bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitive Fluorescent Biosensor Reveals Differential Subcellular Regulation of PKC
Authors: Su Qi , Zhang Jing , Lin Wei , Zhang Jin-Fan , Newton Alexandra C. , Mehta Sohum , Yang Jing , Zhang Jin 
Published: March 2024

AbstractThe protein kinase C (PKC) family of serine/threonine kinases, which consist of three distinctly regulated subfamilies, have long been established as critical for a variety of cellular functions. However, how PKC enzymes are regulated at different subcellular locations, particularly at emerging signaling hubs such as the ER, lysosome, and Par signaling complexes, is unclear. Here, we present a sensitive Excitation Ratiometric (ExRai) C Kinase Activity Reporter (ExRai-CKAR2) that enables the detection of minute changes in subcellular PKC activity. Using ExRai-CKAR2 in conjunction with an enhanced diacylglycerol (DAG) biosensor capable of detecting intracellular DAG dynamics, we uncover the differential regulation of PKC isoforms at distinct subcellular locations. We find that G-protein coupled receptor (GPCR) stimulation triggers sustained PKC activity at the ER and lysosomes, primarily mediated by Ca2+sensitive conventional PKC (cPKC) and novel PKC (nPKC), respectively, with nPKC showing high basal activity due to elevated basal DAG levels on lysosome membranes. The high sensitivity of ExRai-CKAR2, targeted to either the cytosol or Par-complexes, further enabled us to detect previously inaccessible endogenous atypical PKC (aPKC) activity in 3D organoids. Taken together, ExRai-CKAR2 is a powerful tool for interrogating PKC regulation in response to physiological stimuli.
GTRpmix: A linked general-time reversible model for profile mixture models
Authors: Banos Hector , Wong Thomas KF. , Daneau Justin , Susko Edward , Minh Bui Quang , Lanfear Robert , Brown Matthew W. , Eme Laura , Roger Andrew J. 
Published: March 2024

AbstractProfile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common set of amino acid exchange rates (a matrix of exchangeabilities) and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile.Currently, empirically estimated exchangeability matrices (e.g., the LG or WAG matrices) are widely used for phylogenetic inference under profile mixture models. However, such matrices were originally estimated using site homogeneous models with a single set of equilibrium amino acid frequencies; therefore unlikely to be optimal for site heterogeneous profile mixture models. Here we describe the GTRpmix model, implemented in IQ-TREE2, that allows maximum likelihood estimation of a common set of exchangeabilities for all site classes under any profile mixture model. We show that exchangeability matrices estimated in the presence of a site-heterogeneous profile mixture model differ markedly from the widely used LG matrix and dramatically improve model fit and topological estimation accuracy for empirical test cases.Because the GTRpmix model is computationally expensive, we provide two exchangeability matrices estimated from large concatenated phylogenomic supermatrices under the C60 profile mixture model that can be used as fixed matrices for phylogenetic analyses. One of these, called Eukaryotic Linked Mixture (ELM), is designed for phylogenetic analysis of proteins encoded by nuclear genomes of eukaryotes, and the other, Eukaryotic and Archeal Linked mixture (EAL), for reconstructing relationships between eukaryotes and Archaea. These matrices when combined with profile mixture models fit data much better and have improved topology estimation relative to the empirical LG matrix combined with the same underlying mixture models. Version v2.3.1 of IQ-TREE2 implementing these models is available atwww.iqtree.org.
Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter
Authors: Goyal Parveen , Dhanabalan KanagaVijayan , Scalise Mariafrancesca , Friemann Rosmarie , Indiveri Cesare , Dobson Renwick C.J. , Vinothkumar Kutti R. , Ramaswamy Subramanian 
Published: March 2024

