bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and Characterisation of a Structured, Tuneable, and Transparent 3D Culture Platform for Soil Bacteria
Authors: Rooney Liam M. , Dupuy Lionel X. , Hoskisson Paul A. , McConnell Gail 
Published: June 2023

2.AbstractWe have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.3.Graphical AbstractA step-by-step method for creating a tailored 3D culture medium for study of soil microbes.The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion™ resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion™ particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.
Collagen prolyl 4-hydroxylases have sequence specificity towards different X-Pro-Gly triplets
Authors: Salo Antti M. , Rappu Pekka , Koski M. Kristian , Karjalainen Emma , Izzi Valerio , Drushinin Kati , Miinalainen Ilkka , Käpylä Jarmo , Heino Jyrki , Myllyharju Johanna 
Published: June 2023

ABSTRACTFormation of 4-hydroxyproline (4Hyp) in -X-Pro-Gly- collagen sequences is essential for the thermal stability of collagen molecules. 4Hyp formation is catalyzed by collagen prolyl 4-hydroxylases (C- P4H). Here we identify specific roles for the two main C-P4H isoenzymes by 4Hyp analysis of type I and IV collagens. Loss of C-P4H-I mainly affected prolines preceded by an X-position amino acid with a positively charged or a polar uncharged side chain. In contrast, loss of C-P4H-II affected triplets with a negatively charged glutamate or aspartate in the X-position, and their hydroxylation was found to be important as loss of C-P4H-II alone resulted in reduced collagen melting temperature and altered assembly of collagen fibrils and basement membrane. The C-P4H isoenzyme differences in substrate specificity were explained by selective substrate binding to the active site resulting in differences in Km and Vmax values. In conclusion, this study provides a molecular level explanation for the need of multiple C-P4H isoenzymes to generate collagen molecules capable to assemble into intact extracellular matrix structures.
Performance ofOrbicella faveolatalarval cohorts does not align with previously observed thermal tolerance of adult source populations
Authors: Zhang Yingqi , Gantt Shelby E. , Keister Elise F. , Elder Holland , Kolodziej Graham , Aguilar Catalina , Studivan Michael S. , Williams Dana E. , Kemp Dustin W. , Manzello Derek P. , Enochs Ian C. , Kenkel Carly D. 
Published: June 2023

AbstractOrbicella faveolata, commonly known as the mountainous star coral, is a dominant reef-building species in the Caribbean, but populations have suffered sharp declines since the 1980s due to repeated bleaching and disease-driven mortality. Prior research has shown that inshore adultO. faveolatapopulations in the Florida Keys are able to maintain high coral cover and recover from bleaching faster than their offshore counterparts. However, whether this origin-specific variation in thermal resistance is heritable remains unclear. To address this knowledge gap, we produced purebred and hybrid larval crosses fromO. faveolatagametes collected at two distinct reefs in the Upper Florida Keys, a nearshore site (Cheeca Rocks, CR) and an offshore site (Horseshoe Reef, HR), in two different years (2019, 2021). We then subjected these aposymbiotic larvae to severe (36 °C) and moderate (32 °C) heat challenges to quantify their thermal tolerance. Contrary to our expectation based on patterns of adult thermal tolerance, HR purebred larvae survived better and exhibited gene expression profiles that were less driven by stress response under elevated temperature compared to purebred CR and hybrid larvae. One potential explanation could be compromised reproductive output of CR adult colonies due to repeated summer bleaching events in 2018 and 2019, as gametes originating from CR in 2019 contained less storage lipids than those from HR. These findings provide an important counter-example to the current selective breeding paradigm, that more tolerant parents will yield more tolerant offspring, and highlight the importance of adopting a holistic approach when evaluating larval quality for conservation and restoration purposes.
Reconstructing the evolutionary history of human, simian, and prosimian immunodeficiency viruses
Authors: Ghafari Mahan , Simmonds Peter , Katzourakis Aris 
Published: June 2023

