bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing sarcomere and cellular dynamics in skeletal muscle to improve cell therapies
Authors: Hüttemeister Judith , Rudolph Franziska , Radke Michael H. , Fink Claudia , Friedrich Dhana , Preibisch Stephan , Falcke Martin , Wagner Eva , Lehnart Stephan E. , Gotthardt Michael
Published: February 2024

The giant striated muscle protein titin integrates into the developing sarcomere to form a stable myofilament system that is extended as myocytes fuse. The logistics underlying myofilament assembly and disassembly have started to emerge with the possibility to follow labeled sarcomere components. Here, we generated the mCherry knock-in at titin’s Z-disk to study skeletal muscle development and remodeling. We find titin’s integration into the sarcomere tightly regulated and its unexpected mobility facilitating a homogenous distribution of titin after cell fusion – an integral part of syncytium formation and maturation of skeletal muscle. In adult mCherry-titin mice, treatment of muscle injury by implantation of titin-eGFP myoblasts reveals how myocytes integrate, fuse and contribute to the continuous myofilament system across cell boundaries. Unlike in immature primary cells, titin proteins are retained at the proximal nucleus and do not diffuse across the whole syncytium with implications for future cell-based therapies of skeletal muscle disease.
A Comprehensive Benchmarking Study on Computational Tools for Cross-omics Label Transfer from Single-cell RNA to ATAC Data
Authors: Wang Yuge , Zhao Hongyu
Published: February 2024

With continuous progress of single-cell chromatin accessibility profiling techniques, scATAC-seq has become more commonly used in investigating regulatory genomic regions and their involvement in developmental, evolutionary, and disease-related processes. At the same time, accurate cell type annotation plays a crucial role in comprehending the cellular makeup of complex tissues and uncovering novel cell types. Unfortunately, the majority of existing methods primarily focus on label transfer within scRNA-seq datasets and only a limited number of approaches have been specifically developed for transferring labels from scRNA-seq to scATAC-seq data. Moreover, many methods have been published for the joint embedding of data from the two modalities, which can be used for label transfer by adding a classifier trained on the latent space. Given these available methods, this study presents a comprehensive benchmarking study evaluating 27 computational tools for scATAC-seq label annotations through tasks involving single-cell RNA and ATAC data from various human and mouse tissues. We found that when high quality paired data were available to transfer labels across unpaired data, Bridge and GLUE were the best performers; otherwise, bindSC and GLUE achieved the highest prediction accuracy overall. All these methods were able to use peak-level information instead of purely relying on the gene activities from scATAC-seq. Furthermore, we found that data imbalance, cross-omics dissimilarity on common cell types, data binarization, and the introduction of semi-supervised strategy usually had negative impacts on model performance. In terms of scalability, we found that the most time and memory efficient methods were Bridge and deep-learning-based algorithms like GLUE. Based on the results of this study, we provide several suggestions for future methodology development.
Effects of inbreeding and elevated rearing temperatures on strategic sperm production
Authors: Chung Meng-Han Joseph , Mahmud-Al-Hasan Md , Jennions Michael D. , Head Megan L.
Published: February 2024

Males often strategically modify their rate of sperm production based on the social context, but it remains unclear how environmental and genetic factors shape this plasticity. In freshwater ecosystems, high ambient temperatures often lead to isolated pools of hotter water in which inbreeding occurs. Higher water temperatures and inbreeding can impair fish development, potentially disrupting sperm production. We used guppies (Poecilia reticulata) to investigate how developmental temperature (26 °C or 30 °C) and male inbreeding status (inbred, outbred) influence sperm production in the absence or presence of a female (i.e., sperm priming response). We also tested if sperm priming was affected by whether the female was a relative (sister), and whether she was inbred or outbred. A higher rearing temperature had no effect on the rate of sperm production or the priming response. Inbred males produced significantly more sperm in the presence of an unrelated, outbred female than when no female was present. Conversely, outbred males did not alter sperm production in response to female presence or relatedness. In addition, inbred males showed marginally greater sperm production when exposed to an unrelated female that was outbred rather than inbred, but no difference when exposed to an inbred female that was unrelated versus related. Together, only inbred males increased sperm production in response to the presence of a female, but this depended on her being outbred. This suggests stronger sexual selection on inbred males to allocate ejaculate resources, perhaps due to greater benefits when mating with outbred females in better condition.
gMCSpy: Efficient and accurate computation of Genetic Minimal Cut Sets in Python
Authors: Rodriguez Carlos Javier , Barrena Naroa , Olaverri-Mendizabal Danel , Ochoa Idoia , Valcarcel Luis V. , Planes Francisco J.
Published: February 2024

Motivation

The identification of minimal genetic interventions that modulate metabolic processes constitutes one of the most relevant applications of genome-scale metabolic models (GEMs). The concept of Minimal Cut Sets (MCSs) and its extension at the gene level, genetic Minimal Cut Sets (gMCSs), have attracted increasing interest in the field of Systems Biology to address this task. Different computational tools have been developed to calculate MCSs and gMCSs using both commercial and open-source software.

