bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting episodic evolution through Bayesian inference of molecular clock models
Authors: Tay John H , Baele Guy , Duchene Sebastian 
Published: June 2023

AbstractMolecular evolutionary rate variation is a key aspect of the evolution of many organisms that can be modelled using molecular clock models. For example, fixed local clocks revealed the role of episodic evolution in the emergence of SARS-CoV-2 variants of concern. Like all statistical models, however, the reliability of such inferences is contingent on an assessment of statistical evidence. We present a novel Bayesian phylogenetic approach for detecting episodic evolution. It consists of computing Bayes factors, as the ratio of posterior and prior odds of evolutionary rate increases, effectively quantifying support for the effect size. We conducted an extensive simulation study to illustrate the power of this method and benchmarked it to formal model comparison of a range of molecular clock models using (log) marginal likelihood estimation, and to inference under a random local clock model. Quantifying support for the effect size has higher sensitivity than formal model testing and is straight-forward to compute, because it only needs samples from the posterior and prior distribution. However, formal model testing has the advantage of accommodating a wide range molecular clock models. We also assessed the ability of an automated approach, known as the random local clock, where branches under episodic evolution may be detected without theira prioridefinition. In an empirical analysis of a data set of SARS-CoV-2 genomes, we find ‘very strong’ evidence for episodic evolution. Our results provide guidelines and practical methods for Bayesian detection of episodic evolution, as well as avenues for further research into this phenomenon.
Heat-evolved algal symbionts enhance bleaching tolerance of adult corals without trade-off against growth
Authors: Chan Wing Yan , Rudd David , Meyers Luka , Topa Sanjida H. , van Oppen Madeleine J. H. 
Published: June 2023

ABSTRACTOcean warming has caused coral mass bleaching and mortality worldwide and the persistence of symbiotic reef-building corals requires rapid acclimation or adaptation. Experimental evolution of the coral’s microalgal symbionts followed by their introduction into coral is one potential method to enhance coral thermotolerance. Heat-evolved microalgal symbionts of the generalist species,Cladocopium proliferum(strain SS8), were exposed to elevated temperature (31°C) for ∼10 years, and were introduced into chemically bleached adult fragments of the scleractinian coral,Galaxea fascicularis. The new symbionts persisted for the five months of the experiment and enhanced adult coral thermotolerance compared with corals that were inoculated with the wild-typeC. proliferumstrain. Thermotolerance of SS8-corals was similar to that of coral fragments from the same colony hosting the homologous symbiont,Durusdiniumsp., which is naturally heat-tolerant. However, SS8-coral fragments exhibited faster growth and recovered cell density and photochemical efficiency more quickly following chemical bleaching and inoculation under ambient temperature relative toDurusdinium-corals. Mass spectrometry imaging suggests that algal pigments involved in photobiology and oxidative stress were the greatest contributors to the thermotolerance differences between coral hosting heat-evolved versus wild-typeC. proliferum. These pigments may have increased photoprotection in the heat-evolved symbionts. Our findings show that adult coral thermotolerance can be enhanced via the uptake of exogenously supplied, heat-evolved symbionts, without a trade-off against growth under ambient temperature. Heat-evolvedC. proliferumremains in the corals in moderate abundance two years after its first inoculation, suggesting long-term stability of this novel symbiosis.
DNA conserved in diverse animals since the Precambrian controls genes for embryonic development
Authors: Frith Martin C. , Ni Shengliang 
Published: June 2023

SummaryDNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly-related animals, like vertebrates and arthropods. This is mysterious, because development of such animals is partly organized by homologous genes with similar complex expression patterns, termed “deep homology”.Here we report twenty-five regulatory DNA segments conserved across bilaterian animals, of which seven are also conserved in cnidaria (coral and sea anemone). They control developmental genes (e.g.Nr2f, Ptch, Rfx1/3, Sall, Smad6, Sp5, Tbx2/3), including six homeobox genes:Gsx, Hmx, Meis, Msx, Six1/2, andZfhx3/4. The segments contain perfectly or near-perfectly conserved CCAAT boxes, E-boxes, and other sequences recognized by regulatory proteins. More such DNA conservation will surely be found soon, as more genomes are published and sequence comparison is optimized. This reveals a control system for animal development conserved since the Precambrian.
A combined computational-biochemical approach offers an accelerated path to membrane protein solubilization
Authors: Pierce Mariah R. , Ji Jingjing , Novak Sadie X. , Sieburg Michelle A. , Nangia Shikha , Hougland James L. 
Published: June 2023

AbstractMembrane proteins are difficult to isolate and purify due to their dependence on the surrounding lipid membrane for structural stability. Detergents are often used to solubilize these proteins, with this approach requiring a careful balance between protein solubilization and denaturation. Determining which detergent is most appropriate for a given protein has largely been done empirically through screening, which requires large amounts of membrane protein and associated resources. Here we describe an alternative to conventional detergent screening using a computational modeling approach to identify the most likely candidate detergents for solubilizing a protein of interest. We demonstrate our approach using ghrelinO-acyltransferase (GOAT), a member of the membrane-boundO-acyltransferase (MBOAT) family of integral membrane enzymes that has not been solubilized or purified in active form. A computationally derived GOAT structural model provides the only structural information required for this approach. Using computational analysis of detergent ability to penetrate phospholipid bilayers and stabilize the GOAT structure, a panel of common detergents were rank ordered for their proposed ability to solubilize GOAT. Independently, we biologically screened these detergents for their solubilization of fluorescently tagged GOAT constructs. We found computational prediction of protein structural stabilization was the better predictor of detergent solubilization ability, but neither approach was effective for predicting detergents that would support GOAT enzymatic function. The current rapid expansion of membrane protein computational models lacking experimental structural information and our computational detergent screening approach can greatly improve the efficiency of membrane protein detergent solubilization supporting downstream functional and structural studies.
An oncogenic isoform of septin 9 promotes the formation of juxtanuclear invadopodia by reducing nuclear deformability
Authors: Okletey Joshua , Angelis Dimitrios , Jones Tia M. , Montagna Cristina , Spiliotis Elias T. 
Published: June 2023

SUMMARYInvadopodia are extracellular matrix (ECM) degrading structures, which promote cancer cell invasion. The nucleus is increasingly viewed as a mechanosensory organelle that determines migratory strategies. However, how the nucleus crosstalks with invadopodia is little known. Here, we report that the oncogenic septin 9 isoform 1 (SEPT9_i1) is a component of breast cancer invadopodia. SEPT9_i1 depletion diminishes invadopodia formation and the clustering of invadopodia precursor components TKS5 and cortactin. This phenotype is characterized by deformed nuclei, and nuclear envelopes with folds and grooves. We show that SEPT9_i1 localizes to the nuclear envelope and juxtanuclear invadopodia. Moreover, exogenous lamin A rescues nuclear morphology and juxtanuclear TKS5 clusters. Importantly, SEPT9_i1 is required for the amplification of juxtanuclear invadopodia, which is induced by the epidermal growth factor. We posit that nuclei of low deformability favor the formation of juxtanuclear invadopodia in a SEPT9_i1-dependent manner, which functions as a tunable mechanism for overcoming ECM impenetrability.HighlightsThe oncogenic SEPT9_i1 is enriched in breast cancer invadopodia in 2D and 3D ECMSEPT9_i1 promotes invadopodia precursor clustering and invadopodia elongationSEPT9_i1 localizes to the nuclear envelope and reduces nuclear deformabilitySEPT9_i1 is required for EGF-induced amplification of juxtanuclear invadopodiaeTOC BlurbInvadopodia promote the invasion of metastatic cancers. The nucleus is a mechanosensory organelle that determines migratory strategies, but how it crosstalks with invadopodia is unknown. Okletey et al show that the oncogenic isoform SEPT9_i1 promotes nuclear envelope stability and the formation of invadopodia at juxtanuclear areas of the plasma membrane.
Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains
Authors: Radmall Kaitlin S. , Shukla Prakash K. , Leng Andrew M. , Chandrasekharan Mahesh B. 
Published: June 2023

