bluuebunny/crossref_metadata_2025 huggingface dataset:
Vulnerability to climate change for narrowly ranged species: the case of Ecuadorian endemicMagnolia mercedesiarum
Authors: Shalisko V. , Vázquez-García J. A. , Villalobos-Arámbula A. R. , Muñiz-Castro M. A.
Published: November 2018

Species vulnerability to climate change has been inferred using species distribution models from an example of the recently discoveredMagnolia mercedesiarum(sect.Talauma, Magnoliaceae), a narrowly ranged species endemic to moist tropical forests in the eastern Ecuadorian Andes. The environmental conditions within the current species distribution area has been compared with conditions projected to 2050 and 2070, using data from the HadGEM2-ES model in two CO2 emission scenarios: RCP4.5 and RCP8.5. The ecological niche modelling allowed determination of parameters of climatic environmental conditions that control current species distribution to produce a hypothesis on probable changes in spatial pattern of suitable habitats in future scenarios. Within the current species distribution area ofM. mercedesiarum, significant reduction of habitat suitability was projected for both emission scenarios, combined with a lack of nearby areas with adequate environmental conditions. Several disjunct sites of high habitat suitability were found to emerge in the Colombian Andes, but they seem unreachable by this tree species in the scope of a few decades, due to intrinsic dispersal limitations. The reduction of habitat suitability and improbability of distribution area shift to adjacent geographic locations could mean a high species vulnerability to climate change. The species could be at risk of extinction if it does not possess hidden phenotypical plasticity and potential for fast adaptation to climate change.
Waddington Revisited: Organ transformation by environmental disruption of epigenetic memory
Authors: Snir Orli , Elgart Michael , Ciabrelli Filippo , Dagan Shlomi , Aviezer Iris , Stoops Elizabeth , Cavalli Giacomo , Soen Yoav
Published: November 2018

Despite major progress in mechanistic understanding of epigenetic reprogramming of cells, the basis of ‘organ reprograming’ by (epi-)gene-environment interactions remained largely obscured. Here we use the ether-induced haltere-to-wing transformations as a model for epigenetic “reprogramming” at the whole organism level. Our findings support a mechanistic chain of events explaining why and how brief embryonic exposure to ether leads to organ transformation manifested at the larval stage and on. We show that ether interferes with protein integrity in the egg leading to altered deployment of Hsp90 and repression of Trithorax-mediated establishment of H3K4 tri-methylations. This repression pre-disposes early methylated Ubx targets and wing genes for later up-regulation in the larval haltere disc, hence the wing-like outcome. Consistent with compromised protein integrity during the exposure, the severity of bithorax transformation is increased by genetic or chemical reduction of Hsp90 function. Moreover, a joint reduction inHsp90andtrxgene dosage can cause bithorax transformations without exposure to ether. These findings implicate environmental disruption of protein integrity at the onset of histone methylations with a modification of epigenetic memory, which in turn, supports a morphogenetic shift towards an ancestral-like body plan. The morphogenetic impact of chaperone response during a major setup of epigenetic patterns may be a general scheme for organ reprogramming by environmental cues.
ACAT: A Fast and Powerful P-value Combination Method for Rare-variant Analysis in Sequencing Studies
Authors: Liu Yaowu , Chen Sixing , Li Zilin , Morrison Alanna C. , Boerwinkle Eric , Lin Xihong
Published: November 2018

Set-based analysis that jointly tests the association of variants in a group has emerged as a popular tool for analyzing rare and low-frequency variants in sequencing studies. The existing set-based tests can suffer significant power loss when only a small proportion of variants are causal, and their powers can be sensitive to the number, effect sizes and effect directions of the causal variants and the choices of weights. Here we propose an Aggregated Cauchy Association Test (ACAT), a general, powerful and computationally efficient p-value combination method to boost power in sequencing studies. First, by combining variant-level p-values, we use ACAT to construct a set-based test (ACAT-V) that is particularly powerful in the presence of only a small number of casual variants in a variant set. Second, by combining different variant set-level p-values, we use ACAT to construct an omnibus test (ACAT-O) that combines the strength of multiple complimentary set-based tests including the burden test, Sequence Kernel Association Test (SKAT) and ACAT-V. Through analysis of extensively simulated data and the whole-genome sequencing data from the Atherosclerosis Risk in Communities (ARIC) study, we demonstrate that ACAT-V complements the SKAT and burden test, and that ACAT-O has a substantially more robust and higher power than the alternative tests.
Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Authors: Schwarzkopf Enrique J. , Motamayor Juan C. , Cornejo Omar E.
Published: November 2018