Results

Here, we presentgMCSpy, an efficient Python package to calculate gMCSs in GEMs using both commercial and non-commercial optimization solvers. We show thatgMCSpysubstantially overperforms our previous computational tool GMCS, which exclusively relied on commercial software. Moreover, we comparedgMCSpywith recently published competing algorithms in the literature, finding significant improvements in both accuracy and computation time. All these advances makegMCSpyan attractive tool for researchers in the field of Systems Biology for different applications in health and biotechnology.

Availability and Implementation

The Python packagegMCSpy can be accessed at:https://github.com/PlanesLab/gMCSpy

Contact

fplanes@tecnun.es

Supplementary Information
A universal and effective variational method for destriping: application to light-sheet microscopy, FIB-SEM and remote sensing images
Authors: Rottmayer Niklas , Redenbach Claudia , Fahrbach Florian O.
Published: February 2024

Stripe artifacts are a common problem for various imaging techniques such as light-sheet fluorescence microscopy (LSFM), electron microscopy and remote sensing. These artifacts are characterized by their elongated shapes and compromise image quality and impede further analysis. To address the primary challenge of removing the stripe artifacts while preserving the object structures we present here an improved variational method for stripe removal with intuitive parametrization. Comparison against previously published methods on images from LSFM, FIB-SEM and remote sensing by visual inspection and quantitative metrics demonstrates the superior capability of the approach. Based on synthetic LSFM data obtained by simulation of physical light-propagation we enriched our analysis by the comparison of processed images to ground truth data and quantitatively confirmed that our method outperforms existing solutions in terms of improved removal of artifacts and retention of image structures. The open availability of our solution[1], the flexibility in handling variations in stripe orientation and thickness ensures its broad applicability across diverse imaging scenarios.
Mechanical loading modulates AMPK and mTOR signaling in myblasts
Authors: Zhou Xin , Zhu Shaocun , Li Junhong , Mateus Andre , Backman Ludvig J.
Published: February 2024

Skeletal muscle adaptation to exercise involves various phenotypic changes that enhance metabolic and contractile functions. One key regulator of these adaptive responses is the activation of AMPK, influenced by exercise intensity. However, the mechanistic understanding of AMPK activation during exercise remains incomplete. In this study, we utilized an in vitro model to investigate the effects of mechanical loading on AMPK activation and its interplay with the mTOR signaling pathway. Proteomic analysis of myoblasts subjected to static loading (SL) revealed distinct quantitative protein alterations associated with RNA metabolism, with 10% SL inducing the most pronounced response compared to lower intensity of 5% and 2% as well as control. Additionally, 10% SL suppressed RNA and protein synthesis, while activating AMPK and inhibiting the mTOR pathway. Our RNA sequencing analysis further corroborated these findings, revealing numerous differentially regulated genes and signaling pathways influenced by both AMPK and mTOR. Further examination showed that SL induced changes in mitochondrial biogenesis and the ADP/ATP ratio. These findings provide novel insights into the cellular responses to mechanical loading and shed light on the intricate AMPK-mTOR regulatory network in myoblasts.
Optimization of liver graft function using poly-pharmacological drug cocktail CEPT in a simulated transplant model
Authors: Kharga Anil , Mojoudi Mohammadreza , Chen Huyun , Taggart McLean S. , Dinicu Antonia T. , Ozgur Ozge S. , Uygun Basak , Toner Mehmet , Tessier Shannon N. , Yeh Heidi , Markmann James F. , Longchamp Alban , Uygun Korkut
Published: February 2024

Background

The number of patients in need of a liver transplant far exceeds the supply of available organs. This imbalance could be dramatically reduced should the donor organ pool be expanded by rendering marginal cases transplantable rather than discarded. The poly-pharmacological drug cocktail CEPT (Chroman-1, Emricasan, Polyamine, and Trans-ISRIB (integrated stress inhibitor)) has been found to improve the in-vitro viability of human pluripotent stem cells (hPSCs) following cryopreservation. It is worth exploring CEPT’s ability to inhibit various apoptotic pathways and preserve cellular function for potentially mitigating warm ischemic stress of the anhepatic phase of graft implantation and promoting more rapid graft recovery following reperfusion with continuous treatment.

