bluuebunny/crossref_metadata_2025 huggingface dataset:
A single-cell atlas of pig gastrulation as a resource for comparative embryology
Authors: Simpson Luke , Strange Andrew , Klisch Doris , Kraunsoe Sophie , Azami Takuya , Goszczynski Daniel , Le Triet , Planells Benjamin , Holmes Nadine , Sang Fei , Henson Sonal , Loose Matthew , Nichols Jennifer , Alberio Ramiro
Published: September 2023

Early mammalian gastrulation’s cell-fate decisions are poorly understood due to difficulties obtaining non-rodent embryos. The bilaminar disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-type development, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm (DE). We find early FOXA2+/TBXT-embryonic disc cells directly from DE, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. DE/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon DE differentiation. These findings emphasise the interplay between temporal and topological signalling in early fate decisions during gastrulation.
Metabolic Dependency Shapes Bivalent Antiviral Response in Host Cells in response to poly:IC: The Role of Glutamine
Authors: Lebeau Grégorie , Paulo-Ramos Aurélie , Hoarau Mathilde , El Safadi Daed , Meilhac Olivier , Krejbich-Trotot Pascale , Roche Marjolaine , Viranaicken Wildriss
Published: September 2023

The establishment of effective antiviral responses within host cells is intricately related to their metabolic status, shedding light on immunometabolism. In this study, we investigated the hypothesis that cellular reliance on glutamine metabolism contributes to the development of a potent antiviral response. We evaluated the antiviral response in the presence or absence of L-glutamine in the culture medium, revealing a bivalent response hinging on cellular metabolism. While certain interferon-stimulated genes (ISGs) exhibited higher expression in an oxidative phosphorylation (OXPHOS)-dependent manner, others were surprisingly upregulated in a glycolytic-dependent manner. This metabolic dichotomy was influenced in part by variations in IFN-β expression. We initially demonstrated that the presence of L-glutamine induced an enhancement of OXPHOS in A549 cells. Furthermore, in cells either stimulated poly:IC or infected with Dengue Virus and Zika Virus, a marked increase in ISGs expression was observed in a dose-dependent manner with L-glutamine supplementation. Interestingly, our findings unveiled a metabolic dependency in the expression of specific ISGs. In particular, genes such as ISG54, ISG12 and ISG15 exhibited heightened expression in cells cultured with L-glutamine, corresponding to higher OXPHOS rates and IFN-β signaling. Conversely, the expression of viperin and 2’-5’-oligoadenylate synthetase 1 was inversely related to L-glutamine concentration, suggesting a glycolysis-dependent regulation, confirmed by inhibition experiments. This study highlights the intricate interplay between cellular metabolism, especially glutaminergic and glycolytic, and the establishment of the canonical antiviral response characterized by the expression of antiviral effectors, potentially paving the way for novel strategies to modulate antiviral responses through metabolic interventions.
Single-cell immune multi-omics and repertoire analyses in pancreatic ductal adenocarcinoma reveal differential immunosuppressive mechanisms within different tumour microenvironments
Authors: Sivakumar Shivan , Jainarayanan Ashwin , Arbe-Barnes Edward , Sharma Piyush Kumar , Leathlobhair Maire Ni , Amin Sakina , Heij Lara , Hegde Samarth , Magen Assaf , Tucci Felicia , Sun Bo , Wu Shihong , Anand Nithishwer Mouroug , Slawinski Hubert , Revale Santiago , Nassiri Isar , Webber Jonathon , Frampton Adam , Wiltberger Georg , Neumann Ulf , Charlton Philip , Spiers Laura , Elliott Tim , Sivakumar Pallavur V. , Ratushny Alexander V. , Middleton Mark , Peppa Dimitra , Fairfax Benjamin , Merad Miriam , Dustin Michael L. , Abu-Shah Enas , Bashford-Rogers Rachael
Published: September 2023

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. Understanding the multiple mechanisms by which the tumour evades immune control, and how these mechanisms may be disrupted is critical to developing targeted immunotherapies. Previous studies have shown that higher lymphocyte infiltration is associated with better survival, and here we investigated what mediates these differences. We performed a comprehensive analysis of PDAC-associated immune cells using single cell multi-omics coupled with re-analysis of public PDAC scRNA-seq datasets. We introduce novel single-cell and repertoire analyses that have uncoupled diverse roles and contributions of various immune cell populations within different tumour microenvironments (TMEs). They revealed clear distinctions in the clonal characteristics among different patient groups, provided valuable insights into the mechanisms of immune cell migration and tissue adaptation underlying these disparities. These results point to differential CD4 polarisation of intra-tumoural T cells, differential B cell differentiation, GC reactions, antigen presentation pathways, and distinct cell-cell communication between the myeloid-enriched and adaptive-enriched groups. Overall, we identified two major distinct themes for future immune intervention within PDAC patients between those with higher adaptive versus myeloid immune cell infiltration.
Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures
Authors: Herrington Noah B. , Stein David , Li Yan Chak , Pandey Gaurav , Schlessinger Avner
Published: September 2023

