bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein structure determination using Riemannian approach
Authors: Wei Xian , Li Zhicheng , Li Shijian , Peng Xubiao , Zhao Qing
Published: April 2019

The protein nuclear magnetic resonance (NMR) structure determination is one of the most extensively studied problems due to its increasing importance in biological function analysis. We adopt a novel method, based on one of the matrix completion (MC) techniques–the Riemannian approach, to solve the protein structure determination problem. We formulate the protein structure in terms of low-rank matrix which can be solved by an optimization problem in the Riemannian spectrahedron manifold whose objective function has been delimited with the derived boundary condition. Two efficient algorithms in Riemannian approach-the trust-region (Tr) algorithm and the conjugate gradient (Cg) algorithm are used to reconstruct protein structures. We first use the two algorithms in a toy model and show that the Tr algorithm is more robust. Afterwards, we rebuild the protein structure from the NOE distance information deposited in NMR Restraints Grid (http://restraintsgrid.bmrb.wisc.edu/NRG/MRGridServlet). A dataset with both X-ray crystallographic structure and NMR structure deposited in Protein Data Bank (PDB) is used to statistically evaluate the performance of our method. By comparing both our rebuilt structures and NMR counterparts with the “standard” X-ray structures, we conclude that our rebuilt structures have similar (sometimes even smaller) RMSDs relative to “standard” X-ray structures in contrast with the reference NMR structures. Besides, we also validate our method by comparing the Z-scores between our rebuilt structures with reference structures using Protein Structure Validation Software suit. All the validation scores indicate that the Riemannian approach in MC techniques is valid in reconstructing the protein structures from NOE distance information. The software based on Riemannian approach is freely available athttps://github.com/xubiaopeng/Protein_Recon_MCRiemman.

Author summary

Matrix Completion is a technique widely used in many aspects, such as the global positioning in sensor networks, collaborative filtering in recommendation system for many companies and face recognition, etc. In biology, distance geometry used to be a popular method for reconstructing protein structures related to NMR experiment. However, due to the low quality of the reconstructed results, those methods were replaced by other dynamic methods such as ARIA, CYANA and UNIO. Recently, a new MC technique named Riemannian approach is introduced and proved mathematically, which promotes us to apply it in protein structure determination from NMR measurements. In this paper, by combining the Riemannian approach and some post-processing procedures together, we reconstruct the protein structures from the incomplete distance information measured by NMR. By evaluating our results and comparing with the corresponding PDB NMR deposits, we show that the current Riemannian approach method is valid and at least comparable with (if not better than) the state-of-art methods in NMR structure determination.
Second messengers and divergent HD-GYP enzymes regulate 3’,3’-cGAMP signaling
Authors: Wright Todd A. , Jiang Lucy , Park James J. , Anderson Wyatt A. , Chen Ge , Hallberg Zachary F. , Nan Beiyan , Hammond Ming C.
Published: April 2019

3’,3’-cyclic GMP-AMP (cGAMP) is the third cyclic dinucleotide (CDN) to be discovered in bacteria. No activators of cGAMP signaling have yet been identified, and the signaling pathways for cGAMP have appeared narrowly distributed based upon the characterized synthases, DncV and Hypr GGDEFs. Here we report that the ubiquitous second messenger cyclic AMP (cAMP) is an activator of the Hypr GGDEF enzyme GacB from Myxococcus xanthus. Furthermore, we show that GacB is inhibited directly by cyclic di-GMP, which provides evidence for cross-regulation between different CDN pathways. Finally, we reveal that the HD-GYP enzyme PmxA is a cGAMP-specific phosphodiesterase (GAP) that promotes resistance to osmotic stress in M. xanthus. A signature amino acid change in PmxA was found to reprogram substrate specificity and was applied to predict the presence of non-canonical HD-GYP phosphodiesterases in many bacterial species, including phyla previously not known to utilize cGAMP signaling.
OscoNet: Inferring oscillatory gene networks
Authors: Boukouvalas Alexis , Cutillo Luisa , Marinopoulou Elli , Papalopulu Nancy , Rattray Magnus
Published: April 2019

Motivation

Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cycle, only a few such genes are known. Detecting oscillatory genes from snapshot single-cell experiments is a challenging task due to the lack of time information. Oscope is a recently proposed method to identify co-oscillatory gene pairs using single-cell RNA-seq data. Although promising, the current implementation of Oscope does not provide a principled statistical criterion for selecting oscillatory genes.

Results

We improve the optimisation scheme underlying Oscope and provide a well-calibrated non-parametric hypothesis test to select oscillatory genes at a given FDR threshold. We evaluate performance on synthetic data and three real datasets and show that our approach is more sensitive than the original Oscope formulation, discovering larger sets of known oscillators while-avoiding the need for less interpretable thresholds. We also describe how our proposed pseudo-time estimation method is more accurate in recovering the true cell order for each gene cluster while-requiring substantially less computation time than the extended nearest insertion approach.