Methods

Rat livers without warm ischemia and CEPT supplementation are the healthy control: fresh (n=3) group. Room-temperature warm ischemia was used to replicate the anhepatic phase of graft implantation in the control (n=6) group and the experimental CEPT group (n=6) without and with CEPT supplementation, respectively. Transplantation was modeled by ex-vivo reperfusion at 37°C for six hours with William’s E-based hepatocyte culture media and with CEPT supplementation in the CEPT group.

Results

Livers treated with CEPT during warm ischemia and subsequent reperfusion have improved hepatocellular function as indicated by increased oxygen O2utilization, stable pH, and improved cholangiocyte function indicated by the increased hourly rate of bile production. Furthermore, resistance, an endothelial injury marker, and caspase 3/7, an apoptotic marker, were lower.

Conclusion

To improve the utilization of available donor livers, different stages of the organ transplantation process can be optimized. The anhepatic phase, which includes the period from the removal of the native liver from the recipient to the reperfusion of the donor’s graft liver through the portal vein during graft implantation, can be targeted using CEPT for mitigating warm ischemia-induced injury that occurs during vascular anastomosis.(S1 Fig: Graphical abstract)
Spatial transcriptomics of healthy and fibrotic human liver at single-cell resolution
Authors: Watson Brianna , Paul Biplab , Amir-Zilberstein Liat , Segerstolpe Asa , Rahman Raza Ur , Shih Angela , Deguine Jacques , Xavier Ramnik J. , Moffitt Jeffrey R. , Mullen Alan C.
Published: February 2024

Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cell types and their heterogeneity within the human liver, but the spatial organization at single-cell resolution has not yet been described. Here we apply multiplexed error robust fluorescent in situ hybridization (MERFISH) to map the zonal distribution of hepatocytes, resolve subsets of macrophage and mesenchymal populations, and investigate the relationship between hepatocyte ploidy and gene expression within the healthy human liver. We next integrated spatial information from MERFISH with the more complete transcriptome produced by single-nucleus RNA sequencing (snRNA-seq), revealing zonally enriched receptor-ligand interactions. Finally, analysis of fibrotic liver samples identified two hepatocyte populations that are not restricted to zonal distribution and expand with injury. Together these spatial maps of the healthy and fibrotic liver provide a deeper understanding of the cellular and spatial remodeling that drives disease which, in turn, could provide new avenues for intervention and further study.
Mutualism provides the basis for biodiversity in eco-evolutionary community assembly
Authors: Araujo Gui , Lurgi Miguel
Published: February 2024

Unveiling the ecological and evolutionary mechanisms underpinning the assembly of stable and complex ecosystems is a main focus of community ecology. Ecological theory predicts the necessity of structural constraints on the network of species interactions to allow for growth of complexity in assembling multispecies communities. A promising research avenue is the search for an understanding of how the coexistence of diverse species interaction types could influence the development of complexity and how an ideal composition could arise in nature. We propose an ecological model with mixed interaction types incorporating evolutionary assembly by speciation. This framework allows to investigate the eco-evolutionary assembly on complex species interaction networks with multiple interaction types and its consequences for ecosystem stability. Our results show that highly mutualistic communities are conducive of complexity and promote the emergence of consumer-resource interactions. Furthermore, we show that an evolutionary process is required to produce such condition. Moreover, this evolutionary assembly generates a diversity of outcomes and promotes two distinct types of complexity depending on speciation constraints. Assembled communities are thus either larger (more species) or more connected, in agreement with patterns previously observed in microbial communities. Our results produce invaluable theoretical insight into the mechanisms behind the emergence of ecological complexity and into the roles of mutualism and speciation on community formation.
Predicting Depression in Canadians with or at Risk of Diabetes: A Cross-Sectional Machine Learning Analysis
Authors: Samsel Konrad , Noaeen Mohammad , Tiwana Amrit , Ali Sarra , Guergachi Aziz , Keshavjee Karim , Shakeri Zahra
Published: February 2024

Depression often goes unrecognized in individuals at risk or living with diabetes, presenting considerable challenges for primary care clinicians. Although large language models and other foundation model approaches are drawing significant attention, we systematically compared six established machine learning algorithms-Logistic Regression, Random Forest, AdaBoost, XGBoost, Naive Bayes, and Artificial Neural Networks-chosen for their reliability, interpretability, and feasibility in everyday clinical settings. By benchmarking their performance under real-world constraints, we identified key factors linked to depression risk in diabetes care, including patient sex, age, osteoarthritis, hemoglobin A1c, and body mass index. Although incomplete demographic information and potential label bias limited predictive power, our results demonstrate that a diverse set of clinical features might help pinpoint high-risk patients. They also indicate a need for longitudinal follow-up and richer clinical data to enhance model accuracy. As a practical benchmark for both clinicians and data scientists, this work suggests that machine learning–based risk stratification can improve early detection of depression and inform targeted interventions in diabetic populations.
Predictive processing in biological motion perception: Evidence from human behavior
Authors: Elmas Hüseyin O. , Er Sena , Rezaki Ada D. , Izgi Aysesu , Urgen Buse M. , Boyaci Huseyin , Urgen Burcu A.
Published: February 2024