Our study investigates the possible drivers of recombination hotspots inTheobroma cacaousing ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated population’s FIGL1 protein. FIGL1 has been shown to increase recombination rates inArabidopsisby several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.
Modular, part-based control of gene expression response time using protein degradation tags
Authors: Jones Ethan M , Monette Callan E , Marken John P , Dhawan Sejal , Gibney Theresa , Li Christine , Liu Wukun , Luz-Ricca Alyssa , Ren Xida , Zheng Xingyu , Saha Margaret
Published: November 2018

A fundamental principle of cellular signal processing is the encoding of information within the temporal dynamics of regulatory circuits. If synthetic circuits are to achieve the versatility and effectiveness of naturally-occurring circuits, it is necessary to develop simple, effective methods for the control of the dynamical properties of genetic circuits. However, current approaches to dynamical control often require extensive rewiring of circuit architecture, which hinders their implementation in a variety of systems. Therefore, it is essential that simple, modular, genetic parts-based frameworks are created to control the dynamical properties of circuits. Here we address this need by implementing a modular, genetic parts-based system which tunes the response time of a gene's expression by tuning its degradation rate via the application of protein degradation tags with various affinities to their protease. This system provides a simple, easily-applicable framework for controlling the temporal aspects of genetic circuit behavior.
Optimised CRISPR-Cas9 mediated single molecule imaging for accurate quantification through endogenous expression
Authors: Khan Abdullah O. , White Carl W. , Pike Jeremy A. , Yule Jack , Slater Alexandre , Hill Stephen J. , Poulter Natalie S. , Thomas Steven G. , Morgan Neil V.
Published: November 2018

The use of CRISPR-Cas9 genome editing to introduce endogenously expressed tags has the potential to address a number of the classical limitations of single molecule localisation microscopy. In this work we present the first systematic comparison of inserts introduced through CRISPR- knock in, with the aim of optimising this approach for single molecule imaging. We show that more highly monomeric and codon optimised variants of mEos result in improved expression at the TubA1B locus, despite the use of identical guides, homology templates, and selection strategies. We apply this approach to target the G protein-coupled receptor (GPCR) CXCR4 and show a further insert dependent effect on expression and protein function. Finally, we show that compared to over-expressed CXCR4, endogenously labelled samples allow for accurate single molecule quantification on ligand treatment. This suggests that despite the complications evident in CRISPR mediated labelling, the development of CRISPR-PALM has substantial quantitative benefits.
A Network based Approach to Identify the Genetic Influence Caused by Associated Factors and Disorders for the Parkinsons Disease Progression
Authors: Sakib Najmus , Chowdhury Utpala Nanda , Islam M. Babul , Quinn Julian M.W. , Moni Mohammad Ali
Published: November 2018

Actual causes of Parkinsons disease (PD) are still unknown. In any case, a better comprehension of genetic and ecological influences to the PD and their interaction will assist physicians and patients to evaluate individual hazard for the PD, and definitely, there will be a possibility to find a way to reduce the progression of the PD. We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors for the PD. In this study, we analyzed gene expression microarray data from the PD, ageing (AG), severe alcohol consumption (AC), type II diabetes (T2D), high body fat (HBF), hypercholesterolemia (HC), high dietary fat (HDF), red meat dietary (RMD), sedentary lifestyle (SL), smoking (SM), and control datasets. We have developed genetic associations of various factors with the PD based on the neighborhood-based benchmarking and multilayer network topology.

We identified 1343 significantly dysregulated genes in the PD patients compared to the healthy control, where we have 779 genes down regulated and 544 genes up regulated. 69 genes were highly expressed in both for the PD and alcohol consumption whereas the number of shared genes for the PD and the type II diabetes is 51. However, the PD shared 45, 43 and 42 significantly expressed genes with the ageing, high dietary fat and high body fat respectively. The PD shared less than 40 significant transcripts with other factors. Ontological and pathway analyses have identified significant gene ontology and molecular pathways that enhance our understanding of the fundamental molecular procedure of the PD progression. Therapeutic targets of the PD could be developed using these identified target genes, ontologies and pathways. Our formulated methodologies demonstrate a network-based approach to understand the disease mechanism and the causative reason of the PD, and the identification for therapeutic targets of the PD.
Molecular fingerprints for a novel glucosamine kinase family inActinobacteria
Authors: Manso José A , Nunes-Costa Daniela , Macedo-Ribeiro Sandra , Empadinhas Nuno , Pereira Pedro José Barbosa
Published: November 2018