AbstractPost-translational covalent conjugation of ubiquitin onto proteins or ubiquitination is important in nearly all cellular processes. Steady-state ubiquitination of individual proteinsin vivois maintained by two countering enzymatic activities: conjugation of ubiquitin by E1, E2 and E3 enzymes and removal by deubiquitinases. Here, we deleted one or more genes encoding deubiquitinases in yeast and evaluated the requirements for ubiquitin conjugation onto a target protein. Our proof-of-principle studies demonstrate that absence of relevant deubiquitinase(s) provides a facile and versatile method that can be used to study the nuances of ubiquitin conjugation and deubiquitination of target proteinsin vivo. We verified our method using mutants lacking the deubiquitinases Ubp8 and/or Ubp10 that remove ubiquitin from histone H2B or PCNA. Our studies reveal that the C-terminal coiled-domain of the adapter protein Lge1 and the C-terminal acidic tail of Rad6 E2 contribute to monoubiquitination of histone H2BK123, whereas the distal acidic residues of helix-4 of Rad6, but not the acidic tail, is required for monoubiquitination of PCNA. Further, charged substitution at alanine-120 in the H2B C-terminal helix adversely affected histone H2BK123 monoubiquitination by inhibiting Rad6-Bre1-mediated ubiquitin conjugation and by promoting Ubp8/Ubp10-mediated deubiquitination. In summary, absence of yeast deubiquitinasesUBP8and/orUBP10allows uncovering the regulation of and requirements for ubiquitin addition and removal from their physiological substrates such as histone H2B or PCNAin vivo.
Neural correlates of online action preparation
Authors: Shahbazi Mahdiyar , Ariani Giacomo , Kashefi Mehrdad , Pruszynski J. Andrew , Diedrichsen Jörn 
Published: June 2023

AbstractWhen performing movements in rapid succession, the brain needs to coordinate preparation of an upcoming action with ongoing execution. Here we identify the processes and brain areas involved in this ability. Human participants performed pairs of single-finger presses or three-finger chords in settings where they had to prepare the second movement before or after the first response. Despite matched perceptual and movement requirements, 7T functional MRI revealed increased brain activity in regions along the intra-parietal sulcus and ventral visual stream when actions overlapped. Multivariate analyses suggested that these areas were involved in stimulus identification and action selection. In contrast, the dorsal premotor cortex, known to be involved in planning upcoming movements, showed no discernible signs of heightened activity. This observation suggests that the bottleneck during simultaneous action control and preparation arises at the level of stimulus identification and action selection, whereas movement planning in the premotor cortex can unfold concurrently with execution without interference between the two processes.SummaryThe brain’s ability to prepare for upcoming actions while controlling ongoing movements is a crucial evolutionary adaptation of the action system. However, the neural basis of online action preparation remains largely unknown. We found that superior-parietal and occipito-temporal areas exhibited heightened activation during online preparation. Surprisingly, the dorsal premotor cortex, known to be a crucial structure in motor planning, did not display additional activation for overlapping actions. These findings imply that while motor planning within the premotor cortex can occur in parallel with the execution of ongoing movement, the parallel stimulus identification and action selection in the posterior parietal cortex requires additional neural processes.HighlightsIndividuals prepare upcoming actions while simultaneously controlling ongoing movementWhen these two processes overlap, superior-parietal and occipito-temporal areas show increased activationMultivariate analysis suggests that increased activation arises to resolve simultaneous stimulus identification and action selectionThe premotor cortex, known to be involved in motor planning, coordinates simultaneous planning and execution without extra neural engagement
Selective plane activation structured illumination microscopy
Authors: Temma Kenta , Oketani Ryosuke , Kubo Toshiki , Bando Kazuki , Maeda Shunsuke , Sugiura Kazunori , Matsuda Tomoki , Heintzmann Rainer , Kaminishi Tatsuya , Fukuda Koki , Hamasaki Maho , Nagai Takeharu , Fujita Katsumasa 
Published: June 2023