AbstractN-Acetylneuraminic acid (Neu5Ac) is a negatively charged nine-carbon amino-sugar that is often the peripheral sugar in human cell-surface glycoconjugates. Some bacteria scavenge, import, and metabolize Neu5Ac or redeploy it on their cell surfaces for immune evasion. The import of Neu5Ac by many bacteria is mediated by tripartite ATP-independent periplasmic (TRAP) transporters. We have previously reported the structures of SiaQM, a membrane-embedded component of theHaemophilus influenzaeTRAP transport system, (Currieet al.,2024). However, none of the published structures contain Neu5Ac bound to SiaQM. This information is critical for defining the transport mechanism and for further structure-activity relationship studies. Here, we report the structures ofFusobacterium nucleatumSiaQM with and without Neu5Ac. Both structures are in an inward (cytoplasmic side) facing conformation. The Neu5Ac-bound structure reveals the interactions of Neu5Ac with the transporter and its relationship with the Na+binding sites. Two of the Na+-binding sites are similar to those described previously. We identify a third metal-binding site that is further away and buried in the elevator domain. Ser300 and Ser345 interact with the C1-carboxylate group of Neu5Ac. Proteoliposome-based transport assays showed that Ser300-Neu5Ac interaction is critical for transport, whereas Ser345 is dispensable. Neu5Ac primarily interacts with residues in the elevator domain of the protein, thereby supporting the elevator with an operator mechanism. The residues interacting with Neu5Ac are conserved, providing fundamental information required to design inhibitors against this class of proteins.
Cell fixation improves performance ofin situcrosslinking mass spectrometry while preserving cellular ultrastructure
Authors: Michael Andrew R.M. , Amaral Bruno C. , Ball Kallie L. , Eiriksson Kristen H. , Schriemer David C. 
Published: March 2024

AbstractCrosslinking mass spectrometry (XL-MS) has the potential to map the interactome of the cell with high resolution and depth of coverage. However, currentin vivoXL-MS methods are hampered by crosslinkers that demonstrate low cell permeability and require long reaction times. Consequently, interactome sampling is not high and long incubation times can distort the cell, bringing into question the validity any protein interactions identified by the method. We address these issues with a fast formaldehyde-based fixation method applied prior to the introduction of secondary crosslinkers. Using human A549 cells and a range of reagents, we show that 4% formaldehyde fixation with membrane permeabilization preserves cellular ultrastructure and simultaneously improves reaction conditions forin situXL-MS. Protein labeling yields can be increased even for nominally membrane-permeable reagents, and surprisingly, formaldehyde does not compete with conventional amine-reactive crosslinking reagents. Prefixation with permeabilization uncouples cellular dynamics from crosslinker dynamics, enhancing control over crosslinking yield and permitting the use of any chemical crosslinker.
Novel extracellular matrix architecture on excitatory neurons revealed by HaloTag-HAPLN1
Authors: Sterin Igal , Niazi Ava , Kim Jennifer , Park Joosang , Park Sungjin 
Published: March 2024

AbstractThe brain’s extracellular matrix (ECM) regulates neuronal plasticity and animal behavior. ECM staining shows an aggregated pattern in a net-like structure around a subset of neurons and diffuse staining in the interstitial matrix. However, understanding the structural features of ECM deposition across various neuronal types and subcellular compartments remains limited. To visualize the organization pattern and assembly process of the hyaluronan-scaffolded ECM in the brain, we fused a HaloTag to HAPLN1, which links hyaluronan and proteoglycans. Expression or application of the probe enables us to identify spatial and temporal regulation of ECM deposition and heterogeneity in ECM aggregation among neuronal populations. Dual-color birthdating shows the ECM assembly process in culture andin vivo.Sparse expression in vivo reveals novel forms of ECM architecture around excitatory neurons and developmentally regulated dendritic ECM. Overall, our study uncovers extensive structural features of the brain’ ECM, suggesting diverse roles in regulating neuronal plasticity.
A spectral framework to map QTLs affecting joint differential networks of gene co-expression
Authors: Hu Jiaxin , Weber Jesse N. , Fuess Lauren E. , Steinel Natalie C. , Bolnick Daniel I. , Wang Miaoyan 
Published: March 2024

