bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATAC and SAGA coactivator complexes utilize co-translational assembly, but their cellular localization properties and functions are distinct
Authors: Yayli Gizem , Bernardini Andrea , Mendoza Sanchez Paulina Karen , Scheer Elisabeth , Damilot Mylène , Essabri Karim , Morlet Bastien , Negroni Luc , Vincent Stéphane D. , Timmers HT Marc , Tora László 
Published: August 2023

SummaryTo understand the function of multisubunit complexes it is of key importance to uncover the precise mechanisms that guide their assembly. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the core modules of ATAC (ADA-Two-A-Containing) and SAGA (Spt-Ada-Gcn5-acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. In addition, SAGA complex containing all of its modules forms in the cytoplasm and acetylates non-histones proteins. In contrast, fully assembled ATAC complex cannot be detected in the cytoplasm of mammalian cells. However, endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related coactivators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic abundance and functions are distinct.
Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly
Authors: Liu Xiao , Husby Monica , Stahelin Robert V. , Pienaar Elsje 
Published: August 2023

AbstractEbola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 (BSL-4) laboratories hinders experimental work to advance our understanding of EBOV and evaluation of treatment. In this work, we use a computational model to study the assembly and budding process of EBOV and evaluate the effect of fendiline on these processes. Our results indicate that the assembly of VP40 filaments may follow the nucleation-elongation theory, as it is critical to maintain a pool of VP40 dimer for the maturation and production of virus-like particles (VLPs). We further find that the nucleation-elongation process can also be influenced by phosphatidylserine (PS), which can complicate the efficacy of fendiline, a drug that lowers cellular PS levels. We observe that fendiline may increase VLP production at earlier time points (24 h) and under low concentrations (≤ 2 μM). But this effect is transient and does not change the conclusion that fendiline generally decreases VLP production. We also conclude that fendiline can be more efficient at the stage of VLP budding relative to earlier phases. Combination therapy with a VLP budding step-targeted drug may further increase the treatment efficiency of fendiline. Finally, we also show that fendiline has higher efficacy when VP40 expression is high. While these are single-cell level results based on the VP40 system, it points out a potential way of fendiline application affecting EBOV assembly, which can be further tested in experimental studies with multiple EBOV proteins or live virus.ImportanceEBOV infection can cause deadly hemorrhagic fever, which has a mortality rate around 90% without treatment. The recent outbreaks in Uganda and Democratic Republic of the Congo illustrate its treat to human health. Though two antibody-based treatments are approved, mortality rates in the last outbreak is still higher than 30%. This can partly be due to the requirement of advanced medical facilities for current treatments. As a result, it is very important to develop and evaluate new therapies for EBOV infection, especially those can be easily applied in the developing world. The significance of our research is that we evaluate the potential treatment effect of fendiline on EBOV infection in the VP40 system with a computational approach, which both greatly saves time and lowers cost compared to traditional experimental studies, and provides innovative new tools to study viral protein dynamics.
The Prp19C subunits Cwc15 and Syf2 function in TREX occupancy and transcription elongation
Authors: Henke-Schulz Laura , Minocha Rashmi , Sträßer Katja 
Published: August 2023

ABSTRACTThe Prp19 complex (Prp19C) is conserved from yeast to human and functions in many different processes such as genome stability, splicing and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX in turn couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunits Syf2 and Cwc15 in the interaction of Prp19C and TREX with the transcription machinery, Prp19C and TREX occupancy as well as transcription elongation. Whereas both proteins are important for Prp19C-TREX interaction, Syf2 is needed for full Prp19C occupancy, and Cwc15 is important for the interaction of Prp19C with RNA polymerase II and TREX occupancy. These partially overlapping functions are corroborated by a genetic interaction betweenΔcwc15andΔsyf2. Finally, Cwc15 also interacts genetically with the transcription elongation factor Dst1 and functions in transcription elongation. In summary, we uncover novel roles of the nonessential Prp19C components Syf2 and Cwc15 in Prp19C’s function in transcription elongation.
A unifying computational account of temporal context effects in language across the human cortex
Authors: Vo Vy Ai , Jain Shailee , Beckage Nicole , Chien Hsiang-Yun Sherry , Obinwa Chiadika , Huth Alexander G. 
Published: August 2023

SummaryDeep learning advances have revolutionized computational modeling approaches in neuroscience. However, their black-box nature makes it challenging to use deep learning models to discover new insights about brain function. Focusing on human language processing, we propose a new framework to improve the quality and interpretability of the inferences we make from deep learning-based models. First, we add interpretable components to a deep language model and use it to build a predictive encoding model. Then, we use the model’s predictive abilities to simulate brain responses to controlled stimuli from published experiments. We find that our model, based on a multi-timescale recurrent neural network, captures many previously reported temporal context effects in human cortex. Its failure to capture other effects also highlights important gaps in current language models. Finally, we use this new framework to generate model-based evidence that supports the proposal that different linguistic features are represented at different timescales across cortex.
Number of kinesins engaged in axonal cargo transport: A novel biomarker for neurological disorders
Authors: Hayashi Kumiko , Sasaki Kazuo 
Published: August 2023