Biological motion perception plays a crucial role in understanding the actions of other animals, facilitating effective social interactions. While foundation of biological motion perception is rooted in bottom-up processes, as evidenced by point-light display studies, real-world complexities necessitate the involvement of top-down processes, such as attention and expectation. This study investigates the impact of expectations on biological motion perception using a cued individuation task with point-light display stimuli. We conducted three experiments, each providing advance information about distinct aspects of the subsequent biological motion stimuli – specifically information about action, emotion, and gender. Our results revealed a pattern in the action experiment, where participants demonstrated significantly slower response times for incongruent trials than congruent ones, but only under the 75% cue validity condition. This effect was notably absent in the emotion and gender experiments. Our exploration underscores the multi-faceted nature of biological motion perception, highlighting that while the brain adeptly harnesses prior cues to anticipate and interpret stimuli, the nature and reliability of these cues play a pivotal role on their effects. Specifically, action-related information stands out as an important modulator, possibly due to its evolutionary significance and unique neural processing pathway. These findings not only agree with the principles of predictive processing but also pave the way for future research, emphasizing the need to utilize naturalistic, complex stimuli together with neuroimaging methods to create more comprehensive models of biological motion perception.
Non-cell autonomous OTX2 in the piriform cortex regulates parvalbumin cell maturation states and olfactory-driven behavior
Authors: Gibel-Russo Rachel , Di Nardo Ariel A.
Published: February 2024

The timing of critical periods of juvenile brain plasticity is driven by the maturation of parvalbumin interneurons in the neocortex, a process regulated in part by non-cell autonomous activity of the OTX2 homeoprotein transcription factor. However, the involvement of critical periods in olfactory paleocortex maturation is unknown. Here, we find that the adult mouse piriform cortex parvalbumin interneurons display particularly low molecular maturation that increases in aged animals. Expression analysis of a large panel of genes reveals that an acute increase in piriform cortex OTX2 levels in young adult mice increasesPvalbexpression as well asAdamts9expression, resulting in increased extracellular perineuronal net levels, while reducing OTX2 transfer decreasesPvalbexpression and increasesMmp9expression, resulting in decreased perineuronal net levels. Reduction in OTX2 also stimulates odor-driven cFos activity in piriform cortex parvalbumin cells and disrupts olfactory-driven behavior. Our findings suggest plasticity in piriform cortex involves OTX2 activity on parvalbumin cells and lacks strictly defined critical periods.
SSRI Use During Acute COVID-19 Infection Associated with Lower Risk of Long COVID Among Patients with Depression
Authors: Butzin-Dozier Zachary , Ji Yunwen , Deshpande Sarang , Hurwitz Eric , Coyle Jeremy , Shi Junming (Seraphina) , Mertens Andrew , van der Laan Mark J. , Colford John M. , Patel Rena C. , Hubbard Alan E. ,   the National COVID Cohort Collaborative (N3C) Consortium
Published: February 2024

Background

Long COVID, also known as post-acute sequelae of COVID-19 (PASC), is a poorly understood condition with symptoms across a range of biological domains that often have debilitating consequences. Some have recently suggested that lingering SARS-CoV-2 virus in the gut may impede serotonin production and that low serotonin may drive many Long COVID symptoms across a range of biological systems. Therefore, selective serotonin reuptake inhibitors (SSRIs), which increase synaptic serotonin availability, may prevent or treat Long COVID. SSRIs are commonly prescribed for depression, therefore restricting a study sample to only include patients with depression can reduce the concern of confounding by indication.

Methods

In an observational sample of electronic health records from patients in the National COVID Cohort Collaborative (N3C) with a COVID-19 diagnosis between September 1, 2021, and December 1, 2022, and pre-existing major depressive disorder, the leading indication for SSRI use, we evaluated the relationship between SSRI use at the time of COVID-19 infection and subsequent 12-month risk of Long COVID (defined by ICD-10 code U09.9). We defined SSRI use as a prescription for SSRI medication beginning at least 30 days before COVID-19 infection and not ending before COVID-19 infection. To minimize bias, we estimated the causal associations of interest using a nonparametric approach, targeted maximum likelihood estimation, to aggressively adjust for high-dimensional covariates.