AbstractStudying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called snQTL, to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.Significance statementThis work addresses a key gap in understanding the mechanistic foundations for genotype-phenotype associations. While existing expression quantitative trait loci (eQTL) methods identify candidate loci affecting gene expression variants, they often neglect the crucial role of gene co-expression networks. Here, we develop a network-based QTL framework to map genetic loci affecting the gene co-expression network. Utilizing a tensor-based spectral approach, our snQTL method estimates the differential co-expression patterns and effectively identifies the associated genetic loci. Application of snQTL to three-spined sticklebacks revealed candidate loci missed by standard methods. This work suggests the limitations of current approaches and highlights the potential of network-based functional loci discovery.
Unravelling differential Hes1 dynamics during axis elongation of mouse embryos through single-cell tracking
Authors: el Azhar Yasmine , Schulthess Pascal , van Oostrom Marek J. , Meijer Wilke H.M. , Thomas Wouter M. , Bauer Marianne , Sonnen Katharina F. 
Published: March 2024

SummaryThe intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells. While pre-NT cells display variable, low-amplitude oscillations, PSM cells exhibit synchronized, high-amplitude oscillations. Upon the induction of differentiation, the oscillation amplitude increases in pre-NT cells. Additionally, our study of Notch inhibition on Hes1 oscillations unveiled distinct responses in PSM and pre-NT cells, corresponding to differential Notch ligand expression dynamics. These findings suggest the involvement of separate mechanisms driving Hes1 oscillations. Thus, Hes1 demonstrates dynamic behaviour across adjacent tissues of the embryonic tail, yet the varying oscillation parameters give rise to differences in the information that can be conveyed by these dynamics.
The TTLL10 polyglycylase is stimulated by tubulin glutamylation and inhibited by polyglycylation
Authors: Cummings Steven W. , Li Yan , Spector Jeffrey O. , Kim Christopher , Roll-Mecak Antonina 
Published: March 2024

ABSTRACTMicrotubules in cells have complex and developmentally stereotyped posttranslational modifications that support diverse processes such as cell division, ciliary growth and axonal specification. Glycylation, the addition of glycines, singly (monoglycylation) or in chains (polyglycylation), is primarily found on axonemal microtubules where it functions in cilia maintenance and motility. It is catalyzed by three enzymes in the tubulin tyrosine ligase- like family, TTLL3, 8 and 10. We show that TTLL8 monoglycylates both α- and β-tubulin, unlike TTLL3 which prefers β-tubulin. Microscopy and mass spectrometry show that TTLL10 requires monoglycylation for high affinity microtubule binding and elongates polyglycine chains only from pre-existing glycine branches. Surprisingly, tubulin polyglycylation inhibits TTLL10 recruitment to microtubules proportional with the number of posttranslationally added glycines, suggesting an autonomous mechanism for polyglycine chain length control. In contrast, tubulin glutamylation, which developmentally precedes polyglycylation in cilia, increases TTLL10 recruitment to microtubules, suggesting a mechanism for sequential deposition of tubulin modifications on axonemes. Our work sheds light on how the tubulin code is written by establishing the substrate preference and regulation of TTLL glycylases, and provides a minimal system for generating differentially glycylated microtubules forin vitroanalyses of the tubulin code.
Immersive virtual reality in experiential learning for architecture design education: an action research
Authors: Ummihusna Annisa , Zairul Mohd , Ab Jalil Habibah , Sulaiman Puteri Suhaiza 
Published: March 2024

