nanocrystals interconnected by numerous one-dimensional graphene nanoribbons serves as a promising electrocatalyst for nitrite oxidation.
A high temperature reduction cleaning (HTRC) process: a novel method for conductivity recovery of yttrium-doped barium zirconate electrolytes
Authors: Han Donglin , Iihara Junji , Uemura Shigeaki , Kazumi Kenji , Hiraiwa Chihiro , Majima Masatoshi , Uda Tetsuya
Published: June 2016

A novel high temperature reduction cleaning (HTRC) process to recover the electrical conductivity of Y-doped barium zirconate electrolytes from Ni contamination.
Solvent-triggered relaxative spin state switching of [Fe(HB(pz)3)2] in a closed nano-confinement of NH2-MIL-101(Al)
Authors: Zhao Tian , Boldog Ishtvan , Spasojevic Vojislav , Rotaru Aurelian , Garcia Yann , Janiak Christoph
Published: June 2016

The synthesis of the NH2-MIL-101(Al) Metal–Organic Framework (MOF) with bis(hydrotris(pyrazolyl)borato)iron(ii), [Fe(HB(pz)3)2], added to the reaction medium yielded [Fe(HB(pz)3)2]@NH2-MIL101(Al) encapsulation products, denoted as S@Ms, in the course of a ‘bottle-around-the-ship’ assembly.
Improved performance of a conducting-bridge random access memory using ionic liquids
Authors: Harada A. , Yamaoka H. , Tojo S. , Watanabe K. , Sakaguchi A. , Kinoshita K. , Kishida S. , Fukaya Y. , Matsumoto K. , Hagiwara R. , Sakaguchi H. , Nokami T. , Itoh T.
Published: June 2016

The conducting-bridge random access memory (CB-RAM) is a promising candidate for the next-generation memory.
Controlling armchair and zigzag edges in oxidative cutting of graphene
Authors: Sk Mahasin Alam , Huang Lin , Chen Peng , Lim Kok Hwa
Published: June 2016

DFT calculations reveal that the edges of GNRs and GQDs can be controlled by manipulating the experimental conditions and external strain on a graphene sheet.
Interdomain regulation of the ATPase activity of the ABC transporter haemolysin B from Escherichia coli
Authors: Reimann Sven , Poschmann Gereon , Kanonenberg Kerstin , Stühler Kai , Smits Sander H.J. , Schmitt Lutz
Published: June 2016

Type 1 secretion systems (T1SS) transport a wide range of substrates across both membranes of Gram-negative bacteria and are composed of an outer membrane protein, a membrane fusion protein and an ABC (ATP-binding cassette) transporter. The ABC transporter HlyB (haemolysin B) is part of a T1SS catalysing the export of the toxin HlyA in E. coli. HlyB consists of the canonical transmembrane and nucleotide-binding domains. Additionally, HlyB contains an N-terminal CLD (C39-peptidase-like domain) that interacts with the transport substrate, but its functional relevance is still not precisely defined. In the present paper, we describe the purification and biochemical characterization of detergent-solubilized HlyB in the presence of its transport substrate. Our results exhibit a positive co-operativity in ATP hydrolysis. We characterized further the influence of the CLD on kinetic parameters by using an HlyB variant lacking the CLD (HlyB∆CLD). The biochemical parameters of HlyB∆CLD revealed an increased basal maximum velocity but no change in substrate-binding affinity in comparison with full-length HlyB. We also assigned a distinct interaction of the CLD and a transport substrate (HlyA1), leading to an inhibition of HlyB hydrolytic activity at low HlyA1 concentrations. At higher HlyA1 concentrations, we observed a stimulation of the hydrolytic activities of both HlyB and HlyB∆CLD, which was completely independent of the interaction of HlyA1 with the CLD. Notably, all observed effects on ATPase activity, which were also analysed in detail by mass spectrometry, were independent of the HlyA1 secretion signal. These results assign an interdomain regulatory role for the CLD modulating the hydrolytic activity of HlyB.
The multidrug transporter ABCG2: still more questions than answers
Authors: Horsey Aaron J. , Cox Megan H. , Sarwat Sunehera , Kerr Ian D.
Published: June 2016

