bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct
Authors: Kosno Martyna , Currie Simon L. , Kumar Ashwani , Xing Chao , Rosen Michael K. 
Published: May 2023

AbstractAberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma (NC). Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
Orientia tsutsugamushi:analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium
Authors: Giengkam Suparat , Kullapanich Chitrasak , Wongsantichon Jantana , Adcox Haley E. , Gillespie Joseph J. , Salje Jeanne 
Published: May 2023

AbstractThe rickettsial human pathogenOrientia tsutsugamushi(Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ∼2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra)type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.
Torsion of the heart tube by shortage of progenitor cells : identification ofGreb1las a genetic determinant of criss-cross hearts in mice
Authors: Bernheim Ségolène , Borgel Adrien , Garrec Jean-François Le , Perthame Emeline , Desgrange Audrey , Krezel Wojciech , Raimondi Francesca , Bonnet Damien , Houyel Lucile , Meilhac Sigolène M. 
Published: May 2023

SummaryDespite their burden and impact, most congenital defects remain poorly understood by lack of knowledge of the embryological mechanisms. Here, we identifyGreb1lmutants as the first mouse model of criss-cross heart. Based on 3D quantifications of shape changes, we demonstrate that torsion of the atrioventricular canal occurs together with supero-inferior ventricles at E10.5, after heart looping. Mutants phenocopy specific features of partial deficiency in retinoic acid signalling, suggesting that GREB1L is a novel modulator of this signalling. Spatio-temporal gene mapping and cross-correlated transcriptomic analyses further reveal the role ofGreb1lin maintaining a pool of precursor cells during heart tube elongation, by controlling ribosome biogenesis and cell differentiation. Growth arrest and malposition of the outflow tract are predictive of abnormal tube remodelling in mutants. Our work on a rare cardiac malformation opens novel perspectives on the origin of a broader spectrum of congenital defects associated withGREB1Lin humans.HighlightsGreb1linactivation is the first model of criss-cross heartGrowth arrest of the outflow tract and reduced pole distance are predictive of the torsion of the atrioventricular canal, and also account for associated defects of supero-inferior ventricles and malposition of the great vesselsVentricle position needs to be maintained after heart loopingGREB1L, which is associated in humans with a spectrum of congenital defects, is required to maintain precursor cells, by promoting ribosome biogenesis and restricting cell differentiation.GREB1L is a novel factor involved in retinoic acid signalling.In BriefGREB1Lis associated with a spectrum of congenital defects in humans. Bernheim et al now uncover its function in maintaining a reservoir of precursor cells. Inactivation ofGreb1lin the mouse impairs the elongation of the heart tube leading to criss-cross heart with supero-inferior ventricles.
LTP2hypomorphs show genotype-by-environment interaction in early seedling traits inArabidopsis thaliana
Authors: Alexandre Cristina M , Bubb Kerry L , Schultz Karla M , Lempe Janne , Cuperus Josh T , Queitsch Christine 
Published: May 2023

ABSTRACTIsogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits inArabidopsis thaliana, we found that hypomorphs of the cuticle-related geneLTP2greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Manyltp2hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild type. Differences in epidermal properties and gene expression betweenltp2seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation inltp2hypomorphs, and found that increased expression of its closest paralogLTP1is necessary forltp2phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.
Social navigation: distance and grid-like codes support navigation of abstract social space in human brain
Authors: Liang Zilu , Wu Simeng , Wu Jie , Wang Wenxu , Qin Shaozheng , Liu Chao 
Published: May 2023

AbstractPeople form impressions about others during daily social encounters and infer personality traits from others’ behaviors. Such trait inference is thought to rely on two universal dimensions, i.e., competence and warmth. These two dimensions can be used to construct a ‘social cognitive map’ organizing massive information obtained from social encounters efficiently. Originated from spatial cognition, the neural codes supporting representation and navigation of spatial cognitive map has been widely studied. Recent studies suggest similar neural mechanism subserves the map-like architecture in social cognition as well. Here we investigated how spatial codes operate beyond physical environment and support the representation and navigation of social cognitive map. We designed a social value space defined by two dimensions of competence and warmth. Behaviorally, participants were able to navigate to a learned location from random starting locations in this abstract social space. At neural level, we identified representation of distance in precuneus, fusiform gyrus and middle occipital gyrus. We also found partial evidence of grid-like representation patterns in medial prefrontal cortex and entorhinal cortex. Moreover, the intensity of grid-like response scaled with performance of navigating in social space and social avoidance trait scores. Our findings suggest a neurocognitive mechanism by which social information can be organized into a structured representation namely cognitive map and its relevance to social well-being.
Hippocampal contextualization of social rewards
Authors: Duarte Joana Mendes , Li Kaizhen , Nguyen Robin , Ciocchi Stéphane 
Published: May 2023