Conclusion

OscoNet is a robust and versatile approach to detect oscillatory gene networks from snapshot single-cell data addressing many of the limitations of the original Oscope method.
Measuring shared responses across subjects using intersubject correlation
Authors: Nastase Samuel A. , Gazzola Valeria , Hasson Uri , Keysers Christian
Published: April 2019

Our capacity to jointly represent information about the world underpins our social experience. By leveraging one individual’s brain activity to model another’s, we can measure shared information across brains—even in dynamic, naturalistic scenarios where an explicit response model may be unobtainable. Introducing experimental manipulations allows us to measure, for example, shared responses between speakers and listeners, or between perception and recall. In this tutorial, we develop the logic of intersubject correlation (ISC) analysis and discuss the family of neuroscientific questions that stem from this approach. We also extend this logic to spatially distributed response patterns and functional network estimation. We provide a thorough and accessible treatment of methodological considerations specific to ISC analysis, and outline best practices.
Goal congruency dominates reward value in accounting for behavioral and neural correlates of value-based decision-making
Authors: Frömer Romy , Dean Wolf Carolyn K. , Shenhav Amitai
Published: April 2019

How we engage with a set of options (e.g., items on a menu) is affected both by the rewards they promise and our goal in choosing between them. Typically, our goal is to maximize potential reward and minimize potential punishment. Previous research on value-based decision-making has characterized how people make decisions with this goal in mind, identifying consistent behavioral and neural signatures associated with how rewarding a set of choice options are, overall and relative to one another. However, these studies suffer from a common confound: in each case, more rewarding options were also more congruent with one’s goal of choosing the best option. Previous findings can therefore be accounted for by thereward valueor thegoal congruencyof one’s options. To compare these accounts directly, we had participants make choices while their goal varied between choosing the best or the worst option, resulting in situations where either high-reward or low-reward options were most goal-congruent. We found that goal congruency uniquely accounts for past observations that decision speed varies with the overall value of one’s options. Within brain regions commonly associated with choice value, fMRI activity was associated with both relative and overall goal congruency. These goal congruency correlates were dissociable from separate correlates of the overall reward associated with a choice set (independent of one’s goal). Our findings call for a reinterpretation of previous research on value-based choice, and offer an approach moving forward for disentangling the roles of rewards and goals in how we evaluate our options.

Significance Statement

Whether it is between restaurants or career paths, to make adaptive decisions we must evaluate our options and identify those that are most conducive to our current goal. Dysfunctional decision-making can therefore result from aberrant reward processing (e.g., impulse disorders) or from aberrant goal processing (e.g., OCD, ADHD). By focusing only on how people choose theirfavoriteoption in a choice set (when rewards and goals are aligned), past research has been unable to distinguish the degree to which behavior and neural activity are determined by reward versus goal processing. We disentangle these processes and show that behavior and fMRI activity are differentially influenced by the promised rewards versus the degree to which those rewards align with one’s current goal.
Transcriptional analysis defines TCR and cytokine-stimulated MAIT cells as rapid polyfunctional effector T cells that can coordinate the immune response
Authors: Lamichhane Rajesh , Schneider Marion , de la Harpe Sara M. , Harrop Thomas W. R. , Hannaway Rachel F. , Dearden Peter , Kirman Joanna R. , Tyndall Joel D. A. , Vernall Andrea J. , Ussher James E.
Published: April 2019

MAIT cells are an abundant innate-like T cell population which can be activated via either their T cell receptor (TCR), which recognizes MR1-bound pyrimidine antigens derived from microbial riboflavin biosynthesis, or via cytokines, such as IL-12 and IL-18. In vivo, these two modes of activation may act in concert or independently depending upon the nature of the microbial or inflammatory stimuli. It is unknown, however, how the MAIT cell response differs to the different modes of activation. Here, we define the transcriptional and effector responses of human MAIT cells to TCR and cytokine stimulation. We report that MAIT cells rapidly respond to TCR stimulation through the production of multiple effector cytokines and chemokines, alteration of their cytotoxic granule content and transcription factor expression, and upregulation of co-stimulatory proteins CD40L and 4-1BB. In contrast, cytokine-mediated activation is slower and results in more limited production of cytokines, chemokines, and co-stimulatory proteins; differences in granule content and transcription factor expression are also evident. Therefore, we propose that in infections by riboflavin-synthesizing bacteria, MAIT cells play a key early role in effecting and coordinating the immune response, while in the absence of TCR stimulation (e.g. viral infection) their role is likely to differ.
Optimization and validation of a quadruplex real-time PCR assay for the diagnosis of diphtheria
Authors: Badell Edgar , Guillot Sophie , Tulliez Marie , Pascal Marine , Panunzi Leonardo-Gabriel , Rose Samuel , Litt David , Fry Norman K. , Brisse Sylvain
Published: April 2019