ABSTRACTKinesin motor proteins play crucial roles in anterograde transport of cargo vesicles in neurons, moving them along axons from the cell body towards the synaptic region. Not only the transport force and velocity of single motor protein, but also the number of kinesin molecules involved in transporting a specific cargo, is pivotal for synapse formation. This collective transport by multiple kinesins ensures stable and efficient cargo transport in neurons. Abnormal increases or decreases in the number of engaged kinesin molecules per cargo could potentially act as biomarkers for neurodegenerative diseases such as Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis (ALS), spastic paraplegia, polydactyly syndrome, and virus transport disorders. We review here a model constructed using physical measurements to quantify the number of kinesin molecules associated with their cargo, which could shed light on the molecular mechanisms of neurodegenerative diseases related to axonal transport.
The structure of immature tick-borne encephalitis virus
Authors: Anastasina Maria , Füzik Tibor , Domanska Aušra , Pulkkinen Lauri IA , Šmerdová Lenka , Formanová Petra Pokorná , Straková Petra , Nováček Jiří , Růžek Daniel , Plevka Pavel , Butcher Sarah J 
Published: August 2023

AbstractTick-borne encephalitis virus (TBEV) is a medically important flavivirus that poses a significant health threat in Europe and Asia. However, the structure of the immature form of TBEV remains unknown. Here, we employed state-of-the-art cryogenic electron microscopy (cryoEM) to determine the structure of the immature TBEV particle. The immature TBEV particle has a diameter of 56 nm and its surface glycoproteins are organised into spikes characteristic of immature flaviviruses. The cryoEM reconstructions of the whole virus and of the individual spike enabled us to build atomic models of the major viral components, the E and prM proteins. The insights obtained from our study provide a foundation for understanding the early stages of TBEV assembly and maturation. The pr domains of prM have a critical role in holding the heterohexameric prM3E3 spikes in metastable conformation. Destabilisation of the prM furin-sensitive loop at acidic pH facilitates its processing. The prM cleavage, the collapse of E protein ectodomains onto the virion surface concurrent with significant movement of the membrane domains of both E and M, and release of the pr fragment from the particle render the virus mature and infectious. This knowledge contributes to our understanding of the flavivirus life cycle.
Carbapenem- and cefiderocol-resistantEnterobacteralesin surface waters in Kumasi, Ashanti Region, Ghana
Authors: Eger Elias , Homeier-Bachmann Timo , Adade Eugene , Dreyer Sylvia , Heiden Stefan E. , Tawiah Patrick Ofori , Sylverken Augustina Angelina , Knauf Sascha , Schaufler Katharina 
Published: August 2023

ABSTRACTThis study investigated the presence of extended-spectrum β-lactamase-producingEnterobacteralesin selected surface waters in the Ashanti Region in Ghana. Subsequent genomic analysis revealed that one-fifth of the isolates were genotypically carbapenem-resistant. Phenotypic susceptibility testing not only confirmed their carbapenem resistance, but also uncovered two cefiderocol-resistant isolates.
ArreSTick Motif is Responsible for GPCR-β-Arrestin Binding Stability and Extends Phosphorylation-Dependent β-arrestin Interactions to Non-Receptor Proteins
Authors: Tóth András Dávid , Soltész-Katona Eszter , Kis Katalin , Guti Viktor , Gilzer Sharon , Prokop Susanne , Boros Roxána , Misák Ádám , Balla András , Várnai Péter , Turiák Lilla , Ács András , Drahos László , Inoue Asuka , Hunyady László , Turu Gábor 
Published: August 2023

AbstractThe binding and function of β-arrestins are regulated by specific phosphorylation motifs present in G protein-coupled receptors (GPCRs). However, the exact arrangement of phosphorylated amino acids responsible for establishing a stable interaction remains unclear. To investigate this pattern, we employed a 1D sequence convolution model trained on a dataset of GPCRs that have established β-arrestin binding properties. This approach allowed us to identify the amino acid pattern required for GPCRs to form stable interactions with β-arrestins. This motif was named “arreSTick.” Our data show that the model predicts the strength of the coupling between GPCRs and β-arrestins with high accuracy, as well as the specific location of the interaction within the receptor sequence. Furthermore, we show that the arreSTick pattern is not limited to GPCRs, and is also present in numerous non-receptor proteins. Using a proximity biotinylation assay and mass spectrometry analysis, we demonstrate that the arreSTick motif controls the interaction between numerous non-receptor proteins and β-arrestins. For example, the HIV-1 Tat Specific Factor 1 (HTSF1 or HTATSF1), a nuclear transcription factor, contains the arreSTick pattern, and our data show that its subcellular localization is influenced by its coupling to β-arrestin2. Our findings unveil a broader regulatory role for β-arrestins in phosphorylation-dependent interactions, extending beyond GPCRs to encompass non-receptor proteins as well.
Performance and allocation can simultaneously shape behaviour in fire-disturbed populations of root vole
Authors: Boratyński Jan S. , Iwińska Karolina , Wirowska Martyna , Borowski Zbigniew , Solecki Paweł , Ciesielski Mariusz , Boratyński Zbyszek 
Published: August 2023