SummaryWhile paleovirological evidence supports the idea that the ancestors of modern simian (SIV) and prosimian (pSIV) immunodeficiency viruses have been evolving in nonhuman primates for millions of years, standard molecular clock methods calibrated using contemporary sequences significantly underestimate their times of origin. This discrepancy is attributed to the time-dependent nature of evolutionary rate estimates whereby the rate of virus evolution varies with respect to the time window of its measurement. While biogeographical calibrations may provide better estimates across intermediate timescales, there is currently no unifying framework that can allow inference of lentiviral ages across all relevant timescales. Here we showed that by correcting for such time-dependent rate effects using the recently developed Prisoner-of-War evolutionary model, we can successfully reconstruct the evolutionary history of human, simian, and prosimian immunodeficiency viruses across vastly different timescales and allowed estimates of the age of lineages that gave rise to HIV-1 and HIV-2. The model also predicted that the most recent common ancestor of SIV and pSIV lived around 21 million years ago, suggesting that the most likely explanation for the origins of primate lentiviruses is a terrestrial transfer of lentiviruses between African and Malagasy primates during the last episode of colonisation of Madagascar. Infections have entered via a land bridge in a group of mammals or through a nonprimate vector or transfer mediated by an aerial vector species. We also found that the most recent common ancestor of SIVs lived nearly a million years ago and that some SIV lineages codiverged with their hosts for several hundreds of thousands of years. The predicted long evolutionary timescales of SIVs and potential for close virus/host co-adaptation is consistent with their reduced or minimal pathogenicity in their native hosts, contrasting with the very recent evolutionary origins of highly pathogenic HIV strains in humans.
Inter individual variability in neuronal expression of heat shock protein genes predicts stress survival inCaenorhabditis elegans
Authors: Todtenhaupt Pia , Murdoch Sharlene , Vallejos Catalina A. , Casanueva Olivia , Chauve Laetitia 
Published: June 2023

ABSTRACTDespite being isogenic and grown under controlled conditions,C. eleganspopulations exhibit widespread inter-individual variability in many traits, making it an ideal model organism to investigate non-genetic influences on phenotypic diversity. Our particular interest is to study the consequences of inter-individual variability in genes encoding heat shock proteins, which are expressed at low levels under non-stimulated conditions. To robustly quantify inter-individual gene expression, we developed a novel pipeline that combines a highly efficient cDNA extraction method with a high-throughput qPCR nanofluidics technology with a bespoke computational analysis. We validated our approach by benchmarking againstin vivoreporters. We also screened among hundreds of stress inducible genes, and identified a regulon formed by transcripts belonging to the inducible heat shock protein family. We demonstrate, using a bipartitein vivofluorescent reporter, that the inter-individual variability in the stress regulon stems mostly from anterior neurons. Our studies demonstrate for the first time that, under physiological and unstimulated conditions, the variable expression of neural stress responses has cross-tissue consequences for fitness at the individual worm level, suggesting an adaptive role under variable environmental conditions.
The human Dicer helicase domain mediates ATP hydrolysis and RNA rearrangement
Authors: Ciechanowska Kinga , Szczepanska Agnieszka , Szpotkowski Kamil , Wojcik Klaudia , Urbanowicz Anna , Kurzynska-Kokorniak Anna 
Published: June 2023

AbstractVertebrates have one Dicer ortholog that generates both microRNAs (miRNAs) and small interfering RNAs (siRNAs), in contrast to the multiple Dicer-like proteins found in flies and plants. Here, we focus on the functions of the human Dicer (hDicer) helicase domain. The helicase domain of hDicer is known to recognize pre-miRNA substrates through interactions with their apical loop regions. Besides interacting with canonical substrates, the hDicer helicase domain has also been suggested to bind many different cellular RNAs; however, a comprehensive study of the biochemical activities and substrate specificity of the hDicer helicase domain towards different nucleic acids has yet to be undertaken. Here, we conduct such an analysis and reveal that full-length hDicer, through its helicase domain, hydrolyzes ATP. We also show that the hDicer helicase domain binds single-but not double-stranded RNAs and DNAs and that a structural rearrangement of the substrate accompanies the binding of single-stranded RNAs. This RNA rearrangement activity is ATP-independent. Our findings open new avenues for future studies aimed at defining the cellular activities of hDicer that may be associated with these newly described biochemical properties.
Cryo-electron microscopy of cytoskeletal ‘fibril’ involved inSpiroplasmaswimming
Authors: Sasajima Yuya , Kato Takayuki , Miyata Tomoko , Kiyama Hana , Kawamoto Akihiro , Makino Fumiaki , Namba Keiichi , Miyata Makoto 
Published: June 2023