AbstractAcquiring and exploiting memories of rewarding experiences is critical for survival. The spatial environment in which a rewarding stimulus is encountered regulates memory retrieval. The ventral hippocampus (vH) has been implicated in contextual memories involving rewarding stimuli such as food, social cues or drugs. Yet, the spatial representations and circuits underlying contextual memories of socially rewarding stimuli are poorly understood. Here, usingin vivoelectrophysiological recordings during a social reward contextual conditioning paradigm in mice, we showed that vH neurons discriminate between contexts with neutral or acquired social reward value and exhibit a preferential remapping of their place fields to the context previously paired with social reward cues. The formation of context-discriminating vH neurons following learning was contingent upon the presence of salient reinforcers. Moreover, vH neurons showed different contextual representations during retrieval of social reward and fear contextual memories, suggesting different vH circuits underlie positively and negatively valenced contextual memories. Finally, optogenetic inhibition of locus coeruleus (LC) projections in the vH selectively disrupted social reward contextual memory by impairing vH contextual representations. Collectively, our findings reveal that the vH integrates contextual and social reward information, with memory encoding of these representations supported by input from the LC.
Cryo-EM structures of both ends of the actin filament explain why the barbed end elongates faster than the pointed end
Authors: Chou Steven Z. , Pollard Thomas D. 
Published: May 2023

AbstractActin filament ends are the sites of subunit addition during elongation and subunit loss during depolymerization. Prior work established the kinetics and thermodynamics of the assembly reactions at both ends but not the structural basis of their differences. Cryo-EM reconstructions of the barbed end at 3.1 Å resolution and the pointed end at 3.5 Å reveal distinct conformations at the two ends. These conformations explain why barbed ends elongate faster than pointed ends and why pointed ends rapidly dissociate the γ-phosphate released from ATP hydrolysis during assembly. The D-loop of the penultimate subunit at the pointed end is folded onto the terminal subunit, precluding its binding incoming actin monomers, and gates on the phosphate release channels of both subunits are wide open. The samples were prepared with FH2 dimers from fission yeast formin Cdc12. The barbed end reconstruction has extra density that may be partial occupancy by the FH2 domains.Significance StatementCells depend cytoplasmic filaments assembled from the protein actin for their physical integrity, as tracks for myosin motor proteins and movements of the whole cell and internal organelles. Actin filaments elongate and shrink at their ends by adding or dissociating single actin molecules. We used cryo-electron microscopy to determine the structures of the two ends of actin filaments at 3.5 Å resolution for the slowly growing pointed end and 3.1 Å for the rapidly growing barbed end. These structures reveal why barbed ends grow faster than the pointed ends, why the rate at the pointed end is not diffusion-limited and why the pointed end has a low affinity for the γ-phosphate released from bound ATP inside the filament.
Lipid-anchored Proteasomes Control Membrane Protein Homeostasis
Authors: Zhang Ruizhu , Pan Shuxian , Zheng Suya , Liao Qingqing , Jiang Zhaodi , Wang Dixian , Li Xuemei , Hu Ao , Li Xinran , Zhu Yezhang , Shen Xiaoqi , Lei Jing , Zhong Siming , Zhang Xiaomei , Huang Lingyun , Wang Xiaorong , Huang Lan , Shen Li , Song Bao-Liang , Zhao Jingwei , Wang Zhiping , Yang Bing , Guo Xing 
Published: May 2023

AbstractProtein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation (ERAD) and membrane protein trafficking. Rpt2G2A/G2Ahomozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation bymyristoyl-anchoredproteasomes (MAPs) in health and disease.
Spatiotemporal velocities, aggregation, and false dispersion: numerical considerations for the modeling of colonial and motile harmful algae
Authors: Opfer Jackie , Hondzo Miki , Voller V.R. 
Published: May 2023

Purpose
The purpose of this study is to investigate the errors arising from the numerical treatment of model processes, paying particular attention to the impact of key system features including widely variable dispersion coefficients, spatiotemporal velocities of algal cells, and the aggregation of algae from single cells to large colonies. An advection–dispersion model has been presented to describe the vertical transport of colonial and motile harmful algae in a lake environment.

Design/methodology/approach
Model performance is examined for two different numerical treatments of the advective term: first-order upwind and quadratic upwind with a stability-preserving flux limiter (SMART). To determine how these schemes impact predictions, comparisons are made across a sequence of models with increasing complexity.

Findings
Using first-order upwinding for advection–dispersion calculations with a time oscillating velocity field leads to oscillatory numerical dispersion. Subjecting an initially uniform distribution of large-sized algal colonies to a spatiotemporal velocity creates a concentration pulse, which reaches a steady-state width at high-grid Peclet numbers when using the SMART scheme; the pulse exhibits contraction–expansion behavior throughout a velocity cycle at all Peclet numbers when using first-order upwinding. When aggregation dynamics are included with advection-dominated spatiotemporal transport, results indicate the SMART scheme predicts larger peak concentration values than those predicted by first-order upwind, but peak location and the time to large colony appearance remain largely unchanged between the two advective schemes.