AbstractResolution enhancement in structured illumination microscopy is hindered when volumetric samples are observed owing to background signals from out-of-focus planes. In this study, we utilized selective plane illumination and reversibly photoswitchable fluorescent proteins to realize structured illumination within the focal plane and eliminate the out-of-focus background. We demonstrated high-resolution fluorescence imaging of volumetric samples, including dense fluorescent objects in a cell spheroid.
Male and female syringeal muscles exhibit superfast shortening velocities in Zebra finches
Authors: Gladman Nicholas W. , Elemans Coen P. H. 
Published: June 2023

AbstractVocalisations play a key role in the communication behaviour of many vertebrates. Vocal production requires extremely precise motor control, which is executed by superfast vocal muscles that can operate at cycle frequencies over 100 Hz and up to 250 Hz. The mechanical performance of these muscles has been quantified with isometric performance and the workloop technique, but due to methodological limitations we lack a key muscle property characterising muscle performance, the force-velocity (FV) relationship. Here we establish a method that allows quantification of the FV relationship in extremely fast muscles, and test if the maximal shortening velocity of zebra finch syringeal muscles is different between males and females. We show that syringeal muscles exhibit extremely high maximal shortening velocities of 46 L0s-1, far exceeding most other vocal and skeletal muscles, and that isometric properties positively correlate with maximal shortening velocities. While male and female muscles differ in isometric speed measures, maximal shortening velocity surprisingly is not sex-dependent. We also show that cyclical methods to measure force-length properties used in classical laryngeal studies give the same result as conventional stepwise methodologies, suggesting either approach is appropriate. Next to force, instantaneous power also trades for speed, further highlighting these muscles are tuned to operate at high frequencies. We argue that the high thermal dependence of superfast vocal muscle performance may impact vocal behaviour.Summary statementZebra finch syringeal muscle exhibits superfast shortening of 46 L0s-1. Shortening is not sex-specific but correlates with isometric performance – faster twitches and tetani are associated with faster shortening.
Evaluating the compliance of environmental management systems: evidence from Moroccan banks
Authors: Ibenrissoul Abdelmajid , Benjouid Zakaria , Kammoun Souhaila 
Published: June 2023

PurposeThe purpose of the study is to evaluate the compliance of environmental risk management systems implemented by Moroccan banks with ISO 14001 certification or environmental charters.Design/methodology/approachData were collected through the distribution of an environmental risk management questionnaire to all Moroccan banks’ branches, business centers and various central entities. The study uses regression analysis to model the relationship between environmental management system (EMS) compliance and environmental management explanatory variables to identify the most relevant indicators that can explain the effectiveness and reliability of an EMS.FindingsEmpirical evidence reveals that the evaluation of EMS compliance in Moroccan banks should consider two categories of variables: the first category is related to the culture of environmental risk management, and the second one is related to environmental management practices.Originality/valueThe results show that the “information” variables play a key role in the overall design of an EMS and represent essential variables in the general definition of the environmental policy and in raising awareness and providing information on the bank’s commitment to a pro-environmental approach. The “application” variables confirm that environmental management practices need to be put in place to manage the different environmental risks. The study raises some managerial implications and further research directions.
Extending UTAUT with competitive pressure for SMEs digitalization adoption in two European nations: a multi-group analysis
Authors: Kwarteng Michael Adu , Ntsiful Alex , Diego Lerma Fernando Plata , Novák Petr 
Published: June 2023

