bluuebunny/crossref_metadata_2025_split huggingface dataset:
An apple long-chain acyl-CoA synthetase 2 gene enhances plant resistance to abiotic stress by regulating the accumulation of cuticular wax
Authors: Zhang Chun-Ling , Hu Xing , Zhang Ya-Li , Liu Yang , Wang Gui-Luan , You Chun-Xiang , Li Yuan-Yuan , Hao Yu-Jin 
Published: June 2020

Abstract
Apple cuticular wax can protect plants from environmental stress, determine fruit luster and improve postharvest fruit storage quality. In recent years, dry weather, soil salinization and adverse environmental conditions have led to declines in apple fruit quality. However, few studies have reported the molecular mechanisms of apple cuticular wax biosynthesis. In this study, we identified a long-chain acyl-CoA synthetase MdLACS2 gene from apple. The MdLACS2 protein contained an AMP-binding domain and demonstrated long-chain acyl-CoA synthetase activity. MdLACS2 transgenic Arabidopsis exhibited reductions in epidermal permeability and water loss; change in the expression of genes related to cuticular wax biosynthesis, transport and transcriptional regulation; and differences in the composition and ultrastructure of cuticular wax. Moreover, the accumulation of cuticular wax enhanced the resistance of MdLACS2 transgenic plants to drought and salt stress. The main protein functional interaction networks of LACS2 were predicted, revealing a preliminary molecular regulation pathway for MdLACS2-mediated wax biosynthesis in apple. Our study provides candidate genes for breeding apple varieties and rootstocks with better fruit quality and higher stress resistance.
Challenges in pain assessment and management among individuals with intellectual and developmental disabilities
Authors: Barney Chantel C. , Andersen Randi D. , Defrin Ruth , Genik Lara M. , McGuire Brian E. , Symons Frank J. 
Published: June 2020

Abstract

Introduction:
Intellectual and developmental disabilities (IDD) include conditions associated with physical, learning, language, behavioural, and/or intellectual impairment. Pain is a common and debilitating secondary condition compromising functional abilities and quality of life.

Objectives:
This article addresses scientific and clinical challenges in pain assessment and management in individuals with severe IDD.

Methods:
This Clinical Update aligns with the 2019 IASP Global Year Against Pain in the Vulnerable and selectively reviews recurring issues as well as the best available evidence and practice.

Results:
The past decade of pain research has involved the development of standardized assessment tools appropriate for individuals with severe IDD; however, there is little empirical evidence that pain is being better assessed or managed clinically. There is limited evidence available to inform effective pain management practices; therefore, treatment approaches are largely empiric and highly variable. This is problematic because individuals with IDD are at risk of developing drug-related side effects, and treatment approaches effective for other populations may exacerbate pain in IDD populations. Scientifically, we are especially challenged by biases in self-reported and proxy-reported pain scores, identifying valid outcome measures for treatment trials, being able to adequately power studies due to small sample sizes, and our inability to easily explore the underlying pain mechanisms due to compromised ability to self-report.

Conclusion:
Despite the critical challenges, new developments in research and knowledge translation activities in pain and IDD continue to emerge, and there are ongoing international collaborations.
A thermostable, closed, SARS-CoV-2 spike protein trimer
Authors: Xiong Xiaoli , Qu Kun , Ciazynska Katarzyna A. , Hosmillo Myra , Carter Andrew P. , Ebrahimi Soraya , Ke Zunlong , Scheres Sjors H.W. , Bergamaschi Laura , Grice Guinevere L. , Zhang Ying ,   The CITIID-NIHR COVID-19 BioResource Collaboration, Nathan James A. , Baker Stephen , James Leo C. , Baxendale Helen E. , Goodfellow Ian , Doffinger Rainer , Briggs John A.G. 
Published: June 2020

AbstractThe spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.
Identifying persistent structures in multiscale ‘omics data
Authors: Zheng Fan , Zhang She , Churas Christopher , Pratt Dexter , Bahar Ivet , Ideker Trey 
Published: June 2020

AbstractIn any ‘omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of “persistent homology”, drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.
Transposable element mobilization in interspecific yeast hybrids
Authors: Heil Caiti Smukowski , Patterson Kira , Hickey Angela Shang-Mei , Alcantara Erica , Dunham Maitreya J. 
Published: June 2020

AbstractBarbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements inSaccharomyces cerevisiae x Saccharomyces uvaruminterspecific yeast hybrids.S. cerevisiaehave a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relativeS. uvarumhave lost the Ty elements active inS. cerevisiae. While the regulation system of Ty elements is known inS. cerevisiae, it is unclear how Ty elements are regulated in otherSaccharomycesspecies, and what mechanisms contributed to the loss of most classes of Ty elements inS. uvarum. Therefore, we first assessed whether transposable elements could insert in theS. uvarumsub-genome of aS. cerevisiaexS. uvarumhybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in theS. uvarumgenome. We then used anin vivoreporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.
Modulation of inhibitory communication coordinates looking and reaching
Authors: Hagan Maureen A. , Pesaran Bijan 
Published: June 2020

SummaryLooking and reaching are controlled by different brain regions and coordinated during natural behaviour1–3. Understanding how flexible, natural behaviours like coordinated looking-and-reaching are controlled depends on understanding how neurons in different regions of the brain communicate4. Excitatory multiregional communication recruits neural coherence in a gamma-frequency (40-90 Hz) band5. Inhibitory control mechanisms are also required to flexibly control behaviour6, but little is known about how neurons in one region transiently suppress individual neurons in another to support behaviour. How does neuronal firing in a sender-region transiently suppress firing in a receiver-region? Here, we study inhibitory communication during a flexible, natural behaviour, termed gaze-anchoring, in which saccades are transiently inhibited by coordinated reaches. During gaze-anchoring, we find that neurons in the reach region of the posterior parietal cortex can inhibit neuronal firing in the parietal saccade region to suppress eye movements and improve reach accuracy. Importantly, suppression is transient, only present around the coordinated reach, and greatest when reach neurons fire spikes at a particular phase of beta-frequency (15-25 Hz) activity, not gamma-frequency activity. Our work provides evidence in the activity of single neurons for a novel mechanism of inhibitory communication in which beta-frequency neural coherence transiently inhibits multiregional communication to flexibly coordinate our natural behaviour.
Environmental and physiological factors affecting high-throughput measurements of bacterial growth
Authors: Atolia Esha , Cesar Spencer , Arjes Heidi A. , Rajendram Manohary , Shi Handuo , Knapp Benjamin D. , Khare Somya , Aranda-Díaz Andrés , Lenski Richard E. , Huang Kerwyn Casey 
Published: June 2020

AbstractBacterial growth in nutrient-rich and starvation conditions is intrinsically tied to the environmental history and physiological state of the population. While high-throughput technologies have enabled rapid analyses of mutant libraries, technical and biological challenges complicate data collection and interpretation. Here, we present a framework for the execution and analysis of growth measurements with improved accuracy over standard approaches. Using this framework, we demonstrate key biological insights that emerge from consideration of culturing conditions and history. We determined that quantification of the background absorbance in each well of a multi-well plate is critical for accurate measurements of maximal growth rate. Using mathematical modeling, we demonstrated that maximal growth rate is dependent on initial cell density, which distorts comparisons across strains with variable lag properties. We established a multiple-passage protocol that alleviates the substantial effects of glycerol on growth in carbon-poor media, and we tracked growth rate-mediated fitness increases observed during a long-term evolution ofEscherichia coliin low glucose concentrations. Finally, we showed that growth ofBacillus subtilisin the presence of glycerol induces a long lag in the next passage due to inhibition of a large fraction of the population. Transposon mutagenesis linked this phenotype to the incorporation of glycerol into lipoteichoic acids, revealing a new role for these envelope components in resuming growth after starvation. Together, our investigations underscore the complex physiology of bacteria during bulk passaging and the importance of robust strategies to understand and quantify growth.Abstract ImportanceHow starved bacteria adapt to and multiply in replete nutrient conditions is intimately linked to their history of previous growth, their physiological state, and the surrounding environment. While automated equipment has enabled high-throughput growth measurements, data interpretation and knowledge gaps regarding the determinants of growth kinetics complicate comparisons between strains. Here, we present a framework for growth measurements that improves accuracy and attenuates the effects of growth history. We determined that background absorbance quantification and multiple passaging cycles allows for accurate growth-rate measurements even in carbon-poor media, which we used to reveal growth-rate increases during long-term laboratory evolution ofEscherichia coli. Using mathematical modeling, we showed that maximum growth rate depends on initial cell density. Finally, we demonstrated that growth ofBacillus subtiliswith glycerol inhibits the future growth of most of the population, due to lipoteichoic-acid synthesis. These studies highlight the challenges of accurate quantification of bacterial growth behaviors.
Haplotype of RNASE 3 polymorphisms is associated with severe malaria in an Indian population
Authors: Mukhi Benudhar , Gupta Himanshu , Wassmer Samuel C. , Anvikar Anupkumar R. , Ghosh Susanta Kumar 
Published: June 2020

