bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding the CRISPR toolbox by engineering Cas12a orthologs of metagenomic discovery
Authors: Tao Dagang , Xu Bingrong , Li Sheng , Liu Hailong , Shi Suyu , Wang Yuan , Zhao Changzhi , Ruan Jinxue , Fu Liangliang , Huang Xingxu , Li Xinyun , Zhao Shuhong , Xie Shengsong
Published: September 2024

Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility in genome editing and molecular diagnostic applications. However, the widespread adoption of CRISPR-Cas12a nucleases and their variants has been hindered by the requirement for a specific protospacer adjacent motif (PAM), relatively low CRISPR RNA (crRNA) activity and the inability to multiplex nucleic acid detection alone. To overcome these limitations, we employed a comprehensive framework combined with AlphaFold2 tode novomine 1,261 previously unexploited Cas12a orthologs from the global microbiome. Following experimental analysis, we identified the most promising 21 Cas12a nuclease orthologs and designated them “Genie scissor 12” (Gs12). Our analysis uncovered two exceptional variants among these newly identified orthologs: Gs12-10, a first natural PAM-less Cas12a ortholog, which can recognize 52 distinct PAM types, representing a significant 1.8-fold expansion in recognition range compared to the relative LbCas12a PAM; and Gs12-7MAX, an engineered variant of Gs12-7 that exhibited 1.27-fold higher editing efficiency than enAsCas12a-HF. Furthermore, we harnessed Gs12-1, Gs12-4, Gs12-9, and Gs12-18, along with their corresponding engineered crRNAs, to develop a powerful four-channel multiplexed CRISPR-based nucleic acid detection system. The discovery of diverse functions in Cas12a offers a deeper understanding of the CRISPR/Cas12a family. Also, it holds great promise for expanding its applications and uncovering the untapped potential of other CRISPR/Cas systems.

Graphical Abstract
TvAP65 inTrichomonas vaginalisPromotes HPV Infection by Interacting with Host Molecules
Authors: Mei Xuefang , Sheng Wanxin , Zhang Yani , Tian Wenjie , Tian Xiaowei , Yang Zhenke , Wang Shuai , Zhang Zhenchao
Published: September 2024

Cervical cancer induced by human papillomavirus (HPV) infection poses a serious threat to women’s health. Studies have shown thatTrichomonas vaginalis(T. vaginalis), which is widely prevalent globally, can facilitate HPV infection. However, the underlying mechanism remains unclear. This study found thatT. vaginalissignificantly enhanced HPV infection in HaCaT cells and mouse vaginas throughin vivoandin vitroexperiments, and promoted the expression of HPV membrane receptor molecules CD151 and HSPG2. The HPV infection rate and CD151/HSPG2 expression levels were significantly decreased after reducing the expression ofT. vaginalisadhesion protein 65 (TvAP65). In contrast, both HPV infection rates and CD151/HSPG2 expression were significantly increased in HaCaT cells over-expressing TvAP65. When both TvAP65 inT. vaginalisand CD151/HSPG2 in HaCaT cells were knocked down simultaneously, the infection rate of HPV in HaCaT cells was further reduced. These results suggest that TvAP65 promotes HPV infection by up-regulating the expression of CD151 and HSPG2. Furthermore, this study knocked down the 12 interacting molecules of TvAP65 in HaCaT cells one by one, and found that the HPV infection rate was significantly reduced afterT. vaginalisinfected HaCaT cells with low expression of FTH1, SPCS1, ATP5MC3, ITGB7, PMEPA1 or REEP5. Among them, SPCS1 played the most significant role. Simultaneous knockdown of TvAP65 and SPCS1 further significantly down-regulated the infection rate of HPV in HaCaT cells. Moreover, this molecule also down-regulated the promoting effect ofT. vaginalison HSPG2/CD151 expression. These results imply that SPCS1 plays an important role inT. vaginalispromoting HSPG2/CD151 expression and HPV infection. This study not only further proved thatT. vaginaliscan promote HPV infection but also explores the molecular mechanism by which TvAP65, through its interaction with SPCS1, up-regulates the expression of HSPG2 and CD151, thereby facilitating HPV infection. This provides a theoretical basis for clarifying the mechanism of co-infection betweenT. vaginalisand HPV.
Entorhinal grid-like codes for visual space during memory formation
Authors: Graichen Luise P. , Linder Magdalena S. , Keuter Lars , Jensen Ole , Doeller Christian F. , Lamm Claus , Staudigl Tobias , Wagner Isabella C.
Published: September 2024

