bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple rotavirus species encode fusion-associated small transmembrane (FAST) proteins with cell type-specific activity
Authors: Veletanlic Vanesa , Sartalamacchia Kylie , Diller Julia R. , Ogden Kristen M.
Published: April 2023

Fusion-associated small transmembrane (FAST) proteins are viral nonstructural proteins that mediate cell-cell fusion to form multinucleated syncytia. We previously reported that human species B rotavirus NSP1-1 is a FAST protein that induces syncytia in primate epithelial cells but not rodent fibroblasts. We hypothesized that the NSP1-1 proteins of other rotavirus species could also mediate cell-cell fusion and that fusion activity might be limited to cell types derived from homologous hosts. To test this hypothesis, we predicted the structure and domain organization of NSP1-1 proteins of species B rotavirus from a human, goat, and pig, species G rotavirus from a pigeon and turkey, and species I rotavirus from a dog and cat. We cloned these sequences into plasmids and transiently expressed the NSP1-1 proteins in avian, canine, hamster, human, porcine, and simian cells. Regardless of host origin of the virus, each NSP1-1 protein induced syncytia in primate cells, while few induced syncytia in other cell types. To identify the domains that determined cell-specific fusion activity for human species B rotavirus NSP1-1, we engineered chimeric proteins containing domain exchanges with the p10 FAST protein from Nelson Bay orthoreovirus. Using the chimeric proteins, we found that the N-terminal and transmembrane domains determined the cell type specificity of fusion activity. Although the species and cell type criteria for fusion activity remain unclear, these findings suggest that rotavirus species B, G, and I NSP1-1 are functional FAST proteins whose N termini play a role in specifying the cells in which they mediate syncytia formation.

IMPORTANCE

Mechanisms of membrane fusion and determinants of host range for pathogens remain poorly understood. Improved understanding of these concepts could open new areas for therapeutic development and shed light on virus epidemiology. Our analyses of NSP1-1 proteins from species B, G, and I rotaviruses provide insights into the diversity of domain features tolerated by functional FAST proteins. Further, the observation that all putative FAST proteins tested can induce syncytia formation in at least some cell types provides evidence that rotaviruses that encode NSP1-1 proteins are fusogenic viruses. Finally, although the criteria for their specificity remain unclear, our observations regarding fusion capacities of different NSP1-1 proteins and of chimeric FAST proteins suggest a potential role for rotavirus FAST proteins in determining the efficiency of viral replication within a given host or cell type.
Classifier for the Rapid Simultaneous Determination of Sleep-Wake States and Seizures in Mice
Authors: Harvey Brandon J. , Olah Viktor J. , Aiani Lauren M. , Rosenberg Lucie I. , Pedersen Nigel P.
Published: April 2023

Independent automated scoring of sleep-wake and seizures have recently been achieved; however, the combined scoring of both states has yet to be reported. Mouse models of epilepsy typically demonstrate an abnormal electroencephalographic (EEG) background with significant variability between mice, making combined scoring a more difficult classification problem for manual and automated scoring. Given the extensive EEG variability between epileptic mice, large group sizes are needed for most studies. As large datasets are unwieldy and impractical to score manually, automatic seizure and sleep-wake classification are warranted. To this end, we developed an accurate automated classifier of sleep-wake states, seizures, and the post-ictal state. Our benchmark was a classification accuracy at or above the 93% level of human inter-rater agreement. Given the failure of parametric scoring in the setting of altered baseline EEGs, we adopted a machine-learning approach. We created several multi-layer neural network architectures that were trained on human-scored training data from an extensive repository of continuous recordings of electrocorticogram (ECoG), left and right hippocampal local field potential (HPC-L and HPC-R), and electromyogram (EMG) in the murine intra-amygdala kainic acid model of medial temporal lobe epilepsy. We then compared different network models, finding a bidirectional long short-term memory (BiLSTM) design to show the best performance with validation and test portions of the dataset. The SWISC (sleep-wake and the ictal state classifier) achieved >93% scoring accuracy in all categories for epileptic and non-epileptic mice. Classification performance was principally dependent on hippocampal signals and performed well without EMG. Additionally, performance is within desirable limits for recording montages featuring only ECoG channels, expanding its potential scope. This accurate classifier will allow for rapid combined sleep-wake and seizure scoring in mouse models of epilepsy and other neurologic diseases with varying EEG abnormalities, thereby facilitating rigorous experiments with larger numbers of mice.
Analysis of the Combined Effect of rs699 and rs5051 on Angiotensinogen Expression and Hypertension
Authors: Powell Nicholas R. , Shugg Tyler , Leighty Jacob , Martin Matthew , Kreutz Rolf P. , Eadon Michael T. , Lai Dongbing , Lu Tao , Skaar Todd C.
Published: April 2023

