bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Pore Complex Acetylation Regulates mRNA Export and Cell Cycle Commitment in Budding Yeast
Authors: Gomar-Alba Mercè , Pozharskaia Vasilisa , Schaal Celia , Kumar Arun , Jacquel Basile , Charvin Gilles , Igual J. Carlos , Mendoza Manuel 
Published: September 2021

AbstractNuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyl-transferases (KATs) promote transcription through acetylation of chromatin-associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export. Acetylation of Nup60 recruits to the nuclear basket the mRNA export factor Sac3, the scaffolding subunit of the Transcription and Export 2 (TREX-2) complex. Esa1-dependent nuclear export of mRNAs promotes entry into S phase, and is inhibited by the Hos3 deacetylase in G1 daughter cells to restrain their premature commitment to a new cell division cycle. This mechanism also inhibits expression of the nutrient-regulated GAL1 gene specifically in daughter cells. These results reveal how acetylation contributes to the functional plasticity of NPCs in specific cell types, and demonstrate how the evolutionarily conserved NuA4 complex regulates gene expression dually at the level of transcription and mRNA export, by modifying the nucleoplasmic entrance to nuclear pores.
Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere
Authors: Lidbury Ian D.E.A. , Raguideau Sebastien , Liu Senlin , Murphy Andrew R. J. , Stark Richard , Borsetto Chiara , Fraser Tandra , Goodall Andrew , Bottrill Andrew , Jones Alex , Bending Gary D. , Tibbet Mark , Hammond John P. , Quince Chris , Scanlan David J. , Pandhal Jagroop , Wellington Elizabeth M. H. 
Published: September 2021

AbstractThe advance of DNA sequencing technologies has drastically changed our perception of the complexity and structure of the plant microbiome and its role in augmenting plant health. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and their specific functional role is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (meta-exoproteomics) expressed in the rhizosphere of Brassica spp. First, we validated our method in the laboratory by successfully identifying proteins related to the host plant (Brassica rapa) and a bacterial inoculant, Pseudomonas putida BIRD-1, revealing the latter expressed numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients. Next, we analysed natural field-soil microbial communities associated with Brassica napus L (Oil Seed rape). By combining deep-sequencing metagenomics with meta-exoproteomics, a total of 1882 proteins were identified in bulk and rhizosphere samples. Importantly, meta-exoproteomics identified a clear shift (p<0.001) in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. By providing the first meta-proteomic level assessment of the ‘active’ plant microbiome at the field-scale, this study demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant: microbe interactions driving plant growth.
Small proline-rich proteins (SPRRs) are epidermally produced antimicrobial proteins that defend the cutaneous barrier by direct bacterial membrane disruption
Authors: Zhang Chenlu , Hu Zehan , Lone Abdul G. , Artami Methinee , Edwards Marshall , Zouboulis Christos C. , Stein Maggie , Harris-Tryon Tamia A. 
Published: September 2021

AbstractHuman skin functions as a physical barrier, preventing the entry of foreign pathogens while also accommodating a myriad of commensal microorganisms. A key contributor to the skin landscape is the sebaceous gland. Mice devoid of sebocytes are prone to skin infection, yet our understanding of how sebocytes function in host defense is incomplete. Here we show that the small proline-rich proteins, SPRR1 and SPRR2 are bactericidal in skin. SPRR1B and SPPR2A were induced in human sebocytes by exposure to the bacterial cell wall component lipopolysaccharide (LPS). Further, LPS injected into mouse skin triggered the expression of the mouse SPRR orthologous genes, Sprr1a and Sprr2a, through stimulation of MYD88. Both mouse and human SPRR proteins displayed potent bactericidal activity against MRSA (methicillin-resistant Staphylococcus aureus), Pseudomonas aeruginosa and skin commensals. Thus, Sprr1a-/-;Sprr2a-/- mice are more susceptible to MRSA and Pseudomonas aeruginosa skin infection. Lastly, mechanistic studies demonstrate that SPRR proteins exert their bactericidal activity through binding and disruption of the bacterial membrane. Taken together, these findings provide insight into the regulation and antimicrobial function of SPRR proteins in skin and how the skin defends the host against systemic infection.
High-altitude adaptation and incipient speciation in geladas
Authors: Chiou Kenneth L. , Janiak Mareike C. , Schneider-Crease India , Sen Sharmi , Ayele Ferehiwot , Chuma Idrissa S. , Knauf Sascha , Lemma Alemayehu , Signore Anthony V. , D’Ippolito Anthony M. , Abebe Belayneh , Haile Abebaw Azanaw , Kebede Fanuel , Fashing Peter J. , Nguyen Nga , McCann Colleen , Houck Marlys L. , Wall Jeffrey D. , Burrell Andrew S. , Bergey Christina M. , Rogers Jeffrey , Phillips-Conroy Jane E. , Jolly Clifford J. , Melin Amanda D. , Storz Jay F. , Lu Amy , Beehner Jacinta C. , Bergman Thore J. , Snyder-Mackler Noah 
Published: September 2021