Eye movements, such as saccades, allow us to gather information about the environment and, in this way, can shape memory. In non-human primates, saccades are associated with the activity of grid cells in the entorhinal cortex. Grid cells are essential for spatial navigation, but whether saccade-based grid-like signals play a role in human memory formation is currently unclear. Here, human participants underwent functional magnetic resonance imaging (fMRI) and continuous eye gaze monitoring while studying scene images. Recognition memory was probed immediately thereafter. Results revealed saccade-based grid-like codes in the left entorhinal cortex while participants studied the scene images, a finding that was replicated with an independent data set reported here. The grid-related effects were time-locked to activation increases in the frontal eye fields. Most importantly, saccade-based grid-like codes were associated with recognition memory, such that grid-like codes were lower the better participants performed in subsequently recognizing the scene images. Collectively, our findings suggest an entorhinal map of visual space that is timed with neural activity in oculomotor regions, supporting memory formation.
Purkinje cell intrinsic activity shapes cerebellar development and function
Authors: Osório Catarina , White Joshua J. , Solé Paula Torrents , Mandemaker Nienke , Olivero Federico , Kirwan Freya , de Winter Fred , Regolo Eleonora , Fiocchi Francesca Romana , Serra Inês , Tjon Saffira , Ozgur Zeliha , van den Hout Mirjam C.G.N. , van Ijcken Wilfred F. J. , López-Bendito Guillermina , Badura Aleksandra , Lim Lynette , van Woerden Geeske , Schonewille Martijn
Published: September 2024

The emergence of functional cerebellar circuits is heavily influenced by activity-dependent processes. However, the role of intrinsic activity in Purkinje neurons, independent of external input, in driving cerebellar development remains less understood. Here, we demonstrate that before synaptic networks mature, Purkinje cell intrinsic activity is essential for regulating dendrite growth, establishing connections with cerebellar nuclei, and ensuring proper cerebellar function. Disrupting this activity during the postnatal period impairs motor function, with earlier disruptions causing more severe effects. Importantly, only disruptions during early development lead to pronounced defects in cellular morphology, highlighting key temporal windows for dendritic growth and maturation. Transcriptomic analysis revealed that early intrinsic activity drives the expression of activity-dependent genes, such asPrkcgandCar8, which are essential for dendritic growth. Our findings emphasize the importance of temporally-specific intrinsic activity in Purkinje cells for guiding cerebellar circuit development, providing a potential common mechanism underlying cerebellum-related disorders.
The wheat NLR protein PM3b localizes to endoplasmic reticulum-plasma membrane contact sites and interacts with AVRPM3b2/c2through its LRR domain
Authors: Isaksson Jonatan , Kunz Lukas , Flückiger Simon , Widrig Victoria , Keller Beat
Published: September 2024

Plant nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular immune receptors that directly or indirectly perceive pathogen derived effector proteins to induce an immune response. NLRs display diverse sub-cellular localizations, which are associated with the capacity of the immune receptor to confer disease resistance and recognize its corresponding avirulence effector. In wheat, the NLR PM3b recognizes the wheat powdery mildew effector AVRPM3b2/c2and we examined the molecular mechanism underlying this recognition. We show that PM3b and other PM3 variants localize to endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (EPCS) while AVRPM3b2/c2localizes to the nucleocytoplasmic space. Additionally, we found that PM3b interacts in planta with AVRPM3b2/c2through its LRR domain. We further demonstrate that full length PM3b interaction with AVRPM3b2/c2is considerably weaker than for the isolated PM3b LRR domain or the susceptible PM3 variant PM3CS, indicating that activation of PM3b leads to dissociation of the complex. In line with this: We observed a strong interaction between PM3b and AVRPM3b2/c2in a P-loop mutant of PM3b which was unable to initiate a cell death response, or when an inactive variant of AVRPM3b2/c2was used. We propose that PM3b transiently interacts with AVRPM3b2/c2through residues in the LRR which are conserved among PM3 variants while the amino acids necessary for full activation and cell death signaling are unique to PM3b. Our data suggests that PM3b localization and interaction with AVRPM3b2/c2differs from other well studied NLRs and further highlights the mechanistic diversity in NLR-mediated responses against pathogens in plants.
End of preservation normothermic machine perfusion of porcine kidneys after ischaemic injury reprograms metabolism and induces fibrosis after transplant despite unchanged function: insights from the renal proteome
Authors: Mulvey John Francis , Snashall Corinna , Rozenberg Kaithlyn , Lo Faro M. Letizia , Eijken Marco , Lohmann Stine , Moers Cyril , Leuvenink Henri , Baan Carla , Hoogduijn Martin , Keller Anna Krarup , Sutton Chris , Hunter James , Jespersen Bente , Ploeg Rutger , Shaheed Sadr
Published: September 2024

Normothermic machine perfusion (NMP) after initial hypothermic preservation of donor kidneys prior to transplantation is becoming a clinical reality, but the precise molecular mechanisms through which the graft is impacted remain only partially characterised. Using an unbiased proteomic methodology, we found that auto transplantation of is chaemically injured porcine kidneys resulted in an activation of the stress response 14 days after transplantation, as well as in selective changes in the proteins responsible for the metabolism of organic acids. The addition of 4 hours of NMP at the end of organ preservation (endNMP) resulted in coordinated changes to the renal proteome at 14 days when compared with the effect of transplant after preservation by hypothermic machine perfusion alone: most notably increased fibrosis and widespread additional reprogramming of metabolism. These findings were supported by intersection with single cell transcriptomics data which suggested an enrichment of proteins predominantly expressed in fibroblasts in kidneys with end of preservation NMP 14 days post-transplant compared to healthy kidneys. Our data showed that the addition of endNMP to existing preservation strategies resulted in a different molecular phenotype after transplantation, despite unchanged filtration function. In addition to potentially conferring benefits, NMP may also result in potentially detrimental molecular changes and thus protocols should be carefully evaluated to derive optimal clinical outcomes.
Plant Mobile Domain protein-DNA motif modules counteract Polycomb silencing to stabilize gene expression
Authors: Pélissier Thierry , Jarry Lucas , Olivier Margaux , Dajoux Gabin , Pélissier Marie-Noëlle Pouch- , Courtois Charles , Descombin Julie , Picault Nathalie , Moissiard Guillaume , Mathieu Olivier
Published: September 2024