Protein kinase function and interactions with drugs are controlled in part by the movement of the DFG and ɑC-Helix motifs, which enable kinases to adopt various conformational states. Small molecule ligands elicit therapeutic effects with distinct selectivity profiles and residence times that often depend on the kinase conformation(s) they bind. However, the limited availability of experimentally determined structural data for kinases in inactive states restricts drug discovery efforts for this major protein family. Modern AI-based structural modeling methods hold potential for exploring the previously experimentally uncharted druggable conformational space for kinases. Here, we first evaluated the currently explored conformational space of kinases in the PDB and models generated by AlphaFold2 (AF2) (1) and ESMFold (2), two prominent AI-based structure prediction methods. We then investigated AF2’s ability to predict kinase structures in different conformations at various multiple sequence alignment (MSA) depths, based on this parameter’s ability to explore conformational diversity. Our results showed a bias within the PDB and predicted structural models generated by AF2 and ESMFold toward structures of kinases in the active state over alternative conformations, particularly those conformations controlled by the DFG motif. Finally, we demonstrate that predicting kinase structures using AF2 at lower MSA depths allows the exploration of the space of these alternative conformations, including identifying previously unobserved conformations for 398 kinases. The results of our analysis of structural modeling by AF2 create a new avenue for the pursuit of new therapeutic agents against a notoriously difficult-to-target family of proteins.

Significance Statement

Greater abundance of kinase structural data in inactive conformations, currently lacking in structural databases, would improve our understanding of how protein kinases function and expand drug discovery and development for this family of therapeutic targets. Modern approaches utilizing artificial intelligence and machine learning have potential for efficiently capturing novel protein conformations. We provide evidence for a bias within AlphaFold2 and ESMFold to predict structures of kinases in their active states, similar to their overrepresentation in the PDB. We show that lowering the AlphaFold2 algorithm’s multiple sequence alignment depth can help explore kinase conformational space more broadly. It can also enable the prediction of hundreds of kinase structures in novel conformations, many of whose models are likely viable for drug discovery.
Multifaceted proteome analysis at solubility, redox, and expression dimensions for target identification
Authors: Saei Amir Ata , Lundin Albin , Lyu Hezheng , Gharibi Hassan , Luo Huqiao , Teppo Jaakko , Zhang Xuepei , Gaetani Massimiliano , Végvári Ákos , Holmdahl Rikard , Gygi Steven P. , Zubarev Roman A.
Published: September 2023

Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, we devise the first high- throughput redox proteomics approach integrated with expression analysis (REX) and combine it with Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, we analyzed HCT116 cells treated with auranofin, showing great improvement compared with previous such studies. Then we applied PISA-REX to study proteome remodeling upon stimulation of human monocytes by interferon α. We also studied the proteome changes in plasmacytoid dendritic cells isolated from wild type vs.Ncf1- mutant mice treated with interferon α, showing that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.
AToxoplasma gondiiputative arginine transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation
Authors: Piro Federica , Masci Silvia , Kannan Geetha , Focaia Riccardo , Schultz Tracey L. , Carruthers Vern B. , Di Cristina Manlio
Published: September 2023

Toxoplasma gondiiis a protozoan parasite that infects a broad spectrum of hosts and can colonize many organs and cell types. The ability to reside within a wide range of different niches requires substantial adaptability to diverse microenvironments. Very little is known about how this parasite senses various milieus and adapts its metabolism to survive, replicate during the acute stage, and then differentiate to the chronic stage. Most eukaryotes, from yeast to mammals, rely on a nutrient sensing machinery involving the TORC complex as master regulator of cell growth and cell cycle progression. The lysosome functions as a signaling hub where TORC complex assembles and is activated by transceptors, which both sense and transport amino acids, including the arginine transceptor SLC38A9. While most of the TORC components are lost inT. gondii, indicating the evolution of a distinct nutrient sensing mechanism, the parasite’s lysosomal plant-like vacuolar compartment (PLVAC) may still serve as a sensory platform for controlling parasite growth and differentiation. Using SLC38A9 to query theT. gondiiproteome, we identified four putative amino acid transporters, termed TgAAT1-4, that structurally resemble the SLC38A9 arginine transceptor. Assessing their expression and sub-cellular localization, we found that one of them, TgAAT1, localized to the PLVAC and is necessary for normal parasite extracellular survival and bradyzoite differentiation. Moreover, we show that TgAAT1 is involved in the PLVAC efflux of arginine, an amino acid playing a key role inT. gondiidifferentiation, further supporting the hypothesis that TgAAT1 might play a role in nutrient sensing.