Results

We analyzed a sample (n= 506,903) of patients with a diagnosis of major depressive disorder before COVID-19 diagnosis, where 124,928 (25%) were using an SSRI. We found that SSRI users had a significantly lower risk of Long COVID compared to nonusers (adjusted causal relative risk 0.90, 95% CI (0.86, 0.94)).

Conclusion

These findings suggest that SSRI use during COVID-19 infection may be protective against Long COVID, supporting the hypothesis that serotonin may be a key mechanistic biomarker of Long COVID.
Evaluating Cochlear Implant Stimulation Strategies Through Wide-field Calcium Imaging of the Auditory Cortex
Authors: Castellaro Bruno , Yip Tony Ka Wing , Peng Fei , Muhammad Zeeshan , Fang Shiyi , Nelken Israel , Schnupp Jan
Published: February 2024

Cochlear Implants (CI) are an effective neuroprosthesis for humans with profound hearing loss, enabling deaf adults to have phone calls without lipreading and babies to have successful language development. However, CIs have significant limitations in complex hearing situations, motivating the need for further research, including studies in animal models. Here, we demonstrate the usefulness of wide field Ca++ imaging in assessing different CI stimulation strategies. One major challenge in electrophysiology in CI animals lies in excluding the CI electric artifacts from the recording, since they are orders of magnitude larger than the amplitude of action potentials. Also, electrophysiology can rarely sample large areas of neuropil at high spatial resolution. To circumvent these problems, we have set up an imaging system allowing us to monitor neural activity in the auditory cortex (AC) of CI supplied rats using the Ca++ sensitive dye OGB. Here we describe an initial experiment with this setup, in which we recorded cortical responses to 4 different stimulation patterns which were delivered across 3 CI channels to the contralateral ear. We then investigated two parameters that have been shown to affect intelligibility in CI users: pulse rate and relative pulse timing across CI channels. While pulse rate had only a very modest effect on the discriminability of the neural responses, the stimulation mode had a major effect, with simultaneous pulse timing, perhaps surprisingly, allowing much better pattern discrimination than interleaved sampling. The result suggests that allowing collisions of pulses on neighboring channels may not always be detrimental, at least if partial overlaps of pulses, in which anodic and cathodic pulse phases might cancel, are avoided.
The Effect on Speech-in-Noise Perception of Real Faces and Synthetic Faces Generated with either Deep Neural Networks or the Facial Action Coding System
Authors: Yu Yingjia , Lado Anastasia , Zhang Yue , Magnotti John F. , Beauchamp Michael S.
Published: February 2024

The prevalence of synthetic talking faces in both commercial and academic environments is increasing as the technology to generate them grows more powerful and available. While it has long been known that seeing the face of the talker improves human perception of speech-in-noise, recent studies have shown that synthetic talking faces generated by deep neural networks (DNNs) are also able to improve human perception of speech-in-noise. However, in previous studies the benefit provided by DNN synthetic faces was only about half that of real human talkers. We sought to determine whether synthetic talking faces generated by an alternative method would provide a greater perceptual benefit. The facial action coding system (FACS) is a comprehensive system for measuring visually discernible facial movements. Because the action units that comprise FACS are linked to specific muscle groups, synthetic talking faces generated by FACS might have greater verisimilitude than DNN synthetic faces which do not reference an explicit model of the facial musculature. We tested the ability of human observers to identity speech-in-noise accompanied by a blank screen; the real face of the talker; and synthetic talking face generated either by DNN or FACS. We replicated previous findings of a large benefit for seeing the face of a real talker for speech-in-noise perception and a smaller benefit for DNN synthetic faces. FACS faces also improved perception, but only to the same degree as DNN faces. Analysis at the phoneme level showed that the performance of DNN and FACS faces was particularly poor for phonemes that involve interactions between the teeth and lips, such as /f/, /v/, and /th/. Inspection of single video frames revealed that the characteristic visual features for these phonemes were weak or absent in synthetic faces. Modeling the realvs.synthetic difference showed that increasing the realism of a few phonemes could substantially increase the overall perceptual benefit of synthetic faces, providing a roadmap for improving communication in this rapidly developing domain.
Neural ensembles that encode affective mechanical and heat pain in mouse spinal cord
Authors: Zhang Ming-Dong , Kupari Jussi , Su Jie , Hu Yizhou , Magnusson Kajsa A. , Calvo-En-rique Laura , Usoskin Dmitry , Albisetti Gioele W , Leavitt Andrew D , Zeilhofer Hanns Ulrich , Hökfelt Tomas , Lagerström Malin C. , Ernfors Patrik
Published: February 2024