In plants and animals, Polycomb group (PcG) proteins are crucial for development, regulating gene expression through H3K27me3 deposition and subsequent gene silencing. While Polycomb silencing target specification is increasingly understood, it remains unclear how certain genes with apparent silencing-attracting features escape this process. Here, we show that the plant mobile domain C (PMD-C) containing proteins MAINTENANCE OF MERISTEMS (MAIN), MAIN-LIKE 1 (MAIL1) and MAIL2 oppose Polycomb silencing at numerous actively transcribed genes in Arabidopsis. Mutations inMAIN,MAIL1orMAIL2result in PcG-dependent ectopic H3K27me3 deposition, often associated with transcriptional repression. We show that MAIL1, which functions in concert with MAIN, and MAIL2 target distinct gene sets and associate with chromatin at specific DNA sequence motifs. We demonstrate that the integrity of these motif sequences is essential for promoting expression and antagonizing H3K27me3 deposition. Our results unveil a novel system opposing Polycomb silencing involving PMD-C protein-DNA motif modules, expanding our understanding of eukaryotic gene regulation mechanisms.
EnteropathogenicEscherichia coliinducesEntamoeba histolyticaLévy-like movement on fibronectin-rich substrate by reducing traction forces
Authors: Guo Yuanning , Ye Jun , Odeh Anas , Trebicz-Geffen Meirav , Wolfenson Haguy , Ankri Serge
Published: September 2024

Amebiasis, caused byEntamoeba histolytica, is a global health concern, affecting millions and causing significant mortality, particularly in areas with poor sanitation. Although recent studies have examinedE. histolytica’s interaction with human intestinal microbes, the impact of bacterial presence on the parasite’s motility, mechanical forces, and their potential role in altering invasiveness have not been fully elucidated. In this study, we utilized a micropillar-array system combined with live imaging to investigate the effects of enteropathogenicEscherichia colionE. histolytica’s motility characteristics, F-actin spatial localization, and traction force exerted on fibronectin-coated substrates. Our findings indicate that co-incubation withE. colisignificantly enhances the motility ofE. histolytica, as evidenced by the enhancement of Lévy-like movement patterns, i.e., increased directionality and velocity. This increased motility is accompanied by a reduction in F-actin-dependent traction forces and podosome-like structures on fibronectin-coated substrates, but with increased F-actin localization in the upper part of the cytoplasm. These findings highlight the role of physical interactions and cellular behaviors in modulating the parasite’s virulence, providing new insights into the mechanistic basis of its pathogenicity.

Author Summary

Amebiasis, caused by the protozoan parasiteEntamoeba histolytica, is a major global health issue, affecting around 50 million people and resulting in 100,000 deaths annually. The disease is transmitted through contaminated food and water. Upon reaching the intestines, which are teeming with bacteria,E. histolyticabegins its invasion by removing the protective mucus layer, followed by adhering to and detaching enterocytes, leading to the disruption and degradation of the epithelial barrier. Afterwards,E. histolyticainvades along the fibronectin-rich basement membrane deep into the crypts of Lieberkühn, eventually penetrating the fibronectin- rich lamina propria. This leads to further tissue destruction and potential dissemination to distant organs, causing severe complications. In our study, we explored how the presence of enteropathogenic bacteria affects the parasite’s motility and mechanical force generation, both of which are key to its pathogenicity. Using a micropillar-array system and live imaging, we found that exposure to enteropathogenicEscherichia colisignificantly increasesE. histolytica’s motility while reducing its traction force on fibronectin-rich matrices. These changes in behavior highlight the role of bacterial interactions in enhancing the parasite’s virulence. Our findings provide important insights into the mechanistic basis ofE. histolytica’s pathogenicity, offering potential avenues for new treatments against amebiasis.
Self-immunity towards a novel competence-induced streptococcal murein hydrolase is mediated by a Fem-transferase-like protein
Authors: Mårli Marita Torrissen , Arntzen Magnus Øverlie , Allred Jennie Ann , Schultheiss Anna Teigen , Oppegaard Oddvar , Kjos Morten , Straume Daniel
Published: September 2024