ABCG2 is one of at least three human ATP binding cassette (ABC) transporters which can facilitate the export from cells of a wide range of chemically unrelated drug molecules. This capacity for multidrug transport is not only a confounding factor in chemotherapy, but is also one of the more perplexing phenomena in transporter biochemistry. Since its discovery in the last decade of the 20th century much has been revealed about ABCG2’s localization, physiological function and its broad substrate range. There have also been many investigations of its structure and molecular mechanism. In this mini review article we take a Rumsfeldian approach to ABCG2 and essentially ask what we do know about this transporter, and what we will need to know about this transporter if we wish to use modulation of ABCG2 activity as a therapeutic approach.
Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions
Authors: Hussain Rohanah , Harding Stephen E. , Hughes Charlotte S. , Ma Pikyee , Patching Simon G. , Edara Shalini , Siligardi Giuliano , Henderson Peter J.F. , Phillips-Jones Mary K.
Published: June 2016

This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developed at Leeds alongside Professor Steve Baldwin to whom this review is dedicated. It also reviews two biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins–synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs.
Membrane proteins: always an insoluble problem?
Authors: Rawlings Andrea E.
Published: June 2016

Membrane proteins play crucial roles in cellular processes and are often important pharmacological drug targets. The hydrophobic properties of these proteins make full structural and functional characterization challenging because of the need to use detergents or other solubilizing agents when extracting them from their native lipid membranes. To aid membrane protein research, new methodologies are required to allow these proteins to be expressed and purified cheaply, easily, in high yield and to provide water soluble proteins for subsequent study. This mini review focuses on the relatively new area of water soluble membrane proteins and in particular two innovative approaches: the redesign of membrane proteins to yield water soluble variants and how adding solubilizing fusion proteins can help to overcome these challenges. This review also looks at naturally occurring membrane proteins, which are able to exist as stable, functional, water soluble assemblies with no alteration to their native sequence.
Discovery of functional monoclonal antibodies targeting G-protein-coupled receptors and ion channels
Authors: Wilkinson Trevor C.I.
Published: June 2016

The development of recombinant antibody therapeutics is a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Despite this growth, however, certain classes of important molecular targets have remained intractable to therapeutic antibodies due to complexity of the target molecules. These complex target molecules include G-protein-coupled receptors and ion channels which represent a large potential target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these target proteins. Given this opportunity, substantial effort has been applied to address the technical challenges of targeting these complex membrane proteins with monoclonal antibodies. In this review recent progress made in the strategies for discovery of functional monoclonal antibodies for these challenging membrane protein targets is addressed.
How to move an amphipathic molecule across a lipid bilayer: different mechanisms for different ABC transporters?
Authors: Theodoulou Frederica L. , Carrier David J. , Schaedler Theresia A. , Baldwin Stephen A. , Baker Alison
Published: June 2016

Import of β-oxidation substrates into peroxisomes is mediated by ATP binding cassette (ABC) transporters belonging to subfamily D. In order to enter the β-oxidation pathway, fatty acids are activated by conversion to fatty acyl-CoA esters, a reaction which is catalysed by acyl-CoA synthetases (ACSs). Here, we present evidence for an unusual transport mechanism, in which fatty acyl-CoA substrates are accepted by ABC subclass D protein (ABCD) transporters, cleaved by the transporters during transit across the lipid bilayer to release CoA, and ultimately re-esterified in the peroxisome lumen by ACSs which interact with the transporter. We propose that this solves the biophysical problem of moving an amphipathic molecule across the peroxisomal membrane, since the intrinsic thioesterase activity of the transporter permits separate membrane translocation pathways for the hydrophobic fatty acid moiety and the polar CoA moiety. The cleavage/re-esterification mechanism also has the potential to control entry of disparate substrates into the β-oxidation pathway when coupled with distinct peroxisomal ACSs. A different solution to the movement of amphipathic molecules across a lipid bilayer is deployed by the bacterial lipid-linked oligosaccharide (LLO) flippase, PglK, in which the hydrophilic head group and the hydrophobic polyprenyl tail of the substrate are proposed to have distinct translocation pathways but are not chemically separated during transport. We discuss a speculative alternating access model for ABCD proteins based on the mammalian ABC transporter associated with antigen processing (TAP) and compare it to the novel mechanism suggested by the recent PglK crystal structures and biochemical data.
Protein translocation: what's the problem?
Authors: Corey Robin A. , Allen William J. , Collinson Ian
Published: June 2016