AbstractSurvival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.
A conserved glutamate residue in RPM1-interacting protein4 is ADP-ribosylated by Pseudomonas effector AvrRpm2 to activate RPM1-mediated response
Authors: Yoon Minsoo , Middleditch Martin , Rikkerink Erik 
Published: September 2021

ABSTRACTGram-negative bacterial plant pathogens directly inject effectors into their hosts to hijack and manipulate metabolism, eluding the frontier surveillance at the cell surface. The effector AvrRpm1Pma from Pseudomonas syringae pv. maculicola functions as an ADP-ribosyl transferase, modifying RPM1-interacting protein4 (RIN4), leading to the activation of Arabidopsis resistance protein RPM1. We identified the ADP-ribosyl transferase activity of another bacterial effector AvrRpm2Psa from Pseudomonas syringae pv. actinidiae via infection using a Pseudomonas syringae pv. tomato strain following Agrobacterium-mediated transient expression of RIN4 in N. benthamiana. We conducted mutational analysis in combination with mass spectrometry to genetically locate the modified residue. We show that a conserved glutamate residue (E156) of AtRIN4 is the target site for AvrRpm2Psa by demonstrating the modified AtRIN4 with E156A substitution is no longer ADP-ribosylated. Accordingly, naturally occurring soybean and snap bean RIN4 homologs with no glutamate at the positions corresponding to the E156 of AtRIN4 are not ADP-ribosylated by AvrRpm2Psa. In contrast with another effector AvrB, modifications of potential phosphorylation sites including T166 in AtRIN4 affected neither ADP-ribosylation nor RPM1 activation by AvrRpm2Psa. This study suggests that separate biochemical reactions by different pathogen effectors may trigger the activation of the same resistance protein through distinct modifications of RIN4.One sentence summaryA conserved glutamate residue (E156) in the C-NOI domain of RPM1-interacting protein4 is ADP-ribosylated by Pseudomonas effector AvrRpm2 to activate RPM1-mediated defence response, independently of phosphorylation at T166.
Fast and interpretable non-negative matrix factorization for atlas-scale single cell data
Authors: DeBruine Zachary J. , Pospisilik J. Andrew , Triche Timothy J. 
Published: September 2021

AbstractNon-negative matrix factorization (NMF) is a popular method for analyzing strictly positive data due to its relatively straightforward interpretation. However, NMF has a reputation as a less efficient alternative to the singular value decomposition (SVD), a standard operation that is highly optimized in most linear algebra libraries. Sparse single-cell sequencing assays, now feasible in thousands of subjects and millions of cells, generate data matrices with tens of thousands of strictly non-negative transcript abundance entries. We present an extremely fast NMF implementation made available in the RcppML (Rcpp Machine Learning library) R package that rivals the runtimes of state-of-the-art Singular Value Decomposition (SVD). NMF can now be run quickly on desktop computers to analyze sparse single-cell datasets consisting of hundreds of thousands of cells. Our method improves upon current NMF implementations by introducing a scaling diagonal to increase interpretability, guarantee consistent regularization penalties across different random initializations, and symmetry in symmetric factorizations. We use our method to show how NMF models learned on standard log-normalized count data are interpretable dimensional reductions, describe interpretable patterns of coordinated gene activities, and explain biologically relevant metadata. We believe NMF has the potential to replace PCA in most single-cell analyses, and the presented NMF implementation overcomes previous challenges with long runtime.
Nanobody-Functionalized Cellulose for Capturing and Containing SARS-CoV-2
Authors: Sun Xin , Yang Shaobo , Al-Dossary Amal A. , Broitman Shana , Ni Yun , Yang Mengdi , Li Jiahe 
Published: September 2021