AbstractSpiroplasma, parasitic or commensal bacteria, can swim by switching the handedness of its helical cell body. A helical cell body is formed by an internal ribbon of MreB, an actin superfamily, andSpiroplasma-specific fibril proteins. Here we have solved the structure of the fibril filament by single-particle cryo-electron microscopy at 3.6 Å resolution and built its atomic structure. The structure is composed of repeated rings and cylinders. The N-terminal cylinder of the fibril protein shows a structure similar to that of S-adenosylhomocysteine nucleosidase, while the C-terminal ring does not show similarity to other proteins. The filament is nonpolar and flexible, possessing a helical pitch of 700 nm, consistent with cell helicity. Cryo-electron tomography revealed aligned several MreB filaments in the center of the ribbon, flanked by membrane-binding fibril filaments through electrostatic interactions. This study discusses the evolution and roles of the fibril filament.
Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins
Authors: Zheng Lirong , Zan Bing , Yang Yu , Zhou Bingxin , Wu Banghao , Feng Yan , Liu Qian , Hong Liang 
Published: June 2023

AbstractProkaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicated that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.
(Re)Investigating the pathways between instructional leadership, collective teacher efficacy, and teacher commitment: a multilevel analysis
Authors: Thien Lei Mee , Darmawan Igusti Ngurah , Adams Donnie 
Published: June 2023

PurposeThis study aims to investigate the direct and indirect relationships among principal instructional leadership, collective teacher efficacy, and teacher commitment using multilevel analysis.Design/methodology/approachThis study employed quantitative cross-sectional research design. Data were collected from 1,328 teachers selected from 71 Malaysian primary schools.FindingsThe direct relationship between instructional leadership and teacher commitment was significant at the school level. Similarly, instructional leadership exhibits a significant direct effect on collective teacher efficacy. Collective teacher efficacy also has a significant direct effect on teacher commitment. The results also indicate a significant indirect effect at school level between instructional leadership and teacher commitment through collective teacher efficacy.Research limitations/implicationsThe multilevel analysis among instructional leadership, collective teacher efficacy, and teacher commitment warrant further investigations with larger sample sizes at both group and individual levels.Originality/valueThis study supplements previous findings by contributing more rigorous empirical evidence using multilevel analysis. The findings extend current knowledge in the principal instructional leadership literature in the context of a Southeast Asian country.
The more perceived training effectiveness, the greater the risk of voluntary separation: testing a turnover intent model among police officers in Taiwan
Authors: Lin Wen-Yu , Lai Yung-Lien , Luo Fei , Kuo Shih-ya , Chang Kwang-Ming 
Published: June 2023

Purpose Building on Lambert’s (2001) work on turnover intent in law enforcement, this study examines how organizational characteristics and job attitudes along with job satisfaction, and organizational commitment affect turnover intent among Taiwanese police officers.Design/methodology/approach Data were collected from the New Taipei City Police Department (NTCPD) in the summer of 2012 via stratified random sampling (N = 1,035). Structural equation modeling was employed to examine factors affecting turnover intent.Findings Job satisfaction and organizational commitment reduced the risk of turnover, while job stressors and training effectiveness directly increased the risk. Worthy of note, officers with a Central Police University degree and who were married had a lower risk of turnover.Originality/value This study applies Lambert’s (2001) turnover intent model in law enforcement agencies developed in the West to a non-western policing setting. The use of SEM assures the robustness of the findings. Some noteworthy contrasts in findings from Western and non-Western settings are presented.
Limiting scaring activities reduces economic costs associated with foraging barnacle geese: Results from an individual‐based model
Authors: de Jager Monique , Buitendijk Nelleke H. , Baveco Johannes M. , van Els Paul , Nolet Bart A. 
Published: June 2023

Abstract

With increasing numbers of large grazing birds on agricultural grassland, conflict with farmers is rising. One management approach to alleviate conflict allows foraging on dedicated agricultural land (accommodation areas) and nature reserves, combined with scaring on remaining agricultural land. Here, we examine the cost‐effectiveness of these measures by studying the influence on barnacle goose distribution and associated economic damage.