Hypertension (HTN) involves genetic variability in the renin-angiotensin system and characterizing this variability will help advance precision antihypertensive treatments. We previously reported that angiotensinogen (AGT) mRNA is endogenously bound by mir-122-5p and that rs699 A>G significantly decreases reporter mRNA in the functional mirSNP assay PASSPORT-seq. TheAGTpromoter variant rs5051 C>T is in linkage disequilibrium (LD) with rs699 A>G and increasesAGTtranscription. We hypothesized that the increasedAGTby rs5051 C>T counterbalancesAGTdecrease by rs699 A>G, and when these variants occur independently, would translate to HTN-related phenotypes. The independent effect of each of these variants is understudied due to their LD, therefore, we usedin silico, in vitro, in vivo, and retrospective clinical and biobank analyses to assess HTN andAGTexpression phenotypes where rs699 A>G occurs independently from rs5051 C>T.In silico, rs699 A>G is predicted to increase mir-122-5p binding strength by 3%. Mir-eCLIP assay results show that rs699 is 40-45 nucleotides from the strongest microRNA binding site in theAGTmRNA. Unexpectedly, rs699 A>G increasesAGTmRNA in a plasmid cDNA HepG2 expression model. GTEx and UK Biobank analyses demonstrate that liverAGTexpression and HTN phenotypes were not different when rs699 A>G occurs independently from rs5051 C>T, allowing us to reject the original hypothesis. However, both GTEx and ourin vitroexperiments suggest rs699 A>G confers cell-type specific effects onAGTmRNA abundance. We found that rs5051 C>T and rs699 A>G significantly associate with systolic blood pressure in Black participants in the UK Biobank, demonstrating a 4-fold larger effect than in White participants. Further studies are warranted to determine if the altered antihypertensive response in Black individuals might be due to rs5051 C>T or rs699 A>G. Studies like this will help clinicians move beyond the use of race as a surrogate for genotype.
Lustro: High-throughput optogenetic experiments enabled by automation and a yeast optogenetic toolkit
Authors: Harmer Zachary P , McClean Megan N
Published: April 2023

Optogenetic systems use genetically-encoded light-sensitive proteins to control cellular processes. This provides the potential to orthogonally control cells with light, however these systems require many design-build-test cycles to achieve a functional design and multiple illumination variables need to be laboriously tuned for optimal stimulation. We combine laboratory automation and a modular cloning scheme to enable high-throughput construction and characterization of optogenetic split transcription factors inSaccharomyces cerevisiae. We expand the yeast optogenetic toolkit to include variants of the cryptochromes and Enhanced Magnets, incorporate these light-sensitive dimerizers into split transcription factors, and automate illumination and measurement of cultures in a 96-well microplate format for high-throughput characterization. We use this approach to rationally design and test an optimized Enhanced Magnet transcription factor with improved light-sensitive gene expression. This approach is generalizable to high-throughput characterization of optogenetic systems across a range of biological systems and applications.
Targeted RNA Condensation in Living Cells via Genetically Encodable Triplet Repeat Tags
Authors: Xue Zhaolin , Ren Kewei , Wu Rigumula , Sun Zhining , Zheng Ru , Tian Qian , Ali Ahsan Ausaf , Mi Lan , You Mingxu
Published: April 2023

Living systems contain various functional membraneless organelles that can segregate selective proteins and RNAs via liquid–liquid phase separation. Inspired by nature, many synthetic compartments have been engineered in vitro and in living cells, mostly focused on protein-scaffolded systems. Herein, we introduce a nature-inspired genetically encoded RNA tag to program cellular condensate formations and recruit non-phase-transition target RNAs to achieve functional modulation. In our system, different lengths of CAG-repeat tags were tested as the self-assembled scaffold to drive multivalent condensate formation. Various selective target messenger RNAs and noncoding RNAs can be compartmentalized into these condensates. With the help of fluorogenic RNA aptamers, we have systematically studied the formation dynamics, spatial distributions, sizes, and densities of these cellular RNA condensates. The regulation functions of these CAG-repeat tags on the cellular RNA localization, lifetime, RNA–protein interactions, and gene expression have also been investigated. Considering the importance of RNA condensation in both health and disease conditions, these genetically encodable modular and self-assembled tags can be potentially widely used for chemical biology and synthetic biology studies.
Robust Removal of Slow Artifactual Dynamics Induced by Deep Brain Stimulation in Local Field Potential Recordings using SVD-based Adaptive Filtering
Authors: Bahador Nooshin , Saha Josh , Rezaei Mohammad R. , Saha Utpal , Ghahremani Ayda , Chen Robert , Lankarany Milad
Published: April 2023