We came together in Leeds to commemorate and celebrate the life and achievements of Prof. Stephen Baldwin. For many years we, together with Sheena Radford and Roman Tuma (colleagues also of the University of Leeds), have worked together on the problem of protein translocation through the essential and ubiquitous Sec system. Inspired and helped by Steve we may finally be making progress. My seminar described our latest hypothesis for the molecular mechanism of protein translocation, supported by results collected in Bristol and Leeds on the tractable bacterial secretion process–commonly known as the Sec system; work that will be published elsewhere. Below is a description of the alternative and contested models for protein translocation that we all have been contemplating for many years. This review will consider their pros and cons.
Synthesis of chemically modified DNA
Authors: Shivalingam Arun , Brown Tom
Published: June 2016

Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to ‘write’ long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion.
Transport mechanism of a glutamate transporter homologue GltPh
Authors: Ji Yurui , Postis Vincent L.G. , Wang Yingying , Bartlam Mark , Goldman Adrian
Published: June 2016

Glutamate transporters are responsible for uptake of the neurotransmitter glutamate in mammalian central nervous systems. Their archaeal homologue GltPh, an aspartate transporter isolated from Pyrococcus horikoshii, has been the focus of extensive studies through crystallography, MD simulations and single-molecule FRET (smFRET). Here, we summarize the recent research progress on GltPh, in the hope of gaining some insights into the transport mechanism of this aspartate transporter.
Detecting and positioning of traffic incidents via video‐based analysis of traffic states in a road segment
Authors: Ren Jianqiang , Chen Yangzhou , Xin Le , Shi Jianjun , Li Baotong , Liu Yinan
Published: June 2016

Non‐recurrent traffic incidents (accidents, stalled vehicles and spilled loads) often bring about traffic congestion and even secondary accidents. Detecting and positioning them quickly and accurately has important significance for early warning, timely incident‐disposal and speedy congestion‐evacuation. This study proposes a video‐based detecting and positioning method by analysing distribution characteristics of traffic states in a road segment. Each lane in the monitored segment is divided into a cluster of cells. Traffic parameters in each cell, including flow rate, average travel speed and average space occupancy, are obtained by detecting and tracking traffic objects (vehicles and spilled loads). On the basis of the parameters, traffic states in the cells are judged via a fuzzy‐identification method. For each congested cell, a feature vector is constructed by taking its state together with states of its upstream and downstream neighbouring cells in the same lane. Then, a support vector machine classifier is trained to detect incident point. If a cell is judged to be corresponding to an incident point at least for two successive time periods, an incident is detected and its position is calculated based on the identity number of the cell. Experiments prove the efficiency and practicability of the proposed method.
Flexibility arrangements in the African Union: a way out of the integration conundrum?
Authors: Fagbayibo Babatunde
Published: June 2016

The transformation of the Organisation of African Unity (OAU) to the African Union (AU) in 2002 was seen as a positive development in the process of continental integration in Africa. With an institutional architecture largely inspired by the European Union (EU) model, the AU was positioned to infuse new and vibrant energy into the stagnated process of achieving deeper unity. After a decade of existence, little has been achieved in terms of deepening continental integration. It is against this background that this article considers the feasibility of adopting legal frameworks for flexibility arrangements in the AU. What this implies is the establishment of legal arrangements that could enable member states with similar interests to pursue integrative objectives at a determinable and attainable pace and speed. This article examines the possibility of placing key integrative objectives such as democratic governance, trade and immigration within the context of a flexibility approach. Lessons are drawn from the operation of flexibility arrangements in the EU, Asia and regional economic communities across the African continent to further buttress the essence of this idea.
The impact of familiarization strategies on the missing-letter effect
Authors: Plamondon Andréanne , Roy-Charland Annie , Chamberland Justin , Quenneville Joannie , Laforge Christian
Published: June 2016