We present an individual/agent‐based model of barnacle geese (Branta leucopsis) foraging on grasslands in Friesland, the Netherlands. The model is parameterized using field observations and GPS‐tracks and allows simulation of management scenarios, differing in scaring probability and accommodation area size, with different potential management costs.

Our model shows that, while yield loss decreases with higher scaring probabilities, costs of damage appraisal increase because geese graze on more fields. With small accommodation areas, achieving high scaring probabilities takes more effort and could result in goose population decline. Total management costs are lowest without scaring activity.

Synthesis and applications. Considering costs of active scaring and the need to maintain the barnacle goose population in a favourable conservation status, our model suggests that the most cost‐effective scenario is to prevent disturbance of geese. A high scaring probability could be beneficial if applied in small areas, for example around sensitive crops or airfields. Scaring in large areas could result in costs outweighing benefits and a declining barnacle goose population.
Attention Focus and Attention Framework: A Configuration Perspective of Attention to Innovation
Authors: Cai Jing , Canales J. Ignacio 
Published: June 2023

AbstractThe current understanding of the unique contribution of single factors to attention may underestimate the complexity involved in attention allocation. This study aims to design an attention framework and examine the interdependencies between organisational and contextual factors that affect firm attention to exploitation, exploration, and ambidexterity. Drawing on a longitudinal study from 2008 to 2021, we use a configurational approach and identify seven distinct attention configurations as a result of different factor interdependencies, shedding light on how stability in attention configurations produces consistent attention focus. We also identify four change pathways that illustrate how configurations could be modified in response to radical environmental changes. Our study contributes to the attention‐based view by stressing the importance of two alignments that explain a firm's high performance: between attention and contextual factors; between attention and organisational factors. Methodologically, the novelty of the configurational approach is its ability to capture configuration stability in normal external conditions and trace sudden changes in attention focus and configuration paths under extreme external conditions. This study also enhances exploitation and exploration research on managing attention configuration pathways in terms of path flexibility, path emergence, and path deterioration.
Evaluation of the genetic viability of metapopulation scenarios for the Iberian lynx
Authors: Pacín C. , Garrote G. , Godoy J. A. 
Published: June 2023

AbstractThe Iberian lynx has shown a favourable demographic trajectory in the last decade as a result of the conservation measures adopted which are still ongoing. However, the viability of the species is still compromised by genetic factors. Here, we used the GESP software that predicts the effective population size (Ne) and inbreeding accumulation (∆f) over time in metapopulations, to find realistic scenarios that guarantee the genetic viability of this species. We proposed as genetic targets that Ne of the metapopulation (NeMeta) should exceed 500 in 20 generations (long term), whereas ∆f of the subpopulations (∆fx) should not exceed 0.05 in five generations (short term). The current Iberian lynx metapopulation configuration, with the expected subpopulations sizes at carrying capacity (5 subpops.; Ne1 = 100, Ne2,3,4,5 = 25), does not reach the long‐term goal, with a NeMeta ~ 150 in 20 generations. The results indicate that the long‐term genetic viability of the metapopulation requires an increase in the subpopulation size of 50–200%, the creation of at least 8 new subpopulations, and migration rates close to 0.1 between neighbouring subpopulations, comprising 2165 effective individuals (ca. 1100 breeding females). In addition, a minimum migration rate of 0.05 into the smallest subpopulations of Ne = 25 (i.e. 1.25 migrants/generation) is needed to avoid excessive inbreeding accumulation (short‐term goal). Larger subpopulations are preferable to several smaller subpopulations with the same number of effective individuals, even when the latter are well connected. Although these requirements seem challenging to achieve in the short‐medium term, the study provides key information for informed decision making by environmental managers and policymakers. The conclusions drawn here apply to other carnivores in need of conservation.