AbstractMetabolic physiology and animal personality are often considered linked to each other, shaping ecological and evolutionary strategies along a life-history continuum. The energy allocation model predicts a negative while the performance model predicts a positive correlation between the rate of metabolic processes and behaviours, such as activity level. The models might operate simultaneously but depending on the context one can predominate over the other, determining expression of alternative pro- and reactive behavioural strategies. Large-scale fires, such as the one that burnt wetlands of Biebrza National Park (NE Poland), degrade natural habitats, affect amount of food and shelters and modify predatory-prey interactions. Fires pose also direct threat to survival of local populations, such as the wetland specialist root vole (Microtus oeconomus). We hypothesized that fire disturbance, by changing environmental context and selective regimes, determines mechanisms linking physiology and behaviour. Positive relation found among most studies, predicted by the performance model, would revert to negative relation, predicted by the allocation model, affecting animals ecological strategy in disturbed habitat. We repeatedly measured maintenance and exercise metabolic rates and activity behaviour on voles from post-fire and unburnt populations. Repeatable maintenance metabolism and activity level were positively correlated, but more labile exercise metabolism did not explain behaviour. The correlations were not strongly affected by fire disturbance, but voles from post-fire habitat had higher maintenance but not maximum metabolism and moved shorter distances than individuals from unburnt area. The results suggest that performance model predominates, while habitat disturbance might reveal some allocation constraints on physiology-personality linkage.Summary statementContrasting ’allocation’ and ’performance’ models, for energetics-behaviour linkage, were tested in context of fire-disturbance. Positive (performance) correlation predominated but animals from burned habitat had elevated metabolism and suppressed exploration (allocation).
Nutrient learning, perception and generalization differ among wild pollinator species
Authors: Pietrantuono Ana Laura , Fernández-Arhex Valeria , Sandoz Jean-Christophe , Requier Fabrice 
Published: August 2023

AbstractLearning is the process through which skills, knowledge, behaviors are acquired and developed. Through life experiences, pollinator insects, learn to associate odor or visual stimuli from flowers with a rewarding food as pollen or nectar. This capability allows them to obtain resources efficiently and provides a valuable pollination service. Here, we compared the learning capability among different wild pollinator insects by mean of experiments based on the recent Free-Moving Proboscis Extension Response (FMPER) technique. Specifically, we evaluated the process of perception, learning and generalization between pollen enriched with different concentrations of fatty acid (which play a critical role in the survival, development and reproduction of many animals). We compared the associative learning in two castes of bumble bees (queens and workers ofBombus terrestris), honey bees (Apis mellifera), solitary bees (Ruizanthedella mutabilis) and non-bee pollinator species (the hoverflyEristalis tenax). Our results reveal that learning performances differed among bumble bee social castes, with queens acquiring learning odorants more effectively than workers. Likewise, learning performances differed among the four species of insect pollinators. Honey bees acquired odor-sucrose association more rapidly than the other species. Likewise, bumble bees learned better than the solitary bee species and the hoverfly. The pattern of generalization among odorant stimuli as also different among the studied species, with honey bees showing stronger generalization and hoverflies showing more specific response patterns. Studying the learning behavior in insect pollinators provides valuable information for the conservation of these species and services they provide, through adapted pollinator-friendly schemes matching their behavioral performances.
Cell growth and nutrient availability control the mitotic exit signaling network in budding yeast
Authors: Talavera Rafael A. , Prichard Beth E. , Sommer Robert A. , Leitao Ricardo M. , Sarabia Christopher J. , Hazir Semin , Paulo Joao A. , Gygi Steven P. , Kellogg Douglas R. 
Published: August 2023