Deep brain stimulation (DBS) is widely used as a treatment option for patients with movement disorders. In addition to its clinical impact, DBS has been utilized in the field of cognitive neuroscience wherein the answers to several fundamental questions underpinning the mechanisms of neuromodulation in decision making rely on how a burst of DBS pulses, usually delivered at clinical frequency, i.e., 130 Hz, perturb participants’ choices. It was observed that neural activities recorded during DBS were contaminated with stereotype large artifacts, which lasts for a few milliseconds, as well as a low-frequency (slow) signal (∼1-2 Hz) that can persist for hundreds of milliseconds. While the focus of the most of methods for removing DBS artifact was on the former, the artifact removal of the slow signal has not been addressed. In this work, we propose a new method based on combining singular value decomposition (SVD) and normalized adaptive filtering to remove both large (fast) and slow artifacts in local field potentials recorded during a cognitive task in which bursts of DBS were utilized. Using synthetic data, we show that our proposed algorithm outperforms four commonly used techniques in the literature, namely, (1) Normalized least mean square adaptive filtering, (2) Optimal FIR Wiener filtering, (3) Gaussian model matching, and (4) Moving average. The algorithm’s capabilities are further demonstrated by its ability to effectively remove DBS artifacts in local field potentials recorded from the subthalamic nucleus during a verbal Stroop task, highlighting its utility in real-world applications.
Resolving the temporal splenic proteome during fungal infection for discovery of putative dual perspective biomarker signatures
Authors: Muselius Benjamin , Roux-Dalvai Florence , Droit Arnaud , Geddes-McAlister Jennifer
Published: April 2023

Fungal pathogens are emerging threats to global health with the rise of incidence associated with climate change and increased geographical distribution; factors also influencing host susceptibility to infection. Accurate detection and diagnosis of fungal infections is paramount to offer rapid and effective therapeutic options. For improved diagnostics, the discovery and development of protein biomarkers presents a promising avenue; however, this approach requires aprioriknowledge of infection hallmarks. To uncover putative novel biomarkers of disease, profiling of the host immune response and pathogen virulence factor production is indispensable. In this study, we use mass spectrometry-based proteomics to resolve the temporal proteome ofCryptococcus neoformansinfection of the spleen following a murine model of infection. Dual perspective proteome profiling defines global remodeling of the host over a time course of infection, confirming activation of immune associated proteins in response to fungal invasion. Conversely, pathogen proteomes detect well-characterizedC. neoformansvirulence determinants, along with novel mapped patterns of pathogenesis during the progression of disease. Together, our innovative systematic approach confirms immune protection against fungal pathogens and explores the discovery of putative biomarker signatures from complementary biological systems to monitor the presence and progression of cryptococcal disease.
Bioorthogonal photocatalytic quinone methide decaging for cell-cell interaction labeling
Authors: Zhang Yan , Liu Shibo , Guo Fuhu , Qin Shan , Zhou Nan , Fan Xinyuan , Chen Peng R.
Published: April 2023

Cell-cell interactions (CCIs) play crucial roles in directing diverse biological processes in multicellular organisms, making the high-sensitivity and selectivity characterization of the diverse CCIs in high demand yet still challenging. We herein introduced a bioorthogonal photocatalytic quinone methide decaging-enabled cell-cell interaction labeling strategy (CAT-Cell) for sensitive and spatiotemporally resolved profiling of multitype CCIs. By adapting an optimized quinone methide probe for interacting cell labeling, we demonstrated the excellent capacity of CAT-Cell for capturing CCIs directed by various receptor-ligand pairs (e.g., CD40-CD40L, TCR-pMHC) and further showed its compatibility with tumor-specific targeting systems. Finally, we used CAT-Cell to detect cytotoxic cells (e.g., antigenspecific T cells, Natural Killer cells) in mouse models containing splenocyte mixtures and tumor samples. By leveraging the bioorthogonal photocatalytic decaging chemistry, CAT-Cell offers as a nongenetic, non-invasive and universal toolbox for profiling diverse CCIs under physiological-relevant settings.
Exploiting rodent cell blocks for intrinsic resistance to HIV-1 gene expression in human T cells
Authors: Behrens Ryan T. , Rajashekar Jyothi Krishnaswamy , Bruce James W. , Evans Edward L. , Hansen Amelia M. , Salazar-Quiroz Natalia , Simons Lacy M. , Ahlquist Paul , Hultquist Judd F. , Kumar Priti , Sherer Nathan M.
Published: April 2023

HIV-1 virion production is inefficient in cells derived from mice and other rodents reflecting cell-intrinsic defects to interactions between the HIV-1 auxiliary proteins Tat and Rev and host dependency factors CCNT1 (Cyclin T1) and XPO1 (Exportin-1, also known as CRM1), respectively. In human cells, Tat binds CCNT1 to enhance viral RNA transcription and Rev recruits XPO1 to mediate the nuclear export of intron-containing viral RNA. In mouse cells, Tat’s interactions with CCNT1 are inefficient, mapped to a single species-specific residue Y261 instead of C261 in human. Rev interacts poorly with murine XPO1, mapped to a trio of amino acids T411/V412/S414 instead of P411/M412/F414 in humans. To determine if these discrete species-specific regions of otherwise conserved housekeeping proteins represent viable targets for inhibiting Tat and Rev function in humans, herein we recoded (“mousified”) each in human CD4+ T cells using precision CRISPR/Cas9-facilitated gene editing. Both edits yielded cells refractory to Rev or Tat activity, respectively, with isolated, isogenic CCNT1.C261Y cell lines remarkable in their capacity to exhibit near total inactivation of viral gene expression for all X4 and R5-tropic HIV-1 strains tested, and even the more distantly related lentiviruses including HIV-2 and SIVagm. These studies validate minor and naturally-occurring, species-specific differences in otherwise conserved human host factors as compelling targets for achieving broad-acting cell-intrinsic resistance to HIV’s post-integration phases.