Actinobacteriahave long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has been suggested as a mechanism for incorporation of this extracellular material into secondary metabolite biosynthesis, but experimental evidence of specific glucosamine kinases inActinobacteriais lacking. Here, we present the molecular fingerprints for the identification of a unique family of actinobacterial glucosamine kinases. Structural and biochemical studies on a distinctive kinase from the soil bacteriumStreptacidiphilus jiangxiensisunveiled its preference for glucosamine and provided structural evidence of a phosphoryl transfer to this substrate. Conservation of glucosamine-contacting residues across a large number of uncharacterized actinobacterial proteins unveiled a specific glucosamine-binding sequence motif. This family of kinases and their genetic context may represent the missing link for the incorporation of environmental glucosamine into the antibiotic biosynthesis pathways inActinobacteriaand can be explored to enhance antibiotic production.
Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome
Authors: Faull Sarah V. , Lau Andy. M. C. , Martens Chloe , Ahdash Zainab , Yebenes Hugo , Schmidt Carla , Beuron Fabienne , Cronin Nora B. , Morris Edward P. , Politis Argyris
Published: November 2018

Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 (N8) from activated Cullins. The structure of stable CSN-CRL can be used to understand this mechanism of regulation. Here we present the first structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (MS). These structures reveal a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen deuterium exchange-MS we show that CRL2 binding and conformational activation of CSN5/CSN6 occur in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identified novel sensory regions of the CSN that mediate its stepwise activation mechanism and provide a framework for better understanding the regulatory mechanism of other Cullin family members.

One sentence summary

Structure and dynamics of the CSN-CRL2 complexes assessed by cryo-electron microscopy and structural mass spectrometry.
The fine-scale landscape of immunity and parasitism in a wild ungulate population
Authors: Albery Gregory F. , Becker Daniel J. , Kenyon Fiona , Nussey Daniel H. , Pemberton Josephine M.
Published: November 2018

Spatial heterogeneity in parasite susceptibility and exposure is a common source of confounding variation in disease ecology studies. However, it is not known whether spatial autocorrelation acts on immunity in particular at small scales, within wild animal populations, and whether this predicts spatial patterns in infection. Here we used a well-mixed wild population of individually recognised red deer (Cervus elaphus) inhabiting a heterogeneous landscape to investigate fine-scale spatial patterns of immunity and parasitism. We noninvasively collected 842 faecal samples from 141 females with known ranging behaviour over two years. We quantified total and helminth-specific mucosal antibodies and counted propagules of three gastrointestinal helminth taxa. These data were analysed with linear mixed models using the Integrated Nested Laplace Approximation (INLA), using a Stochastic Partial Differentiation Equation approach (SPDE) to control for and quantify spatial autocorrelation. We also investigated whether spatial patterns of immunity and parasitism changed seasonally. We discovered substantial spatial heterogeneity in general and helminth-specific antibody levels and parasitism with two helminth taxa, all of which exhibited contrasting seasonal variation in their spatial patterns. Notably, strongyle nematode intensity did not align with density hotspots, while Fasciola hepatica intensity appeared to be strongly influenced by the presence of wet grazing. In addition, antibody hotspots did not correlate with distributions of any parasites. Our results suggest spatial heterogeneity may be an important factor affecting immunity and parasitism in a wide range of study systems. We discuss these findings with regards to the design of sampling regimes and public health interventions, and suggest that disease ecology studies investigate spatial heterogeneity more regularly to enhance their results, even when examining small geographic areas.
Habitat-Net: Segmentation of habitat images using deep learning
Authors: Abrams Jesse F. , Vashishtha Anand , Wong Seth T. , Nguyen An , Mohamed Azlan , Wieser Sebastian , Kuijper Arjan , Wilting Andreas , Mukhopadhyay Anirban
Published: November 2018

Understanding environmental factors that influence forest health, as well as the occurrence and abundance of wildlife, is a central topic in forestry and ecology. However, the manual processing of field habitat data is time-consuming and months are often needed to progress from data collection to data interpretation. Computer-assisted tools, such as deep-learning applications can significantly shortening the time to process the data while maintaining a high level of accuracy. Here, we propose Habitat-Net: a novel method based on Convolutional Neural Networks (CNN) to segment habitat images of tropical rainforests. Habitat-Net takes color images as input and after multiple layers of convolution and deconvolution, produces a binary segmentation of the input image. We worked on two different types of habitat datasets that are widely used in ecological studies to characterize the forest conditions: canopy closure and understory vegetation. We trained the model with 800 canopy images and 700 understory images separately and then used 149 canopy and 172 understory images to test the performance of Habitat-Net. We compared the performance of Habitat-Net with a simple threshold based method, a manual processing by a second researcher and a CNN approach called U-Net upon which Habitat-Net is based. Habitat-Net, U-Net and simple thresholding reduced total processing time to milliseconds per image, compared to 45 seconds per image for manual processing. However, the higher mean Dice coefficient of Habitat-Net (0.94 for canopy and 0.95 for understory) indicates that accuracy of Habitat-Net is higher than that of both the simple thresholding (0.64, 0.83) and U-Net (0.89, 0.94). Habitat-Net will be of great relevance for ecologists and foresters, who need to monitor changes in their forest structures. The automated workflow not only reduces the time, it also standardizes the analytical pipeline and, thus, reduces the degree of uncertainty that would be introduced by manual processing of images by different people (either over time or between study sites). Furthermore, it provides the opportunity to collect and process more images from the field, which might increase the accuracy of the method. Although datasets from other habitats might need an annotated dataset to first train the model, the overall time required to process habitat photos will be reduced, particularly for large projects.
Anin vivoknockdown strategy reveals multiple functions for circMbl
Authors: Pamudurti Nagarjuna Reddy , Konakondla-Jacob Vinay Vikas , Krishnamoorthy Aishwarya , Ashwal-Fluss Reut , Bartok Osnat , Wüst Stas , Seitz Katerina , Maya Roni , Lerner Noam , Patop Ines Lucia , Rizzoli Silvio , Beautus Tsevi , Kadener Sebastian
Published: November 2018