Acute pain is an unpleasant experience caused by noxious stimuli. How the spinal neural circuits attribute differences in quality of noxious information remains unknown. By means of genetic capturing, activity manipulation and single cell RNA sequencing, we identified distinct neural ensembles in mouse spinal cord encoding mechanical and heat pain. Re-activation or silencing of these ensembles potentiated or stopped, respectively, affective but not reflex behaviour without altering pain behaviour to cross stimuli modality. Within ensembles, polymodal Gal+inhibitory neurons with monosynaptic contacts to A-fiber sensory neurons gated affective pain independent of modality. Peripheral nerve injury led to microglia driven inflammation and an ensemble transition with decreased recruitment of Gal+inhibitory neurons and increased excitatory drive. However, activating Gal+neurons reversed hypersensitivity associated with neuropathy. Our results reveal the existence of a spinal representation which forms the neural basis of the discriminative and affective qualities of acute pain and that these neurons are under the control of a shared feed-forward inhibition.
Ramping Dynamics in the Frontal Cortex Unfold Over Multiple Timescales During Motor Planning
Authors: Affan R.O. , Bright I.M. , Pemberton L.N. , Cruzado N.A. , Scott B.B. , Howard M.W.
Published: February 2024

Plans are formulated and refined over the period leading to their execution, ensuring that the appropriate behavior is enacted at just the right time. While existing evidence suggests that memory circuits convey the passage of time through diverse neuronal responses, it remains unclear whether the neural circuits involved in planning behavior exhibit analogous temporal dynamics. Using publicly available data, we analyzed how activity in the frontal motor cortex evolves during motor planning. Individual neurons exhibited diverse ramping activity throughout a delay interval that preceded a planned movement. The collective activity of these neurons was useful for making temporal predictions that became increasingly precise as the movement time approached. This temporal diversity gave rise to a spectrum of encoding patterns, ranging from stable to dynamic representations of the upcoming movement. Our results indicate that neural activity unfolds over multiple timescales during motor planning, suggesting a shared mechanism in the brain for processing temporal information related to both past memories and future plans.
Reconceptualizing programmed transcriptional slippage in RNA viruses
Authors: Valli Adrian A. , Domingo-Calap María Luisa , González de Prádena Alfonso , García Juan Antonio , Cui Hongguang , Desbiez Cécile , Lopez-Moya Juan José
Published: February 2024

RNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of such, named programmed transcriptional slippage (PTS), is defined by the insertion of an additional A at Anmotifs (n ≥ 6) of newly synthetized viral transcripts to get access to overlapping open reading frames (ORFs). Although key proteins from Ebolavirus and potyvirids (members of thePotyviridaefamily) are expressed via PTS, available information about this phenomenon is very scarce. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases in which PTS does not fit with its current definition. In summary, we observe (i) high rate of single nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8stretch, and (iii) significant changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of full-genome sequences from potyvirids shows a widespread occurrence of species-specific An/Un(n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. In conclusion, our data prompt to broaden PTS definition in RNA viruses. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a revaluation of PTS significance during infections of RNA viruses is required.

IMPORTANCE

Programmed transcriptional slippage (PTS) is used by RNA viruses as another strategy to maximise the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they insert an untemplated A in An motifs (n ≥ 6) in a small fraction of newly synthesised viral RNAs. As a consequence, ribosomes can get access to overlapping open reading frames (ORFs) when translating those particular transcripts. Here, using plant-infecting RNA viruses as models, we discover cases challenging the previously stablished definition of viral PTS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that PTS might be more relevant during RNA virus evolution and infection processes than previously assumed.
(p)ppGpp-mediated GTP homeostasis ensures the survival and antibiotic tolerance ofStaphylococcus aureusduring starvation by preserving the proton motive force
Authors: Salzer Andrea , Ingrassia Sophia , Sauer Lisa , Rapp Johanna , Dobritz Ronja , Müller Jennifer , Link Hannes , Wolz Christiane
Published: February 2024

Upon nutrient limitation bacteria enter a nongrowing state, which allow bacterial survival and antibiotic tolerance. The mechanisms whether and how the messenger molecule (p)ppGpp contributes to the transition in Firmicutes is debated. Here we show forStaphylococcus aureusthat (p)ppGpp-dependent restriction of the GTP pool is essential for the culturability of starved cells and for antibiotic tolerance. Elevated GTP levels in a starving (p)ppGpp-deficient mutant lead to a division-incompetent, dormant state characterized by reduced metabolic activity and alterations in membrane function and architecture. GTP level control of nucleotide sensitive promoters result in transcriptional downregulation of gene of the TCA cycle and electron transport chain. Increasing transcription ofqoxABCD, a terminal oxidase of the respiratory chain, through mutation of the transcriptional start site partially restored the culturability of the (p)ppGpp-deficient mutant. Furthermore, we showed that the maintenance of proton motive force under nutritional stress contributes to antibiotic tolerance, supporting the idea of applying (p)ppGpp or PMF inhibitors to combat antibiotic-tolerant bacteria.
A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis
Authors: Pérez-Burgos María , Herfurth Marco , Kaczmarczyk Andreas , Harms Andrea , Huber Katrin , Jenal Urs , Glatter Timo , Søgaard-Andersen Lotte
Published: February 2024