Diphtheria is caused by toxigenic strains ofCorynebacterium diphtheriae, Corynebacterium ulceransandCorynebacterium pseudotuberculosis. For diagnostic purposes, species identification and detection of toxigenic strains (diphtheria toxin (tox)-positive strains) is typically performed using end-point PCR. A faster quadruplex real-time PCR (qPCR) was recently developed (De Zoysaet al. J Med Microbiol. 2016 65(12):1521-1527). Here, we present an improvement of the quadruplex method, in which a 16S rRNA gene target was added as an internal processing control, providing confirmation of the presence of bacterial DNA in the assays. This improved qPCR method was validated using 36 bacterial isolates and 16 clinical samples. The method allows detection of thetoxgene and distinguishingC. diphtheriae(including the newly described speciesC. belfantii) fromC. ulceransandC. pseudotuberculosis. Complete diagnostic specificity, sensitivity and experimental robustness of the method to temperature and reagent concentration variations were demonstrated. The lower limit of detection forC. diphtheriae, C. ulceransandtoxtargets was 1.86 genome copies per 5 μL reaction volume. Finally, the method was successfully used on two distinct qPCR technologies (LightCycler 480, Roche Diagnostics and Rotor-Gene Q, Qiagen) and in two laboratories (Institut Pasteur, Paris, France and Public Health England – National Infection Service, London, UK). This work describes validation of the improved qPCR quadruplex method and supports its implementation for the biological diagnosis of diphtheria.
ADSoluble aggregates present in cerebrospinal fluid change in size and mechanism of toxicity during Alzheimer’s disease progression
Authors: De Suman , Whiten Daniel R. , Ruggeri Francesco S. , Hughes Craig , Rodrigues Margarida , Sideris Dimitrios I. , Taylor Christopher G. , Aprile Francesco A. , Muyldermans Serge , Knowles Tuomas P. J. , Vendruscolo Michele , Bryant Clare , Blennow Kaj , Skoog Ingmar , Kern Silke , Zetterberg Henrik , Klenerman David
Published: April 2019

Soluble aggregates of amyloid-β (Aβ) have been associated with neuronal and synaptic loss in Alzheimer’s disease (AD). However, despite significant recent progress, the mechanisms by which these aggregated species contribute to disease progression are not fully determined. As the analysis of human cerebrospinal fluid (CSF) provides an accessible window into the molecular changes associated with the disease progression, we studied the soluble Aβ aggregates present in CSF samples from individuals with AD, mild cognitive impairment (MCI) and healthy controls. We found that these aggregates vary structurally and in their mechanisms of toxicity. More small aggregates of Aβ that can cause membrane permeabilization already found in MCI; in established AD, the aggregates were larger and more prone to elicit a pro-inflammatory response in glial cells. These results suggest that different neurotoxic mechanisms are prevalent at different stages of AD.
Solving the first novel protein structure by 3D micro-crystal electron diffraction
Authors: Xu H. , Lebrette H. , Clabbers M.T.B. , Zhao J. , Griese J.J. , Zou X. , Högbom M.
Published: April 2019

Micro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure – an R2lox enzyme – solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.
Drosophilaribosomal protein S5b is essential for oogenesis and interacts with distinct RNAs
Authors: Kong Jian , Han Hong , Bergalet Julie , Benoit Bouvrette Louis Philip , Hernández Greco , Moon Nam-Sung , Vali Hojatollah , Lécuyer Éric , Lasko Paul
Published: April 2019

InDrosophila melanogasterthere are two genes encoding ribosomal protein S5,RpS5aandRpS5b.Here, we demonstrate thatRpS5bis required for oogenesis. Females lackingRpS5bproduce ovaries with numerous developmental defects that undergo widespread apoptosis in mid-oogenesis. Females lacking germlineRpS5aare fully fertile, but germline expression of interfering RNA targeting germlineRpS5ain anRpS5bmutant background worsened theRpS5bphenotype and blocked oogenesis before egg chambers form. A broad spectrum of mRNAs co-purified in immunoprecipitations with RpS5a, while RpS5b-associated mRNAs were specifically enriched for GO terms related to mitochondrial electron transport and cellular metabolic processes. Consistent with this,RpS5bmitochondrial fractions are depleted for proteins linked to oxidative phosphorylation and mitochondrial respiration, andRpS5bmitochondria tended to form large clusters and had more heterogeneous morphology than those from controls. We conclude that RpS5b-containing ribosomes preferentially associate with particular mRNAs and serve an essential function in oogenesis.
Composition and structure of synaptic ectosomes exporting antigen receptor linked to functional CD40 ligand from helper T-cells
Authors: Saliba David G. , Céspedes-Donoso Pablo F. , Bálint Štefan , Compeer Ewoud B. , Valvo Salvatore , Korobchevskaya Kseniya , Mayya Viveka , Peng Yanchun , Dong Tao , Tognoli Maria-Laura , O’Neill Eric , Bonham Sarah , Fischer Roman , Kessler Benedikt M. , Dustin Michael L.
Published: April 2019