Murein hydrolases (or peptidoglycan hydrolases) play diverse roles in bacteria, from controlled remodeling of the bacterial cell wall to lytic agents. In streptococci, a subset of these hydrolases is associated with competence-induced fratricide, a process where bacteria kill closely related cells to release DNA that can be taken up during natural transformation. Here, we characterize ScrM, a competence-induced murein hydrolase fromStreptococcus dysgalactiaecomprising a CHAP domain, an SH3b domain and an uncharacterized C-terminal domain (CCD). ScrM displayed lytic activity against pyogenic and salivarius group streptococci. Microscopy analysis of fluorescent fusions revealed that ScrM specifically localizes to the division zone of sensitive cells, with binding and localization mediated primarily by CCD. Upon competence induction, cells became immune to ScrM due to expression of ScrI, a Fem-transferase-like protein. We show by LC-MS/MS that ScrI incorporates Thr in place of Ala into the interpeptide bridges of peptidoglycan, which in turn prevents ScrM binding to the division zone, thereby protecting the cells from self-lysis during competence. ScrM and ScrI are conserved among pyogenic streptococcal pathogens and represent new players in the cell wall biogenesis of these bacteria that may form a platform for development of novel antimicrobial strategies.
Evaluation of antibacterial activity of ethanolic extracts ofRuta chalepensis, Hippocratea excelsa, Litsea glaucescensandWaltheria americanaagainst methicillin-resistantStaphylococcus aureus
Authors: Salvador Martínez Margarita , Fuentes Gutiérrez José Fernando , Tescucano Alonso Alonso Rubén , Martínez González Gabriel
Published: September 2024

Antimicrobial resistance is still a problem today, with increasingly limited therapeutic options.Staphylococcus aureuscauses infections of the skin, soft tissues and contains a high degree of pathogenicity. The objective of this work was to determine the antibacterial activity of ethanol extracts from several plants at different concentrations against strains ofStaphylococcus aureusresistant and sensitive to methicillin, using the Kirby-Bauer method. The ethanolic extract of Rue (Ruta chalepensis) shows a significantly higher antibacterial activity than the extracts of Cancerina (Hippocratea excelsa), Laurel (Litsea glaucescens) and Tapacola (Waltheria americana) alone and in combination. Phenolic compounds, anthocyanins and flavonoids were determined. Rue may contribute to the potential identification of a natural alternative therapy against methicillin resistantStaphylococcus aureus.
Unified Sampling and Ranking for Protein Docking with DFMDock
Authors: Chu Lee-Shin , Sarma Sudeep , Gray Jeffrey J.
Published: September 2024

Diffusion models have shown promise in addressing the protein docking problem. Traditionally, these models are used solely for sampling docked poses, with a separate confidence model for ranking. We introduce DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework. DFMDock features two output heads: one for predicting forces and the other for predicting energies. The forces are trained using a denoising force matching objective, while the energy gradients are trained to align with the forces. This design enables our model to sample using the predicted forces and rank poses using the predicted energies, thereby eliminating the need for an additional confidence model. Our approach outperforms the previous diffusion model for protein docking, DiffDock-PP, with a sampling success rate of 44% compared to its 8%, and a Top-1 ranking success rate of 16% compared to 0% on the Docking Benchmark 5.5 test set. In successful decoy cases, the DFMDock Energy forms a binding funnel similar to the physics-based Rosetta Energy, suggesting that DFMDock can capture the underlying energy landscape.
Predictive influences on memory encoding: investigating oscillations and the N400 event-related potential component
Authors: Jano Sophie Louise , Schlesewsky Matthias , Chatburn Alex , Coussens Scott , Cross Zachariah R , Bornkessel-Schlesewsky Ina
Published: September 2024

To effectively function in an ever-changing environment, the brain is proposed to make predictions about upcoming information. However, the association between prediction and memory formation and the role of between-subject neural variability in this relationship is unclear. To shed light on the relationship between prediction and memory, the present study reanalysed data from Jano, Chatburn, and colleagues (2024). In the original experiment, participants were exposed to naturalistic images in predictable and unpredictable four-item sequences, after which their memory was tested using an old/new paradigm. In the present analysis (N = 46), N400 amplitude and oscillatory power during learning was measured to gauge processes related to prediction error and memory encoding, respectively. This activity was compared with subsequent memory outcomes and individual alpha frequency (IAF) calculated at rest. Linear mixed-effects regressions revealed an alpha power subsequent memory effect that was not related to the amplitude of the N400, suggesting that memory encoding may occur independently of the level of prediction error. Notably, IAF influenced the relationship between theta power, N400 amplitude and subsequent memory, implying that the electrophysiological conditions for successful memory formation differ between individuals. Consequently, the degree to which prediction errors (presumably gauged via the N400) drive memory encoding could depend on inter-individual variability in intrinsic neural activity. These findings emphasise the flexible nature of memory, whilst having potential implications for prediction error-driven accounts of learning.
MetaLab Platform Enables Comprehensive DDA and DIA Metaproteomics Analysis
Authors: Cheng Kai , Ning Zhibin , Zhang Xu , Duan Haonan , Mayne Janice , Figeys Daniel
Published: September 2024

Metaproteomics studies the collective protein composition of complex microbial communities, providing insights into microbial roles in various environments. Despite its importance, metaproteomic data analysis is challenging due to the data’s large and heterogeneous nature. While Data-Independent Acquisition (DIA) mode enhances proteomics sensitivity, it traditionally requires Data-Dependent Acquisition (DDA) results to build the library for peptide identification.