Circular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. circRNAs are enriched in the brain and accumulate with age in flies, worms and mice. Despite their abundance, little is known about their functions, especially in the context of whole organisms. Here we report the development and use of shRNAs to knock down and study the function of circMbl, the most abundant circRNA inDrosophila.This circRNA is highly conserved through evolution and is generated from the locus of the essential splicing factormuscleblind(mbl). Briefly, we generated flies in which circMbl is reduced more than 90% without measurable off-target effects in the hosting gene as well as in other RNAs. These flies display specific defects that suggest roles of circMbl in muscle and neural tissues during development and in adult flies. More specifically, whole organism downregulation of circMbl leads to male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. Moreover, these phenotypes are recapitulated by a second shRNA targeting circMbl. Importantly, knockdown and overexpression of circMbl affect mostly the same genes but in the opposite direction. Last but not least, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level likely by acting in multiple tissues. Moreover, here we provide the first proof of functionality of circRNAs inDrosophilaas well as a methodological approach that enables the comprehensive study of circRNAsin vivo.

SIGNIFICANCE STATEMENT

Circular RNAs (circRNAs) are highly abundant and evolutionary conserved RNAs of mostly unknown functions. Here we report the development and use of a shRNA-based system to knockdown specific circRNAsin vivo. We generated flies in which circMbl, the most abundant circRNA is reduced more than 90% without measurable off-target effects. These flies display male developmental lethality, altered gene expression, behavioral defects, wing posture- and flight defects. These phenotypes are recapitulated by a second shRNA targeting circMbl. Moreover, downregulation of circMbl in the fly central nervous system caused abnormal synaptic function. Together, our results demonstrate the functionality of circMbl at the organismal level and provide a methodological approach that enables the comprehensive study of circRNAsin vivo.
Self-agency built with sensorimotor processing: Decoding self-other action attribution in the human brain
Authors: Ohata Ryu , Asai Tomohisa , Kadota Hiroshi , Shigemasu Hiroaki , Ogawa Kenji , Imamizu Hiroshi
Published: November 2018

A sense of agency can be defined as a subjective experience that I am the one who is causing or generating an action. Several brain regions have been proposed as neural substrates of the subjective experience; however, how the information is processed and organized by each region to achieve the sense of agency still remains unclear. In this study, we have clarified the neural representations corresponding to three processes namely, sensorimotor error, feeling of agency, and judgment of agency. Specifically, we found that the widespread sensorimotor areas represent sensorimotor error information. The right inferior parietal lobe represents the information solely on self-/other-attribution even during movements, which corresponds to the feeling of agency. Finally, the right inferior frontal gyrus shows a distinct representation between self- and other-attribution immediately before reporting the judgment on the movement attribution. These results suggest that the brain builds a sense of agency by developing distinct types of information each corresponding to the three processes with the passage of time.
A Toolbox of IgG Subclass-Switched Recombinant Monoclonal Antibodies for Enhanced Multiplex Immunolabeling of Brain
Authors: Andrews Nicolas P. , Boeckman Justin X. , Manning Colleen F. , Nguyen Joe T. , Bechtold Hannah , Dumitras Camelia , Gong Belvin , Nguyen Kimberly , List Deborah van der , Murray Karl D. , Engebrecht JoAnne , Trimmer James S.
Published: November 2018