AbstractSevere malaria (SM) caused by Plasmodium falciparum (Pf) infection has been associated with life-threatening anemia, metabolic acidosis, cerebral malaria and multiorgan dysfunction. It may lead to death if not treated promptly. RNASE 3 has been linked to Pf growth inhibition and its polymorphisms found associated with SM and cerebral malaria in African populations. This study aimed to assess the association of RNASE 3 polymorphisms with SM in an Indian population. RNASE 3 gene and flanking regions were amplified followed by direct DNA sequencing in 151 Indian patients who visited Wenlock District Government Hospital, Mangalore, Karnataka, India. Allele, genotype and haplotype frequencies were compared between patients with SM (n=47) and uncomplicated malaria (UM; n=104). Homozygous mutant genotype was only found for rs2233860 polymorphism (<1% frequency). No significant genetic associations were found for RNASE 3 polymorphism genotypes and alleles in Indian SM patients. C-G-G haplotype of rs2233859, rs2073342 and rs2233860 polymorphisms was correlated significantly with SM patients (OR=3.03; p<0.001). Overall, these results suggest that RNASE 3 gene plays a role in susceptibility to severe malaria.
Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
Authors: Coventry Brian , Baker David 
Published: June 2020

AbstractIn aqueous solution, polar groups make hydrogen bonds with water, and hence burial of such groups in the interior of a protein is unfavorable unless the loss of hydrogen bonds with water is compensated by formation of new ones with other protein groups. Hence, buried “unsatisfied” polar groups making no hydrogen bonds are very rare in proteins. Efficiently representing the energetic cost of unsatisfied hydrogen bonds with a pairwise-decomposable energy term during protein design is challenging since whether or not a group is satisfied depends on all of its neighbors. Here we describe a method for assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are penalized. The penalty can be any quadratic function of the number of unsatisfied polar groups, and can be computed very rapidly. We show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the number of buried unsatisfied polar groups.
A critical role for MSR1 in vesicular stomatitis virus infection of the central nervous system
Authors: Yang Duomeng , Lin Tao , Harrison Andrew G. , Geng Tingting , Wang Huadong , Wang Penghua 
Published: June 2020

AbstractMacrophage scavenger receptor 1 (MSR1) plays an important role in host defense to bacterial infections, M2 macrophage polarization and lipid homeostasis. However, its physiological function in viral pathogenesis remains poorly defined. Herein, we report that MSR1 facilitates vesicular stomatitis virus (VSV) infection in the spinal cord. Msr1-deficient (Msr1-/-) mice presented reduced morbidity and mortality following lethal VSV infection, along with normal viremia and antiviral innate immune responses, compared toMsr1+/-littermates and wild-type mice. Msr1 expression was selectively upregulated in the spinal cord, which was the predominant target of VSV infection. The viral load in the spinal cord was positively correlated with Msr1 expression level and was reduced inMsr1-/-mice. Through its extracellular domain, MSR1 interacted with VSV surface glycoprotein and facilitated its cellular entry. In conclusion, our results demonstrate that MSR1 serves as a cellular entry receptor for VSV and facilitates its infection specifically in the spinal cord.
A multiplex CRISPR interference tool for virulence gene interrogation in an intracellular pathogen
Authors: Ellis Nicole A. , Kim Byoungkwan , Machner Matthias P. 
Published: June 2020