IMPORTANCE

T. gondiiis a highly successful parasite infecting a broad range of warm-blood organisms including about one third of all humans. AlthoughToxoplasmainfections rarely result in symptomatic disease in individuals with a healthy immune system, the incredibly high number of persons infected along with the risk of severe infection in immunocompromised patients and the potential link of chronic infection to mental disorders make this infection a significant public health concern. As a result, there is a pressing need for new treatment approaches that are both effective and well-tolerated. The limitations in understanding howToxoplasma gondiimanages its metabolism to adapt to changing environments and triggers its transformation into bradyzoites have hindered the discovery of vulnerabilities in its metabolic pathways or nutrient acquisition mechanisms to identify new therapeutic targets. In this work, we have shown that the lysosome-like organelle PLVAC, acting through the putative arginine transporter TgAAT1, plays a pivotal role in regulating the parasite’s extracellular survival and differentiation into bradyzoites.
Estrogen prevents age-dependent beige adipogenesis failure through NAMPT-controlled ER stress pathway
Authors: Park Jooman , Hu Ruoci , Xiong Shaolei , Qian Yanyu , El-Sabbagh Asma Sana , Ibrahim Meram , Song Qing , Yan Gege , Song Zhenyuan , Mahmoud Abeer M. , He Yanlin , Layden Brian T. , Chen Jiwang , Ong Sang-Ging , Xu Pingwen , Jiang Yuwei
Published: September 2023

Thermogenic beige adipocytes are recognized as potential therapeutic targets for combating metabolic diseases. However, the metabolic advantages they offer are compromised with aging. Here, we show that treating mice with estrogen (E2), a hormone that decreases with age, to mice can counteract the aging- related decline in beige adipocyte formation when subjected to cold, while concurrently enhancing energy expenditure and improving glucose tolerance. Mechanistically, we find that nicotinamide phosphoribosyltranferase (NAMPT) plays a pivotal role in facilitating the formation of E2-induced beige adipocytes, which subsequently suppresses the onset of age-related ER stress. Furthermore, we found that targeting NAMPT signaling, either genetically or pharmacologically, can restore the formation of beige adipocytes by increasing the number of perivascular adipocyte progenitor cells. Conversely, the absence of NAMPT signaling prevents this process. In conclusion, our findings shed light on the mechanisms governing the age-dependent impairment of beige adipocyte formation and underscore the E2-NAMPT controlled ER stress as a key regulator of this process.

Highlights

Estrogen restores beige adipocyte failure along with improved energy metabolism in old mice.

Estrogen enhances the thermogenic gene program by mitigating age-induced ER stress.

Estrogen enhances the beige adipogenesis derived from SMA+ APCs.

Inhibiting the NAMPT signaling pathway abolishes estrogen-promoted beige adipogenesis.
The Quest for Dynamic Consistency — A Comparison of OpenSim Tools for Residual Reduction in Simulations of Human Running
Authors: Fox Aaron S.
Published: September 2023

The use of synchronous kinematic and kinetic data in simulations of human running will typically lead to dynamic inconsistencies (i.e. residual forces and moments) being present. Minimising the residual forces and moments in such simulations is important to ensure plausible model outputs (e.g. joint moments, muscle forces) are obtained. A variety of approaches suitable for residual reduction are available in OpenSim, however a detailed comparison of these is yet to be conducted. This study compared a variety of OpenSim tools applicable for residual reduction in simulations of human running. A series of approaches (i.e. singular and iterative Residual Reduction Algorithm,MocoTrack, AddBiomechanics) designed to reduce residual forces and moments were examined using an existing dataset of 10 male participants running on a treadmill at 5.0 m·s-1(n= 3 gait cycles per participant). The computational time, resultant residual forces and moments, and output joint kinematics and kinetics from each approach were compared. A computational cost to residual reduction trade-off was identified, where lower residual forces and moments were achieved using approaches that required longer computational times. All of the tested approaches regularly reduced residual forces below recommended thresholds, however only theMocoTrackapproach could consistently achieve acceptable levels for residual moments. TheAddBiomechanicsandMocoTrackapproaches produced variable lower and upper body kinematics, respectively, versus the remaining approaches; with minimal other qualitative differences were identified between joint kinematics from each approach. Joint kinetics were qualitatively similar between approaches, howeverMocoTrackgenerated much noisier joint kinetic signals. TheMocoTrackapproach was the most consistent and best performing approach for reducing residuals to near-zero levels, at the cost of longer computational times and potentially noisier joint kinetic signals. This study provides OpenSim users with evidence to inform decision-making at the residual reduction step of their modelling and simulation workflow when analysing human running.
Versatile Tissue-Injectable Hydrogels with Extended Hydrolytic Release of Bioactive Protein Therapeutics
Authors: Nealy Eric S. , Reed Steven J. , Adelmund Steve M. , Badeau Barry A. , Shadish Jared A. , Girard Emily J. , Pakiam Fiona J. , Mhyre Andrew J. , Price Jason P. , Sarkar Surojit , Kalia Vandana , DeForest Cole A. , Olson James M.
Published: September 2023