When reading a text and searching for a target letter, readers make more omissions of the target letter if it is embedded in frequent function words than if it is in rare content words. While word frequency effects are consistently found, few studies have examined the impacts of passage familiarity on the missing-letter effect and studies that have present conflicting evidence. The present study examines the effects of passage familiarity, as well as the impacts of passage familiarization strategy promoting surface or deep encoding, on the missing-letter effect. Participants were familiarized with a passage by retyping a text, replacing all common nouns with synonyms, or generating a text on the same topic as that of the original text, and then completed a letter search task on the familiar passage as well as an unfamiliar passage. In Experiment 1, when both familiar and unfamiliar passages use the same words, results revealed fewer omissions for the retyping and synonyms conditions. However, in Experiment 2, when different words are used in both types of texts, no effect of familiarization strategy was observed. Furthermore, the missing-letter effect is maintained in all conditions, adding support to the robustness of the effect regardless of familiarity with the text.
Phosphorylation of the RNA-binding protein Dazl by MAPKAP kinase 2 regulates spermatogenesis
Authors: Williams Patrick A. , Krug Michael S. , McMillan Emily A. , Peake Jasmine D. , Davis Tara L. , Cocklin Simon , Strochlic Todd I.
Published: June 2016

Developing male germ cells are exquisitely sensitive to environmental insults such as heat and oxidative stress. An additional characteristic of these cells is their unique dependence on RNA-binding proteins for regulating posttranscriptional gene expression and translational control. Here we provide a mechanistic link unifying these two features. We show that the germ cell–specific RNA-binding protein deleted in azoospermia-like (Dazl) is phosphorylated by MAPKAP kinase 2 (MK2), a stress-induced protein kinase activated downstream of p38 MAPK. We demonstrate that phosphorylation of Dazl by MK2 on an evolutionarily conserved serine residue inhibits its interaction with poly(A)-binding protein, resulting in reduced translation of Dazl-regulated target RNAs. We further show that transgenic expression of wild-type human Dazl but not a phosphomimetic form in the Drosophila male germline can restore fertility to flies deficient in boule, the Drosophila orthologue of human Dazl. These results illuminate a novel role for MK2 in spermatogenesis, expand the repertoire of RNA-binding proteins phosphorylated by this kinase, and suggest that signaling by the p38-MK2 pathway is a negative regulator of spermatogenesis via phosphorylation of Dazl.
Aftershock seismicity and tectonic setting of the 2015 September 16 Mw 8.3 Illapel earthquake, Central Chile
Authors: Lange Dietrich , Geersen Jacob , Barrientos Sergio , Moreno Marcos , Grevemeyer Ingo , Contreras-Reyes Eduardo , Kopp Heidrun
Published: June 2016

Powerful subduction zone earthquakes rupture thousands of square kilometres along continental margins but at certain locations earthquake rupture terminates. To date, detailed knowledge of the parameters that govern seismic rupture and aftershocks is still incomplete. On 2015 September 16, the Mw 8.3 Illapel earthquake ruptured a 200 km long stretch of the Central Chilean subduction zone, triggering a tsunami and causing significant damage. Here, we analyse the temporal and spatial pattern of the coseismic rupture and aftershocks in relation to the tectonic setting in the earthquake area. Aftershocks cluster around the area of maximum coseismic slip, in particular in lateral and downdip direction. During the first 24 hr after the main shock, aftershocks migrated in both lateral directions with velocities of approximately 2.5 and 5 km hr−1. At the southern rupture boundary, aftershocks cluster around individual subducted seamounts that are related to the downthrusting Juan Fernández Ridge. In the northern part of the rupture area, aftershocks separate into an upper cluster (above 25 km depth) and a lower cluster (below 35 km depth). This dual seismic–aseismic transition in downdip direction is also observed in the interseismic period suggesting that it may represent a persistent feature for the Central Chilean subduction zone.
Reported Distribution of Aedes (Stegomyia) aegypti and Aedes (Stegomyia) albopictus in the United States, 1995-2016 (Diptera: Culicidae)
Authors: Hahn Micah B , Eisen Rebecca J , Eisen Lars , Boegler Karen A , Moore Chester G , McAllister Janet , Savage Harry M , Mutebi John-Paul
Published: June 2016

Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) transmit arboviruses that are increasing threats to human health in the Americas, particularly dengue, chikungunya, and Zika viruses. Epidemics of the associated arboviral diseases have been limited to South and Central America, Mexico, and the Caribbean in the Western Hemisphere, with only minor localized outbreaks in the United States. Nevertheless, accurate and up-to-date information for the geographical ranges of Ae. aegypti and Ae. albopictus in the United States is urgently needed to guide surveillance and enhance control capacity for these mosquitoes. We compiled county records for presence of Ae. aegypti and Ae. albopictus in the United States from 1995-2016, presented here in map format. Records were derived from the Centers for Disease Control and Prevention ArboNET database, VectorMap, the published literature, and a survey of mosquito control agencies, university researchers, and state and local health departments. Between January 1995 and March 2016, 183 counties from 26 states and the District of Columbia reported occurrence of Ae. aegypti, and 1,241 counties from 40 states and the District of Columbia reported occurrence of Ae. albopictus. During the same time period, Ae. aegypti was collected in 3 or more years from 94 counties from 14 states and the District of Columbia, and Ae. albopictus was collected during 3 or more years from 514 counties in 34 states and the District of Columbia. Our findings underscore the need for systematic surveillance of Ae. aegypti and Ae. albopictus in the United States and delineate areas with risk for the transmission of these introduced arboviruses.
Bevacizumab in high-grade glioma patients following intraparenchymal hemorrhage
Authors: Lin Xuling , Daras Mariza , Pentsova Elena , Nolan Craig P. , Gavrilovic Igor T. , DeAngelis Lisa M. , Kaley Thomas J.
Published: June 2016

Background

Intraparenchymal hemorrhage (IPH) is a relative contraindication to bevacizumab therapy, an anti-vascular endothelial growth factor (VEGF) monoclonal antibody approved for the treatment of recurrent glioblastoma. However, in patients with symptomatic enhancing tumors and poor functional status, bevacizumab may be the only beneficial therapeutic option.

Methods

We retrospectively reviewed all patients with high-grade glioma who were treated between January 1, 2005 and December 31, 2014 with bevacizumab despite prior IPH.

Results

Eighteen patients met our study criteria. There were 12 women and 6 men with a median age of 56 years. Tumor types were glioblastoma (n = 15), anaplastic astrocytoma (n = 2), and anaplastic oligodendroglioma (n = 1). Seventeen patients had prior spontaneous intratumoral bleed (13 grade 1–2; 4 grade 3–4); the 1 remaining patient had a grade 3 bleed due to cerebral venous thrombosis. Among them, identifiable risk factors for hemorrhage were anti-VEGF therapy, anticoagulation use, thrombocytopenia, and hypertension; seven had no identifiable risk factors. The median duration from IPH to (re-)initiation of bevacizumab was 113 days (range 13–1367). Brain imaging performed prior to bevacizumab treatment showed persistent or evolving hemorrhage in 8 patients and complete resolution in 10 patients. With a median follow-up duration of 137 days after bevacizumab re-initiation, only 1 (6%) of the 18 patients re-bled; this patient had an anaplastic oligodendroglioma and developed a grade 2 intratumoral bleed after 3 doses of bevacizumab.

Conclusions

The incidence of re-bleed is rare. Bevacizumab use was safe in patients with recurrent high-grade glioma following IPH for whom no other meaningful treatment options existed.
SPGGEN: a computer program for retrieval of space-group information in several settings and generator-containing space-group symbols
Authors: Shmueli Uri
Published: June 2016

A brief outline of the algorithm for the derivation of a space group is followed by a detailed description of the explicit space-group symbols here employed. These space-group symbols are unique insofar as they contain explicitly the generators of the space group dealt with. Next, the implementation of the above in a computer program,SPGGEN, is briefly discussed and the options presented by the program are outlined. Briefly, these options are (i) conventional derivation of the space group from an explicit symbol, including a user-defined one; (ii) such derivation from the conventional space-group number only; (iii) introduction of a general setting into the derivation; (iv) introduction of a Cartesian setting into the derivation; and (v) treatment of some non-conventional settings of orthorhombic space groups. This is followed by a detailed comparison withInternational Tables for Crystallography, Vol. A, and by examples of the output ofSPGGEN. A complete tabulation of the explicit three-dimensional space-group symbols is readily accessed.
Mixed convection squeezing three-dimensional flow in a rotating channel filled with nanofluid
Authors: Mahanthesh B , Gireesha B J , Gorla R S R
Published: June 2016

Purpose

– The purpose of this paper is to numerically solve the problem of an unsteady squeezing three-dimensional flow and heat transfer of a nanofluid in rotating vertical channel of stretching left plane. The fluid is assumed to be Newtonian, incompressible and electrically conducting embedded with nanoparticles. Effect of internal heat generation/ absorption is also considered in energy equation. Four different types of nanoparticles are considered, namely, copper (Cu), alumina (Al2O3), silver (Ag) and titanium oxide (TiO2) with the base fluid as water. Maxwell-Garnetts and Brinkman models are, respectively, employed to calculate the effective thermal conductivity and viscosity of the nanofluid.

