bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibitor-induced oxidation of the nucleus and cytosol in
Arabidopsis thaliana:
implications for organelle to nucleus retrograde signalling
Authors: Karpinska Barbara , Alomrani Sarah Owdah , Foyer Christine H.
Published: August 2017

Concepts of organelle-to-nucleus signalling pathways are largely based on genetic screens involving inhibitors of chloroplast and mitochondrial functions such as norflurazon, lincomycin (LINC), antimycin A (ANT) and salicylhydroxamic acid. These inhibitors favour enhanced cellular oxidation, but their precise effects on the cellular redox state are unknown. Using the
in vivo
reduction–oxidation (redox) reporter, roGFP2, inhibitor-induced changes in the glutathione redox potentials of the nuclei and cytosol were measured in
Arabidopsis thaliana
root, epidermal and stomatal guard cells, together with the expression of nuclear-encoded chloroplast and mitochondrial marker genes. All the chloroplast and mitochondrial inhibitors increased the degree of oxidation in the nuclei and cytosol. However, inhibitor-induced oxidation was less marked in stomatal guard cells than in epidermal or root cells. Moreover, LINC and ANT caused a greater oxidation of guard cell nuclei than the cytosol. Chloroplast and mitochondrial inhibitors significantly decreased the abundance of
LHCA1
and
LHCB1
transcripts. The levels of
WHY1
,
WHY3
and
LEA5
transcripts were increased in the presence of inhibitors. Chloroplast inhibitors decreased
AOXA1
mRNA levels, while mitochondrial inhibitors had the opposite effect. Inhibitors that are used to characterize retrograde signalling pathways therefore have similar general effects on cellular redox state and gene expression.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Quantifying the efficiency of photoprotection
Authors: Ruban Alexander V.
Published: August 2017

A novel emerging technology for the assessment of the photoprotective ‘power’ of non-photochemical fluorescence quenching (NPQ) has been reviewed and its insightful outcomes are explained using several examples. The principles of the method are described in detail as well as the work undertaken for its justification. This pulse amplitude modulated chlorophyll fluorescence approach has been applied for the past 5 years to quantify the photoprotective effectiveness of the NPQ and the light tolerance in
Arabidopsis
plants grown under various light conditions, during ontogenetic development as well as in a range of mutants impaired in carotenoid and protein biosynthesis. The future applications of this approach for the assessment of crop plant light tolerance are outlined. The perspective of obtaining detailed information about how the extent of photoinhibition and photoprotection can affect plant development, growth and productivity is highlighted, including the potential for us to predict the influence of environmental elements on plant performance and yield of crops. The novel methodology can be used to build up comprehensive light tolerance databases for various current and emerging varieties of crops that are grown outdoors as well as in artificial light environments, in order to optimize for the best environmental conditions that enable high crop productivity.

This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395
Authors: Petitjean Marie , Martak Daniel , Silvant Alicia , Bertrand Xavier , Valot Benoit , Hocquet Didier
Published: August 2017

Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen with several clones being frequently associated with outbreaks in hospital settings. ST395 is among these so-called ‘international’ clones. We aimed here to define the biological features that could have helped the implantation and spread of the clone ST395 in hospital settings. The complete genome of a multidrug resistant index isolate (DHS01) of a large hospital outbreak was analysed. We identified DHS01-specific genetic elements, among which were identified those shared with a panel of six independent ST395 isolates responsible for outbreaks in other hospitals. DHS01 has the fifth largest chromosome of the species (7.1 Mbp), with most of its 1555 accessory genes borne by either genomic islands (GIs, n=48) or integrative and conjugative elements (ICEs, n=5). DHS01 is multidrug resistant mostly due to chromosomal mutations. It displayed signatures of adaptation to chronic infection in part due to the loss of a 131 kbp chromosomal fragment. Four GIs were specific to the clone ST395 and contained genes involved in metabolism (GI-4), in virulence (GI-6) and in resistance to copper (GI-7). GI-7 harboured an array of six copper transporters and was shared with non-pathogenic Pseudomonas sp. retrieved from copper-contaminated environments. Copper resistance was confirmed phenotypically in all other ST395 isolates and possibly accounted for the spreading capability of the clone in hospital outbreaks, where water networks have been incriminated. This suggests that genes transferred from copper-polluted environments may have favoured the implantation and spread of the international clone P. aeruginosa ST395 in hospital settings.
Somatic genome editing with the RCAS/TVA-CRISPR/Cas9 system for precision tumor modeling
Authors: Oldrini Barbara , Curiel-García Álvaro , Marques Carolina , Matia Veronica , Uluçkan Özge , Torres-Ruiz Raul , Rodriguez-Perales Sandra , Huse Jason T. , Squatrito Massimo
Published: August 2017