Hydrogels generally have broad utilization in healthcare due to their tunable structures, high water content, and inherent biocompatibility. FDA-approved applications of hydrogels include spinal cord regeneration, skin fillers, and local therapeutic delivery. Drawbacks exist in the clinical hydrogel space, largely pertaining to inconsistent therapeutic exposure, short-lived release windows, and difficulties inserting the polymer into tissue. In this study, we engineered injectable, biocompatible hydrogels that function as a local protein therapeutic depot with a high degree of user-customizability. We showcase a PEG-based hydrogel functionalized with bioorthogonal strain-promoted azide-alkyne cycloaddition (SPAAC) handles for its polymerization and functionalization with a variety of payloads. Small-molecule and protein cargos, including chemokines and antibodies, were site-specifically modified with hydrolysable “azidoesters” of varying hydrophobicity via direct chemical conjugation or sortase-mediated transpeptidation. These hydrolysable esters afforded extended release of payloads linked to our hydrogels beyond diffusion; with timescales spanning days to months dependent on ester hydrophobicity. Injected hydrogels polymerizein situand remain in tissue over extended periods of time. Hydrogel-delivered protein payloads elicit biological activity after being modified with SPAAC-compatible linkers, as demonstrated by the successful recruitment of murine T-cells to a mouse melanoma model by hydrolytically released murine CXCL10. These results highlight a highly versatile, customizable hydrogel-based delivery system for local delivery of protein therapeutics with payload release profiles appropriate for a variety of clinical needs.

Translational Impact

We developed injectable hydrogels that provide loco-regional, controlled release of protein therapeutics. Local delivery is especially suitable for potent, protein-based drugs like chemokines and monoclonal antibodies whose systemic toxicities can be life threatening. Our hydrogel is equipped with slowly hydrolyzing linkers for transient payload coupling, prolonging its therapeutic window and minimizing the need for repeat surgeries in a clinical setting. A range of release profiles, spanning days to over a month, and a broad compatibility to therapeutically relevant, recombinant proteins provide clinicians with flexible therapeutic options to suit a variety of circumstances.
Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets
Authors: Schmidt Nicola , Sielemann Katharina , Breitenbach Sarah , Fuchs Jörg , Pucker Boas , Weisshaar Bernd , Holtgräwe Daniela , Heitkam Tony
Published: September 2023

Background

Sugar beet (Beta vulgarissubsp.vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation.

Results

We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet generaBetaandPatellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome.

Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the sectionCorollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity inBetaandPatellifoliaspecies to the formation of patchwork chromosomes inCorollinae/Nanaespecies.

Conclusions

We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.
Dog Ecology and Rabies Knowledge, Attitude and Practice (KAP) in the Northern Communal Areas of Namibia
Authors: Tenzin Tenzin , Hikufe Emmanuel , Hedimbi Nehemia , Athingo Rauna , Shikongo Beatrice , Shuro Thompson , Iipinge Johannes , Herman Nelson , Naunyango Matias , Haufiku Frenada , Peter Josephat , Hango Laina , Gottlieb Sara , Shoombe Kenneth , Denzin Nicolai , Busch Frank , Lohr Frederic , Letshwenyo Moetapele , Torres Gregorio , Freuling Conrad M. , Müller Thomas , Shilongo Albertina
Published: September 2023

