bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ubiquitination mediates protein localization in RNA virus-infected cells
Authors: Shi Shihua , Iesmantavicius Vytautas , Sabu Amit Santhu , Soneson Charlotte , Kohler Hubertus , Sanchez Jacint , Ghosh Sucheta , Cao Chun , Huang Yong , Matthias Gabriele , Yamauchi Yohei , Matthias Patrick , Wang Longlong 
Published: August 2024

AbstractViruses trigger monocytes’ proinflammatory and antiviral responses. Ubiquitination, a post-translational modification primarily marking proteins for degradation, regulates cellular responses to virus infection. However, a comprehensive analysis of virus-induced ubiquitination in monocytes is lacking. Here we identified a widespread increase of ubiquitination under viral RNA challenge or influenza infection in monocytes. Systematic proteome studies revealed that influenza infection elicits dynamic ubiquitinome alterations, with a notable transition from early to late stage. Most of this increased ubiquitination is not proteolytic and targets proteins involved in subcellular localization, such as the mitochondrial protein COA7 which, when ubiquitinated during infection, translocates to the nucleus and inhibits stress granules formation and TNF-α expression. Blocking ubiquitination halts viral ribonucleoprotein’s nuclear export, highlighting ubiquitination’s importance for protein localization during virus infection.
Semi-Automatic Segmentation ofPseudomonas koreensisandEscherichia colifor Bacterial Growth Characterization
Authors: Alvarado-Ruiz Diana A. , Ordaz-Hernández Keny , Díaz-Jiménez Lourdes , Lara-Cadena Grecia L. , González-López Roberto , Vargas-Gutiérrez Gregorio , Castelán Mario 
Published: August 2024

AbstractBacterial characterization is a crucial discipline within microbiology. Given the manual and labor-intensive nature of this task, our aim is to introduce a semi-automatic segmentation method that enhances efficiency while preserving the rich details of bacterial colonies. We propose using the k-means clusterization algorithm to analyze and segment images of bacterial cultures, specifically those ofPseudomonas koreensisandEscherichia coli. Unlike existing methods that focus primarily on colony counting, our approach emphasizes morphological characterization. In some bacterial cultures, colonies are not well-defined, making manual counting or other automated counting methods unfeasible; i.e. the bacterial growth area is not easily identifiable, thus precise growth tracking is not feasible. Our method enables bacterial growth characterization even in these cases. Our computer vision system identifies and quantifies the diverse morphologies withinP. koreensisandE. colicultures, determining their relative occupancy in an image. Our approach provides valuable insights into the composition, growth patterns, and developmental stages of bacterial colonies, designed to assist both novice and expert microbiologists in bacterial analysis.
Annotation of piRNA source loci in the genome of non-model insects
Authors: Halbach Rebecca , van Rij Ronald P. 
Published: August 2024

AbstractThe PIWI-interacting RNA (piRNA) pathway plays a crucial role in the defense of metazoan genomes against parasitic transposable elements. The major source of piRNAs in the model organismDrosophila melanogasterare defective transposon copies located in piRNA clusters – genomic regions with a high piRNA density that are thought to serve as an immunological memory of past invasion by those elements. Different approaches have been used to annotate piRNA clusters in model organisms like flies, mice and rats, and software such as proTRAC or piClust are available for piRNA cluster annotation. However, these software often make assumptions based on current knowledge of piRNA clusters from (mostly vertebrate) model organisms, which do not necessarily hold true for non-model insects in which the piRNA pathway is less understood. Here we describe a simple piRNA cluster annotation approach that utilizes very little assumptions on the biology of the piRNA pathway. The pipeline has been validated on mosquito genomes but can be easily used for other non-model insect species as well.
Calcium transfer from the ER to other organelles for optimal signaling inToxoplasma gondii
Authors: Li Zhu-Hong , Asady Beejan , Chang Le , Hortua Triana Miryam Andrea , Li Catherine , Coppens Isabelle , Moreno Silvia N.J. 
Published: August 2024

