bluuebunny/crossref_metadata_2025 huggingface dataset:
Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumor progression
Authors: Burger Gerhard A , Nesenberend Daphne N , Lems Carlijn M , Hille Sander C , Beltman Joost B
Published: February 2022

Epithelial-Mesenchymal Transition (EMT) and immunoevasion through upregulation of Programmed Death-Ligand 1 (PD-L1) are important drivers of cancer progression. While EMT has been proposed to facilitate PD-L1-mediated immunosuppression, the molecular mechanisms of their interaction remain obscure. Here we provide insight into these mechanisms by proposing a mathematical model that describes the crosstalk between EMT and Interferon gamma (IFNγ)-induced PD-L1 expression. Our model shows that via interaction with microRNA-200 (miR-200), the multistability of the EMT regulatory circuit is mirrored in the PD-L1 levels, which are further amplified by IFNγ stimulation. This IFNγ-mediated effect is most prominent for cells in a fully mesenchymal state, and less strong for those in an epithelial or partially mesenchymal state. Additionally, bi-directional crosstalk between miR-200 and PD-L1 implies that IFNγ stimulation allows cells to undergo EMT for lower amounts of inducing signal, and that IFNγ presence accelerates EMT and decelerates Mesenchymal-Epithelial Transition (MET). Overall, our model agrees with published findings and provides insight into possible mechanisms behind EMT-mediated immune-evasion; and primary, adaptive, or acquired resistance to immunotherapy. Our model can be used as a starting point to explore additional crosstalk mechanisms, as an improved understanding of these mechanisms is indispensable for developing better diagnostic and therapeutic options for cancer patients.
Data-driven dynamical modelling of a pathogen-infected plant gene regulatory network: a comparative analysis
Authors: Foo Mathias , Dony Leander , He Fei
Published: February 2022

Recent advances in synthetic biology have enabled the design of genetic feedback control circuits that could be implemented to build resilient plants against pathogen attacks. To facilitate the proper design of these genetic feedback control circuits, an accurate model that is able to capture the vital dynamical behaviour of the pathogen-infected plant is required. In this study, using a data-driven modelling approach, we develop and compare four dynamical models (i.e. linear, Michaelis-Menten, standard S-System and extended S-System) of a pathogen-infected plant gene regulatory network (GRN). These models are then assessed across several criteria, i.e. ease of identifying the type of gene regulation, the predictive capability, Akaike Information Criterion (AIC) and the robustness to parameter uncertainty to determine its viability of modelling the pathogen-infected plant GRN. Using our defined ranking score, our analyses show that while the extended S-System model ranks highest in the overall comparison, the performance of the linear model is more consistent throughout the comparison, making it the preferred model for this pathogen-infected plant GRN.
DisPhaseDB, an integrative database of diseases related variations in liquid-liquid phase separation proteins
Authors: Navarro Alvaro , Orti Fernando , Martínez-Pérez Elizabeth , Simonetti Franco , Iserte Javier , Marino-Buslje Cristina
Published: February 2022

Motivation

Proteins involved in liquid-liquid phase separation (LLPS) and membraneless organelles (MLOs) are recognized to be decisive for many biological processes and also responsible for several diseases. The recent explosion of research in the area still lacks tools for the analysis and data integration among different repositories. Currently, there is not a comprehensive and dedicated database that collects all disease-related variations in combination with the protein location, biological role in the MLO and all the metadata available for each protein and disease. Disease related protein variants and additional features are dispersed and the user has to navigate many databases, with different focus, formats and often not user friendly.

Results

We present DisPhaseDB, a database dedicated to disease related variants of LLPS proteins and/or are involved in MLOs. It integrates 10 databases, contains 5.741 proteins, 1.660.059 variants and 4.051 disease terms. It also offers intuitive navigation and an informative display. It constitutes a pivotal starting point for further analysis, encouraging the development of new computational tools.

Availability and Implementation

The database is freely available at http://disphasedb.leloir.org.ar.

Contact

jiserte@leloir.org.ar and cmb@leloir.org.ar

Graphical abstract
Tau seeding without tauopathy
Authors: LaCroix Michael S. , Hitt Brian D. , Beaver Joshua D. , Estill-Terpack Sandi-Jo , Gleason Kelly , Tamminga Carol A. , Evers Bret M. , White Charles L. , Diamond Marc I.
Published: February 2022

Neurodegenerative tauopathies such as Alzheimer’s disease (AD) are caused by brain accumulation of tau assemblies. Evidence suggests tau functions as a prion, and cells and animals efficiently propagate unique tau assemblies. This suggests a dedicated cellular replication machinery, with normal physiologic function for tau seeds. Consequently, we hypothesized that healthy control brains would have seeding activity. We recently developed a novel monoclonal antibody (MD3.1) specific for tau seeds. We used this antibody to immunopurify tau from the parietal and cerebellar cortices of 19 healthy subjects ranging 19-65 years. We detected seeding in the parietal cortex, but not in the cerebellum, or in wild-type or human tau knockin mice, suggesting that cellular/genetic context dictates development of seed-competent tau. Seeding did not correlate with subject age or brain tau levels. Dot blot analyses revealed no AT8 immunoreactivity above background levels in parietal and cerebellar extracts and <1/100 of that present in AD. Based on binding to a panel of antibodies, the conformational characteristics of control seeds differed from AD, suggesting a unique underlying assembly, or structural ensemble. Tau’s ability to adopt self-replicating conformations under non-pathogenic conditions may reflect normal function that goes awry in disease states.
Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data
Authors: Inward Rhys P. D. , Parag Kris V. , Faria Nuno R.
Published: February 2022