Phenotypic heterogeneity in bacteria results from stochastic processes or deterministic genetic programs. These deterministic programs often incorporate the versatile second messenger c-di-GMP, and by deploying c-di-GMP metabolizing enzyme(s) asymmetrically during cell division give rise to daughter cells with different c-di-GMP levels. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent genetic program that is hardwired into the cell cycle ofMyxococcus xanthusto minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity switched on during cytokinesis, resulting in a dramatic but transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating mirror-symmetric, phenotypically similar daughters with correct motility behaviours. These findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations ensure the formation of dissimilar or similar daughter cells.
YraN is a helicase-associated nuclease fostering extended recombination events by natural transformation
Authors: Hardy Léo , Plantade Julie , Morales Violette , Mazzamuro Fanny , Rocha Eduardo P. C. , Polard Patrice , Charpentier Xavier
Published: February 2024

Natural transformation is a widespread molecular pathway of horizontal gene transfer involving the uptake and recombination of exogenous DNA. Exogenous DNA follows a pathway involving genes sequentially required for its capture, internalization, protection, and recombination with the chromosome. Most of these genes were identified through the isolation of transformation-defective mutants and/or based on their expression preceding natural transformation. Yet, genes required for key steps of the pathway remain elusive. We sought to identify any missing component by comparing Tn-seq data obtained in two distantly-related transformable diderm species, the human pathogenLegionella pneumophilaand the cyanobacteriumSynechococcus elongatus. We identifiedyraN, a widespread and highly conserved gene of unknown function required for natural transformation. We provide evidence that YraN is a nuclease associated with the ComM helicase, which cooperate to process the D-loop formed by the invasion of the transforming DNA in the chromosomal DNA strands. We propose a model in which cleavage of the displaced strand by YraN can promote the recombination of transforming DNA, leading to extended recombination events. The identification of this YraN/ComM nuclease/helicase system supports the hypothesis that bacteria possess a conserved pathway for the transport and recombination of exogenous DNA.

Significance

Many bacteria use a dedicated pathway to internalize and integrate extracellular DNA into their chromosome. This allows them to naturally acquire genes, or gene variants, that can confer them new traits, hence the term of natural transformation. Although reported nearly a century ago by Frederick Griffith, several aspects of the mechanism of natural transformation remain elusive. Specifically, it is not clear whether or not all the conserved molecular players of the pathway have been identified. We queried two distinct bacterial species for any gene that would be required for natural transformation. We confirmed all core players of the pathway, but also uncovered a highly conserved one, YraN. We provide evidence that YraN is an endonuclease, which in association with the ComM helicase, promotes the efficient integration of the extracellular DNA in the bacterial chromosome.
Simulation and analysis of micro-textured rough curved surface based on fractal characterization method
Authors: Zhu Chunxia , Meng Xianling
Published: February 2024

Purpose

Micro-texture is processed on the surface to reduce the friction of the contact surface, and its application is more and more extensive. The purpose of this paper is to create a texture function model to study the influence of surface parameters on the accuracy of the simulated surface so that it can more accurately reflect the characteristics of the real micro-textured surface.

Design/methodology/approach

The microstructure function model of rough surfaces is established based on fractal geometry and polar coordinate theory. The offset angle θ is introduced into the fractal geometry function to make the surface asperity normal perpendicular to the tangent of the surface. The 2D and 3D contour surfaces of the surface groove texture are analyzed by MATLAB simulation. The effects of fractal parameters (D and G) and texture parameter h on the curvature of the surface micro-texture model were studied.

Findings

This paper more accurately characterizes the textured 3D curved surface, especially the surface curvature. The scale coefficient G significantly affects curvature, and the influence of fractal dimension D and texture parameters on curvature can be ignored.

Originality/value

The micro-texture model of the rough surface was successfully established, and the range of fractal parameters was determined. It provides a new method for the study of surface micro-texture tribology.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-09-2023-0298/
The market reaction of real estate companies to the announcement of the Russian–Ukrainian invasion
Authors: Yudaruddin Rizky , Lesmana Dadang
Published: February 2024

Purpose

This study aims to investigate the market reaction in the real estate market to the announcement of Russia’s invasion of Ukraine.