Importance

Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 editing to engineer “mousified” versions of two of these proteins, CCNT1 and XPO1, in human T cells. CCNT1 and XPO1 are essential for efficient HIV-1 transcription and viral RNA transport, respectively, making them intriguing targets for gene-based inactivation of virus replication. Targeting either gene yielded antiviral phenotypes, with isogenic CCNT1-modified cell lines confirmed to exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cells. These results provide proof of concept for targeting CCNT1 (and potentially XPO1) in the context of one or more functional HIV-1 cure strategies.
A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits
Authors: Sechkar Kirill , Perrino Giansimone , Stan Guy-Bart
Published: April 2023

Synthetic genes compete among themselves and with the host cell’s genes for expression machinery, exhibiting resource couplings that affect the dynamics of cellular processes. The modeling of such couplings can be facilitated by simplifying the kinetics of resource-substrate binding. Model-guided design allows to counter unwanted indirect interactions by using biomolecular controllers or tuning the biocircuit’s parameters. However, resource-aware biocircuit design in bacteria is complicated by the interdependence of resource availability and cell growth rate, which significantly affects biocircuit performance. This phenomenon can be captured by coarse-grained models of the whole bacterial cell. The level of detail in these models must balance accurate representation of metabolic regulation against model simplicity and interpretability.

We propose a coarse-grainedE. colicell model that combines the ease of simplified resource coupling analysis with the appreciation of bacterial growth regulation mechanisms. Reliably capturing known growth phenomena, it enables numerical prototyping of biocircuits and derivation of analytical relations which can guide the design process. By reproducing several distinct empirical laws observed in prior studies, our model provides a unifying framework for previously disjoint experimental observations. Finally, we propose a novel biomolecular controller that achieves near-perfect adaptation of cell-wide ribosome availability to changes in synthetic gene expression. Showcasing our model’s usefulness, we use it to determine the controller’s setpoint and operation range from its constituent genes’ parameters.
Multiple Brain Activation Patterns for the Same Perceptual Decision-Making Task
Authors: Nakuci Johan , Yeon Jiown , Haddara Nadia , Kim Ji-Hyun , Kim Sung-Phil , Rahnev Dobromir
Published: April 2023

Meaningful variation in internal states that impacts cognition and behavior remains challenging to discover and characterize. Here we leveraged trial-to-trial fluctuations in the brain-wide signal recorded using functional MRI to test if distinct sets of brain regions are activated on different trials when accomplishing the same task. Across three different perceptual decision-making experiments, we estimated the brain activations for each trial. We then clustered the trials based on their similarity using modularity-maximization, a data-driven classification method. In each experiment, we found multiple distinct but stable subtypes of trials, suggesting that the same task can be accomplished in the presence of widely varying brain activation patterns. Surprisingly, in all experiments, one of the subtypes exhibited strong activation in the default mode network, which is typically thought to decrease in activity during tasks that require externally focused attention. The remaining subtypes were characterized by activations in different task-positive areas. The default mode network subtype was characterized by behavioral signatures that were similar to the other subtypes exhibiting activation with task-positive regions. These findings demonstrate that the same perceptual decision-making task is accomplished through multiple brain activation patterns.
scART: recognizing cell clusters and constructing trajectory from single-cell epigenomic data
Authors: Guo Jingxin , Li Jingyu , Huang Fei , Chen Jiadong , Shen Li
Published: April 2023

The development of single-cell assay for transposase-accessible chromatin using sequencing data (scATAC-seq) has allowed the characterization of epigenetic heterogeneity at single-cell resolution. However, the sparse and noisy nature of scATAC-seq data poses unique computational challenges. To address this, we introduce scART, a novel bioinformatics tool specifically designed for scATAC-seq data analysis. scART utilizes analytical methods highly stable for processing sparse and noisy data, such as k-nearest neighbor (KNN) imputation, Term Frequency-Inverse Document Frequency (TF-IDF) weighting scheme, and the cosine similarity metric to identify underlying cellular heterogeneity in scATAC-seq data. It accurately and robustly identifies cell identities, particularly in data with low sequencing depth, and constructs the trajectory of cellular states. As a demonstration of its utility, scART successfully reconstructed the development trajectory of the embryonic mouse forebrain and uncovered the dynamics of layer-specific neurogenesis. scART is available at GitHub.
Archaeal self-activating GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis
Authors: Korf Lukas , Ye Xing , Vogt Marian S. , Steinchen Wieland , Watad Mohamed , Tourte Maxime , Sivabalasarma Shamphavi , Albers Sonja-Verena , Essen Lars-Oliver
Published: April 2023