Cell communication through extracellular vesicles is an emerging topic in biology, including communication between cells of the immune system. Planar supported lipid bilayers (PSLBs) presenting T cell receptor (TCR) ligands and intercellular adhesion molecule-1 (ICAM-1) induce budding of extracellular microvesicles enriched in functional TCR, defined here as synaptic ectosomes (SE), from helper T cells. SE bind peptide-MHC directly exporting TCR into the synaptic cleft, but their ability to incorporate other effectors is unknown. Here, we utilized bead supported lipid bilayers (BSLB) to capture SE from single immunological synapses (IS), determined SE composition by immunofluorescence flow cytometry and enriched SE for proteomic analysis by particle sorting. Our results demonstrate selective enrichment of CD40 ligand (CD40L) and inducible T-cell costimulator (ICOS) in SE in response to addition of CD40 and ICOS ligand (ICOSL), respectively, to SLB presenting TCR ligands and ICAM-1. TCR triggering mobilized intracellular CD40L to the T cells surface at the IS, where it engaged CD40 to enable sorting into SE. SEs were enriched in tetraspanins and bone marrow stromal cell antigen 2 (BST-2) by immunofluorescence and TCR signalling and endosomal sorting complexes required for transport by proteomics. Super-resolution microscopy demonstrated that CD40L is present in microclusters within CD81 defined SE that are spatially segregated from TCR/ICOS/BST-2 microclusters. CD40L in SE retains the capacity to induce dendritic cell (DC) maturation and cytokine production. SE enabled helper T cells to release effectors physically linked to TCR.

One Sentence Summary

TCR and CD40L microclusters can be linked in synaptic ectosomes (extracellular vesicles) that are released in the immunological synapse by helper T cells and induce dendritic cell maturation and cytokine production.
Interplay Between Short-range Attraction and Long-range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes
Authors: Alshareedah Ibraheem , Kaur Taranpreet , Ngo Jason , Seppala Hannah , Djomnang Kounatse Liz-Audrey , Wang Wei , Moosa Mahdi Muhammad , Banerjee Priya R.
Published: April 2019

In eukaryotic cells, ribonucleoproteins (RNPs) form mesoscale condensates by liquid-liquid phase separation that play essential roles in subcellular dynamic compartmentalization. The formation and dissolution of many RNP condensates are finely dependent on the RNA-to-RNP ratio, giving rise to a window-like phase separation behavior. This is commonly referred to as reentrant liquid condensation (RLC). Here, using RNP-inspired polypeptides with low-complexity RNA-binding sequences as well as the C-terminal disordered domain of the ribonucleoprotein FUS as model systems, we investigate the molecular driving forces underlying this non-monotonous phase transition. We show that an interplay between short-range cation-π attractions and long-range electrostatic forces governs the heterotypic RLC of RNP-RNA complexes. Short-range attractions, which can be encoded by both polypeptide chain primary sequence and nucleic acid base sequence, are activated by RNP-RNA condensate formation. After activation, the short-range forces regulate material properties of polypeptide-RNA condensates and subsequently oppose their reentrant dissolution. In the presence of excess RNA, a competition between short-range attraction and long-range electrostatic repulsion drives the formation of a colloid-like cluster phase. With increasing short-range attraction, the fluid dynamics of the cluster phase is arrested, leading to the formation of a colloidal gel. Our results reveal that phase behavior, supramolecular organization, and material states of RNP-RNA assemblies are controlled by a dynamic interplay between molecular interactions at different length scales.
Seasonal Change of Microbial Diversity and Its Relation with Soil Chemical Properties in Orchard
Authors: Luo Xuhui , Wang Mingkuang , Hu Guiping , Weng Boqi
Published: April 2019

This study aimed to determine the microbial diversity of different soil depths (0-5 and 5-20 cm) in a subtropical orchard during different seasons (i.e., Spring, Summer and Autumn) for enrich the knowledgements on micorbes roles in orchard ecosystem balance. In tracking experiments conducted in an orchard (established in 1996), the phospholipid fatty acid (PLFA) biomarker method was employed to know soil microbial system. Total PLFAs concentration did not vary significantly between soil depths but changed between seasons. It peaked in the summer at 258.97 ± 23.48 μg g-1soil from 0-5 cm and at 270.99 ± 58.94 μg g-1soil from 5-20 cm. A total of 33 microbial fatty acid biomarkers were observed and identified in the sampled soil. Quantities of PLFAs for 29 microbe groups varied significantly between seasons, except for 15:0 iso 3OH, 15:1 iso G, 16:0 2OH, and 17:0 iso 3OH. The bacterial PLFAs and fungal and actinomycotic PLFAs in the orchard soil collected in Summer were significantly higher than in the Spring or Autumn (P< 0.01). The number of soil microorganism species (Richness) and the Simpson and Shannon-Wiener indexes were all the highest in summer. The total PLFAs, bacterial PLFAs, fungal PLFAs, actinomycotic PLFAs, Richness, or the Simpson and Shannon-Wiener indexes were all significantly negatively correlated with soil pH, total carbon (TOC), total nitrogen (TN) and cation-exchange capacity (CEC) (P< 0.05).
NOTCH1 signaling establishes the medullary thymic epithelial cell progenitor pool during mouse fetal development
Authors: Li Jie , Gordon Julie , Chen Edward L. Y. , Wu Luying , Zúñiga-Pflücker Juan Carlos , Manley Nancy R.
Published: April 2019