ABSTRACTCa2+signaling in cells begins with the opening of Ca2+channels in either the plasma membrane (PM) or the endoplasmic reticulum (ER) and results in a dramatic increase in the physiologically low (<100 nM) cytosolic Ca2+level. The temporal and spatial Ca2+levels are well regulated to enable precise and specific activation of critical biological processes. Ca2+signaling regulates pathogenic features of apicomplexan parasites likeToxoplasma gondiiwhich infects approximately one-third of the world’s population.T. gondiirelies on Ca2+signals to stimulate traits of its infection cycle and several Ca2+signaling elements play essential roles in its parasitic cycle. Active egress, an essential step for the infection cycle ofT. gondiiis preceded by a large increase in cytosolic Ca2+most likely by release from intracellular stores. Intracellular parasites take up Ca2+from the host cell during host Ca2+signaling events to replenish intracellular stores. In this work, we investigated the mechanism by which intracellular stores are replenished with Ca2+and demonstrated a central role for the SERCA-Ca2+-ATPase in keeping not only the ER filled with Ca2+but also other stores. We show mitochondrial Ca2+uptake, by transfer of Ca2+from the ER likely through membrane contact sites. We propose a central role for the ER in sequestering and redistributing calcium to other intracellular organelles following influx at the PM.HIGHLIGHTSTheT. gondiiER efficiently takes up Ca2+that enters the cytosol from the extracellular milieu.Filling of acidic stores inT. gondiiappears to be dependent on the filling of the ERThe mitochondrion ofT. gondiihas no direct access to extracellular calcium but is able to take up Ca2+by transfer from the ER and/or acidic stores
PhOxi-seq detects enzyme-dependent m2G in multiple RNA types
Authors: Klimontova Marie , Kim Chung Kimberley Chung , Zhang Han , Kouzarides Tony , Bannister Andrew J , Hili Ryan 
Published: August 2024

ABSTRACTIn recent years, RNA-modifying enzymes have gained significant attention due to their impact on critical RNA-based processes, and consequently human pathology. However, identifying sites of modifications throughout the transcriptome remains challenging largely due to the lack of accurate and sensitive detection technologies. Recently, we described PhOxi-seq as a method capable of confirming known sites of m2G within abundant classes of RNA, namely purified rRNA and purified tRNA. Here, we further explore the selectivity of PhOxi-seq and describe an optimised PhOxi-seq workflow, coupled to a novel bioinformatic pipeline, that is capable of detecting enzyme-dependent m2G sites throughout the transcriptome, including low abundant mRNAs. In this way, we generated the first database of high confidence sites of THUMPD3-dependent m2G in multiple RNA classes within a human cancer cell line and further identify non-THUMPD3 controlled sites throughout the transcriptome.
The ubiquitin-proteasome system regulates the formation of specialized ribosomes during high salt stress in yeast
Authors: Yang Yoon-Mo , Karbstein Katrin 
Published: August 2024

AbstractRps26-deficient ribosomes are a physiologically relevant ribosome population which arises during osmotic stress to support the translation of mRNAs involved in the response to high salt in yeast. They are formed by binding of the chaperone Tsr2 to fully assembled ribosomes to release Rps26 when intracellular Na+concentrations rise. Tsr2-mediated Rps26 release is reversible, enabling a rapid response that conserves ribosomes. However, because the concentration of Tsr2 relative to ribosomes is low, how the released Rps26•Tsr2 complex is managed to allow for accumulation of Rps26-deficient ribosomes to nearly 50% of all ribosomes remains unclear. Here we show that released Rps26 is degraded via the Pro/N-degron pathway, enabling the accumulation of Rps26-deficient ribosomes. Substitution of the N-terminal proline of Rps26 to serine increases the stability of free Rps26, limits the accumulation of Rps26-deficient ribosomes and renders yeast sensitive to high salt. The GID-complex, an E3 ubiquitin ligase, and its adaptor Gid4, mediate polyubiquitination of Rps26 at Lys66 and Lys70. Moreover, this ubiquitination event is required for Rps26 degradation, the accumulation of Rps26-deficient ribosomes and the high salt stress resistance. Together, the data show that targeted degradation of released Rps26 from the Rps26•Tsr2 complex allows Tsr2 to be recycled, thus facilitating multiple rounds of Rps26 release.
EmergingClostridioides difficileribotypes have divergent metabolic phenotypes
Authors: Midani Firas S. , Danhof Heather A. , Mathew Nathanael , Ardis Colleen K. , Garey Kevin W. , Spinler Jennifer K. , Britton Robert A. 
Published: August 2024