AbstractIn the absence of target cleavage, catalytically inactive dCas9 imposes transcriptional gene repression by sterically precluding RNA polymerase activity at a given gene to which it was directed by CRISPR (cr)RNAs. This gene silencing technology, referred to as CRISPRinterference (CRISPRi), has been employed in various bacterial species to interrogate genes, mostly individually or in pairs. Here, we developed a multiplex CRISPRi platform in the pathogenLegionella pneumophilacapable of silencing up to ten genes simultaneously. Constraints on precursor-crRNA expression by Rho-dependent transcription termination were overcome by combining a strong processive promoter with aboxAelement upstream of a repeat/spacer array. Using crRNAs directed against virulence protein-encoding genes, we demonstrated that CRISPRi is fully functional not only during growth in axenic media, but also during macrophage infection, and that gene depletion by CRISPRi fully recapitulated the growth defect of deletion strains. Importantly, by altering the position of crRNA-encoding spacers within the repeat/spacer array, our platform achieved the gradual depletion of targets that was mirrored by the severity in phenotypes. Multiplex CRISPRi thus holds great promise for probing large sets of genes in bulk in order to decipher virulence strategies ofL. pneumophilaand other bacterial pathogens.
Persistence of alternative reproductive tactics: a test of game theoretic predictions
Authors: Garrison Courtney R. , Sakaluk Scott K. , Dochtermann Ned A. 
Published: June 2020

AbstractIn many species, males produce signals to attract females. However, in some species and populations, only some males produce these signals with other males competing for and intercepting reproductive opportunities. In these systems, at least three tactics are expected:always signal, signal only when others are not (assessors), andnever signal. The expected representation of these tactics within a population is frequently unknown in part because the costs of signaling (C) and the fitness value of a single reproductive bout (V) are difficult to quantify. Using a game-theoretic model, we predicted that thealways signalstrategy should only be present in a population if the fitness value of calling is greater than twice the cost (2C < V). We found thatalways signalmales are apparently absent in decorated crickets (Gryllodes sigillatus), at least in our sampling of a laboratory housed population. Moreover, males were not strict assessors and instead signaled infrequently (30% of the time) when signaling by others was constant. Males also exhibited substantial among-individual variation in the propensity to call when other males were not signaling (τ = 0.3). Our results indicate a high relative cost of signaling (2C > V). The presence of among-individual variation in propensity to call is also suggestive of underlying genetic variation and a mixed evolutionary stable strategy. More generally, the apparent high cost of signaling and presence of variation in calling propensity suggests that reduced-cost strategies should spread quickly in populations.
Employee performance management: charting the field from 1998 to 2018
Authors: Maley Jane Frances , Dabic Marina , Moeller Miriam 
Published: June 2020

PurposeThe purpose of this paper is to study the development and consider the future of one of the most controversial areas of human resource development – employee performance management (PM).Design/methodology/approachThrough bibliometrics, a multiple correspondence analysis identifies the main research directions of PM studies and provides a map of descriptors and a list of authors, along with a framework to track PM literature over 20 years (1998–2018).FindingsScholars have attempted to address some of the questions raised by earlier researchers. However, critical questions remain unanswered, and there is increasing dissatisfaction with the process. The most glaring yet unaddressed problem with PM is poor employee acceptability of the process.Practical implicationsIf the research gaps are addressed, the lack of acceptability of the PM could be resolved and more effectively managed in the future.Originality/valueThe study particularly addresses poor employee “acceptability” of the PM process, a subject that has received limited attention by scholars.
Corporate payout policy: does product market competition matter? Evidence from Australia
Authors: Pham Hai-yen , Chung Richard , Bao Ben-Hsien , Min Byung-Seong 
Published: June 2020

PurposeThe purpose of this paper is to examine the impact of product market competition on dividend payout and share repurchases in Australia in which a full dividend imputation system has been in place since 1987.Design/methodology/approachPanel data estimation with industry and year-fixed effects is employed to examine the role of industry competition on dividend payout and share repurchases. The paper uses a sample of ASX200 non-financial firms, including 4,272 observations over the period 1992–2015. To address the endogeneity problem, the authors utilize the event of Australia–United States Free Trade Agreement (AUSFTA), which became effective on 01 January 2005, and perform a difference-in-difference analysis.FindingsThe authors find that firms operating in competitive markets are likely to pay more dividends and repurchase more shares to reduce agency costs. The positive relation between industry competition and dividends is stronger among firms where the CEO and the Chairman of the Board are the same person and among firms with higher market-to-book ratio and higher standard deviation of stock returns. The study results are robust when the authors account for the impact of franking credit on dividend payment. In the difference-in-difference analysis, the authors find strong evidence of a casual relation that product competition drives changes in dividend policy.Practical implicationsThe findings are consistent with the notion that intense product market competition can mitigate agency conflicts between managers and shareholders and with the information signalling explanation of market competition. As such, regulators may want to introduce policies that encourage more market competition (e.g. market deregulation) to enhance market efficiency.Originality/valueThis study incorporates product market competition in explaining the firm payout policy.