In 2021, a comprehensive dog demographic questionnaire combined with a KAP survey were conducted in the northern communal areas (NCAs) of Namibia with the aim of gaining a better understanding of dog populations, owner behaviour, and knowledge, attitudes and practices (KAP) relating to rabies. The survey of 3,726 households across the eight regions of the NCAs provided insights that will inform interventions on order to improve human rabies prevention and Namibia’s dog rabies control strategy. The results showed a relatively low average human/dog ratio (HDR) of 5.4:1 indicating a surprisingly high dog population of at least 272,000 dogs in the NCAs, 93% of which appear to be owned but are free-roaming. Data analysis revealed opportunities but also highlighted needs for improvements in rabies surveillance and mass dog vaccinations. Although knowledge, attitude, and practice scores towards epidemiologic and clinical aspects, human rabies prevention, and canine rabies vaccination were deemed to be acceptable, the survey nevertheless revealed deficiencies in some of the population. Interestingly, data seemed to indicate a certain number of unreported human rabies cases. Other findings included the very high number of dogs. However, only 50% of dog-owning households reported having vaccinated their dogs. In order to address these issues, the planning, announcement, and implementation of mass dog vaccination campaigns need to be adapted to achieve adequate vaccination coverage. Another focus needs to be on rabies awareness and education if Namibia is to be significantly contributing to the global goal of “Zero by 30”.

Author Summary

As a neglected disease, rabies remains a major One Health problem in Africa and Asia. Here we report the results of an extensive community survey on dog ownership and knowledge, attitudes and practices (KAP) related to rabies control and prevention, covering the Northern Communal Areas of Namibia. Our results showed that the dog population is large with a human/dog ratio (HDR) of 5.4:1, of which the vast majority is free-roaming thus supporting disease transmission but complicating control efforts. The majority of people across this part of Namibia were aware of rabies and had acceptable levels of attitudes and practices. While dog bite incidences per 100,000 people were high, ranging between 262 and 1,369, more than 90% of bite victims reported having visited a hospital after a bite incident. Still, gaps in dog rabies surveillance exist and incomplete or missing post exposure prophylaxes caused human casualties and call for ongoing interventions aimed at increasing knowledge and awareness.
NMR structure of the carboxy-terminal domain of the Ea22 pro-lysogenic protein from lambda bacteriophage
Authors: Goddard Cameron , Nejman-Faleńczyk Bożena , Donaldson Logan W
Published: September 2023

Theea22gene resides in a relatively uncharacterized region of the lambda bacteriophage genome between theexoandxisgenes and is among the earliest genes transcribed upon infection. In lambda and Shiga toxin-producing phages found in enterohemorrhagicE. coli(EHEC) associated with food poisoning, Ea22 favors a lysogenic over lytic developmental state. The Ea22 protein may be considered in terms of three domains: a short amino-terminal domain, a coiled-coiled domain, and a carboxy-terminal domain (CTD). While the full-length protein is tetrameric, the CTD is dimeric when expressed individually. Here, we report the NMR solution structure of the Ea22 CTD that is described by a mixed alpha-beta fold with a dimer interface reinforced by salt bridges. A conserved mobile loop may serve as a ligand for an unknown host protein that works with Ea22 to promote bacterial survival and the formation of new lysogens. From sequence and structural comparisons, the CTD distinguishes lambda Ea22 from homologs encoded by Shiga toxin-producing bacteriophages.
Loss ofRND3/RHOEcontrols entosis throughLAMP1expression in hepatocellular carcinoma
Authors: Basbous Sara , Dif Lydia , Dantzer Camille , Di-Tommaso Sylvaine , Dupuy Jean-William , Bioulac-Sage Paulette , Raymond Anne-Aurélie , Desdouets Chantal , Saltel Frédéric , Moreau Violaine
Published: September 2023

Entosis is a process that leads to the formation of cell-in-cell structures commonly found in cancers. Here, we identified entosis in hepatocellular carcinoma and the loss of Rnd3 as an efficient inducer of this mechanism. We characterized the different stages and the molecular regulators of entosis induced after Rnd3 silencing. We demonstrated that this process depends on RhoA/ROCK pathway, but not on E-cadherin. The proteomic profiling of entotic cells allowed us to identify LAMP1 as a protein upregulated by Rnd3 silencing and implicated not only in the degradation final stage of entosis, but also in the full mechanism. Moreover, we found a positive correlation between the presence of entotic cells and the metastatic potential of tumors in human patient samples. Altogether, these data suggest the involvement of entosis in liver tumor progression and highlight a new perspective for entosis analysis in medicine research as a novel therapeutic target.
Rof is a key regulator of Rho and transcription termination in bacteria
Authors: Zhang Jing , Zhang Shuo , Zhou Wei , Zhang Xiang , Li Guanjin , Li Luoxuan , Lin Xingyu , Liu Fang , Gao Yue , Chen Zhenguo , Chao Yanjie , Wang Chengyuan
Published: September 2023

Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report the cryogenic electron microscopy structure of Rho-Rof antitermination complex. The structure shows that Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof’s N-terminal α-helix is key in facilitating Rof-Rho interactions. Rof binds to Rho’s primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo assays inSalmonella Typhimuriumshow that Rof is required for virulence gene expression and host cell invasion, unveiling a novel physiological function of Rof and transcription termination in bacterial pathogenesis.
Chemoproteomic profiling of 8-oxoguanosine-sensitive RNA-protein interactions
Authors: Villers Jennifer , McCann Smith Eliana , DeLiberto Amanda N. , Arguello A. Emilia , Nyaanga Joy , Kleiner Ralph E.
Published: September 2023