PurposeChallenges of conducting site visit activities, a vital component of architecture learning during the recent pandemic have proved our unreadiness in facing the digital future. The lack of understanding of learning technology has affected the education experience. Thus, there is a need to investigate immersive learning technology such as immersive virtual reality (IVR) to replace students’ concrete experience in the current learning setting. This study aims to answer: (1) What is the influence of IVR in experiential learning (EL) in enhancing the personal spatial experience? (2) Does IVR in EL influence students' approach to learning during the architecture design process?Design/methodology/approachThe research was conducted as an action research design approach. Action research was employed in the first-year architecture design studio by the lecturer as a practitioner-researcher. The personal spatial experience survey was performed in the earlier phase to identify the students’ prior spatial experience. Architectural Spatial Experience Simulation (ASES) a learning tool was implemented and assessed with Architecture Design Learning Assessment (ADLA) rubric, which was developed to evaluate EL and student’s approach to learning during the architecture design learning process.FindingsThe outcomes revealed that ASES as a learning tool in EL could improve the participants’ spatial experience, particularly those with minimal prior personal spatial experience. ASES was recognized to enhance the participants’ EL experience and encourage changes in student’s approach to learning from surface to deep learning.Originality/valueThis research benefits the architecture design learning process by offering a learning tool and a framework to resolve challenges in performing site visit activities and digital learning. It also contributes by expanding the EL theory and students’ approach to learning knowledge in the architecture education field.
Getting by with a little help from friends and family: mediation model between loneliness and depressive symptoms amongst Portuguese students
Authors: Kulari Genta 
Published: March 2024

PurposeThe purpose of this study is to analyse the mediating effect of friends and family as sources of perceived social support in the relationship between loneliness and depressive symptoms.Design/methodology/approachSurvey data sample consisted of 733 university students from January to May 2023. Participants completed the UCLA loneliness scales, Multidimensional Scale of Perceived Social Support (MPSS) and Depression, Anxiety and Stress Scale (DASS-21). The SPSS programme with PROCESS macro (Model 6) was used to test the hypothesis regarding the mediation effect.FindingsThe bootstrap analysis found that friends as a source of social support mediated the relationship between loneliness and depressive symptoms. Similarly, loneliness had a significant indirect effect on depressive symptoms through the mediation of family as a source of social support. Moreover, it was found that the relationships of friends and family as sources of social support mediated the association of the aforementioned variables.Originality/valueThis research advances our understanding of social support sources from friends and family amongst university students whilst providing suggestions for interventions tackling loneliness and depressive symptoms in a university setting.
Sweden's quest for shelter: ‘Nonalignment' and NATO membership
Authors: Thorhallsson Baldur , Stude Vidal Thomas 
Published: March 2024

AbstractThis paper posits that, contrary to conventional wisdom, Sweden's decision to join the North Atlantic Treaty Organisation (NATO) and end its official policy of ‘nonalignment’ is neither very surprising nor radical in nature. Utilising the shelter theory framework, we examine the Swedish case to shed a new light on the economic, societal and political shelter‐seeking policy choices that led to Stockholm's NATO application in May of 2022. The analysis finds that Sweden's established strategy of seeking shelter from Western powers eventually induced and facilitated close military cooperation with NATO—ultimately leading to accession on 7 March 2024. The decision to join the Alliance should, therefore, be understood as a culmination, building on a historically flexible approach to neutrality and previously established shelter arrangements that were deemed in 2022, after Russia's full‐scale invasion of Ukraine and subsequent developments in Finland, to be no longer sufficient in deterring or responding to new threat dynamics. The case indicates that shelter theory accurately captures the foreign policy strategy of a small neutral and later nonaligned state. However, analysing Sweden's move towards NATO within the given framework also presents an opportunity for theory development; specifically, the theory ought to more meticulously examine three small‐state shelter‐seeking features, namely, how societal and economic shelter relations may precede and, therefore, affect political shelter strategies (or vice versa), the role of ‘critical junctures’ in the theory; and finally, how small states may be affected by each other's shelter‐seeking strategies.
Impact of the early COVID‐19 pandemic on adult mental health‐related dispensed medications, hospitalizations and specialist outpatient visits in Norway and Sweden: Interrupted time series analysis
Authors: Moreno‐Martos David , Zhao Jing , Li Huiqi , Nyberg Fredrik , Bjørndal Ludvig Daae , Hajiebrahimi Mohammadhossein , Wettermark Björn , Aakjær Mia , Andersen Morten , Sessa Maurizio , Lupattelli Angela , Nordeng Hedvig , Morales Daniel R. 
Published: March 2024