The cortical and medullary thymic epithelial cell (cTEC and mTEC) lineages are essential for inducing T cell lineage commitment, T cell positive selection and the establishment of self-tolerance, but the mechanisms controlling their fetal specification and differentiation are poorly understood. Here, we show that Notch signaling is required to specify and expand the mTEC lineage. Notch1 is expressed by and active in TEC progenitors. Deletion of Notch1 in TECs resulted in depletion of mTEC progenitors and dramatic reductions in mTECs during fetal stages, consistent with defects in mTEC specification and progenitor expansion. Conversely, forced Notch signaling in all TEC resulted in widespread expression of mTEC progenitor markers and profound defects in TEC differentiation. In addition, lineage-tracing analysis indicated that all mTECs have a history of receiving a Notch signal, consistent with Notch signaling occurring in mTEC progenitors. Interestingly, this lineage analysis also showed that cTECs are divided between Notch lineage-positive and lineage-negative populations, identifying a previously unknown complexity in the cTEC lineage.
Congruence of location-specific transcriptional programs in intestinal organoids during long-term culture
Authors: van der Hee B. , Madsen O. , Smidt H. , Wells J.M.
Published: April 2019

The emergence of intestinal organoids, as a stem cell-based self-renewable model system, has led to many studies on intestinal development and cell-cell signaling. However, potential issues regarding the phenotypic stability and reproducibility of the methodology during culture still needs to be addressed for different organoids. Here we investigated the transcriptomes of intestinal organoids derived from the same pig as well as batch-to-batch variation of organoids derived from different pigs over long-term passage. The set of genes expressed in organoids closely resembled that of the tissue of origin, including location specific functions, for at least 17 passages. Minor differences in gene expression were observed between individual organoid cultures. In contrast, most tissue-specific genes were not expressed in the transformed jejunum cell line IPECJ2, which also showed gene expression consistent with cancer phenotypes. We conclude that intestinal organoids provide a robust and stable model for translational research with clear advantages over transformed cells.
Cryo-EM Structures of Four Polymorphic TDP-43 Amyloid Cores
Authors: Cao Qin , Boyer David R. , Sawaya Michael R. , Ge Peng , Eisenberg David S.
Published: April 2019

Summary Paragraph

TDP-43 is an essential DNA/RNA processing protein that undergoes both functional and pathogenic aggregation. Functional TDP-43 aggregates are reversible, forming transient species such as nuclear bodies, stress granules, and myo-granules1–3. In contrast pathogenic TDP-43 aggregates are irreversible, forming stable intracellular amyloid-like inclusions4,5. These inclusions are the primary pathology of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP)6. Disease-associated, hereditary mutations in TDP-43 are known to accelerate the deposition of irreversible aggregates in the cytoplasm7. Reversible TDP-43 aggregation has been shown to precede the formation of irreversible amyloid fibrils similar to the behavior of proteins hnRNPA1 and FUS8–10. Still unknown, however, are the structural features of TDP-43 fibrils that confer both reversibility and irreversibility and how hereditary mutations can impose irreversible aggregation. Here, we determined the structures of amyloid fibrils formed by two segments previously reported to be the pathogenic cores of TDP-43 aggregation7,11,12; these are termed SegA (residues 311-360) and SegB A315E (residues 286-331 containing the ALS hereditary mutation A315E). SegA forms three polymorphs, all with dagger-shaped folds. SegB forms R-shaped folds. All four polymorphs have folds confined to two dimensions, and are stabilized by hydrophobic cores and peripheral hydrogen bonds. Energetic analysis suggests that the dagger-shaped polymorphs are examples of the irreversible fibril structures of TDP-43, whereas the SegB polymorph may participate in both reversible and irreversible fibril structure. Our structure suggests how the A315E mutation may convert this polymorph to the irreversible type and lead to mutation-enhanced pathology.
RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit
Authors: Allepuz-Fuster Paula , O’Brien Michael J. , González-Polo Noelia , Pereira Bianca , Dhoondia Zuzer , Ansari Athar , Calvo Olga
Published: April 2019

Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in therpb4Δ mutant. In contrast to the other looping-defective mutants,rpb4Δ cells do not exhibit a transcription termination defect.RPB4overexpression, however, rescued the transcription termination and gene looping defect ofsua7-1, a mutant of TFIIB. Furthermore,RPB4overexpression rescued thessu72-2gene looping defect, whileSSU72overexpression restored the formation of gene loops inrpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised inrpb4Δ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.
Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes byEscherichia coli
Authors: Jindal Srijan , Yang Lei , Day Philip J. , Kell Douglas B.
Published: April 2019