ABSTRACTThe highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 217 million people, claiming ~ 4.5 million lives to date. Although mandatory quarantines, lockdowns, and vaccinations help curb viral transmission, safe and effective preventative measures remain urgently needed. Here, we present a generic strategy for containing SARS-CoV-2 by cellulose materials. Specifically, we developed a bifunctional fusion protein consisting of a cellulose-binding domain and a nanobody (Nb) targeting the receptor-binding domain of SARS-CoV-2. The immobilization of the fusion proteins on cellulose substrates enhanced the capture efficiency of Nbs against SARS-CoV-2 pseudoviruses of the wildtype and the D614G variant, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography with highly porous cellulose for neutralizing virus from contaminated fluids in a continuous and cost-effective fashion. Taken together, our work leverages low-cost cellulose materials and recently developed Nbs to provide a complementary approach to addressing the pandemic.IMPORTANCEThe ongoing efforts to address the COVID-19 pandemic center around the development of point-of-care diagnostics, preventative measures, and therapeutic strategies against COVID-19. In contrast to existing work, we have provided a complementary approach to target and contain SARS-CoV-2 from contaminated fluids and surfaces. Specifically, we present a generic strategy for the capture and containing of SARS-CoV-2 by cellulose-based substrates. This was archived by developing a bifunctional fusion protein consisting of both a cellulose-binding domain and a nanobody specific for the receptor-binding domain of SARS-CoV-2. As a proof-of-concept, our fusion protein-coated cellulose substrates exhibited enhanced capture efficiency against SARS-CoV-2 pseudovirus of both wildtype and the D614G mutant variants, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography with highly porous cellulose for neutralizing the virus from contaminated fluids in a highly continuous and cost-effective fashion.
Root-specific reduction of cytokinin perception enhances shoot growth with an alteration of trans-zeatin distribution in Arabidopsis thaliana
Authors: Monden Kota , Kojima Mikiko , Takebayashi Yumiko , Suzuki Takamasa , Nakagawa Tsuyoshi , Sakakibara Hitoshi , Hachiya Takushi 
Published: September 2021

AbstractCompelling evidence demonstrates that root-derived cytokinins (CKs) contribute to shoot growth via long-distance transport; therefore, we hypothesized that an increase in root-derived CKs enhances shoot growth. To demonstrate this, we grafted Arabidopsis Col-0 (WT) scion onto rootstock originated from WT or a double-knockout line of CK receptors AHK2 and AHK3 (ahk23) because the knockout line over accumulates CKs in the body due to feedback homeostasis regulation. The grafted plants (scion/rootstock: WT/WT and WT/ahk23) were grown in vermiculite pots or solid media under high and low nitrogen regimes for vegetative growth and biochemical analysis. The root-specific deficiency of AHK2 and AHK3 increased root concentrations of trans-zeatin (tZ)-type and N6-(Δ2-isopentenyl) adenine (iP)-type CKs, induced CK biosynthesis genes, and repressed CK degradation genes in the root. Shoot growth, shoot concentrations of tZ-type CKs, and shoot expression of CK-inducible marker genes were consistently larger in the WT/ahk23 plants than in the WT/WT plants. Moreover, the root-specific deficiency of AHK2 and AHK3 enhanced shoot growth in the WT scion more strongly than in the ahk23 scion. Given that tZ-type CKs are predominantly produced from iP-type CKs in the root and xylem-mobile, it is concluded that the root-specific reduction of CK perception would enhance shoot growth by increasing the amount of root-derived tZ-type CKs and their perception by the shoot. This study will present a novel approach to improve plant growth and productivity.
The dynamic relationship of knowledge management processes and project success: modeling the mediating role of knowledge worker satisfaction
Authors: Shahzadi Anum , Li Shuangyan , Sahibzada Umar Farooq , Malik Mehwish , Khalid Roshi , Afshan Gul 
Published: September 2021

PurposeConstructed upon a knowledge-based view, the purpose of this paper aims to empirically examine the entrepreneurial leadership impact as knowledge management enabler on knowledge management processes and knowledge management processes on project success. The study further ascertains the mediating role of knowledge worker satisfaction among knowledge management processes and project success.Design/methodology/approachUsing the data collected from 302 project workers from the software industry, China. The research used structural equation modeling (SEM) to analyze the hypothesis relationships using smart-PLS 3.2.9.FindingsThe outcome of the study reveals that entrepreneurial leadership has a substantial significant impact on knowledge management processes, and knowledge management processes influence project success via knowledge worker satisfaction as a mediator both directly and indirectly. Moreover, the study found partial mediation of knowledge worker satisfaction between knowledge management processes and project success.Practical implicationsThe current research identifies that entrepreneurial leadership may play a role in fostering knowledge management processes in project-based organizations (e.g. software industry) that can use the knowledge management processes to increase their chances of project success. More broadly, the current study contributes to the entrepreneurial leadership, knowledge management processes, knowledge worker satisfaction and project success existing literature and strengthens the relationship and suggest that how project manager's value knowledge worker satisfaction and help organizations gain competitive advantage and project success.Originality/valueAlthough there is an increased significance of knowledge management in the software industry, there is a lack of research that examines the enabling factors and outcomes of knowledge management practices. The present study is one of the first studies to ascertain the relationship of entrepreneurial leadership, knowledge management processes, knowledge worker satisfaction and project success. This is one of the initial researches that not only empirically examines the interrelationships among these variables but also enlighten insights into the current literature by instantaneous investigation of the mediating role of knowledge worker satisfaction.
The global business cycle and speculative demand for crude oil
Authors: Neves Elisabete , Oliveira Vítor , Leite Joana , Henriques Carla 
Published: September 2021