Design/methodology/approach

– Using suitable similarity transformations, the governing partial differential equations are transformed into set of ordinary differential equations. Resultant equations have been solved numerically using Runge-Kutta-Fehlberg fourth fifth order method for different values of the governing parameters. Effects of pertinent parameters on normal, axial and tangential components of velocity and temperature distributions are presented through graphs and discussed in detail. Further, effects of nanoparticle volume fraction, squeezing parameter, suction/injection parameter and heat source/sink parameter on skin friction and local Nusselt number profiles for different nanoparticles are presented in tables and analyzed.

Findings

– Squeezing effect enhances the temperature field and consequently reduces the heat transfer rate. Large values of mixed convection parameter showed a significant effect on velocity components. Also, in many heat transfer applications, nanofluids are potentially useful because of their novel properties. They exhibit high-thermal conductivity compared to the base fluids. Further, squeezing and rotation effects are desirable in control the heat transfer.

Originality/value

– Three-dimensional mixed convection flows over in rotating vertical channel filled with nanofluid are very rare in the literature. Mixed convection squeezing three-dimensional flow in a rotating channel filled with nanofluid is first time investigated.
Effects of magnetic field and viscous dissipation on entropy generation of mixed convection in porous lid-driven cavity with corner heater
Authors: Ahmed Sameh E , Öztop Hakan F. , Al-Salem Khaled
Published: June 2016

Purpose

– The purpose of this paper is to investigate the effects of magnetic field and viscous dissipation on mixed convection heat transfer, fluid flow and entropy generation in a porous media filled square enclosure heated with corner isothermal heater.

Design/methodology/approach

– Finite volume method has been used to solve governing equations. A code is developed by FORTRAN and entropy generation is calculated from the obtained results of velocities and temperature. Results are presented via streamlines, isotherms, local and mean Nusselt number for different values of Richardson number (0.001=Ri=100), Hartmann number (0.001=Ha=100), Darcy number (0.001=Da=0.1), length of heaters (0.25=hx=hy=0.75) and viscous dissipation factors (10−4=ε=10−6).

Findings

– It is observed that entropy is generated mostly due to lid-driven wall and right side of the heater. Entropy generation decreases with increasing of Hartmann number and heat transfer increases with decreasing of viscous parameter.

Originality/value

– The originality of this work is to application of magnetic field and viscous dissipation on entropy generation in a lid-driven cavity with corner heater. Here, both corner heater and the external forces are original parameters.
Integrating unorganized volunteers in emergency response management
Authors: Skar Marit , Sydnes Maria , Sydnes Are Kristoffer
Published: June 2016

Purpose

– When emergencies occur, ordinary members of the public are often the first to respond. However, their use and integration in emergency response remain a challenge. The purpose of this paper is to explore mechanisms and strategies for integrating unorganized volunteers in emergency response.

Design/methodology/approach

– This is a qualitative case study. A series of anonymized, semi-structured interviews were conducted with representatives of the key emergency response organizations – the police, ambulance service, fire and rescue service, and the Red Cross, located in the city of Tromsø. In addition, regulatory documents used by these organizations were examined, including laws, contingency plans, procedural handbooks and checklists.

Findings

– Professional responders acknowledge the resource unorganized volunteers may represent when additional capacity is needed. However, being uncertain about their availability and competence, professional responders find it hard to integrate unorganized volunteers through formal mechanisms as contingency planning and exercises, but rather rely on informal and individual case-by-case considerations. The local Red Cross, who are part of the established response system, are developing procedures to integrate unorganized volunteers through training, exercises and response operations. This provides an innovative hybrid approach to volunteer management.

Originality/value

– Available research provides limited information and advice on how to integrate unorganized volunteers effectively in emergencies. This study provides insights in formal and informal mechanisms of integrating unorganized volunteers in emergency response. It also provides lessons from a case of volunteer management through the Red Cross.