Cellular nucleic acids are subject to assault by endogenous and exogenous agents that can perturb the flow of genetic information. Oxidative stress leads to the accumulation of 8-oxoguanine (8OG) on DNA and RNA. 8OG lesions on mRNA negatively impact translation, but their effect on global RNA-protein interactions is largely unknown. Here, we apply an RNA chemical proteomics approach to investigate the effect of 8OG on RNA-protein binding. We find proteins that bind preferentially to 8OG-modified RNA, including IGF2BP1-3 and hnRNPD, and proteins that are repelled by 8OG such as RBM4. We characterize these interactions using biochemical and biophysical assays to quantify the effect of 8OG on binding and show that a single 8OG abolishes binding of RBM4 to its preferred CGG-containing substrate. Taken together, our work establishes the molecular consequences of 8OG on cellular RNA-protein binding and provides a framework for interrogating the role of RNA oxidation in biological systems.
Engineering Quorum Quenching Acylases with Improved Kinetic and Biochemical Properties
Authors: Sompiyachoke Kitty , Elias Mikael H.
Published: September 2023

Many Gram-negative bacteria respond toN-acyl-L-homoserine lactone (AHL) signals to coordinate phenotypes such as biofilm formation and virulence factor production. Quorum-quenching enzymes, such as acylases, chemically degrade AHL signals, prevent signal reception by bacteria, and inhibit undesirable traits related to biofilm. These capabilities make these enzymes appealing candidates for controlling microbes. Yet, enzyme candidates with high activity levels, high substrate specificity for specific interference, and that are capable of being formulated into materials are needed. In this work, we undertook engineering efforts against two AHL acylases, PvdQ and MacQ, to obtain improved acylase variants. The engineering of acylase is complicated by low-throughput enzymatic assays. To alleviate this challenge, we report a time-course kinetic assay for AHL acylase that tracks the real-time production of homoserine lactone. Using the protein one-stop shop server (PROSS), we identified variants of PvdQ that were significantly stabilized, with melting point increases of up to 13.2 °C, which translated into high resistance against organic solvents and increased compatibility with material coatings. We also generated mutants of MacQ with considerably improved kinetic properties, with >10-fold increases againstN-butyryl-L-homoserine lactone andN-hexanoyl-L-homoserine lactone. In fact, the variants presented here exhibit unique combinations of stability and activity levels. Accordingly, these changes resulted in increased quenching abilities using a biosensor model and greater inhibition of virulence factor production ofPseudomonas aeruginosaPA14. While the crystal structure of one of the MacQ variants, M1, did not reveal obvious structural determinants explaining the observed changes in kinetics, it allowed for the capture of an acyl-enzyme intermediate that confirms a previously hypothesized catalytic mechanism of AHL acylases.

Abstract Figure
Antecedents of voice endorsement: a communication perspective
Authors: Wang Tingxi , Xu Yue , Li Jie
Published: September 2023

Purpose

The final effectiveness of employee voice largely depends on voice endorsement. This study aims to review, assess, analyze and synthesize the emerging literature on voice endorsement by focusing on its antecedents to promote future research from a comprehensive perspective.

Design/methodology/approach

Based on an integrative review of the literature, the authors conducted a content analysis of 53 peer-reviewed journal articles.

Findings

Building on the Shannon–Weaver communication model, this paper summarizes that factors influencing voice endorsement can be classified into five prominent aspects: voicer, voiced idea, contextual factors and noises, voice channel (medium) and voice receiver.

Practical implications

This research holds important implications for practice, providing practical guidelines for employees to speak up, for leaders to endorse voice and for organizations to maintain sustainable development by making full use of employee voice.

Originality/value

This review enriches voice endorsement research by introducing a communication framework to synthesize its antecedents and extends the application of the communication model in organization research. Additionally, the authors offer directions for future research.
Effect of populism on the internationalization of emerging market firms
Authors: Alcaraz Jorge , Martinez-Suarez Julio , Montoya Miguel A.
Published: September 2023

Purpose

This paper aims to determine whether policy uncertainty caused by institutional decay in countries with populist rulers influences the internationalization decision of emerging market firms (EMFs).

Design/methodology/approach

The study used binary logit analysis on firms from Latin American countries undertaking cross-border greenfield investment projects.

Findings

The results suggest that internationalization decision is demotivated by policy uncertainty generated by populist chief executives and promoted by that of political parties.