Originality/value
To the best of the authors’ knowledge, this study is the first numerical investigation of a novel advection–dispersion model of vertical algal transport. In addition, a generalized expression for the effective dispersion coefficient of temporally variable flow fields is presented.
Industrial revolution and environmental sustainability: an analytical interpretation of research constituents in Industry 4.0
Authors: Malik Arun , Sharma Shamneesh , Batra Isha , Sharma Chetan , Kaswan Mahender Singh , Garza-Reyes Jose Arturo 
Published: May 2023

PurposeEnvironmental sustainability is quickly becoming one of the most critical issues in industry development. This study aims to conduct a systematic literature review through which the author can provide various research areas to work on for future researchers and provide insight into Industry 4.0 and environmental sustainability.Design/methodology/approachThis study accomplishes this by performing a backward analysis using text mining on the Scopus database. Latent semantic analysis (LSA) was used to analyze the corpus of 4,364 articles published between 2013 and 2023. The authors generated ten clusters using keywords in the industrial revolution and environmental sustainability domain, highlighting ten research avenues for further exploration.FindingsIn this study, three research questions discuss the role of environmental sustainability with Industry 4.0. The author predicted ten clusters treated as recent trends on which more insight is required from future researchers. The authors provided year-wise analysis, top authors, top countries, top sources and network analysis related to the topic. Finally, the study provided industrialization’s effect on environmental sustainability and the future aspect of automation.Research limitations/implicationsThe reliability of the current study may be compromised, notwithstanding the size of the sample used. Poor retrieval of the literature corpus can be attributed to the limitations imposed by the search words, synonyms, string construction and variety of search engines used, as well as to the accurate exclusion of results for which the search string is insufficient.Originality/valueThis research is the first-ever study in which a natural language processing technique is implemented to predict future research areas based on the keywords–document relationship.
Empowering leadership for contextual performance: serial mediation of organizational support and commitment
Authors: Pazetto Celliane Ferraz , Luiz Thiago Tomaz , Beuren Ilse Maria 
Published: May 2023

PurposeThis study analyzes, from the perspective of social exchange theory, the influence of empowering leadership on contextual performance mediated by perceived organizational support (POS) and affective organizational commitment (AOC).Design/methodology/approachA survey was carried out with 182 employees of the Best Companies to Work in Brazil. Data analysis was performed by structural equation modeling (SEM) and by fuzzy set qualitative comparative analysis (fsQCA).FindingsResults demonstrate that empowering leadership directly influences higher contextual performance and indirectly through the mediation of AOC, but not through POS. Serial mediation confirms that the model's variables self-promote each other to ultimately foster higher performance. Furthermore, all solutions to obtain high contextual performance include empowering leadership in the dimension of trust in the high performance of employees.Research limitations/implicationsThe statistical support for the serial mediation indicates that empowering leadership promotes POS, which influences AOC that finally promotes the employee's contextual performance. However, this study's model does not include employees' task performance; our results add to the contextual performance literature.Practical implicationsThe study highlights the role of the empowering leadership style in the organizational context, an aspect that deserves attention from the managers and organizations due to its effect on employee performance.Originality/valueThe study adds a new framework to the literature, which can be used by organizations to promote contextual performance. The variables, which include contextual and individual factors, foster the employee's contextual performance in a joint and self-promoting way. Contextual performance exceeds the manager's technical attributions; it covers psychological and discretionary behaviors.
Does CSR contribute to the financial sector's financial stability? The moderating role of a sustainability committee
Authors: Orazalin Nurlan , Kuzey Cemil , Uyar Ali , Karaman Abdullah S. 
Published: May 2023

PurposeThis study tests whether corporate social responsibility (CSR) performance is a predictor of the financial sector's financial stability (FS), with the moderation of a sustainability committee.Design/methodology/approachThe sample covers financial sector firms included in the Thomson Reuters Eikon database. The analyses are based on 8,840 firm-year observations for the years between 2002 and 2019 and the country-firm-year fixed-effects (FE) regression analysis is executed.FindingsThe results reveal that CSR initiatives contribute to the financial sector's FS as a whole and the sector's three individual sub-sectors. This proven significant association holds for all sub-sectors, namely insurance, banking, and investment banking. Moreover, the moderation analysis reveals the prominent role of a sustainability committee in bridging CSR performance (CSRP) with FS.Research limitations/implicationsThe findings highlight that meeting societies' expectations pays back in the form of greater FS in the financial sector.Practical implicationsThe findings suggest that CSR engagement helps the financial sector firms manage their risks and alleviates exposure to insolvency. This is because CSR performance promotes firms' accountability and transparency toward stakeholders. The results help motivate managers to pursue CSR goals more seriously to ensure FS. The moderation analysis implies that sustainability committees develop policies and practices to integrate the non-financial and financial goals of the firm.Originality/valueAlthough prior studies have examined the link between CSR and financial performance (FP) in the financial sector, those studies have largely ignored FS in terms of risk-adjusted performance. Besides, prior studies have exclusively focused on the banking sector, but the authors concentrate on the banking, insurance, and investment banking sectors.