AbstractCell growth is required for cell cycle progression. The amount of growth required for cell cycle progression is reduced in poor nutrients, which leads to a reduction in cell size. In budding yeast, nutrients influence cell size by modulating the duration and extent of bud growth, which occurs predominantly in mitosis. However, the mechanisms are unknown. Here, we used mass spectrometry to identify proteins that mediate the effects of nutrients on bud growth. This led to the discovery that nutrients regulate numerous components of the Mitotic Exit Network (MEN), which controls exit from mitosis. A key component of the MEN undergoes gradual multi-site phosphorylation during bud growth that is dependent upon growth and correlated with the extent of growth. Furthermore, activation of the MEN is sufficient to over-ride a growth requirement for mitotic exit. The data suggest a model in which the MEN integrates signals regarding cell growth and nutrient availability to ensure that mitotic exit occurs only when sufficient growth has occurred.
Linking high-performance work systems and happiness at work: role of career aspiration and thriving
Authors: Qamar Faisal , Soomro Shuaib Ahmed , Kundi Yasir Mansoor 
Published: August 2023

PurposeThis study utilizes self-determination theory (SDT) to understand how high-performance work systems (HPWS) may foster happiness at work through serial transmission pathways of career aspiration and thriving at work.Design/methodology/approachThe study uses data collected from a sample of 309 employees working in various organizations. It uses multilevel, multisource and time-lagged data and applied Mplus 8.0 for hypotheses testing.FindingsThe study findings reveal a positive relationship between HPWS and career aspiration. Career aspiration was positively related to thriving at work and thriving at work was positively associated with happiness at work. Moreover, career aspiration mediated the relationship between HPWS and thriving at work. Whereas, thriving at work mediated the relationship between career aspiration and happiness at work. The results also support the serial mediation of career aspiration and thriving at work between HPWS and happiness at work.Practical implicationsThe findings have important implications for organizational practice. Practitioners should consider implementing pro-employee HPWS to support employees' career aspirations and enhance their thriving experience, which may increase their happiness at work.Originality/valueThis is one of the few studies investigating individual-level serial mediators between departmental-level HPWS and employee happiness at work.
Recognising the recovering addict with Honneth: an intervention into the stigmatising language debate in the alcohol and other drugs field
Authors: Walmsley Ian 
Published: August 2023

Purpose
The purpose of this paper is to assess the impact of the recommendation to replace identity-first language with person-first language on people who self-identify as recovering addicts as part of a recovery programme. Narcotics Anonymous (NA) will be used to illustrate the contextualised nature of the recovering addict identity.

Design/methodology/approach
To demonstrate the value of the recovering addict identity and social relations in NA, this paper draws on Axel Honneth’s theory of mutual recognition and self-formation.

Findings
Person-first language overlooks the significance of identity-first language to people in 12-step recovery. This oversight is linked to the logic of stigma reduction which excludes all identity-first language by association rather than assessing the impact of such terms on a case-by-case basis. Honneth’s theory is used to show how the recovering addict identity facilitates self-confidence and self-esteem through relations of mutual recognition in NA.

Research limitations/implications
The argument excludes people who identify as recovering addicts, but do not attend 12-step groups. Further research would be needed to understand how the recommendation to use person-first language instead of identity-first language impacts upon other recovery communities and pathways.

Practical implications
The recommendation to replace identity-first language with person-first language might result in 12-step fellowships becoming marginalised within the broader academic and policy and practice arena. Language preferences can become a contentious issue when 12-step groups and their members enter the wider recovery arena where their preferred terminology is viewed as stigmatising and dehumanising.

Originality/value
To the best of the author’s knowledge, this is the first article to propose an alternative theoretical framework to stigma reduction for judging morally appropriate language in the alcohol and drugs field.
Review of tribological properties of polyimide-based composite materials
Authors: Yan Jiayuan , Zhang Xiaoliang , Wang Yanming 
Published: August 2023

Purpose
As a high-performance engineering plastic, polyimide (PI) is widely used in the aerospace, electronics and automotive industries. This paper aims to review the latest progress in the tribological properties of PI-based composites, especially the effects of nanofiller selection, composite structure design and material modification on the tribological and mechanical properties of PI-matrix composites.

Design/methodology/approach
The preparation technology of PI and its composites is introduced and the effects of carbon nanotubes (CNTs), carbon fibers (CFs), graphene and its derivatives on the mechanical and tribological properties of PI-based composites are discussed. The effects of different nanofillers on tensile strength, tensile modulus, coefficient of friction and wear rate of PI-based composites are compared.

Findings
CNTs can serve as the strengthening and lubricating phase of PI, whereas CFs can significantly enhance the mechanical properties of the matrix. Two-dimensional graphene and its derivatives have a high modulus of elasticity and self-lubricating properties, making them ideal nanofillers to improve the lubrication performance of PI. In addition, copolymerization can improve the fracture toughness and impact resistance of PI, thereby enhancing its mechanical properties.

Originality/value
The mechanical and tribological properties of PI matrix composites vary depending on the nanofiller. Compared with nanofibers and nanoparticles, layered reinforcements can better improve the friction properties of PI composites. The synergistic effect of different composite fillers will become an important research system in the field of tribology in the future.