ABSTRACTClostridioides difficileis a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. AlthoughC. difficileis a genetically diverse species, certain ribotypes are overrepresented in human infections. It is unknown if metabolic adaptations are essential for the emergence of these epidemic ribotypes. Here, we tested carbon substrate utilization by 88C. difficileisolates and looked for differences in growth between 22 ribotypes. By profiling clinical isolates, we assert thatC. difficileis a generalist species capable of growing on a variety of carbon substrates. Further,C. difficilestrains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, althoughC. difficileClade 5 is the most evolutionary distant clade and often detected in animals, it displayed more robust growth on simple dietary sugars than Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy ofC. difficileand demonstrate lineage-specific metabolic capabilities. In addition, our approach can be adapted to the study of additional pathogens to ascertain their metabolic niches in the gut.IMPORTANCEThe gut pathogenClostridioides difficileutilizes a wide range of carbon sources. Microbial communities can be rationally designed to combatC. difficileby depleting its preferred nutrients in the gut. However,C. difficileis genetically diverse with hundreds of identified ribotypes and most of its metabolic studies were performed with lab-adapted strains. Here, we profiled carbon metabolism by a myriad ofC. difficileclinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that the most genetically distant clade grew robustly on simple dietary sugars, posing intriguing questions about the adaptation ofC. difficileto the human gut. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.
Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in a prominent gut symbiont
Authors: Flanagan Kayla , Gassner Kirsten , Lang Michaela , Ozelyte Jurgita , Hausmann Bela , Crepaz Daniel , Pjevac Petra , Gasche Christoph , Berry David , Vesely Cornelia , Pereira Fatima C. 
Published: August 2024

AbstractIn the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. In this study, we aimed to explore the ability of miR-21, a miRNA that we found decreased in stool samples from IBS patients, to associate with and regulate gut microbiome function. Incubation of human faecal microbiota with miR-21 revealed a rapid association with microbial cells, reproducible across multiple donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently-labelled miR-21 identified organisms belonging to the generaBacteroides,Limosilactobacillus,Ruminococcus, orCoprococcuswhich predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensalBacteroides thetaiotaomicronrevealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.
Sequence action representations contextualize during rapid skill learning
Authors: Dash Debadatta , Iwane Fumiaki , Hayward William , Salamanca-Giron Roberto , Bonstrup Marlene , Buch Ethan , Cohen Leonardo G 
Published: August 2024

AbstractActivities of daily living rely on our ability to acquire new motor skills composed of precise action sequences. Early learning of a new sequential skill is characterized by steep performance improvements that develop predominantly during rest intervals interspersed with practice, a form of rapid consolidation. Here, we ask if the millisecond level neural representation of an action performed at different locations within a skill sequence contextually differentiates or remains stable as learning evolves. Optimization of machine learning decoders to classify sequence-embedded finger movements from MEG activity reached approximately 94% accuracy. The representation manifolds of the same action performed in different sequence contexts progressively differentiated during rest periods of early learning, predicting skill gains. We conclude that sequence action representations contextually differentiate during early skill learning, an issue relevant to brain-computer interface applications in neurorehabilitation.
Does psychological empowerment transmit the effects of organizational justice on employees' knowledge sharing? A study on the Indian hospitality industry
Authors: Srivastava Shalini , Singh Anupriya , Bali Shivani 
Published: August 2024

PurposeThis paper aims to investigate the associations between organizational justice dimensions and employees' knowledge sharing (KS) while studying the mediating role of psychological empowerment (PE) in context of the Indian hospitality industry. It is also aimed to investigate the association between KS and innovative work behavior (IWB).Design/methodology/approachA mediation model was verified utilizing three-wave survey data from 293 employees working in hotels situated in northern India. Hypotheses were tested using AMOS and PROCESS Model 4.FindingsThere are significant associations between justice dimensions and KS, and PE mediates these relationships. Additionally, employees' KS has a positive effect on their IWB.Practical implicationsOrganizations must promote justice and psychologically empower their employees to facilitate KS. Our study also highlights the significance of employees' KS in encouraging their IWBs. HR leaders and managers have an important role in facilitating the right work environment, in which employees experience fairness and empowerment.Originality/valueThis paper is the first to investigate linkages between justice dimensions, PE, KS and IWB in context of the Indian hospitality industry. Furthermore, this study has made the maiden attempt of asserting the mediating role of PE in the relationship between justice dimensions and KS.
Drivers of platform ecosystem adoption: does innovation capability translate these drivers into improved firm performance
Authors: Sun Xinbo , Abdullahi Usman Magaji 
Published: August 2024