It has been gradually established that the vast majority of human tumors are extraordinarily heterogeneous at a genetic level. To accurately recapitulate this complexity, it is now evident that in vivo animal models of cancers will require to recreate not just a handful of simple genetic alterations, but possibly dozens and increasingly intricate. Here, we have combined the RCAS/TVA system with the CRISPR/Cas9 genome editing tools for precise modeling of human tumors. We show that somatic deletion in neural stem cells (NSCs) of a variety of known tumor suppressor genes (Trp53, Cdkn2a and Pten), in combination with the expression of an oncogene driver, leads to high-grade glioma formation. Moreover, by simultaneous delivery of pairs of guide RNAs (gRNAs) we generated different gene fusions, either by chromosomal deletion (Bcan-Ntrk1) or by chromosomal translocation (Myb-Qk), and we show that they have transforming potential in vitro and in vivo. Lastly, using homology-directed-repair (HDR), we also produced tumors carrying the Braf V600E mutation, frequently identified in a variety of subtypes of gliomas. In summary, we have developed an extremely powerful and versatile mouse model for in vivo somatic genome editing, that will elicit the generation of more accurate cancer models particularly appropriate for pre-clinical testing.
Global accumulation of circRNAs during aging inCaenorhabditis elegans
Authors: Cortés-López Mariela , Gruner Matthew , Cooper Daphne A. , Gruner Hannah N. , Voda Alexandru-Ioan , der Linden Alexander van , Miura Pedro
Published: August 2017

Circular RNAs (CircRNAs) are a newly appreciated class of RNAs that lack free 5´ and 3´ ends, are expressed by the thousands in diverse forms of life, and are mostly of enigmatic function. Ostensibly due to their resistance to exonucleases, circRNAs are known to be exceptionally stable. Here, we examined the global profile of circRNAs inC. elegansduring aging by performing ribo-depleted total RNA-seq from the fourth larval stage (L4) through 10-day old adults. Using stringent bioinformatic criteria and experimental validation, we annotated 1,166 circRNAs, including 575 newly discovered circRNAs. These circRNAs were derived from 797 genes with diverse functions, including genes involved in the determination of lifespan. A massive accumulation of circRNAs during aging was uncovered. Many hundreds of circRNAs were significantly increased among the aging time-points and increases of select circRNAs by over 40-fold during aging were quantified by qRT-PCR. The age-accumulation of circRNAs was not accompanied by increased expression of linear RNAs from the same host genes. We attribute the global scale of circRNA age-accumulation to the high composition of postmitotic cells in adultC. elegans, coupled with the high resistance of circRNAs to decay. These findings suggest that the exceptional stability of circRNAs might explain age-accumulation trends observed from neural tissues of other organisms, which also have a high composition of post-mitotic cells. Given the suitability ofC. elegansfor aging research, it is now poised as an excellent model system to determine if there are functional consequences of circRNA accumulation during aging.
A stable beneficial symbiotic relationship between endophytic fungusSchizophyllum communeand host plantPanax ginseng
Authors: Zhai Xin , Chen Ling , Jia Min , Li Changhui , Shen Hui , Ye Bingzhu , Qin Luping , Han Ting
Published: August 2017

Endophytes and plants can establish specific long-term symbiosis through the accumulation of secondary metabolites. Interactions between microbial inhabitants represent a novel area of study for natural products research. In this study, a strain of endophyte 3R-2 that can enhance the biomass and contents of ginsenoside Rc, ginsenoside Rg2 and ginsenoside Rg3 ofPanax ginsenghairy roots was screened out via HPLC, which was identified asSchizophyllum communethrough the morphological and molecular identification. On the base, we found the infection of the endophyte were obviously observed widely in theP. ginsengand the strain formed a stable relationship withP. ginsenghairy roots in parenchyma cells around through tissues embedding slicing, HE ammonium silver staining and immunofluorescence staining. On the other hand, elicitors of fungus 3R-2 can also significantly promote hairy root growth and contents of several ginsenosides, even several times higher than 3R-2 mycelium did. Moreover,S. commune3R-2 mycelium and its elicitor could enhance the transcriptional activity of key genes during the ginsenosides biosynthetic pathway dramatically. Thus, endophyteS. commune3R-2 and its elicitor change the chemical substance content by regulating the expression of genes involved in the secondary metabolite biosynthetic pathway.
HNRNPA1 promotes recognition of splice site decoys by U2AF2in vivo
Authors: Howard Jonathan M. , Lin Hai , Kim Garam , Draper Jolene M , Haeussler Maximilian , Katzman Sol , Toloue Masoud , Liu Yunlong , Sanford Jeremy R.
Published: August 2017

Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay oftrans-acting RNA binding proteins (RBPs) with myriadcis-regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on non-coding regions (introns). One of the earliest events in this process is recognition of the 3’ splice site by U2 small nuclear RNA auxiliary factor 2 (U2AF2). Splicing regulators, such as the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), influence spliceosome assembly bothin vitroandin vivo, but their mechanisms of action remain poorly described on a global scale. HNRNPA1 also promotes proof reading of 3’ss sequences though a direct interaction with the U2AF heterodimer. To determine how HNRNPA1 regulates U2AF-RNA interactions in vivo, we analyzed U2AF2 RNA binding specificity using individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) in control- and HNRNPA1 over-expression cells. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3’ splice sites of alternative cassette exons but not constitutive exons upon HNRNPA1 over-expression. A subset of these events shows a concomitant increase of U2AF2 crosslinking at distal intronic regions, suggesting a shift of U2AF2 to “decoy” binding sites. Of the many non-canonical U2AF2 binding sites, Alu-derived RNA sequences represented one of the most abundant classes of HNRNPA1-dependent decoys. Splicing reporter assays demonstrated that mutation of U2AF2 decoy sites inhibited HNRNPA1-dependent exon skippingin vivo. We propose that HNRNPA1 regulates exon definition by modulating the interaction of U2AF2 with decoy orbona fide3’ splice sites.
A bestiary of localized sequence rearrangements in human DNA
Authors: Frith Martin C. , Khan Sofia
Published: August 2017

Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing methods (e.g. PacBio, nanopore) are promising for this task, because one read may encompass a whole complex mutation. We describe an analysis pipeline to characterize arbitrarily-complex “local” mutations, i.e. intrachromosomal mutations encompassed by one DNA read. We apply it to nanopore and PacBio reads from one human cell line (NA12878), and survey sequence rearrangements, both real and artifactual. Almost all the real rearrangements belong to recurring patterns or motifs: the most common is tandem multiplication (e.g. heptuplication), but there are also complex patterns such as localized shattering, which resembles DNA damage by radiation. Gene conversions are identified, including one between hemoglobin gamma genes. This study demonstrates a way to find intricate rearrangements with any number of duplications, deletions, and repositionings. It demonstrates a probability-based method to resolve ambiguous rearrangements involving highly similar sequences, as occurs in gene conversion. We present a catalog of local rearrangements in one human cell line, and show which rearrangement patterns occur.
Nanopore sequencing enables near-completede novoassembly ofSaccharomyces cerevisiaereference strain CEN.PK113-7D
Authors: Salazar Alex N. , Gorter de Vries Arthur R. , van den Broek Marcel , Wijsman Melanie , de la Torre Cortés Pilar , Brickwedde Anja , Brouwers Nick , Daran Jean-Marc G. , Abeel Thomas
Published: August 2017

The haploidSaccharomyces cerevisiaestrain CEN.PK113-7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and the assumption of perfect homology to S288C for scaffolding introduces bias.

In this study, we obtained a near-complete genome assembly of CEN.PK113-7D using only Oxford Nanopore Technology’s MinION sequencing platform. 15 of the 16 chromosomes, the mitochondrial genome, and the 2-micron plasmid are assembled in single contigs and all but one chromosome starts or ends in a telomere cap. This improved genome assembly contains 770 Kbp of added sequence containing 248 gene annotations in comparison to the previous assembly of CEN.PK113-7D. Many of these genes encode functions determining fitness in specific growth conditions and are therefore highly relevant for various industrial applications. Furthermore, we discovered a translocation between chromosomes III and VIII which caused misidentification of aMALlocus in the previous CEN.PK113-7D assembly. This study demonstrates the power of long-read sequencing by providing a high-quality reference assembly and annotation of CEN.PK113-7D and places a caveat on assumed genome stability of microorganisms.
A genomics approach reveals the global genetic polymorphism, structure and functional diversity of ten accessions of the marine model diatomPhaeodactylum tricornutum
Authors: Rastogi Achal , Vieira FRJ , Deton-Cabanillas Anne-Flore , Veluchamy Alaguraj , Cantrel Catherine , Wang Gaohong , Vanormelingen Pieter , Bowler Chris , Piganeau Gwenael , Hu Hanhua , Tirichine Leila
Published: August 2017

Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world’s ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatomPhaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal ofP. tricornutumin the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
Beer produced via hydrodynamic cavitation retains higher amounts of xanthohumol and other hops prenylflavonoids
Authors: Ciriminna Rosaria , Albanese Lorenzo , Stefano Vita Di , Delisi Riccardo , Avellone Giuseppe , Meneguzzo Francesco , Pagliaro Mario
Published: August 2017

A fraction of the most valuable bioactive compounds in beer comes from hop’s polyphenols, mainly flavonoids, some of which are unique to inflorescences of that flowering plant. Although far from pharmacologically relevant concentrations, the intake of low doses of xanthohumol and related prenylflavonoids found in beer contributes to significant preventive actions with regards to certain diseases, such as cardiovascular and neurodegenerative, as well as to distinct chemopreventive effects on certain cancer types. Hence the efforts to explore both ingredients and methods able to enhance the concentration of such bioactive compounds in the final beers. A novel brewing method assisted by hydrodynamic cavitation was proved able, under suitable process conditions, to retain or generate higher amounts of xanthohumol, desmethylxanthohumol and 6-geranylnaringenin, extending recent evidence about different food and respective bioproducts, as well as adding to its distinct benefits to the brewing process.
N-terminal sumoylation of centromeric histone H3 variant Cse4 regulates its proteolysis to prevent mislocalization to non-centromeric chromatin
Authors: Ohkuni Kentaro , Levy-Myers Reuben , Warren Jack , Au Wei-Chun , Takahashi Yoshimitsu , Baker Richard E. , Basrai Munira A.
Published: August 2017

Stringent regulation of cellular levels of evolutionarily conserved centromeric histone H3 variant (CENP-A in humans, CID in flies, Cse4 in yeast) prevents its mislocalization to non-centromeric chromatin. Overexpression and mislocalization of CENP-A has been observed in cancers and leads to aneuploidy in yeast, flies, and human cells. Ubiquitin-mediated proteolysis of Cse4 by E3 ligases such as Psh1 and Sumo-Targeted Ubiquitin Ligase (STUbL) Slx5 prevent mislocalization of Cse4. Previously, we identified Siz1 and Siz2 as the major E3 ligases for sumoylation of Cse4. In this study, we identify lysine 65 (K65) in Cse4 as a SUMO site and show that sumoylation of Cse4 K65 regulates its ubiquitin-mediated proteolysis by Slx5. Strains expressingcse4 K65Rexhibit reduced levels of sumoylated and ubiquitinated Cse4in vivo. Furthermore, co-immunoprecipitation experiments reveal reduced interaction of cse4 K65R with Slx5. Defects in sumoylation of cse4 K65R contribute to increased stability and mislocalization of cse4 K65R under normal physiological conditions. Based on the increased stability of cse4 K65R inpsh1∆strains but not inslx5∆strains, we conclude that Slx5 targets sumoylated Cse4 K65 for ubiquitination-mediated proteolysis independent of Psh1. In summary, we have identified and characterized the physiological role of Cse4 sumoylation and determined that sumoylation of Cse4 K65 regulates ubiquitin-mediated proteolysis and prevents mislocalization of Cse4 which is required for genome stability.
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
Authors: MacGilvray Matthew E. , Shishkova Evgenia , Chasman Deborah , Place Michael , Gitter Anthony , Coon Joshua J. , Gasch Audrey P.
Published: August 2017

Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized inSaccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. The method uses integer linear programming (ILP) to integrate stress-responsive phospho-proteome responses in wild-type and mutant strains, predicted phosphorylation motifs on groups of coregulated peptides, and published protein interaction data. A key advance is that by grouping peptides into submodules before inference, the method can overcome missing protein interactions in published datasets to predict novel, stress-dependent protein interactions and phosphorylation events. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress.
Deciphering Functional Redundancy in the Human Microbiome
Authors: Tian Liang , Wang Xu-Wen , Wu Ang-Kun , Fan Yuhang , Friedman Jonathan , Dahlin Amber , Waldor Matthew K. , Weinstock George M. , Weiss Scott T. , Liu Yang-Yu
Published: August 2017