Three GPN-loop GTPases, GPN1-GPN3, are central to the maturation and trafficking of eukaryotic RNA polymerase II. This GTPase family is widely represented in archaea but typically occurs as single paralogs. Structural analysis of the GTP- and GDP-bound states of theSulfolobus acidocaldariusGPN enzyme (SaGPN) showed that this central GPN-loop GTPase adopts two distinct quaternary structures. In the GTP-bound form the γ-phosphate induces a tensed dimeric arrangement by interacting with the GPN region that is relaxed upon hydrolysis to GDP. Consequently, a rocking-like motion of the two protomers causes a major allosteric structural change towards the roof-like helices. Using a lock-switch-rock (LSR) mechanism, homo- and heterodimeric GPN-like GTPases are locked in the GTP-bound state and undergo large conformational changes upon GTP hydrolysis. AΔsaGPNstrain ofS. acidocaldariuswas characterized by impaired motility and major changes in the proteome underscoring its functional relevance forS. acidocaldarius in vivo.

Significance Statement

GPN-loop GTPases have been found to be crucial for eukaryotic RNA polymerase II assembly and nuclear trafficking. Despite their ubiquitous occurrence in eukaryotes and archaea the mechanism by which these self-activating GTPases mediate their function is unknown. Our study on an archaeal representative fromSulfolobus acidocaldariusshowed that these dimeric GTPases undergo large-scale conformational changes upon GTP hydrolysis, which can be summarized as a lock-switch-rock mechanism. The observed requirement ofSaGPN for motility appears to be due to its large footprint on the archaeal proteome.
Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications
Authors: Guerrero Rafael F. , Dorji Tandin , Harris Ra’Mal M. , Shoulders Matthew D. , Ogbunugafor C. Brandon
Published: April 2023

The term “druggability” describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variant’s sensitivity across a breadth of drugs in a panel, or a given drug’s range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16β-lactamase alleles and sevenβ-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel (“variant vulnerability”), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target (“drug applicability”). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G x G x E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).
Microtubule search-and-capture model evaluates the effect of chromosomal volume conservation on spindle assembly during mitosis
Authors: Nayak Pinaki , Chatterjee Saptarshi , Paul Raja
Published: April 2023

Variation in the chromosome numbers can arise from the erroneous mitosis or fusion and fission of chromosomes. While the mitotic errors lead to an increase or decrease in the overall chromosomal substance in the daughter cells, fission and fusion keep this conserved. Variations in chromosome numbers are assumed to be a crucial driver of speciation. For example, the members of the muntjac species are known to have very different karyotypes with the chromosome numbers varying from 2n= 70 + 3Bin the brown brocket deer to 2n= 46 in the Chinese muntjac and 2n= 6/7 in the Indian muntjac. The chromosomal content in the nucleus of these closely related mammals is roughly the same and various chromosome fusion and fission pathways have been suggested as the evolution process of these karyotypes. Similar trends can also be found in lepidoptera and yeast species which show a wide variation of chromosome numbers. The effect of chromosome number variation on the spindle assembly time and accuracy is still not properly addressed. We computationally investigate the effect of conservation of the total chromosomal substance on the spindle assembly during prometaphase. Our results suggest that chromosomal fusion pathways aid the microtubule-driven Search and Capture of the kinetochore in cells with monocentric chromosomes. We further report a comparative analysis of the site and percentage of amphitelic captures, dependence on cell shape, position of the kinetochore in respect of chromosomal volume partitioning.
Dose-dependent progression of multiple low dose streptozotocin-induced diabetes in mice
Authors: Bauer Brandon M. , Bhattacharya Supriyo , Bloom-Saldana Elizabeth , Irimia Jose M. , Fueger Patrick T.
Published: April 2023

This study investigated the effects of different multiple low doses of streptozotocin (STZ), namely 35 and 55 mg/kg, on the onset and progression of diabetes in mice. Both doses are commonly used in research, and while both induced a loss of beta cell mass, they had distinct effects on whole glucose tolerance, beta cell function and gene transcription. Mice treated with 55 mg/kg became rapidly glucose intolerant, whereas those treated with 35 mg/kg had a slower onset and remained glucose tolerant for up to a week before becoming equally glucose intolerant as the 55 mg/kg group. Beta cell mass loss was similar between the two groups, but the 35 mg/kg-treated mice had improved glucose-stimulated insulin secretion in gold-standard hyperglycemic clamp studies. Transcriptomic analysis revealed that the 55 mg/kg dose caused disruptions in nearly five times as many genes as the 35 mg/kg dose in isolated pancreatic islets. Pathways that were downregulated in both doses were more downregulated in the 55 mg/kg-treated mice, while pathways that were upregulated in both doses were more upregulated in the 35 mg/kg treated mice. Moreover, we observed a differential downregulation in the 55 mg/kg-treated islets of beta cell characteristic pathways, such as exocytosis or hormone secretion. On the other hand, apoptosis was differentially upregulated in 35 mg/kg-treated islets, suggesting different transcriptional mechanisms in the onset of STZ-induced damage in the islets. This study demonstrates that the two STZ doses induce distinctly mechanistic progressions for the loss of functional beta cell mass.
Thermodynamically consistent determination of free energies and rates in kinetic cycle models
Authors: Kenney Ian M. , Beckstein Oliver
Published: April 2023