This paper introduces an updated version of MetaLab, a software solution that streamlines metaproteomic analysis by supporting both DDA and DIA modes across various mass spectrometry (MS) platforms, including Orbitrap and timsTOF. MetaLab’s key feature is its ability to perform DIA analysis without DDA results, allowing more experimental flexibility. It incorporates a deep learning strategy to train a neural network model, enhancing the accuracy and coverage of DIA results.

Evaluations using diverse datasets demonstrate MetaLab’s robust performance in accuracy and sensitivity. Benchmarks from large-scale human gut microbiome studies show that MetaLab increases peptide identification by 2.7 times compared to conventional methods. MetaLab is a versatile tool that facilitates comprehensive and flexible metaproteomic data analysis, aiding researchers in exploring microbial communities’ functionality and dynamics.
The role of temporal sensitivity of synaptic plasticity in representation learning
Authors: Rubisch Patricia , Stefan Melanie I , Hennig Matthias H
Published: September 2024

Synaptic plasticity, the process by which synapses change in an activity-dependent manner, is assumed to be the basis of learning. Recent experiments demonstrated that synaptic plasticity not only depends on excitatory activity but also on the rate and the timing of inhibitory events. Hypothesising that the regulatory effect of inhibition is mediated by membrane potential hyper-polarisation, we identify a trade-off between temporal precision and magnitude of the inhibitory regulation of plasticity in three different voltage-dependent plasticity models. We show that in recurrent networks all three models develop receptive fields from naturalistic input, yet the temporal precision of inhibitory regulation is critical for the separation and heterogeneity of the resulting representation.
The usual and unusual functions of thioredoxins in the metabolism and stress-response of sulfate-reducing bacteria
Authors: Majumder Erica L.-W. , Hou Liyuan , Whittle Fawn B. , Fitriasari Sharien , Trotter Valentine V. , Butland Gareth P. , Petzold Chris , Wall Judy D.
Published: September 2024

Thioredoxins are small, universal, disulfide isomerase proteins with required functions in oxidative stress response and RNA synthesis, among others. However, little is known about how anaerobic organisms maintain their intracellular redox balance or how thioredoxins may function differently under anaerobic metabolism. In this study, we investigated the roles of thioredoxins in sulfate-reducing microorganisms (SRMs). SRMs use sulfate as their primary electron acceptor in respiration to produce sulfide and are found in various environments including marine, freshwater sediments, guts and biofilms on ferrous metals where corrosion occurs. We found SRMs lack common redox maintenance molecules and macromolecules but have many and varied thioredoxins belonging to three types. Then, we probed their functions in the model SRM,Desulfovibrio vulgarisHildenborough (DvH), by anin vivodisulfide bond capture proteomics experiment in both non-stressed and oxidatively stressed conditions. Our results demonstrated that thioredoxin 1 (Trx1) was essential in DvH and selectively responded to oxidative stress. Our data supported its role in RNA synthesis and energy transduction since Trx1 interacted with DsrC and QmoB. Thioredoxin 3 (Trx3), an atypical thioredoxin, was observed to have roles in sulfur transfer and dissimilatory sulfur metabolism. Next, DvH thioredoxin system protein encoding genes were deleted and single deletion mutant strains were tested for growth phenotypes under a variety of different electron donors, acceptors and toxic metal stresses. It is found that dissimilatory sulfate reduction improves resistance of DvH to metal stress. It appeared the sulfide provided certain protection to DvH from silver and uranium stress.

Importance

We put forth new functions for thioredoxins and a more robust understanding of sulfate reducing microorganisms physiology. Thioredoxin is of general interest because it has been widely studied for redox homeostasis or cancer therapies dealing with the excess of reactive oxygen species (ROS). Our results indicated that these proteins do have functions in stress response, even in microorganisms that generate large amounts of sulfide. We also identified interaction partners for an atypical thioredoxin, suggesting distinct roles from conserved thioredoxin. Mechanisms of metal stress response were found to be different than direct oxidative stress. Thioredoxin did not appear to be involved in uranium reduction electron transfer pathways, contradicting a hypothesis from the literature.
Structure-guided design and synthesis of C22- and C32-modified FK520 analogs with enhanced activity against human pathogenic fungi
Authors: Dome Patrick A. , Jeong Pyeonghwa , Nam Gibeom , Jang Hongjun , Rivera Angela , Averette Anna Floyd , Park Eunchong , Liao Tzu-Chieh , Ciofani Maria , Wu Jianli , Chi Jen-Tsan Ashley , Venters Ronald A. , Park Hyun-Ju , Steinbach William J. , Juvvadi Praveen R. , Heitman Joseph , Hong Jiyong
Published: September 2024