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved1-5---implying an ecological property known asfunctional redundancy. Such functional redundancy is thought to underlie the stability and resilience of the human microbiome6,7, but its origin is elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network --- a bipartite graph that links microbes to the genes in their genomes. We show that this network exhibits several topological features, such as highly nested structure and fat-tailed gene degree distribution, which favor high functional redundancy. To explain the origins of these topological features, we develop a simple genome evolution model that explicitly considers selection pressure, and the processes of gene gain and loss, and horizontal gene transfer. We find that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with both highly nested structure and fat-tailed gene degree distribution, and consequently favor high functional redundancy. These findings provide insights into the relationships between structure and function in complex microbial communities. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.
Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types
Authors: Gong Jingqi QX , Sobie Eric A
Published: August 2017

Quantitative mismatches between human physiology and experimental models can present serious limitations for the development of effective therapeutics. We addressed this issue, in the context of cardiac electrophysiology, through mechanistic mathematical modeling combined with statistical analyses. Physiological metrics were simulated in heterogeneous populations describing cardiac myocytes from adult ventricles and those derived from induced pluripotent stem cells (iPSC-CMs). These simulated measures were used to construct a cross-cell type regression model that predicts adult myocyte drug responses from iPSC-CM behaviors. We found that quantitatively accurate predictions of responses to selective or non-selective drugs could be generated based on iPSC-CM responses and that the method can be extended to predict drug responses in diseased as well as healthy cells. This cross-cell type model can be of great value in drug development, and the approach, which can be applied to other fields, represents an important strategy for overcoming experimental model limitations.
Dlic1deletion impaired cerebellar development in mouse
Authors: Kong Shanshan , Tao Wufan
Published: August 2017

The cerebellum is an important model system to study Central Nervous System, it has a striking morphology consisting of folia separated by fissures of different lengths, and the molecules controlling the process of cerebellar development have been unclear. In this study, we report an unrecognized contribution ofDlic1to the postnatal development of murine cerebellum.Dlic1encodes a light intermediate chain of cytoplasmic dynein 1, it is a subunit unique to the cytoplasmic form of dynein, and how it contributes to dynein function is not fully understood. Our data show thatDlic1deletion leads to impaired cerebellar development, foliation and fissuration, the volume of the cerebellum was evidently reduced. Consistent with the histological defects,Dlic1knockout mice show defective motor coordination, this strongly indicates the fundamental role ofDlic1in cerebellar development and function. Purkinje cells are located within the cerebellum and form synapses with granule cells. InDlic1-/-mice, Purkinje cells display reduced dendritic complexity and the distribution of dynein in Purkinje cell layer is changed. We also found thatDlic1deletion reduced the protein levels of dynein subunits and leads to the defective assembling of dynein subunits. These data indicate thatDlic1may affect cerebellar development through affecting the normal function of dynein.

Abbreviations

Dlic1

cytoplasmic dynein 1 light intermediate chain

CNS

central nervous system

MEF

mouse embryo fibroblast
The wavevector substar group in reciprocal space and its representation
Authors: Kim Il Hwan , Pak Jong Ok , Kim Il Hun , Kim Song Won , Li Lin
Published: August 2017

A new concept of the wavevector substar group is established which, in the study of translational symmetry breaking of a crystal, only considers the particular arms of the wavevector star taking part in the phase transition; this is in contrast with the traditional Landau theory which considers all of the arms of the wavevector star. It is shown that this new concept can be used effectively to investigate the interesting physical properties of crystals associated with translational symmetry breaking. It is shown that studies on complicated phase transitions related to reducible representations, such as those in perovskite KMnF3multiferroics and the high-temperature superconductor La2/3Mg1/2W1/2O3(La4Mg3W3O18), are much simplified by the new concept. The theory of the wavevector substar group and its representation is a powerful mathematical tool for the study of various symmetry-breaking phenomena in solid-state crystals.
Close-packed structure dynamics with finite-range interaction: computational mechanics with individual layer interaction
Authors: Rodriguez-Horta Edwin , Estevez-Rams Ernesto , Lora-Serrano Raimundo , Neder Reinhard
Published: August 2017