Kinetic and thermodynamic models of biological systems are commonly used to connect microscopic features to system function in a bottom-up multiscale approach. The parameters of such models—free energy differences for equilibrium properties and in general rates for equilibrium and out-of-equilibrium observables—have to be measured by different experiments or calculated from multiple computer simulations. All such parameters necessarily come with uncertainties so that when they are naively combined in a full model of the process of interest, they will generally violate fundamental statistical mechanical equalities, namely detailed balance and an equality of forward/backward rate products in cycles due to T. Hill. If left uncorrected, such models can produce arbitrary outputs that are physically inconsistent. Here we develop a maximum likelihood approach (namedmultibind) based on the so-called potential graph to combine kinetic or thermodynamic measurements to yield state resolved models that are thermodynamically consistent while being most consistent with the provided data and their uncertainties. We demonstrate the approach with two theoretical models, a generic two-proton binding site and a simplified model of a sodium/proton antiporter. We also describe an algorithm to use themultibindapproach to solve the inverse problem of determining microscopic quantities from macroscopic measurements and as an example we predict the microscopic pKas and protonation states of a small organic molecule from 1D NMR data. Themultibindapproach is applicable to any thermodynamic or kinetic model that describes a system as transitions between well-defined states with associated free energy differences or rates between these states. A Python packagemultibind, which implements the approach described here, is made publicly available under the MIT Open Source license.

WHY IT MATTERS

The increase in computational efficiency and rapid advances in methodology for quantitative free energy and rate calculations has allowed for the construction of increasingly complex thermodynamic or kinetic “bottom-up” models of chemical and biological processes. These multi-scale models serve as a framework for analyzing aspects of cellular function in terms of microscopic, molecular properties and provide an opportunity to connect molecular mechanisms to cellular function. The underlying model parameters—free energy differences or rates—are constrained by thermodynamic identities over cycles of states but these identities are not necessarily obeyed during model construction, thus potentially leading to inconsistent models. We address these inconsistencies through the use of a maximum likelihood approach for free energies and rates to adjust the model parameters in such a way that they are maximally consistent with the input parameters and exactly fulfill the thermodynamic cycle constraints. This approach enables formulation of thermodynamically consistent multi-scale models from simulated or experimental measurements.
Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings
Authors: Schröder Martin , Renatus Martin , Liang Xiaoyou , Meili Fabian , Zoller Thomas , Ferrand Sandrine , Gauter Francois , Li Xiaoyan , Sigoillot Fred , Gleim Scott , Stachyra Marie-Therese , Thomas Jason , Begue Damien , Lefeuvre Peggy , Andraos-Rey Rita , Chung BoYee , Ma Renate , Carbonneau Seth , Pinch Benika , Hofmann Andreas , Schirle Markus , Schmiedberg Niko , Imbach Patricia , Gorses Delphine , Calkins Keith , Bauer-Probst Bea , Maschlej Magdalena , Niederst Matt , Maher Rob , Henault Martin , Alford John , Ahrne Erik , Hollingworth Greg , Thomä Nicolas H. , Vulpetti Anna , Radimerski Thomas , Holzer Philipp , Thoma Claudio R.
Published: April 2023

Targeted protein degradation (TPD) of neo-substrates with proteolysis targeting chimeras (PROTACs) or molecular glues has emerged as a key modality in exploring new biology as well as designing new drug candidates where catalytic inhibition is neither efficacious nor an option. TPD is mediated through harnessing E3 ligases and redirecting them to ubiquitinatede novotarget proteins for subsequent proteasomal degradation. Until recently, E3 ligase chemical matter available for mediating TPD has been limited to a relatively low number of ligases, considering that over 600 E3 ligases are encoded by the human genome. In addition, the most utilized ligase for TPD approaches, CRBN, has been observed to be downregulated in settings of acquired resistance to immunomodulatory inhibitory drugs (IMiDs). IMiDs are molecular glues that target IKZF transcription factors to CRBN for degradation. Resistance is potentially accelerated by non-essentiality of CRBN for cell viability. Here we investigated if the essential E3 ligase receptor DCAF1 can be harnessed for TPD utilizing a potent, non-covalent DCAF1 binder. We show that this binder, selective for the CRL4DCAF1E3 ligase complex, can be functionalized into an efficient DCAF1-BRD9 PROTAC. Chemical and genetic rescue experiments confirm specific degradation via the CRL4DCAF1E3 ligase. We further highlight the versatility of DCAF1 for TPD by developing a DCAF1-dasatininb PROTAC targeting multiple cytosolic and membrane bound tyrosine kinases. We expand these findings towards Bruton’s tyrosine kinase (BTK) selective PROTACs and through extensive optimization and characterization efforts share key observations that led to a potent and selective DCAF1-BTK PROTAC (DBt-10). Finally, with this PROTAC DBt-10, we show rescue of BTK degradation in a BTK-dependent, CRBN-degradation-resistant cell line and provide a rationale for E3 ligase swap to overcome CRBN mediated resistance.
I am done now! Linking workplace incivility to job search behaviour and employee silence
Authors: Singh Lata Bajpai , Srivastava Sachitaa , Bhumika Bhumika
Published: April 2023