PurposeThis paper aims to better understand if speculative activity is a factor or even the main factor in the run-up of oil prices in the spot market, particularly in the recent price bubble that occurred in the period from mid-2003 to 2008.Design/methodology/approachThe methodology used is based on an existing vector autoregressive model proposed by Kilian and Murphy (2014), which is a structural model of the global market for crude oil that accounts for flow demand and flow supply shocks and speculative demand oil shocks.FindingsFrom the output of the authors’ structural model, the authors ruled out speculation as a factor of rising oil prices. The authors have found instead that the rapid oil demand caused by an unexpected increase in the global business cycle is the most accurate culprit. Despite the change of perspective in the speculative component, the authors’ conclusions concur with the findings of Kilian and Murphy (2014) and others.Originality/valueAs far as the authors are aware, this is the first time that a study has used as a spread oil variable, a speculative component of the real price, replacing the oil inventories considered by Kilian and Murphy (2014). Another contribution is that the model used allows estimating traditional oil demand elasticity in production and oil supply elasticity in spread movements, casting doubt on existing models with perfect price-inelastic output for crude oil.
How far the ownership structure is relevant for CSR performance? An empirical investigation
Authors: Pareek Ritu , Sahu Tarak Nath 
Published: September 2021

PurposeTaking hints from the lacunas in the field of ownership structure and corporate social responsibility (CSR) performance of the firms in India, especially when the moderating effect of certain corporate governance mechanism comes into play, this study aims to attempt to fulfill the gap by exploring the ownership structure of the firm (i.e. foreign ownership, institutional ownership and government ownership) and the CSR performance of the firm, when moderated by board independence of the firm. In an additional analysis, the study explores the non-linear effect of foreign ownership structure on the CSR performance in the Indian context.Design/methodology/approachThe study incorporates a strongly balanced panel data set of 280 non-financial National Stock Exchange 500 listed firms for the study period of 2013–2019. The study uses both static and Arellano–Bond dynamic panel model under generalized method of moments (GMMs) framework to establish the relationship between the studied variables.FindingsThe study acknowledges a positive impact of the foreign investors in the CSR performance of Indian firms with a higher proportion of independent directors on the board. The study further finds a contrarian role of government ownership in Indian context among the sampled firms. The study also in its extended analysis finds a non-linear inverted U-shaped relationship between foreign ownership (FO) and the CSR performance, which shows that FO positively impacts the CSR performance until a threshold level of 34% after which the curve starts declining.Practical implicationsOne of the major implications this study provides for the corporate policymakers is that the firms with a string penchant for philanthropic activities such as CSR should be concerned with attracting more foreign investors in their shareholding. Also, a higher proportion of independent directors on the board boost the engagement of the firm in CSR works.Originality/valueThe moderating effect of board independence in the ownership structure–CSR relationship attempted by this study is a rare attempt in a developing economy, such as India, and offers a fresh dimension to the study. Also, the non-linearity relationship between FO and the CSR performance and the threshold level providing the twofold effect of the variables is an innovative research attempt, especially in regard to a developing country like India.
Cybersecurity educational games: a theoretical framework
Authors: Hwang Mark I. , Helser Susan 
Published: September 2021

Purpose
Computer games that teach cybersecurity concepts have been developed to help both individuals and organizations shore up their defence against cybercrimes. Evidence of the effectiveness of these games has been rather weak, however. This paper aims to guide the design and testing of more effective cybersecurity educational games by developing a theoretical framework.

Design/methodology/approach
A review of the literature is conducted to explore the dependent variable of this research stream, learning outcomes and its relationship with four independent variables, game characteristics, game context, learning theory and user characteristics.

Findings
The dependent variable can be measured by five learning outcomes: information, content, strategic knowledge, eagerness to learn/time spent and behavioral change. Game characteristics refer to features that contribute to a game’s usefulness, interactivity, playfulness or attractiveness. Game context pertains to factors that determine how a game is used, including the target audience, the skill involved and the story. Learning theory explains how learning takes place and can be classified as behaviorism, cognitivism, humanism, social learning or constructivism. User characteristics including gender, age, computer experience, knowledge and perception, are attributes that can impact users’ susceptibility to cybercrimes and hence learning outcomes.

Originality/value
The framework facilitates taking stock of past research and guiding future research. The use of the framework is illustrated in a critique of two research streams. Multiple research directions are discussed for continued research into the design and testing of next-generation cybersecurity computer games.