AimsNorway and Sweden had different early pandemic responses that may have impacted mental health management. The aim was to assess the impact of the early COVID‐19 pandemic on mental health‐related care.MethodsWe used national registries in Norway and Sweden (1 January 2018–31 December 2020) to define 2 cohorts: (i) general adult population; and (ii) mental health adult population. Interrupted times series regression analyses evaluated step and slope changes compared to prepandemic levels for monthly rates of medications (antidepressants, antipsychotics, anxiolytics, hypnotics/sedatives, lithium, opioid analgesics, psychostimulants), hospitalizations (for anxiety, bipolar, depressive/mood, eating and schizophrenia/delusional disorders) and specialist outpatient visits.ResultsIn Norway, immediate reductions occurred in the general population for medications (−12% antidepressants to −7% hypnotics/sedatives) except for antipsychotics; and hospitalizations (−33% anxiety disorders to −17% bipolar disorders). Increasing slope change occurred for all medications except psychostimulants (+1.1%/month hypnotics/sedatives to +1.7%/month antidepressants); and hospitalization for anxiety disorders (+5.5%/month), depressive/mood disorders (+1.7%/month) and schizophrenia/delusional disorders (+2%/month). In Sweden, immediate reductions occurred for antidepressants (−7%) and opioids (−10%) and depressive/mood disorder hospitalizations (−11%) only with increasing slope change in psychostimulant prescribing of (0.9%/month). In contrast to Norway, increasing slope changes occurred in specialist outpatient visits for depressive/mood disorders, eating disorders and schizophrenia/delusional disorders (+1.5, +1.9 and +2.3%/month, respectively). Similar changes occurred in the pre‐existing mental health cohorts.ConclusionDifferences in early COVID‐19 policy response may have contributed to differences in adult mental healthcare provision in Norway and Sweden.
Application of CMV‐IVIg as prophylaxis against cytomegalovirus reactivation in allogeneic hematopoietic stem cell transplantation patients
Authors: Cui Jiaqi , Zhou Yuhang , Zhao Kui , Li Xudong , Zhang Hanyue , Zhang Xiangzhong , Sun Yanling , Long Bing 
Published: March 2024

AbstractCytomegalovirus (CMV) reactivation remains one of the major and life‐threatening complications after allogeneic hematopoietic stem cell transplantation (allo‐HSCT). Yet, there is still a lack of safe and effective ways to prevent CMV reactivation in allo‐HSCT patients. Here, we retrospectively analyzed a cohort of patients who underwent HSCT at our transplant center between 2018 and 2022 to evaluate the efficacy of prophylactic CMV‐specific intravenous immunoglobulin (CMV‐IVIg) against CMV reactivation. After Propensity Score Matching, the CMV reactivation rate was significantly decreased in the CMV‐IVIg group (HR, 2.952; 95% CI,1.492‐5.841; P = .002) compared with the control group. Additionally, the time duration of CMV reactivation (P = .001) and bacterial infection rate (P = .013) were significantly lower in the CMV‐IVIg group. Moreover, prophylactic CMV‐IVIg was more effective in CMV seropositive patients who received ATG as part of GVHD prevention (HR, 8.225; 95% CI,1.809‐37.39; P = .006). In conclusion, CMV‐IVIg is considered an effective and safe way to prevent CMV reactivation in HSCT recipients, which may be related to the acceleration of immune reconstitution in the early stage after transplantation.