Invasive fungal infections are a leading cause of death worldwide. Translating molecular insights into clinical benefits is challenging because fungal pathogens and their hosts share similar eukaryotic physiology. Consequently, current antifungal treatments have limited efficacy, may be poorly fungicidal in the host, can exhibit toxicity, and are increasingly compromised by emerging resistance. We have established that the phosphatase calcineurin (CaN) is required for invasive fungal disease and an attractive target for antifungal drug development. CaN is a druggable target, and there is vast clinical experience with the CaN inhibitors FK506 and cyclosporin A (CsA). However, while FK506 and its natural analog FK520 exhibit antifungal activity, they are also immunosuppressive in the host and thus not fungal-selective. We leverage our pathogenic fungal CaN-FK506-FKBP12 complex X-ray structures and biophysical data to support structure-based ligand design as well as structure–activity relationship analyses of broad-spectrum FK506/FK520 derivatives with potent antifungal activity and reduced immunosuppressive activity. Here we apply molecular docking studies to develop antifungal C22- or C32-modified FK520 derivatives with improved therapeutic index scores. Among them, the C32-modified FK520 derivative JH-FK-44 (7) demonstrates a significantly improved therapeutic index compared to JH-FK-08, our lead compound to date. NMR binding studies with C32-derivatives are consistent with our hypothesis that C32 modifications disrupt the hydrogen bonding network in the human complex while introducing favorable electrostatic and cation–π interactions with the fungal FKBP12 R86 residue. These findings further reinforce calcineurin inhibition as a promising strategy for antifungal therapy.

Significance

Invasive fungal infections cause significant mortality worldwide, and current antifungal treatments are often ineffective, toxic, or face growing resistance. This research identifies calcineurin (CaN), a critical protein for fungal survival, as a potential target for developing new antifungal drugs. Although existing CaN inhibitors such as FK506 (tacrolimus) and FK520 (ascomycin) possess antifungal properties, their immunosuppressive effects limit their clinical utility. By studying the structure of human and fungal FKBP12-FK506 or FK520 complexes with CaN, we have designed and synthesized modified FK520 derivatives with strong antifungal activity and reduced immunosuppressive effects. These new derivatives are expected to have significantly improved therapeutic profiles, offering hope for more effective and safer antifungal treatments.
Directed evolution of aminoacyl-tRNA synthetases throughin vivohypermutation
Authors: Furuhata Yuichi , Rix Gordon , Van Deventer James A. , Liu Chang C.
Published: September 2024

Genetic code expansion (GCE) has become a critical tool in biology by enabling the site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Central to GCE is the development of orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs wherein engineered aaRSs recognize chosen ncAAs and charge them onto tRNAs that decode blank codons (e.g., the amber stop codon). Many orthogonal aaRS/tRNA pairs covering a wide range of ncAAs have been generated by directed evolution, yet the evolution of new aaRS/tRNA pairs by standard strategies remains a labor-intensive process that often produces aaRS/tRNA pairs with suboptimal ncAA incorporation efficiencies. In this study, we present a strategy for evolving aaRSs that leverages OrthoRep to drive their continuous hypermutation in yeast. We demonstrate our strategy in 8 independent aaRS evolution campaigns starting from 4 different aaRS/tRNA parents targeting 7 distinct ncAAs. We observed the rapid evolution of multiple novel aaRSs capable of incorporating an overall range of 13 ncAAs tested into proteins in response to the amber codon. Some evolved systems reached efficiencies for amber codon-specified ncAA-dependent translation comparable to translation with natural amino acids specified by sense codons in yeast. Additionally, we discovered a surprising aaRS that evolved to self-regulate its own expression for greater dependency on ncAAs for translation. These findings demonstrate the potential of OrthoRep-driven aaRS evolution platforms in supporting the continued growth of GCE technologies.
Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks
Authors: Chen Muyuan
Published: September 2024

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores.
The claustrum enhances neural variability by modulating the responsiveness of the prefrontal cortex
Authors: Atilgan Huriye , Lazarte Ivan P. , Packer Adam M.
Published: September 2024

The claustrum is recognized for its significant impact on various cognitive functions and its extensive connections with other brain regions, yet its functional role remains to be fully understood. Here, we utilized an optogenetic approach to investigate the claustrum’s influence on neuronal activity within the dorsal prefrontal cortex (dPFC) of mice. We conducted two-photon calcium imaging to assess dPFC cell responses during exposure to visual stimuli and widefield photostimulation of claustrum axons embedded in the dPFC. We identified three distinct subpopulations of neurons — sensory responsive, opto responsive, and opto-boosted cells — each exhibiting unique response dynamics to combined visual and optogenetic stimuli. Our findings reveal that stimulation of claustrum axons can normalize neuronal responsiveness, while enhancing neural variability, and significantly increasing network homogeneity. Training in a Pavlovian task showed that while enhanced variability with claustrum axon stimulation in neural responses persists, training does not further increase this variability but instead leads to greater network homogeneity. Additionally, we also performed claustrum axon silencing experiments that revealed that the claustrum may operate bidirectionally to maintain enhanced variability and homogeneity in the prefrontal cortex. These results highlight the crucial role of the claustrum in dynamically modulating dPFC activity, impacting both neuronal variability and network synchronization.
Sealing and anti-seepage polyurea coating design method based on nonlinear FEM simulation
Authors: Li Bingqi , Zhang Jilei , Liu Xiaonan , Meng Tianyi
Published: September 2024

Purpose

Structural design theory and method for the polyurea coating system have rarely been developed. The normally used experience-based design method may lead to unsafe, unreasonable and uneconomic results. The purpose of this paper is to investigate the deformation and failure behaviour of the polyurea coating so as to propose a rational design method.