Generating recombinant monoclonal antibodies (R-mAbs) from mAb-producing hybridomas offers numerous advantages that increase the effectiveness, reproducibility, and transparent reporting of research. We report here the generation of a novel resource in the form of a library of recombinant R-mAbs validated for neuroscience research. We cloned immunoglobulin G (IgG) variable domains from cryopreserved hybridoma cells and input them into an integrated pipeline for expression and validation of functional R-mAbs. To improve efficiency over standard protocols, we eliminated aberrant Sp2/0-Ag14 hybridoma-derived variable light transcripts using restriction enzyme trea™ent. Further, we engineered a plasmid backbone that allows for switching of the IgG subclasses without altering target binding specificity to generate R-mAbs useful in simultaneous multiplex labeling experiments not previously possible. The method was also employed to rescue IgG variable sequences and generate functional R-mAbs from a non-viable cryopreserved hybridoma. All R-mAb sequences and plasmids will be archived and disseminated from open source suppliers.
The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells
Authors: Ratzan Wil , Rayaprolu Vamseedhar , Killian Scott E. , Bradley Roger , Kohout Susy C.
Published: November 2018

Voltage-sensing phosphatases (VSPs) are transmembrane proteins that couple changes in membrane potential to hydrolysis of inositol signaling lipids. VSPs catalyze the dephosphorylation of phosphatidylinositol phosphates (PIPs) that regulate diverse aspects of cell membrane physiology including cell division, growth and migration. VSPs are highly conserved among chordates, and their RNA transcripts have been detected in the adult and embryonic stages of frogs, fish, chickens, mice and humans. However, the subcellular localization and biological function of VSP remains unknown. Using reverse transcriptase-PCR (RT-PCR), we show that both Xenopus laevis VSP (Xl-VSP1 and Xl-VSP2) mRNAs are expressed in early embryos, suggesting that both Xl-VSPs are involved in early tadpole development. To understand which embryonic tissues express Xl-VSP mRNA, we used in situ hybridization (ISH) and found Xl-VSP mRNA in both the brain and kidney of NF stage 32-36 embryos. By Western blot analysis with a VSP antibody, we show increasing levels of Xl-VSP protein in the developing embryo, and by immunohistochemistry (IHC), we demonstrate that Xl-VSP protein is specifically localized to the apical membrane of both embryonic and adult kidney tubules. We further characterized the catalytic activity of both Xl-VSP homologs and found that while Xl-VSP1 catalyzes 3- and 5-phosphate removal, Xl-VSP2 is a less efficient 3-phosphatase with different substrate specificity. Our results suggest that Xl-VSP1 and Xl-VSP2 serve different functional roles and that VSPs are an integral component of voltage-dependent PIP signaling pathways during vertebrate kidney tubule development and function.
Trynity controls epidermal barrier function and respiratory tube maturation inDrosophilaby modulating apical extracellular matrix nano-patterning
Authors: Itakura Yuki , Inagaki Sachi , Wada Housei , Hayashi Shigeo
Published: November 2018

The outer surface of insects is covered by the cuticle, which is derived from the apical extracellular matrix (aECM). The aECM is secreted by epidermal cells during embryogenesis. The aECM exhibits large variations in structure, function, and constituent molecules, reflecting the enormous diversity in insect appearances. To investigate the molecular principles of aECM organization and function, here we studied the role of a conserved aECM protein, the ZP domain protein Trynity, inDrosophila melanogaster. We first identifiedtrynityas an essential gene for epidermal barrier function.trynitymutation caused disintegration of the outermost envelope layer of the cuticle, resulting in small- molecule leakage and in growth and molting defects. In addition, the tracheal tubules oftrynitymutants showed defects in pore-like structures of the cuticle, and the mutant tracheal cells failed to absorb luminal proteins and liquid. Our findings indicated thattrynityplays essential roles in organizing nano-level structures in the envelope layer of the cuticle that both restrict molecular trafficking through the epidermis and promote the massive absorption pulse in the trachea.

Summary Statement

The zona pellucida domain protein Trynity controls the structural organization and function of the apical extracellular matrix in the epidermis and trachea ofDrosophila.
qRT-PCR/High Resolution Melting Analyses detected polymorphisms of HSP-70 gene in Zebu cattle
Authors: Onasanya G.O. , Okpeku M. , Thiruvekander K.A. , Sreekumar C. , Tirumurugaan G.K. , Msalya G.M. , anni T. M. S , Olowofeso O. , Fafiolu A.O. , deleke M.A. A , Ikeobi C.O.N.
Published: November 2018