This is the second contribution in a series of papers dealing with dynamical models in equilibrium theories of polytypism. A Hamiltonian introduced by Ahmad & Khan [Phys. Status Solidi B(2000),218, 425–430] avoids the unphysical assignment of interaction terms to fictitious entities given by spins in the Hägg coding of the stacking arrangement. In this paper an analysis of polytype generation and disorder in close-packed structures is made for such a Hamiltonian. Results are compared with a previous analysis using the Ising model. Computational mechanics is the framework under which the analysis is performed. The competing effects of disorder and structure, as given by entropy density and excess entropy, respectively, are discussed. It is argued that the Ahmad & Khan model is simpler and predicts a larger set of polytypes than previous treatments.
Protein structure determination by electron diffraction using a single three-dimensional nanocrystal
Authors: Clabbers M. T. B. , van Genderen E. , Wan W. , Wiegers E. L. , Gruene T. , Abrahams J. P.
Published: August 2017

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3,i.e.no more than 6 × 105unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.
4-{(E)-[(2-Hydroxynaphthalen-1-yl)methylidene]amino}-1,5-dimethyl-2-phenyl-2,3-dihydro-1H-pyrazol-3-one: a new polymorph (β-phase)
Authors: Mohamed Shaaban K. , Mague Joel T. , Akkurt Mehmet , Albayati Mustafa R. , Mohamed Alaa F.
Published: August 2017

The title molecule, C22H19N3O2, is a new polymorphic modification,viz.the β-phase; the α-phase has been previously published [Liang & Wang (2010).Acta Cryst. E66, o1968–o1969]. In the crystal of the β-phase, the molecules pack in helical chains generated by C—H...O hydrogen bonds and offset π–π-stacking interactions. Adjacent chains are associated through C—H...π interactions. In the α-phase, molecules are linked by C—H...O and N—H...O hydrogen bonds, forming layers parallel to the (10-2) plane. In addition, π–π-stacking interactions and C—H...π(ring) interactions consolidate the packing. The packing is compared to that of the α-phase. The title compound was refined as a two-component twin.
Rebel with a cause
Authors: Wong Wilson , Chu May
Published: August 2017

Purpose

The purpose of this paper is to examine the cause and nature of the 2014 Umbrella Movement in Hong Kong and the role of the youth in the movement.

Design/methodology/approach

This paper analyzes the relationship between the serious social and economic problems in Hong Kong, of which the youth often feel the greatest impact, and the demands for a real democratic system made by the Umbrella Movement. It examines the structural roots of the Movement and the role of youths in it.

Findings

The Umbrella Movement is not simply a movement of anger and frustration, but also a movement reflecting some of the serious and legitimate concerns of the people of Hong Kong, especially the youth, who have a high and growing sense of local identity and citizenship. The movement links the major policy and social problems of the post-Handover era to its root cause, which is an undemocratic political system combined with crony capitalism. Unfortunately, the approach taken by the government toward the Movement has been to emphasize its illegal nature and to attempt to divide the opposition by adopting “united front” strategies that pay no serious attention to the problems the Movement has raised. Eventually, this approach will only lead to an outcome of “strong government, weak society” where strong government action in opposition to reformers will weaken the cohesion of society and expose the actual weakness of the state that has no popular legitimacy, going on to create more chaos as a result of its weak governance.

Originality/value

This paper will help both scholars and policymakers to understand the structural and root causes of the Umbrella Movement in Hong Kong and explain why Hong Kong is suffering from a serious problem of weak governance.
Dynamic interactions between sustainability and competitiveness in construction firms
Authors: Chang Rui-Dong , Zuo Jian , Soebarto Veronica , Zhao Zhen-Yu , Zillante George
Published: August 2017

Purpose

Sustainability and competitiveness have received extensive attentions. Despite a large number of studies on sustainability and competitiveness in the construction industry, little research has been conducted to holistically explore the interactions between these two concepts. From a dynamic transition perspective, the purpose of this paper is to link sustainability and competitiveness of construction firms by developing a Sustainability-Competitiveness Dynamic Interaction Framework (SCDIF).

Design/methodology/approach

Conceptual theory-building approach was adopted to develop the conceptual framework. It is an iterative analysis and synthesis process, which involves reading literature, identifying commonalities and differences, synthesizing, proposing an initial framework, collecting additional literature, and revisiting and revising the framework.

Findings

There are complex interactions between sustainability and competitiveness of construction firms. This leads to uncertain relationships between sustainability and competitiveness, which is context dependent. Under evolving economic and socio-political environments, sustainability and competitiveness of construction firms could transition from mutually exclusive to mutually supportive, and finally merge into “sustainable competitiveness.”