Purpose

Remote work has allowed IT professionals to engage in “side hustles”, which is against the law in the Indian labour market. Professionals in the IT industry are constantly being scrutinized due to the emerging “side hustling” culture, and as a result, they are frequently subjected to rude and uncivil behaviour by others. This study aims to examine the outcome of workplace incivility on the employee’s job search behaviour and their silence. Along with this, it examines the intervening effect of organizational cynicism on the interrelation of workplace incivility with job search behaviour and employee silence. It further investigates the buffering role of workplace friendship in the link between workplace incivility and organizational cynicism.

Design/methodology/approach

In this study, a mixed-methods approach was used, which included testing the structural model followed by a qualitative study. In Study 1, the structural model testing of time-lagged primary data from 252 respondents who worked in information technology (IT) or information technology-enabled services was done, whereas Study 2 included a qualitative analysis.

Findings

The findings disclose that workplace incivility is positively connected to job search behaviour and employee silence. Organizational cynicism significantly intervenes in the link between workplace incivility and job search behaviour, and between workplace incivility and employee silence, whereas workplace friendship functions as a moderator in the link between workplace incivility and organizational cynicism. The findings indicate that if an employee experiences incivility at work, then workplace friendship plays an active role in encouraging the cynical behaviour of targeted employees towards their organisation.

Originality/value

In the past, investigators have investigated the concept of workplace incivility; however, to the best of the authors’ knowledge, its impact on job search behaviour is studied for the first time ever, whereas its impact on employee silence is studied for the first time in a moonlighting context in Indian industry. In light of the massive layoffs in India's IT industry because of employees' pursuit of side hustles, the results of this study will help firms better comprehend the negative repercussions of workplace incivility. These effects include employees' reluctance to speak up about problems at work and an increase in their frequency of actively seeking other employment.
Does financial development enhance the growth effect of FDI? A multidimensional analysis in emerging and developing Asia
Authors: An Thu-Ha Thi , Chen Shin-Hui , Yeh Kuo-Chun
Published: April 2023

Purpose

This study examines the role of financial development (FD) in enhancing the growth effect of foreign direct investment (FDI) in emerging and developing Asia from 1996 to 2019.

Design/methodology/approach

The study exploits the new broad-based Financial Development Index of the International Monetary Fund (IMF) and adopts panel smooth transition regression (PSTR) to perform alternative empirical models for a multidimensional analysis of the FD threshold effect in the growth–FDI nexus.

Findings

The results show two thresholds of FD mediating the nonlinear effect of FDI on growth. FD beyond a certain level will enhance the growth effect of FDI, but very high levels of FD will not induce foreign investment to benefit economic growth in emerging and developing Asian economies. The impact of financial institutions on the FDI–growth link is stronger than that of financial markets. Besides, FDI’s effect on growth has an inverted-U shape conditional on financial depth, whereas it is positively associated with the accessibility and efficiency of the financial system.

Practical implications

These results suggest policy implications for emerging and developing Asian countries, emphasizing the other side of “too much finance” and the potential for improvement in the access to and efficiency of the financial system to boost the effects of FDI and FD in the growth of these economies.

Originality/value

The study is the first multifaceted investigation into the influence of FD on the growth effect of FDI. Beyond the previous empirical evidence showing only the impact of credit from banking sector, this study shows different mediating effects of different financial sectors and three dimensions of financing (depth, access and efficiency). The study suggests essential implications for the region in adjusting long-run policies to enhance the FDI–FD–growth link.
A fretting wear model considering formation of tribolayers
Authors: Yang Yulei , Xu Jimin , Liang Yi
Published: April 2023

Purpose

Quantitative fretting wear prediction is of practical significance for industrial components. This study aims to establish a fretting wear model considering the formation of tribolayers and provide better fretting wear prediction.

Design/methodology/approach

Based on the characteristics for the formation of tribolayers, the ratio of fretting amplitude to nominal contact area length in the fretting direction is used to characterize their formation and contribution to the wear volume. The wear volume is then associated with the product of the friction energy and the ratio of fretting amplitude to nominal contact area length.

Findings

Better prediction in the wear volume can be achieved with the proposed fretting wear model by taking the formation of tribolayers into consideration.

Originality/value

The contribution of the formation of tribolayers to the wear volume is considered in the model and better prediction can be achieved.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-01-2023-0004/
Stickiness formation among mobile apps of different social levels: multigroup analysis using the cognitive–affective–conative framework
Authors: Zhou Xingchen , Rau Pei-Luen Patrick , Jie Zhuoni
Published: April 2023

Purpose

This study aims to reveal how mobile app stickiness is formed and how the stickiness formation process differs for apps of different social levels.