Concerns over environmental heat stress have increased in recent years with the realization of global warming effects on environment and subsequently on animal production. Heat stress indicators help to monitor adaptability and survivability of livestock to thermal assault; a consequent effect of global warming. Heat shock proteins (HSPs) are highly conserved and are classified into six groups. Heat shock protein (HSP) 70 gene is a member of molecular chaperone, known to be highly expressed under stressful environmental and physiological conditions. In this study, we used a one-step qReal-Time PCR, followed by high-resolution melting analyses (HRMA) for detection and identification of polymorphism of HSP-70 gene in four extant cattle breeds of (White Fulani, Sokoto Gudali, Red Bororo and Ambala). qRT-PCR/HRMA-based assay detected twelve (12) genetic variant groups of HSP-70 gene. Ambala breed of Nigerian Zebu cattle had the highest number (7) of genetic variants of HSP-70 gene followed by Red Bororo breed (6 genetic variants), Sokoto Gudali breed had 5 genetic variants while White Fulani breed had the least (4 genetic variants) number of genetic variants in the population of Nigerian Zebu cattle breeds examined. We therefore hypothesize that the detected variant groups can be interrogated for their possible effects on thermo-tolerance performance of zebu cattle bred under thermal assaults of tropical conditions.
Human online adaptation to changes in prior probability
Authors: Norton Elyse H. , Acerbi Luigi , Ma Wei Ji , Landy Michael S.
Published: November 2018

Optimal sensory decision-making requires the combination of uncertain sensory signals with prior expectations. The effect of prior probability is often described as a shift in the decision criterion. Can observers track sudden changes in probability? To answer this question, we used a change-point detection paradigm that is frequently used to examine behavior in changing environments. In a pair of orientation-categorization tasks, we investigated the effects of changing probabilities on decision-making. In both tasks, category probability was updated using a sample-and-hold procedure. We developed an ideal Bayesian change-point detection model in which the observer marginalizes over both the current run length (i.e., time since last change) and the current category probability. We compared this model to various alternative models that correspond to different strategies – from approximately Bayesian to simple heuristics – that the observers may have adopted to update their beliefs about probabilities. We find that probability is estimated following an exponential averaging model with a bias towards equal priors, consistent with a conservative bias. The mechanism underlying change of decision criterion is a combination of on-line estimation of prior probability and a stable, long-term equal-probability prior, thus operating at two very different timescales.

Author summary

We demonstrate how people learn and adapt to changes to the probability of occurrence of one of two categories on decision-making under uncertainty. The study combined psychophysical behavioral tasks with computational modeling. We used two behavioral tasks: a typical forced-choice categorization task as well as one in which the observer specified the decision criterion to use on each trial before the stimulus was displayed. We formulated an ideal Bayesian change-point detection model and compared it to several alternative models. We found that the data are best fit by a model that estimates category probability based on recently observed exemplars with a bias towards equal probability. Our results suggest that the brain takes multiple relevant time scales into account when setting category expectations.
The structure of SDS22 provides insights into the mechanism of heterodimer formation with PP1
Authors: Choy Meng S. , Bolik-Coulon Nicolas , Archuleta Tara L. , Peti Wolfgang , Page Rebecca
Published: November 2018

Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured. Here, the 2.9 Å resolution crystal structure of human SDS22 in space groupP212121is reported. SDS22 adopts an LRR fold with the horseshoe-like curvature typical for this family of proteins. The structure results in surfaces with distinct chemical characteristics that are likely to be critical for PP1 binding.
The enrichment ratio of atomic contacts in the crystal structure of isomeric, triply protonated, 4′-functionalized terpyridine cations with [ZnCl4]2− as counter-ion
Authors: Granifo Juan , Suárez Sebastián , Baggio Ricardo
Published: November 2018

We report herein the synthesis, crystallographic analysis and a study of the non-covalent interactions observed in the new 4′-substituted terpyridine-based derivative bis[4′-(isoquinolin-2-ium-4-yl)-4,2′:6′,4′′-terpyridine-1,1′′-diium] tris-[tetrachloridozincate(II)], (C24H19N4)2[ZnCl4]3 or (44TPH3)2[ZnCl4]3, where (44TPH3)3+ is the triply protonated cation 4′-(isoquinolinium-4-yl)-4,2′:6′,4′′ terpyridinium. The compound is similar in its formulation to the recently reported 2,2′:6′,2′′ terpyridinium analogue {bis[4′-(isoquinolin-2-ium-4-yl)-2,2′:6′,2′′-terpyridine-1,1′′-diium] tris[tetrachloridozincate(II)] monohydrate; Granifo et al. (2017). Acta Cryst. C73, 1121–1130}, although rather different and much simpler in its structural features, mainly in the number and type of non-covalent interactions present, as well as in the supramolecular structure they define.
Crystal structure and Hirshfeld surface analysis of (E)-N-[(2-ethoxynaphthalen-1-yl)methylidene]-5,6,7,8-tetrahydronaphthalen-1-amine. Corrigendum
Authors: Kansiz Sevgi , Macit Mustafa , Dege Necmi , Tsapyuk Galyna G.
Published: November 2018