Originality/value

This study uses populist rhetoric to describe policy uncertainty due to chief executives and ruling parties, which influences internationalization decision by increasing anticipated transaction costs. This inquiry identifies populism as a variable that influences EMFs to internationalize, while empirically testing the claim of theoretical scholarship that populism reconfigured the sociopolitical and institutional forces that shape the world’s business. This study further advances institutional theory by offering a fresh perspective on the influence of home instead of host-country institutions on the internationalization motivation of firms due to institutional decay caused by populist regimes.
Disparities in work-integrated learning experiences for students who present as women: an international study of biases, barriers, and challenges
Authors: Bowen Tracey , Drysdale Maureen T.B. , Callaghan Sarah , Smith Sally , Johansson Kristina , Smith Colin , Walsh Barbara , Berg Tessa
Published: September 2023

Purpose

This study identifies gendered disparities among women students participating in work-integrated learning and explores the effects of the disparities on their perceptions on perceived opportunities, competencies, sense of belonging, and professional identity.

Design/methodology/approach

A series of semi-structured focus groups were run with 59 participants at six higher education institutions in four countries (Australia, Canada, Sweden, United Kingdom). All focus groups were designed with the same questions and formatting.

Findings

Thematic analysis of the transcripts revealed two overarching themes, namely perceptions of self and interactions with others in work placements. Theme categories included awareness of self-presentation, sense of autonomy, perceived Allies, emotional labour, barriers to opportunity, sense of belonging, intersections of identity, and validation value.

Originality/value

This study fills an important gap in the international literature about gendered experiences in WIL and highlights inequalities that women experience while on work placements.
Observations from three years of online pandemic learning response on OpenWHO
Authors: Utunen Heini , Appuhamy Ranil , Attias Melissa , Ndiaye Ngouille , George Richelle , Arabi Elham , Tokar Anna
Published: September 2023

Purpose

OpenWHO is the World Health Organization's online learning platform that was launched in 2017. The COVID-19 pandemic led to massive growth in the number of courses, enrolments and reach of the platform. The platform is built on a stable and scalable basis that can host a large volume of learners. The authors aim to identify key factors that led to this growth.

Design/methodology/approach

In this research paper, the authors examined OpenWHO metadata, end-of-course surveys and internal processes using a quantitative approach.

Findings

OpenWHO metadata showed that the platform has hosted over 190 health courses in 65 languages and over seven million course enrolments. Since the onset of the pandemic, there have been more women, older people and people from middle income countries accessing courses than before. Following data analysis of the platform metadata and course production process, it was found that several key factors contributed to the growth of the platform. First, OpenWHO has a standardised course production pathway that ensures efficiency, consistency and quality. Further, providing courses in different languages increased its reach to a variety of populations throughout the world. For this, multi-language translation is achieved through a network of translators and an automated system to ensure the efficient translation of learning products. Lastly, it was found that access was promoted for learners with disabilities by optimising accessibility in course production. Data analysis of learner feedback surveys for selected courses showed that the courses were well received in that learners found it useful to complete courses that were self-paced and flexible. In addition, results indicated that preferred learning methods included videos, downloadable documents, slides, quizzes and learning exercises.

Originality/value

Lessons learnt from the WHO's learning response will help prepare researchers for the next health emergency to ensure timely, equitable access to quality health knowledge for everyone. Findings of this study will provide valuable insights for educators, policymakers and researchers in the field who intend to use online learning to optimise knowledge acquisition and performance.
How to integrate ports into the EU ETS: the CAS approach perspective
Authors: Ayaz İlke Sezin , Bucak Umur , Esmer Soner
Published: September 2023

Purpose

The European Union's Emissions Trading System (EU ETS), which is already one of the EU's most impactful instruments for reducing greenhouse gases (GHGs), will soon include the maritime transport industry. Although ports are this industry's most environmental-friendly component, there are still some barriers to including ports in the system. Therefore, the purpose of the study is to identify these barriers and to reveal the barriers' interrelationships.

Design/methodology/approach

The study was conducted by identifying barriers from a literature review before analyzing the barriers with the Fuzzy DEMATEL method. Finally, based on the Complex Adaptive System Approach, various solutions are proposed to overcome these barriers.

Findings

The identified barriers were grouped into cause-and-effect groups. Two barriers, namely long payback period and high investment costs, were evaluated as triggers of the model while the others were more sensitive to the model.

Research limitations/implications

This study only includes the perceptions of green certificated ports in Türkiye. The results revealed an expectation that elimination of financial concerns will alleviate other barriers to including ports in the system. The study's findings can guide port managers on the integration of the managers' processes into the system.