Design/methodology/approach

This study proposed and validated a stickiness formation model following the cognitive–affective–conative framework. Data were collected from surveys of 1,240 mobile app users and analyzed using structural equation modeling. Multigroup analysis was applied to contrast the stickiness formation process among apps of different social levels.

Findings

This study revealed a causal link between cognitive, affective and conative factors. It found partial mediation effects of trust in the association between perceptions and satisfaction, and the full mediation role of satisfaction and personal investment (PI) in the effects of subjective norm (SN) on stickiness. The multigroup analysis results suggested that social media affordances benefit stickiness through increased PI and strengthened effects of SN on PI. However, it damages stickiness through increased perceived privacy risk (PPR), decreased trust and strengthened effects of PPR on trust.

Originality/value

This study contributes to both stickiness scholars and practitioners, as it builds a model to understand the stickiness formation process and reveals the effects of the “go social” strategy. The novelty of this study is that it examined social influences, considered privacy issues and revealed two mediation mechanisms. The findings can guide the improvement of mobile app stickiness and the application of the “go social” strategy.
The effect of physical education teaching style on exercise habits of college students
Authors: Xu Haibo , Albattat Ahmad , Phuoc Jeong Chun , Wang Baogui
Published: April 2023

Purpose

The purpose of this study is that the teaching style of college physical education (PE) teachers affects the establishment of college students' exercise habits.

Design/methodology/approach

This study uses the teaching style scale for 32 PE teachers and the autonomic motivation and exercise habits scale for 320 college students in the form of self-report.

Findings

Chinese college PE teachers mainly use the teacher-centered reproduction style, and the practice style is the most frequently used; The overall teaching style of college PE teachers was significantly negatively correlated with autonomous motivation and exercise habits. PE teachers' teaching style can negatively affect college students' autonomous motivation, and college students' autonomous motivation can positively affect their exercise habits.

Originality/value

There is a significant negative correlation between the teaching style of college PE teachers and the exercise habits of college students. However, it cannot directly affect the establishment of college students' exercise habits, but is achieved through the mediating role of college students' autonomous motivation.
Close your eyes and open your mind: how closed eyes affect evaluations of utilitarian and hedonic advertising appeals
Authors: Lee Younghwa , Bakpayev Marat , Yoon Sukki , Kim Kacy
Published: April 2023

Purpose

Drawing on embodied cognition and construal level theory perspectives in marketing literature, the purpose of this study is to propose that closed eyes make events appear distant and increase high-level construal and abstract processing, whereas opened eyes make events appear near and increase low-level construal and concrete processing. The authors further argue that high (low) construal level induced by closed (open) eyes increases favoritism toward utilitarian (hedonic) appeals.

Design/methodology/approach

Drawing on embodied cognition and construal level theory, the authors conduct three studies to investigate how consumers form varying distance perceptions and attitudes toward advertising appeals depending on whether they open or close their eyes while contemplating the messages. In Study 1, the authors tested the effects of an advertisement featuring utilitarian versus hedonic appeals in a food waste reduction campaign. In Study 2, the authors tested the effects of an advertisement stressing utilitarian versus hedonic aspects of a brand of travel products. In Study 3, the authors tested the effects of an advertisement for hotel reward products depending on consumption motivations.

Findings

The studies support the hypothesis by showing that when individuals close their eyes, they form abstract processing styles (high-level construal), perceive events as more distant and increase preferences for utilitarian advertising appeals; when they open their eyes, they form concrete processing styles (low-level construal), perceive events as nearer and indicate preferences for hedonic advertising appeals.

Originality/value

The novel insight of this study shows how bodily sensations may affect various types of hedonic and utilitarian advertising appeals. This study contributes to the embodied cognition and construal level literature, but the contribution of this study is particularly important for marketers and advertisers in that the authors show interactions between open or closed eyes, hedonic or utilitarian product aspects and processing styles.
Distributed leadership and teachers' emotional labour: the mediating role of teacher autonomy
Authors: Özdemir Murat , Buyukgoze Hilal , Akman Yener , Topaloğlu Hakan , Çiftçi Kenan
Published: April 2023

Purpose

Teachers' expressing candid and natural emotions during teaching and learning processes is of vital importance for the quality and content of education. Because of that reason, it is necessary to explore factors that have a role in teachers' emotional labour. Therefore, the current study aims to test a novel model developed to explore the direct and indirect relations among distributed leadership, teacher autonomy and emotional labour.

Design/methodology/approach

The study data came from 1,007 teachers working at 81 state high schools located in 12 different regions in Turkey. To test the proposed model, the authors conducted a mediation analysis of structural equation modelling.

Findings

The analysis confirms that teacher autonomy is a prominent mediator in the relationship between distributed leadership and emotional labour.

Originality/value

This study is expected to contribute to the body of research focusing on the effects of leadership on teachers' emotional labour.