We used high-throughput flow cytometry to assess the ability of individual gene knockout strains ofE colito take up two membrane-permeable, cationic fluorescent dyes, viz the carbocyanine diS-C3(5) and the DNA dye SYBR Green. Individual strains showed a large range of distributions of uptake. The range of modal steady-state uptakes for the carbocyanine between the different strains was 36-fold. Knockouts of the ATP synthase α- and β-subunits greatly inhibited uptake, implying that most uptake was ATP-driven rather than being driven by say a membrane potential. Dozens of transporters changed the steady-state uptake of the dye by more than 50% with respect to that of the wild type, in both directions (increased or decreased); knockouts in known influx and efflux transporters behaved as expected, giving confidence in the general strategy. Many of the knockouts with the most reduced uptake were transporter genes of unknown function (‘y-genes’). Similarly, several overexpression variants in the ‘ASKA’ collection had the anticipated, opposite effects. Similar findings were made with SYBR Green (the range being some 69-fold), though despite it too containing a benzimidazole motif there was negligible correlation between its uptake and that of the carbocyanine when compared across the various strains. Overall, we conclude that the uptake of these dyes may be catalysed by a great many transporters of possibly broad and presently unknown specificity. This casts serious doubt upon the use of such dyes as quantitative stains for representing either bioenergetic parameters or the amount of cellular DNA in unfixed cells (in vivo). By contrast, it opens up their potential use as transporter assay substrates in high-throughput screening.
Owners vs executives and decisions vs control
Authors: Andersen Jon Aarum
Published: April 2019

Purpose

Some scholars have claimed that CEOs make decisions, while boards of directors control these decisions by applying the concepts of decision management and decision control. These concepts were suggested more than 30 years ago and are still applied in corporate governance research. They are now challenged on the basis of scholarship on corporate governance and management.

Design/methodology/approach

Corporate governance addresses the authority and responsibility that boards of directors and executives have. Management theory addresses planning and control in corporations.

Findings

The relationship between the owners (the boards of directors) and the top managers is hierarchical. This paper concludes that owners or boards of directors make decisions on main and strategic goals. Decisions cannot be controlled, but the implementation and outcomes of plans can. The latter is managers’ responsibility. The terms “decision management” and “decision control” are undefined and do not describe what takes place in organizations.

Research limitations/implications

This paper does not contain any new empirical data.

Originality/value

Management theory offers clear definitions of decisions, decision-making and control. The concepts of decision management (initiation and implementation) and decision control (ratification and monitoring) neither properly describe who makes major and strategic decisions nor how and who controls the consequences of these decisions.
Conforming to the host country versus being distinct to our home countries
Authors: Abd Hamid Hamizah , O’Kane Conor , Everett André M.
Published: April 2019

Purpose

The purpose of this paper is to examine how ethnic migrant entrepreneurs (EMEs) utilise identity work to build legitimacy in a host country. According to optimal distinctiveness theory (ODT), legitimacy is achieved by balancing conformance and distinctiveness. This paper draws on ODT in the context of ethnic migrant entrepreneurship to examine how EMEs both fit in (conformance) and maintain their uniqueness (distinctiveness) in cross-cultural settings.

Design/methodology/approach

This study adopts a qualitative approach utilising semi-structured interviews to examine the identity work of EMEs from three distinct countries (Indonesia, Pakistan and South Korea (henceforth Korea)) in one host country (Malaysia).

Findings

The results show that EMEs’ identity work incorporates both the blurring and strengthening of host-home country boundaries. Building on this study’s results, the authors develop a model of identity work and three propositions regarding legitimacy building through identity in the context of ethnic migrant entrepreneurship.

Originality/value

Through the model and propositions, this research contributes to the identity, international entrepreneurship and ethnic migrant entrepreneurship discourse by identifying the mechanisms, focus and key features of identity work for entrepreneurs operating in cross-cultural settings. In so doing, this research also offers an alternative interpretation on the apparent divergent views around identity work in the fields of organisation (advocate isomorphism) and entrepreneurship (advocate uniqueness).
Entrepreneuring as an everyday form of resistance
Authors: Sabella Anton Robert , El-Far Mira Taysir
Published: April 2019

Purpose

The purpose of this paper is to problematise the dominant conceptualisation of entrepreneurship by recognising the everyday resistance inherent in mundane entrepreneurial practices. Its principle purpose is to show how entrepreneurial activities enacted by ordinary individuals in a marginalised and oppressed context can be an important means of resisting economic adversity, social marginalisation and political (colonial) domination.

Design/methodology/approach

Framed within de Certeau’s conceptualisation of the practices of everyday life, this study utilises a “focussed ethnography”, relying on “participant observation” and “informal interviews”, to explore the perceptions and experiences of Palestinian women street vendors, and how they use everyday entrepreneurial practices in the open-air market of the Old City of Jerusalem to become socially and politically empowered.

Findings

The arguments in this paper demonstrate how marginalised Palestinian women, who are equipped with a genuine critical vision of their reality and a biophiliac attitude, use entrepreneuring to enact new possibilities for themselves and for their families. Through their entrepreneurial act of street vending, these women exemplify a struggle against economic and socio-political constraints, transforming the act of entrepreneuring from a mere economic practice to an all-encompassing human project, one with a more human face.