In the paper by Kansiz et al. [Acta Cryst. (2018), E74, 1513–1516], the address of the correspondence author is incorrect.
Crystal structure and Hirshfeld surface analysis of two imidazo[1,2-a]pyridine derivatives: N-tert-butyl-2-(4-methoxyphenyl)-5-methylimidazo[1,2-a]pyridin-3-amine and N-tert-butyl-2-[4-(dimethylamino)phenyl]imidazo[1,2-a]pyridin-3-amine
Authors: Dhanalakshmi G. , Ramanjaneyulu Mala , Thennarasu Sathiah , Aravindhan S.
Published: November 2018

In the title imidazo[1,2-a]pyridine derivatives, N-tert-butyl-2-(4-methoxyphenyl)-5-methylimidazo[1,2-a]pyridin-3-amine, C19H23N3O, (I), and N-tert-butyl-2-[4-(dimethylamino)phenyl]imidazo[1,2-a]pyridin-3-amine, C19H24N4, (II), the 4-methoxyphenyl ring in (I) and the 4-(dimethylamino)phenyl ring in (II) are inclined to the respective imidazole rings by 26.69 (9) and 31.35 (10)°. In the crystal of (I), molecules are linked by N—H...N hydrogen bonds, forming chains propagating along the [001] direction. The chains are linked by C—H...π interactions, forming layers parallel to the (010) plane. In (II), the crystal packing also features N—H...N hydrogen bonds, which together with C—H...N hydrogen bonds link molecules to form chains propagating along the c-axis direction. The chains are linked by C—H...π interactions to form layers parallel to the (100) plane. Inversion-related layers are linked by offset π–π interactions [intercentroid distance = 3.577 (1) Å]. The intermolecular interactions of both compounds were analyzed using Hirshfeld surface analysis and two-dimensional fingerprint plots.
The actions of volatile anesthetics: a new perspective
Authors: Weinrich Michael , Worcester David L.
Published: November 2018

This article reviews recent work in applying neutron and X-ray scattering towards the elucidation of the molecular mechanisms of volatile anesthetics. Experimental results on domain mixing in ternary lipid mixtures, and the influence of volatile anesthetics and hydrostatic pressure are placed in the contexts of ion-channel function and receptor trafficking at the postsynaptic density.
3,4,6-Trimethyl-1-phenyl-5-(thiophen-3-yl)-1H-pyrazolo[3,4-b]pyridine
Authors: Loubidi Mohamed , Jouha Jabrane , Tber Zahira , El Hafi Mohamed , Essassi El Mokhtar , Mague Joel T.
Published: November 2018

In the title compound, C19H17N3S, the pyrazolo[3,4-b]pyridine unit is slightly bowed across the C—C bond common to the two rings. In the crystal, ribbons extending along the a-axis direction are formed by C—H...π(ring) interactions. The ribbons are packed into corrugated layers inclined to the ac plane by approximately 22°. The thiophenyl group is rotationally disordered over two sites 180° apart in a 0.606 (2)/0.394 (2) ratio.
1-(3-Hydroxypropyl)-3-phenylquinoxalin-2(1H)-one
Authors: Abad Nadeem , Ramli Youssef , Lahmidi Sanae , El Hafi Mohamed , Essassi El Mokhtar , Mague Joel T.
Published: November 2018

In the title molecule, C17H16N2O2, the quinoxaline portion is slightly folded about the N...N axis with an angle of 4.27 (4)°. In the crystal, O—H...O and weak C—H...O hydrogen bonds link molecules along the b-axis direction. In addition, two sets of weak C—H...π(ring) interactions form a two-dimensional `step' motif parallel to the bc plane.
The impact of cultural values and economic constraints on tourism businesses’ ethical practices
Authors: Skinner Heather
Published: November 2018

Purpose

Anecdotal evidence suggests that in times of economic constraints particularly in countries such as Greece that have long been stereotyped as corrupt, business practices amongst small- and medium-sized organisations that make up the majority of these nations’ tourism operators may become less than ethical or legal. The purpose of this paper is to explore these issues empirically in order to understand the impact of both cultural values and economic constraints on tourism businesses’ practices.

Design/methodology/approach

An exploratory case study using mixed methods has been adopted. Quantitative data were gathered from tourism business owners, managers and employees via questionnaires to establish the nature and scope of various unethical, illegal or immoral practices. Qualitative data were gathered to explore the ways these issues are considered and enacted.

Findings

Results show that there are many unethical and illegal practices that have been witnessed first-hand. Businesses’ attempts at acting in an ethical and socially responsible manner tend to be affected by not only cultural issues, but also economic constraints, yet there remains a desire to act in a way that does not impact negatively on tourists or on the local society and environment.