Originality/value

This study provides novel findings regarding the relationships between barriers hindering ports from involvement in the EU ETS.
Working from home and job satisfaction: evidence from Russia
Authors: Smirnykh Larisa
Published: September 2023

Purpose

This study aims to investigate the impact of working from home and its duration on job satisfaction.

Design/methodology/approach

The analysis was conducted on a representative panel data set from the Russian Longitudinal Monitoring Survey - Higher School of Economics (RLMS-HSE) for 2016–2021 using endogenous regression models. The impact of working from home on job satisfaction before and during the coronavirus disease 2019 (COVID-19) pandemic, and separately for men and women, was analysed.

Findings

Working from home was found to positively affect job satisfaction in the Russian labour market. From 2016 to 2021, men and women who worked from home were more satisfied with their jobs than their counterparts who did not work from home. The positive impact of working from home on job satisfaction was observed before and during the COVID-19 pandemic. However, remote workers (RWR) putting in more than eight hours per day reported lower job satisfaction.

Research limitations/implications

Working from home can be considered as a measure to combat unemployment, increase employment and improve the utilisation (distribution) of human resources. Further research is required to analyse the impact of health issues and the need to care for young children or infirm persons on job satisfaction in remote work. A more detailed analysis is required of the factors that affect the job satisfaction of women who work remotely.

Practical implications

To ensure that labour productivity increases and not decreases, employers are advised to develop more detailed working arrangements and labour management for RWRs. Especially for such assigned workers, task control regulations must be developed. To increase the motivation of individuals to work remotely, overtime should be paid at a higher rate.

Social implications

Unclear working time regulations lead to overwork, irregular working hours and burnout. For RWRs, this leads to lower job satisfaction and a consequent drop in productivity.

Originality/value

The empirical investigation is based on a representative panel of Russian data with six waves. Wide ranges of job characteristics were incorporated as determinants. The problem of causality was investigated. For models with an endogenous regressor, instrumental variables were tested and selected.
Credit risks, national governance and profitability in microfinancing sector: evidence from some emerging economies of world importance
Authors: Singh Kuldeep
Published: September 2023

Purpose

The world order is experiencing unremitting changes. With this, the national governance of emerging economies is also becoming robust. Therefore, the current study examines the efficacy of national governance in the context of emerging economies by investigating its effects on the profitability of the microfinancing sector. Further, the study inspects if national governance mitigates the impact of credit risks to protect profitability.

Design/methodology/approach

The study considers panel data from 224 microfinancing institutions from five economies of world importance: Brazil, Russia, India, China and South Africa (BRICS). The study uses dynamic panel data modeling, particularly the generalized method of moments, alongside multiple univariate and multivariate techniques.

Findings

The findings indicate that credit risks negatively impact profitability. In addition, the study documents a significant positive linkage between national governance and profitability. However, national governance fails to restrict the adverse effects of credit risks. National governance is found to be effective in reducing internal agency problems; the monitoring effects successfully limit the moral hazards due to managers' actions. Conversely, the national governance in these economies misses the mark in regulating the moral hazards due to borrowers' behavior.

Originality/value

The current study provides fresh perspectives on the efficacy of national governance in microfinancing in the setting of emerging economies.
Going home to the gangsters: a preliminary study on the potential link between reintegration support and recidivism amongst female offenders
Authors: Thornton Jessica Leigh
Published: September 2023

Purpose

As the subject of female criminology in South Africa has only recently been dealt with in a qualitative manner, this paper aims to explore if there is a potential link between rehabilitation, reintegration support and recidivism as females are often placed back into the environment which prompted their criminal behaviour, further excluding them from rehabilitative reform, which might lead them to recidivate.

Design/methodology/approach

The research adopted a qualitative approach using in-depth, semi-structured interviews with six participants that were chosen purposively.

Findings

The paper notes a potential link between rehabilitation, reintegration support and recidivism as the female prisoners are imprinted with criminal dispositions since rehabilitation within the correctional facility has no implementation process to ensure that restoration can continue after they have been released.

Research limitations/implications

Due to the limited number of the incarcerated female population and the scope of the preliminary study, the sample comprised of only six female offenders. As such, it contributes to the larger discourse of female criminality, but does not offer any recommendations.

Practical implications

Provides an understanding of the conditions in which the females are released. Allows for the inclusion of the female’s voice on, and reflection of, rehabilitation and recidivism. Notes a link between rehabilitation, reintegration and recidivism. Creates a pathway for further research in the exploration of a gendered reform approach.

Originality/value

While the subject of female criminology in South Africa has only recently been dealt with in a qualitative manner, this study offers an insight into how females who offend are often placed back into the environment which prompted their criminal behaviour.