PurposeIn this article, the authors draw-upon an extended unified theory of acceptance and use of technology (UTAUT) and propose a research model involving performance expectancy (PE), effort expectancy (EE), facilitating conditions (FC) and competitive pressure (CP) as potential salient factors explaining the adoption of digitalization in European SMEs. The authors also postulate that there may be cross-cultural differences, thereby leading us to include the country as a moderator in the model.Design/methodology/approachThe authors validate this model with a cross-cultural sample involving 188 owner-managers from the Czech Republic and Slovakia and through the partial least square structural equation modeling (PLS-SEM) techniques as well as multi-group analysis.FindingsThe results using the study’s global dataset indicate that PE, FC and CP significantly affect owner-managers intentions toward digitalization in SMEs. The authors’ application of the multi-group analysis also suggests that although the two countries differ in digitalization adoption intention, the differences are statistically insignificant. In the conclusion, the authors highlight several implications these findings have for theory and practice.Practical implicationsThe authors recommend that the providers of emerging digital technologies should improve on the performance features of those technologies and ensure they are relevant to the SMEs. By doing so, the adoption of digitalization will grow, because owner-managers of SMEs will have the confidence that adopting such technologies will improve their operations. Second, SMEs are required to provide adequate organizational and technical infrastructure to support digitalization adoption.Originality/valueAside from being among the few attempts to extend the explanatory power of UTAUT with PE, EE, FC and CP in investigating digitalization adoption in SMEs context, this study also validates its model with rigorous methodological approach as well as three datasets (global, Czech Republic and Slovakia) thereby strengthening the validity of the results.
Internal corporate social responsibility in times of uncertainty: does working from home harm the creativity link?
Authors: Lucius Zita K. , Damberg Svenja , Meinel Martin , Ringle Christian M. 
Published: June 2023

Purpose
The purpose of this study is to investigate how working from home (WFH) affects the relationship between internal corporate social responsibility (ICSR) and employee creativity in times of uncertainty when employees’ occupational stress increases and their identification with their company decreases.

Design/methodology/approach
Applying social identity theory, the authors derive and test the hypotheses presented in this study regarding ICSR’s direct effects on employee creativity, given the amount of time they spent on WFH and the role of threat in this relationship. The authors use partial least squares structural equation modeling to analyze the various effects. Via an online questionnaire and using the snowball technique, the authors collected data from 158 participants in different industries in Germany.

Findings
The empirical results of this study show that ICSR activities increase employee creativity, partly by reducing one harmful aspect of stress, namely, threat. In addition, the authors find that WFH moderates this effect, such that the higher the degree of WFH, the weaker the ICSR activities’ effects are.

Research limitations/implications
This study focused on the respondents’ WFH situation during the global COVID-19 pandemic. As such, this research contributes to understanding the roles that modern work practices, human resource management (HRM) and ICSR actions play in respect of employee creativity. The authors expand the theoretical understanding, which is based on social identity theory, by showing that the greater the amount of time spent on WFH, the more it reduces ICSR’s positive effect on employee creativity. The findings of this study open avenues for future research and longitudinal studies that compare the ICSR effects during and after the pandemic, as well as for those that compare WFH and its effects on organizational creativity.

Practical implications
This study shows that managers should encourage appropriate ICSR measures in their organizations and should specifically consider the work setting (i.e. WFH or at the office) as a boundary factor for these measures’ effectiveness. However, ICSR actions, such as anti-discrimination measures, are less effective in respect of building the employee–employer relationship and supporting employees’ identification with and commitment to the company when they work from home. Given the economic benefit of decreased turnover rates and the societal benefit of a company output with higher creativity levels, this study has an impact from both an economic and a societal perspective.

Originality/value
This study sheds light on employee creativity and ICSR’s roles in current HRM practice, which is still underexplored. More importantly, to the best of the authors’ knowledge, this study provides the first empirical evidence of a hitherto overlooked mechanism explaining ICSR activities’ effects on, or their perceived threat to, employee creativity.