Design/methodology/approach

In this study, the fundamental theories concerning the nonlinear analysis of polyurea coating were discussed. Nonlinear Finite Element Method (FEM) models were built to investigate the mechanical behaviour, peeling behaviour and failure mode of the polyurea coating under various conditions, such as surface fracturing, surface hydraulic pressure and reverse hydraulic peeling.

Findings

The main conclusions are as follows. The peeled coating at the crack location exhibits a tensile-bending stress state. Coating material damage may occur at the stress concentration point. The maximum stress increases with the increase in the hydraulic pressure and cohesive strength. The peeling length of the coating decreases with the increase in cohesive strength and increases with the increase in fracture width. The reverse hydraulic pressure-induced blister edge stress concentration is the main trigger of the polyurea coating blistering damage. The blistering height decreases with increasing coating thickness and increases with increasing blistering radius and hydraulic load. The maximum stress increases with increasing blistering radius and hydraulic load. Finally, the frame of design and simple design programme were proposed.

Originality/value

Currently, a design method for polyurea anti-seepage coating can hardly be found. The reason is that the anti-seepage coating has only been recognized as a water-proofing layer, the mechanical behaviour of which has been ignored. This study focused on the mechanical behaviour of the anti-seepage coating and investigated the deformation and failure behaviour of the coating structure under various loading conditions through nonlinear FEM analysis. These research results offer a better understanding concerning the mechanical behaviour and design method of the polyurea anti-seepage coating.
Talent management in the hospitality and tourism industry: the role of societal and organisational culture
Authors: Kravariti Foteini , Jooss Stefan , Tom Dieck M. Claudia , Fountoulaki Paraskevi , Hossain Farhad
Published: September 2024

Purpose

The purpose of this paper is to examine the role of societal and organisational culture on talent management (TM) within the Greek hospitality and tourism (H&T) industry. Specifically, this study tests societal culture’s effect on TM approaches and the mediating role of organisational culture.

Design/methodology/approach

In this quantitative study, the questionnaire sample included employees of all hierarchical levels from three hotels located in northern, central and southern Greece (n = 188). Data analyses were carried out by using the PROCESS Version 4 macro in SPSS.

Findings

The results show that neither societal nor organisational culture are decisive factors in impacting the perceived TM approach. This might be due to the organisations imitating other firms without pre-establishment of societal and organisational fit.

Practical implications

This study emphasises TM’s alignment with both societal and organisational culture. Given the context-specific nature of TM, achieving culture fit can enhance talent acquisition, retention and engagement, ultimately leading to improved talent and overall organisational performance.

Originality/value

This study integrates more centrally a cultural lens into the TM discourse. It provides empirical evidence of TM approaches in the Greek H&T industry, drawing on a multi-stakeholder sample including managers and talents.
The effect of megaproject external social responsibility on community acceptance: the mediating role of public trust
Authors: Aga Deribe Assefa , Beyene Berhanu Belayneh
Published: September 2024

Purpose

By extending corporate social responsibility research to a megaproject context, the purpose of this study is to examine the effect of megaproject external social responsibility (SR) on community acceptance through the mediating role of public trust.

Design/methodology/approach

Drawing from legitimacy theory as well as corporate social responsibility literature, this study developed hypotheses linking the constructs of SR, (public) trust and community acceptance of a megaproject. Thereby, a household survey questionnaire was administered to collect data from randomly selected 328 households in the local community who reside near the construction site of a mega hydropower project in Ethiopia. Guided by structural equation modelling, Smart Partial Least Squares4 (SmartPLS4) was utilized to analyze the data.

Findings

The empirical findings show that community-targeted SR has a significant positive effect on community acceptance of a megaproject, whereas the direct effect of natural environment-targeted SR on community acceptance was found to be non-significant. More importantly, the study reveals that trust in the contractor of the megaproject mediates the relationships between a megaproject SR (fully in the case of the natural environment and partially for community-targeted responsibility) and community acceptance.

Originality/value

The present study contributes to legitimacy theory by illustrating the consequences of megaproject external SR in terms of trust and community acceptance, an issue which has not received adequate attention in the project management literature.
Unveiling environmental excellence: the confluence of green Industrial Internet of Things, circular economy practices and dynamic capabilities in manufacturing firms
Authors: Xu Nan , Shahzad Fakhar , Hu Rui
Published: September 2024

Purpose

To meet environmental performance (EP) goals, this study aims to identify the complex interaction between green Industrial Internet of Things (GIIoT), circular economic practices (CEPs) and dynamic capabilities (DC). This study analyzes how technological, operational and cultural compatibilities enhance GIIoT adoption.

Design/methodology/approach

Data were collected from diverse Chinese manufacturing firms (n = 339) through a quantitative survey. The research model was proposed, and hypotheses were tested using structural equation modeling. Moreover, the robustness of the structural model is further tested using Fuzzy Set Qualitative Comparative Analysis and importance performance map analysis.

Findings

The empirical results indicate that higher organizational compatibilities boost GIIoT adoption and EP. DC was assessed as a higher-order construct to examine its mediation of GIIoT adoption and EP. DC positively mediates GIIoT adoption-EP. Similarly, CEP’s positive impact on EP, partially mediating the relationship between GIIoT adoption and EP, has also been proved.