Research limitations/implications

A SCDIF proposed in this study demonstrates that the interactions between sustainability and competitiveness evolves according to the evolving economic and socio-political environments and firms’ strategies, and thus the relationships and interactions between sustainability and competitiveness are context dependent. This framework helps corporate managers to understand how corporate sustainability and competitiveness interact with each other, thereby informing their decision-making of sustainability strategy. Similarly, the framework provides useful references for policymakers to understand the mechanisms of transitioning industries toward sustainable competitiveness.

Originality/value

The proposed framework offers a new perspective for understanding sustainability and competitiveness. From the dynamic transition perspective, this study effectively illustrates that the interactions between sustainability and competitiveness evolves according to the evolving economic and socio-political environments and firms’ strategies. Compared to existing approaches, the dynamic and holistic approach proposed in this paper provides the capacity to capture the complexity of sustainability and competitiveness.
Stakeholder competency in evaluating the environmental impacts of infrastructure projects using BIM
Authors: Murphy Martina Elizabeth , Nahod Maja-Marija
Published: August 2017

Purpose

Building information modelling (BIM) literature reveals a growing interest in the development of a competency-based approach to manage the long-term goals of BIM implementation in infrastructure projects. One long-term goal is mitigation of environmental impacts (EIs). It is proposed that by integrating environmental systems within the BIM model, the technology can act as an early warning indicator to assist stakeholders identify and evaluate EIs before they become critical to delivery. The purpose of this paper is to assess the effectiveness of BIM in identifying EIs on infrastructure projects and investigate the correlation between stakeholder competency and evaluation of EIs.

Design/methodology/approach

In all, 71 informants that have relevant experience in infrastructure projects were investigated using a two-stage methodology comprising a questionnaire to determine the BIM indicators used to identify EIs and the stakeholder competencies required to assess and evaluate EIs and Behavioural Event Interviews (BEIs) to validate the competencies identified.

Findings

The findings showed that risk assessments are the most critical early warning indicator in identifying EIs specifically when implemented within the cost management process. The key stakeholder competencies required to successfully evaluate EIs were identified as project organisation and building equitable relationships. BEIs showed these stakeholders to also have high levels of behavioural and contextual awareness. This suggests that, contrary to perceived perception, successful management of EIs is more dependent on collaborative working than the acquisition of technical skills. Findings also indicated that Croatian BIM stakeholders are less experienced than UK BIM stakeholders in project implementation and delivery and that less experienced BIM stakeholders require more emphasis on technical knowledge whilst the importance of “soft skills” is more apparent in experienced stakeholders, notably amongst the UK participants.

Originality/value

The implications for infrastructure projects show that effective management of EIs can be achieved through alignment of the BIM model with the cost management plan implemented by stakeholders working collaboratively. Hence, the strategic focus for AEC companies working on infrastructure projects should be the development of staff interpersonal competencies rather than solely on project goals and/or an over-emphasis on technical skills.
Managing the expectations of external stakeholders in construction projects
Authors: Chan Albert P.C. , Oppong Goodenough D.
Published: August 2017

Purpose

The consideration of external stakeholders has proven to be more critical than internal stakeholders in construction projects. The purpose of this paper is to present the diverse expectations of external stakeholder groups, i.e. governmental authorities, general public, and affected local communities, in construction projects. The practical steps to manage the expectations are also outlined.

Design/methodology/approach

A three-stage methodology was adopted for the review. The primary terms “stakeholder,” “project participants,” or “project environment” were first searched in four popularly search engines and eight top journals that publish construction research to retrieve publications. After a second-stage filtering process, the selected data were then analyzed and reviewed in line with the objectives.

Findings

In total, 49 common expectations were identified and classified. The results indicate that each stakeholder group pursues expectations in line with the social, environmental, and economic sustainability objectives. For effective management, project managers (PMs) must know stakeholder opportunities and threats, fulfill social responsibilities, establish common goals, apply appropriate strategies, and enhance stakeholder satisfaction.

Research limitations/implications

The identified expectations are only based on the selected publications. Even though the expectations have been categorized in line with the triple bottom line model, the relative importance of the expectations cannot be ascertained since there is no empirical support.

Practical implications

PMs can play safe by acknowledging the stakeholder expectations and employ such strategies to curtail resulting impacts and maximize mutual benefits. The list of expectations could also be used to promote equitable value optimization in projects, enhance needs fulfillment, and facilitate the evaluation of external stakeholder satisfaction.