Originality/value

This research fills a gap in the literature relating to the ethical stance and practices of tourism entrepreneurs. It also presents an original conceptualisation of these issues in light of their location within the extant literature on ethics, corporate social responsibility and both sustainable and responsible tourism.
Simulation and measurement study of metro wheel wear based on the Archard model
Authors: Zhu AiHua , Yang Si , Li Qiang , Yang JianWei , Li Xi , Xie YiDong
Published: November 2018

Purpose

The purpose of this paper is to study the wear evolution of metro wheels under the conditions of different track sequences, track composition and vehicle load and then to predict wheel wear and to guide its maintenance.

Methodology

By using the SIMPACK and MATLAB software, numerical simulation analysis of metro wheel wear is carried out based on Hertz theory, the FASTSIM algorithm and the Archard model. First of all, the vehicle dynamics model is established to calculate the motion relationship and external forces of wheel-rail in the SIMPACK software. Then, the normal force of wheel-rail is solved based on Hertz theory, and the tangential force of wheel-rail is calculated based on the FASTSIM algorithm through the MATLAB software. Next, in the MATLAB software, the wheel wear is calculated based on the Archard model, and a new wheel profile is obtained. Finally, the new wheel profile is re-input into the vehicle system dynamics model in the SIMPACK software to carry out cyclic calculation of wear.

Findings

The results show that the setting order of different curves has an obvious influence on wear when the proportion of the straight track and the curve is fixed. With the increase in running mileage, the severe wear zone is shifted from tread to flange root under the condition of the sequence-type track, but the wheel wear distribution is basically stable for the unit-type track, and their wear growth rates become closer. In the tracks with different straight-curved ratio, the more proportion the curved tracks occupy, the closer the severe wear zone is shifted to flange root. At the same time, an increase in weight of the vehicle load will aggravate the wheel wear, but it will not change the distribution of wheel wear. Compared with the measured data of one city B type metro in China, the numerical simulation results of wheel wear are nearly the same with the measured data.

Practical implications

These results will be helpful for metro tracks planning and can predict the trend of wheel wear, which has significant importance for the vehicle to do the repair operation. At the same time, the security risks of the vehicle are decreased economically and effectively.

Originality/value

At present, many scholars have studied the influence of metro tracks on wheel wear, but mainly focused on a straight line or a certain radius curve and neglected the influence of track sequence and track composition. This study is the first to examine the influence of track sequence on metro wheel wear by comparing the sequence-type track and unit-type track. The results show that the track sequence has a great influence on the wear distribution. At the same time, the influence of track composition on wheel wear is studied by comparing different straight-curve ratio tracks; therefore, wheel wear can be predicted integrally under different track conditions.
Ownership feature and firm performance via corporate innovation performance
Authors: Nguyen Dung , Nguyen Hoai , Nguyen Kien S.
Published: November 2018

Purpose

The purpose of this paper is to investigate the simultaneous relationship among ownership concentration, innovation and firm performance of the small- and medium-sized enterprises (SMEs) in Vietnam during the 2011–2015. By employing a Conditional Mixed Process (CMP) model, the findings show that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation.

Design/methodology/approach

In this study, the authors propose the adaption of CMP model (Roodman, 2011). The nature of the first stage dependent variable – Innovation – is a binary one while the dependent variable Performance is continuous. Therefore, a model that can adapt the binary nature of the dependent variable and perform the estimation of a system of equations such as CMP model is preferred. The CMP framework is substantially that of seemingly unrelated regression, but with application in a larger scope. This approach is based on a “simulated maximum likelihood method” suggested by Geweke–Hajivassiliou–Keane algorithm.

Findings

By applying CMP method, this study examines the simultaneous relationship among ownership concentration, innovation and firm performance of the SMEs in Vietnam from 2011 to 2015. The findings indicate that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation.

Research limitations/implications

In spite of the efforts to explore the simultaneous relationship among ownership concentration, innovation and firm performance of the SMEs in Vietnam, the study still has some limitations which are promising further research directions. First, the SME surveys by Central Institute for Economic Management do not have much information about other types of ownership including state-owned and foreign ownership. Therefore, possible further studies with richer data sets may explore the impacts of different types of ownership on firm innovation and performance. Second, other types of innovation such as organizational innovation, marketing innovation can also be investigated in further studies in a richer data set for the case of Vietnam SMEs.

Originality/value

The findings show that: there is no impact of ownership concentration on innovation, but it has a positive impact on sales growth; innovation positively affects firm performance; and there exists a positively reverse causality from sales growth to innovation. The policy implications insist on facilitating SMEs with easier access to capital via loans with preferred interest or trust loans without collateral, training programs for the labor force and SME leaders, and reduction of unnecessary administrative procedure.