Originality/value

This research bridges current understanding and contributes useful insights for fostering environmental sustainability inside manufacturing firms and advances the theoretical understanding of technology adoption, sustainable development and dynamic capacity theory. It illuminates the way forward to harmonize and successfully integrate technology, CEP and EP. This research advances the area and gives decision-makers practical advice for creating sustainable and technologically sophisticated organizations.
Top management team stability and outward foreign direct investment of Chinese firms
Authors: Zhan Yun , Liao Jia , Zhao Xiaoyang
Published: September 2024

Purpose

This study aims to investigate the effect of top management team (TMT) stability on outward foreign direct investment (OFDI) of Chinese firms and the moderating effects of state ownership and managerial ownership on this relationship.

Design/methodology/approach

An empirical analysis based on the ordinary least square regression model is conducted using Chinese A-share listed firms that engaged in OFDI from 2008 to 2021.

Findings

TMT stability has a positive effect on firms’ OFDI. Moreover, state ownership significantly strengthens the positive relationship between TMT stability and OFDI, while managerial ownership weakens this positive relationship.

Practical implications

The findings help firms to effectively retain TMT talents and promote the smooth internationalization of firms, thereby enhancing their long-term development capabilities and competitive advantages.

Originality/value

This study expands the investigation of the factors influencing OFDI at the micro level of the TMT, providing valuable decision-making insights for firms.
Does a coach’s reputation affect an athlete’s creativity in team sports?
Authors: Asare Maxwell Kwabena , Schnitzer Martin
Published: September 2024

Purpose

Leadership is a key factor that shapes an athlete’s development, also within team sports; most of this responsibility falls on the coaches. The purpose of this paper is to provide insight into the relationship between a coach’s reputation and athlete creativity as perceived by athletes within team sports.

Design/methodology/approach

The paper examined the reputational construct of coaches vis-a-vis athlete creativity. The researchers surveyed athletes from a variety of team sports and professional levels (N = 203). Structural equation modelling was utilised for testing the hypotheses.

Findings

Findings suggest that a coach’s reputation has a significant influence on the development of an athlete’s creativity. Coach reputation affects the creative development of an athlete, with knowledge sharing and openness to experiences being the principal means of influence.

Originality/value

Our study (1) examines the influence of a coach’s reputation on an athlete’s creativity, (2) tests the role of knowledge sharing in the influence on an athlete’s creativity and (3) considers openness to experiences in the development of an athlete’s creativity.
Surviving in the midst of ‘Nowhere’: Disrupting the conceptualisation of a maternity care desert
Authors: Archer Rose E.
Published: September 2024

The conceptualisation of ‘care deserts’ has gained increased public attention in recent years. This paper engages a reproductive justice framework to investigate the (mis)alignment of a maternity care desert within a predominantly Black rural community in the United States. I draw on a case study of Gadsden County, Florida—a community that is perceived by its members to be a maternity care desert but that is not technically defined as one—to demonstrate how Black birthing people are cultivating a reproductive liberatory consciousness. Semi‐structured interviews with birthing persons and reproductive health experts reveal three overarching processes—naming barriers to health equity, resisting health inequity and cultivating health equity—that characterise a reproductive liberatory consciousness, which I identify as an analytical tool to outline how local social actors are identifying structural constraints as well as developing strategies of communal care and resistance. This work contributes to sociological research on reproductive justice and health equity by exploring the limitations of ‘desert’ frameworks. Pointing to the need to carefully consider the mechanisms that actively disrupt and potentially transform spatial stratifications and inequities, this paper advances a new understanding of birthing space that captures the layered movements of those living within a perceived maternity care desert.
Nonlinear impacts of environmental transport taxes and biofuel consumption on greenhouse emissions in the four largest European Union countries
Authors: Pata Ugur Korkut , Erdogan Sinan , Karlilar Pata Selin , Kartal Mustafa Tevfik
Published: September 2024

Incompatible with the pioneering role of the transportation sector in greenhouse gas (GHG) emissions, this research mainly deals with GHG emissions from the transport sector. In this context, the study looks at the four leading European Union (EU) countries (i.e., Germany, France, Italy, and Spain), investigates emissions from their sub‐types of the transport sector (i.e., aviation, rail, and road), uses environmental transport taxes (ETAX) as the main explanatory variable in the bivariate modeling, and considers biofuel consumption (BIO) as a control factor in the multivariate modeling. The study uses monthly data between 2004 and 2022, bivariate and multivariate quantile‐on‐quantile regression as well, and Granger causality‐in‐quantiles as the main approaches. The results demonstrate that (i) ETAX is completely inefficient on aviation and road transport GHG emissions; (ii) ETAX curbs rail transport GHG emissions in France at only middle quantiles; (iii) with the moderating impact of BIO, ETAX becomes effective in declining aviation, rail, and road transport GHG emissions (iv) BIO has a certainly reversing impact on the nexus between ETAX and transport sector GHG emissions. Overall, the study highlights that ETAX has a stand‐alone ineffective impact in curbing transport sector GHG emissions, but BIO has a certain moderating contribution in this manner. Thus, the study strongly recommends taking further actions, such as more use of BIO as in the case of this study, to support ETAX practices in combating GHG emissions for the EU countries.