Originality/value

This study provides a comprehensive checklist of construction stakeholder expectations which hitherto, is lacked in the literature. Moreover, practical steps to manage the expectations of external stakeholders have been discussed.
Disruption causes and disruption management in supply chains with Chinese suppliers
Authors: Durach Christian F. , Glasen Patrick C. , Straube Frank
Published: August 2017

Purpose

The purpose of this paper is to identify and rank supply chain disruption causes for Western buying firms in the Chinese market; to identify supplier-relationship-specific mitigation strategies to avoid and resist such disruptions; and to develop and propose a framework of relational supply chain disruption management with Chinese suppliers.

Design/methodology/approach

Two group exercises with 42 representatives from Western manufacturing buying firms and nine in-depth interviews were conducted. The group exercises applied the nominal group technique.

Findings

The authors identified and ranked 22 disruption causes in China for Western buying firms. Evaluating the five most urgent causes, 43 mitigation strategies could be identified that build on implementing strategic relationships with Chinese suppliers. A framework of relational supply chain disruption management for Western buying firms was developed with six propositions on primary constructs, mediators, and moderators, highlighting guanxi as a fundamental construct of relations within the Chinese culture.

Research limitations/implications

The findings contribute to theory development at the intersection of risk management and culture. Quantitative testing of the proposed relationships in the framework is needed to derive more reliable conclusions.

Practical implications

The study depicts how cultural differences between Chinese suppliers and Western buyers influence relational supply chain disruption management strategies. Using the study findings, managers of Western buying firms are informed regarding the most pressing disruption causes in the Chinese market and the value and strategic use of Chinese-supplier relationships.

Originality/value

The study provides a valuable contribution to the scant body of literature on disruption management in supply chains with Chinese suppliers. It contributes to our understanding of a successful risk management in the presence of cultural differences.
Developing SCM framework associated with IT-enabled SC network capabilities
Authors: Chen Shyh-Shiuh , Ou-Yang Chao , Chou Tzu-Chuan
Published: August 2017

Purpose

The purpose of this paper is to conceptualize how information technology (IT) enables supply chain (SC) network capabilities, which is to capitalize on SC’s existing set of resources and, at the same time, manage new combinations of SC resources to meet future market needs. The paper also develops SCM framework associated with IT-enabled SC network capabilities.

Design/methodology/approach

Through a case study of a leading Taiwanese petrochemical corporation, qualitative data were gathered on the IT-related SC management practices, in terms of network resource mobilizing and adaptive co-management arrangements to enable SC network capability. This research is based primarily on the interviews of the case company, supplemented by archived documents, published books, and in-depth observations.

Findings

Based on the evidence from the case, this study inductively develops a model that includes the operating processes with IT-enabled activities to achieve ambidextrous SC network capability, and the relevant framework functions in network resources and co-management activities include information co-governance, information interoperability, community engagement strategy, cyber-physical dexterity, and control enactment, which lead the SC alliances improvements for dynamic environmental changes.

Practical implications

Practitioners may derive strategies and tactics from the current findings to help them implement innovative information technologies and setup SC framework, during SC network capability development, to achieve SC’s sustainable competence in a dynamic market.

Originality/value

Researchers and practitioners may obtain a more complete view of IT-enabled SC network capability development. The proposed model reveals that developing IT-enabled SC network capabilities is a dynamic process whereby an organization’s major SC managerial activities are divided into specific network resource mobilizing and adaptive co-management arrangements.
Dependence, trust, and 3PL integration: an empirical study in China
Authors: Huo Baofeng , Liu Chen , Chen Haozhe , Zhao Xiande
Published: August 2017

Purpose

The purpose of this paper is to investigate relationships among dependence, trust, and integration in the Chinese 3PL context. 3PL integration is manifested in two key dimensions: information sharing and process coordination.

Design/methodology/approach

This study develops a dependence-trust-3PL integration-performance model and tests it using structural equation modeling with survey data collected from 361 companies in the Greater China area (i.e. mainland China, Hong Kong, and Taiwan).

Findings

The results show that switch dependence is indirectly related to information sharing and process coordination through goodwill trust, while goal dependence has direct links with both integrative behaviors. The authors also found that only goodwill trust mediates the relationship between dependence and integrative behaviors, while ability trust does not mediate any relationships. Finally, the analysis validated the direct link between process coordination and financial performance, but did not find a significant link between information sharing and financial performance.

Originality/value

Different from most previous studies on similar topics, this study examines the impacts of different types of dependence and trust on different 3PL integration dimensions. As a result, the findings are more specific and have direct relevance to effective 3PL relationship management in China.