PurposeBuilding on the theory of resource-based view (RBV), this paper is determined to explore the key drivers that drive platform ecosystem adoption by small businesses and mediation mechanisms that facilitate the translation of these drivers into improved firm financial and nonfinancial performance.Design/methodology/approachIn this study, structural equation modeling is used to analyze the data. A survey questionnaire was taken from 430 small businesses operating their businesses on various digital platform ecosystems in China to investigate the links between parameters by testing hypotheses. Digital startups operating their businesses on popular Chinese platform ecosystems, including Alibaba, Taobao, Jingdong, Maituan and HelloChe, were chosen.FindingsThe finding deciphers a nuanced interplay of the adoption drivers, with innovation capability emerging as a mediation mechanism translating these drivers into improved financial and non-financial performance.Research limitations/implicationsThe acknowledgment of potential drawbacks, such as the focus on specific drivers of platform ecosystem adoption, highlights the need for future research to explore additional factors that may influence adoption decisions. By examining institutional factors, market conditions or external shocks like the COVID-19 pandemic, researchers can provide a more comprehensive understanding of the complexities surrounding platform ecosystem dynamics and offer insights into adaptive strategies for businesses facing uncertainty.Practical implicationsThe outcome benefits policymakers and ecosystem designers by creating and overseeing platform ecosystems that support the highlighted drivers. This study further serves as a roadmap for both platform owners and prospective small enterprises as they map their path toward the digital frontier.Social implicationsThe findings from the research indicate that small enterprises that embrace platform ecosystems can experience improved financial and non-financial performance, which in turn promotes economic development and the generation of jobs. By utilizing innovative strategies and maximizing their strategic advantages, these enterprises can not only prosper but also make significant contributions to community development and help alleviate joblessness. This highlights the significance of assisting with the incorporation of digital technology in small businesses to achieve wider societal advantages.Originality/valueResearch originality lies in bridging the gap between strategic inputs and measurable outcomes, stressing the vital function of a firm’s innovation in turning ecosystem-driven opportunities into enhanced performance. This means the pivotal role of this study lies in exploring platform ecosystem adoption drivers based on the theory of RBV and the way innovation capability of platform ecosystems facilitates the translation of these drivers into improved financial and nonfinancial performance.
Overall fairness perception and organizational citizenship behaviour: understanding the moderating and mediating factors
Authors: Kyei-Poku Ivy 
Published: August 2024

PurposeSynthesizing theories of leadership, organizational fairness and organizational citizenship behaviour (OCB). This study explores how overall organizational fairness affects OCB by considering the mediating role of organization-based self-esteem (OBSE) and the moderating role of authentic leadership.Design/methodology/approachIn two phases, survey data were collected from 79 job incumbents at a financial company.FindingsThe findings suggest that authentic leadership significantly affects the relationship between overall fairness perceptions and OCB. Moreover, OBSE was found to act as a mediator in this relationship.Research limitations/implicationsAuthentic leadership and organizational self-esteem play crucial roles in fostering a fair work environment that encourages employees to engage in citizenship behaviour. These findings underscore the importance of authentic leadership and OBSE in creating a fair work environment. These findings have implications for human resource management practices and leadership development programs.Originality/valueScholars in organizational behaviour have posited that fairness in the workplace is critical to facilitating effective leadership. However, more research is needed to investigate the interplay and mediating effects of fairness and leadership. The present study offers novel insights into the mediating mechanism of OBSE and its critical role in explaining the positive impact of overall fairness on employees’ OCB.
“A pleasant walk on the Pakihi”: ecological orientations in mid-century nature study
Authors: Kelly Frances Jennifer 
Published: August 2024

PurposeA recent United Nations (2021) report stated that education needs to be concerned with enhancing human relationships with the natural world if we are to work toward building a sustainable future. This paper proposes that educational practices underpinned by an ecological orientation in mid-century Aotearoa offer insights for educators looking to enhance human connection with nature. It also argues that ecological thinking has implications for how research in the history of education might be carried out.Design/methodology/approachThe article responds to recent calls in history of education for researchers to attend to the intertwined ecologies of living and material worlds in research approaches by Maria Tamboukou (2020) and Karin Priem (2022). It conducts a close analysis of a 1952 nature diary, encountered in the national archive, written by a 9-year-old pupil on the West Coast of the South Island. The analysis attends to the human–nature interactions the diary records, and to the resonance of the text in the context of post-war curriculum changes.FindingsPost-war nature study in Aotearoa New Zealand built on an aim to nurture children’s connections with nature and to place. Analysis of an entry from the 1952 nature diary highlights these connections and demonstrates the possibilities for a reframing of human–nature relationships that emerge with an ecological orientation in education. These findings speak to urgent contemporary concerns with environmental sustainability and human–nature relationships.Originality/valueThe paper draws on educational philosophy and theory (Fesmire, 2012; Nicol, 2014) alongside recent conversations in the history of education (Priem, 2022; Grosvenor and Priem, 2022; Tamboukou, 2020) to consider human–nature relationality at the heart of ecological thought. It outlines an approach to archival research that is ecologically oriented, generating openness and receptivity to the material world.