Originality/value

This paper extends the argument for the complex and dynamic nature of the phenomenon and exposes its political nature, hitherto inadequately addressed in existing literature, as well as uncovers the potential of entrepreneurialism to enhance individual empowerment and contribute to meaningful social change. In addition, it addresses the need for scholarly work that focuses on the everyday entrepreneurial activities carried out by ordinary individuals experiencing various forms of oppression in new and challenging spaces, which are seldom acknowledged within the dominant theoretical and research frameworks.
Maritime Cluster Attractiveness Index
Authors: Lagoudis Ioannis , Madentzoglou Eleftherios M. , Theotokas Ioannis N. , Yip Tsz Leung
Published: April 2019

Purpose

The role of clusters in the development and growth of local and national economies has been extensively studied and discussed in global literature. Different methodologies are used for analysing the impact these have in national and regional economies, such as the input–output (IO) and gravity models. This paper aims to detail the methodologies present in the literature and propose a new robust theoretical framework, which facilitates the evaluation and comparison among maritime clusters in terms of attractiveness assisting stakeholders to devise strategies, which will attract companies.

Design/methodology/approach

An index is created composed of five key categories, namely, infrastructure, financing, governance, manpower and institution/legislation. For the analysis of the index, multi-attribute utility theory (MAUT) is used as a tool to evaluate the importance and performance of the different attributes using both quantitative and qualitative criteria. The methodology has been tested via the use the Piraeus maritime cluster.

Findings

The framework has been tested on its robustness and friendliness to the user providing useful insights to the stakeholders. Among the results has been the importance of the finance, manpower and infrastructure attributes, which appear to promote the cluster’s attractiveness. In addition, legislation and institutional partnerships, along with Government support, need to take place improve the performance of the cluster.

Research limitations/implications

A key limitation is the fact that the methodology has been tested in a single case. Applying the methodological framework in a wider sample of clusters will significantly improve the present work.

Originality/value

The proposed model takes further existing research in the field via adopting the philosophy of the World Bank’s Logistics Performance Index. Among the benefits of the proposed index is that it offers the flexibility and robustness to compare among different maritime clusters globally and can be readily used as a benchmarking policy tool at national, regional and global levels at any given point in time and attribute dimension.
Why do clients enrol and continue at sports centres?
Authors: Rodríguez Cañamero Sergio , García-Unanue Jorge , Felipe José Luis , Sánchez-Sánchez Javier , Gallardo Leonor
Published: April 2019

Purpose

The purpose of this paper is to analyse the ways clients find out about a sport centre and the factors that lead them to enrol and influence their satisfaction with their membership. A secondary objective was to determine the reasons for continuing to attend a sport centre and how they influenced satisfaction towards achievement. Finally, the authors aimed to identify differences between reasons for enroling and reasons for continuing at a sport centre.

Design/methodology/approach

A specially developed 16-item questionnaire was sent to 125,000 clients and 21,043 responses were obtained.

Findings

Clients who found out about the centre through a recommendation or the internet were 25 per cent more likely to be satisfied with it than those who knew of the centre due to proximity. Similarly, clients who had a specific motive to continue using the centre, for example, to prepare for a sports competition were twice as likely to be satisfied with their membership as any other group (p<0.001).

Research limitations/implications

It identifies a set of research priorities for the journal and the field.

Practical implications

In conclusion, the option of staying fit is established as the most effective recruitment method for retaining clients at the sport centre.

Originality/value

This paper intends to do is to establish the bases of information and knowledge for the treatment of high motives, as well as for managers of sports centres to remodel their strategies of marketing to attracting customers.
Automated processing strategies for ambient seismic data
Authors: Girard Aaron J. , Shragge Jeffrey
Published: April 2019

Extracting body‐wave arrivals from ambient seismic recordings remains a challenging task, largely because ambient records are usually dominated by surface‐wave energy. Most ambient seismic data‐processing strategies aimed at enhancing body‐wave energy focus on a cross‐correlation plus stack methodology. While this approach is useful for interferometric investigations, it effectively squares the magnitude of unwanted coherent noise events (e.g. surface waves, burst‐like or strong monochromatic energy) that commonly overpower ambient body‐wave signal. Accordingly, coherent noise events are usually treated with a binary accept‐or‐reject decision of individual data windows based on root‐mean‐squared energy considerations. Applying a data‐processing workflow to uncorrelated ambient seismic data represents an alternate strategy for mitigating coherent noise. However, this pre‐stack methodology requires significant computational effort due to the often terabyte‐sized data volumes. To make this approach feasible, we outline an automated processing workflow to automatically identify and mitigate coherent noise events that otherwise does not severely degrade the remaining waveforms. After each processing step, we apply a number of quality control measures to monitor the convergence rate of cross‐correlation plus stack waveforms and for evidence of emerging body‐wave reflection events. We apply the processing flow to an ambient seismic data set acquired on a large‐N array at a mine site near Lalor Lake, Manitoba, Canada. Our quality control analyses suggest that automated preprocessing of uncorrelated ambient seismic recordings successfully mitigates unwanted impulsive and monochromatic coherent noise events. Accordingly, we assert that applying an automated data‐processing approach would be beneficial for body‐wave and other imaging and inversion analyses applied to ambient seismic recordings.
Heterotrophic carbon metabolism and energy acquisition in Candidatus Thioglobus singularis strain PS1, a member of the SUP05 clade of marine Gammaproteobacteria
Authors: Spietz Rachel L. , Lundeen Rachel A. , Zhao Xiaowei , Nicastro Daniela , Ingalls Anitra E. , Morris Robert M.
Published: April 2019