Design/methodology/approach

This study uses the event study method to assess the market reaction to the announcement that Russia is invading Ukraine. The sample in this study comprises 2,325 companies in the real estate market. We also conduct a cross-sectional analysis to determine the influence of the North Atlantic Treaty Organization (NATO) members and company characteristics on market reactions during the invasion.

Findings

The global market reacts significantly negative toward Russia’s invasion of Ukraine. This indicates that the war poses a high geopolitical risk that prompts financial markets down. The authors also demonstrate that emerging and frontier markets react significantly negative to the invasion before and after its announcement. Meanwhile, developed markets tend to react only before the invasion is announced. Furthermore, we find that the NATO members react more strongly than other markets.

Social implications

This result implies that war prompts investors to flee from the stock exchange, while the deeper the country’s involvement, the more investors worry about the risks.

Originality/value

This study is the first to discuss the market reaction to the Russian invasion of Ukrainian, specifically in the real estate market.
Applying the engineering design process to teach the physics course for engineering students using the flipped classroom combined with an instructional design model
Authors: Ngo Van Thien
Published: February 2024

Purpose

This study aims to examine the perceptions of students about learning science and physics using the engineering design process (EDP).

Design/methodology/approach

The study employed a mixed-methods research design: The quantitative session features a pre–post-test control group study. In the qualitative aspect, the study conducted semistructured interviews for data collection. In the experimental group, the flipped classroom (FC) model and an instructional design are combined to design, develop and implement a physics course using the steps of the EDP, while the conventional method was applied to the control group. The respondents are students of the Department of Mechanical Engineering at Cao Thang Technical College in Vietnam for the academic year 2022–2023. The control and experimental groups are composed of 80 students each. An independent sample Mann–Whitney U test is applied to the quantitative data, while thematic analysis is employed for the qualitative data.

Findings

The results demonstrate a statistically significant difference between the experimental and control groups in terms of perceptions about learning science and physics using the EDP, which, when combined with a FC, enhances physics learning for engineering students.

Research limitations/implications

This study implemented the EDP in teaching physics to first-year engineering students in the Department of Mechanical Engineering using the combined FC and instructional design models. The results revealed that a difference exists in the perception of the students in terms of integrating the EDP into learning physics between the experimental and control groups. The experimental group, which underwent the EDP, obtained better results than did the control group, which used the conventional method. The results demonstrated that the EDP encouraged the students to explore and learn new content knowledge by selecting the appropriate solution to the problem. The EDP also helped them integrate new knowledge and engineering skills into mechanical engineering. This research also introduced a new perspective on physics teaching and learning using the EDP for engineering college students.

Practical implications

The research findings are important for teaching and learning physics using EDP in the context of engineering education. Thus, educators can integrate the teaching and learning of physics into the EDP to motivate and engage student learning.

Originality/value

Using the EDP combined with a FC designed under stages of the analyze, design, develop, implement and evaluate (ADDIE) model has enhanced the learning of physics for engineering college students.
Murine models of idiopathic inflammatory myopathies
Authors: Okiyama Naoko , Konishi Risa , Ichimura Yuki
Published: February 2024

Idiopathic inflammatory myopathies (IIMs) are divided into polymyositis and dermatomyositis (DM) with specific cutaneous manifestation. Several myositis‐specific autoantibodies (MSAs) have been identified in IIMs and were found to be associated with distinct clinical features, including anti‐synthetase syndrome (ASyS) and immune‐mediated necrotizing myopathy (IMNM). Moreover, MSA‐related clinical features have been identified even within DM. Although MSAs are valuable for the diagnosis of IIMs, the pathogenic roles of these antibodies remain unknown. To investigate the pathogenesis of IIMs, classical murine models of autoimmune myositis, experimental autoimmune myositis, and C protein‐induced myositis have been established by immunization with muscle‐specific antigens, myosin, and myosin‐binding skeletal C protein, respectively. To according to MSA‐related autoimmunity, a murine model of ASyS was generated by immunization with a murine recombinant histidyl‐transfer RNA (tRNA) synthetase, Jo‐1, in which muscle and lung inflammation are induced depending on acquired immunity. Furthermore, it was found that the transfer of human Immunoglobulin G (IgGs) from patients with IMNM, comprising anti‐signal recognition particles and anti‐3‐hydroxy‐3‐methylglutaryl coenzyme A reductase antibodies, induced complement‐mediated myositis in recipient mice. We found that CD8+ T cell‐mediated myositis can be established depending on autoimmunity against transcriptional intermediary factor 1γ (TIF1γ), an autoantigen for MSAs induced by recombinant human TIF1γ immunization. These new murine models reflecting MSA‐associated IIMs will reveal the immunological mechanisms underlying IIMs.