A hallmark of the SUP05 clade of marine Gammaproteobacteria is the ability to use energy obtained from reduced inorganic sulfur to fuel autotrophic fixation of carbon using RuBisCo. However, some SUP05 also have the genetic potential for heterotrophic growth, raising questions about the roles of SUP05 in the marine carbon cycle. We used genomic reconstructions, physiological growth experiments and proteomics to characterize central carbon and energy metabolism in Candidatus Thioglobus singularis strain PS1, a representative from the SUP05 clade that has the genetic potential for autotrophy and heterotrophy. Here, we show that the addition of individual organic compounds and 0.2 μm filtered diatom lysate significantly enhanced the growth of this bacterium. This positive growth response to organic substrates, combined with expression of a complete TCA cycle, heterotrophic pathways for carbon assimilation, and methylotrophic pathways for energy conversion demonstrate strain PS1's capacity for heterotrophic growth. Further, our inability to verify the expression of RuBisCO suggests that carbon fixation was not critical for growth. These results highlight the metabolic diversity of the SUP05 clade that harbours both primary producers and consumers of organic carbon in the oceans and expand our understanding of specific pathways of organic matter oxidation by the heterotrophic SUP05.
Influence of cognitive impairment on pain assessment and management in the emergency department: A retrospective cross‐sectional study
Authors: Jones Joshua , Sim Tin Fei , Parsons Richard , Hughes Jeff
Published: April 2019

Objectives

To quantify the impact of cognitive impairment on pain assessment and management practices in the ED.

Methods

A retrospective, cross‐sectional study of patient records was conducted for all elderly patients (65 years or older) who presented to the ED of a large Western Australian tertiary hospital with a fracture because of a fall between 6 February and 14 December 2015. Of 327 records identified, 318 were suitable for data extraction. Of these, 120 patients had a cognitive impairment. Primary outcome measures were the method and frequency of pain assessment, and the delay to the administration of a pain intervention after pain was first assessed for patients with and without a cognitive impairment.

Results

Patients with a cognitive impairment were less likely to have their pain assessed with a standardised pain assessment tool (55% vs 91.4%, P < 0.001), and 9.4 times more likely to have their pain assessed using ad hoc assessments only (95% confidence interval 4.6–19.1). The median time between ED presentation and a patient's first pain assessment was longer for patients with cognitive impairment (28 vs 17 min; P < 0.001), as was the time between repeat assessments (81 vs 62 min; P < 0.004). The median times to receive a pain intervention following pain assessment were 51 and 50 min for cognitively intact and impaired patients, respectively (P = 0.209, after adjustment for the first pain score).

Conclusion

Pain is inadequately and inappropriately assessed for elderly patients with a cognitive impairment in the ED, resulting in delays in initiation of pain management.
Long non‐coding RNAs play regulatory roles in acetaminophen‐induced liver injury
Authors: Zheng Jian Xin , Tang Yuan Jia , Yang Tai Hua , Qin Tian , Liu Jin Chuan , Gu Xiang Qian , Xue Feng , Xia Qiang
Published: April 2019

Objective

To explore the expression profile and role of hepatic long non‐coding RNA (lncRNA) in acetaminophen‐induced liver injury mouse model by analyzing lncRNA‐mRNA co‐expression.

Methods

Serum aminotransferase, liver pathology and inflammatory cells were analyzed in mice model at different time points after treated with acetaminophen 300 mg/kg. High‐throughput RNA sequencing was performed to investigate hepatic expression profiles of messenger RNA (mRNA) and lncRNA. The relationship between the lncRNA and mRNA was delineated by the co‐expression network using Cytoscape software. Differential mRNAs co‐expressed with lncRNAs were analyzed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes enrichment. Differential mRNAs and lncRNAs were selected for quantitative reverse transcription polymerase chain reaction validation, and the conservation of lncRNA between human and mouse was analyzed.

Results

Liver injury was more severe at 24 hours than at 6 hours. There was a substantial infiltration of monocytes instead of neutrophil and Kupffer cells at 24 hours compared with 6 hours. The mRNAs co‐expressed with the differential lncRNAs at 24 vs 6 hours were mainly enriched in protein processing in endoplasmic reticulum, MAPK and PPAR signaling pathways. The co‐expression network delineated with four lncRNAs and 94 mRNAs presented the core position of lncRNA in the network. A conservation analysis indicated that four differential mouse lncRNAs (NONMMUT023651.2, NONMMUT029382.2, NONMMUT029383.2 and NONMMUT102053.1) could all be mapped to the relevant human lncRNAs.

Conclusion

Four lncRNAs may play regulatory roles through metabolic and apoptosis‐related pathways during hepatic homeostasis maintenance and repair progress.