SARS-CoV-2 virus genomes are currently being sequenced at an unprecedented pace. The choice of viral sequences used in genetic and epidemiological analysis is important as it can induce biases that detract from the value of these rich datasets. This raises questions about how a set of sequences should be chosen for analysis, and which epidemiological parameters derived from genomic data are sensitive or robust to changes in sampling. We provide initial insights on these largely understudied problems using SARS-CoV-2 genomic sequences from Hong Kong, China, and the Amazonas State, Brazil. We consider sampling schemes that select sequences uniformly, in proportion or reciprocally with case incidence and which simply use all available sequences (unsampled). We apply Birth-Death Skyline and Skygrowth methods to estimate the time-varying reproduction number (Rt) and growth rate (rt) under these strategies as well as related R0 and date of origin parameters. We compare these to estimates from case data derived from EpiFilter, which we use as a reference for assessing bias. We find that both Rt and rt are sensitive to changes in sampling whilst R0 and the date of origin are relatively robust. Moreover, we find that analysis using unsampled datasets, which reflect an opportunistic sampling scheme, result in the most biased Rt and rt estimates for both our Hong Kong and Amazonas case studies. We highlight that sampling strategy choices may be an influential yet neglected component of sequencing analysis pipelines. More targeted attempts at genomic surveillance and epidemic analyses, particularly in settings with limited sequencing capabilities, are necessary to maximise the informativeness of virus genomic datasets.
N-glycans mannosylation controls T-cell development by reprogramming thymocyte commitment, fate and repertoire
Authors: Vicente Manuel M , Alves Inês , Fernandes Ângela , Dias Ana M , Pérez-Anton Elena , Correia Alexandra , Almeida Afonso R M , Rabinovich Gabriel A , Vilanova Manuel , Sousa Ana E , Pinho Salomé S
Published: February 2022

T-cell development is a major physiological process occurring in complex organisms, that ensures the formation of T-cell receptors diverse repertoire, to recognize antigens throughout the life of the organism. The thymus offers a microenvironment for efficient development, where progenitor populations go through maturation steps, which, when not regulated, are associated with disease onset, including autoimmune disorders and cancer. Glycosylation is a major post-translational modification that occurs in virtually all cells, including T lymphocytes, regulating receptor- turnover, affinity and signaling. However, there is a missing knowledge on how glycans regulate lymphocyte development and their impact in T-cell functions. We discovered stage-specific glycosylation profiles in human and murine thymocyte populations. Thereafter, we generated two glycoengineered mouse models displaying N-glycosylation pathway deficiencies, at early DN stages, lacking the Mgat1 or Mgat2 genes. We demonstrated remarkable defects in key T-cell developmental stages, such as ß- and DP-selection, natural regulatory T-cell generation, γδ T development/differentiation and thymic egression, in Mgat1-deficient thymocytes, indicating a pathogenic role of mannose N-glycans in development. We also demonstrated that a single N- glycan antenna (modelled in Mgat2-deficient thymocytes) is sufficient to rescue key developmental processes. In conclusion, we demonstrated that mannosylated thymocytes render a dysregulation in T-cell development, associated with disease.

Graphical abstract
Comparison of common outcome measures for assessing independence in patients diagnosed with disorders of consciousness: A Traumatic Brain Injury Model Systems Study
Authors: Snider Samuel B. , Kowalski Robert G. , Hammond Flora , Izzy Saef , Shih Shirley L. , Rovito Craig , Edlow Brian L. , Zafonte Ross D. , Giacino Joseph T. , Bodien Yelena G.
Published: February 2022

Importance

Patients with disorders of consciousness (DoC) after traumatic brain injury (TBI) recover to varying degrees of functional dependency. Dependency is difficult to measure but critical for outcome interpretation and prognostic counseling. Traditional outcome measures, like the Glasgow Outcome Scale-Extended (GOSE), are mandated by the US Food and Drug Administration for evaluating TBI clinical trial efficacy but have an unknown accuracy for measuring dependency.

Objective

We used the Functional Independence Measure (FIM®) as the reference standard to evaluate how accurately the GOSE and Disability Rating Scale (DRS) assess functional dependency in the world’s largest cohort of patients with DoC after TBI. We propose an alternate, data-driven, approach to measuring dependency.

Design, Setting, and Participants

In this cohort study, we included patients with DoC prospectively enrolled in the longitudinal Traumatic Brain Injury Model Systems National Database (TBIMS NDB). Participants were survivors of moderate/severe TBI with DoC on admission to a US inpatient rehabilitation center between 1988 and 2020, followed 1 year after injury.

Exposure

We examined the classification performance of common TBI outcome measure cutpoints (GOSE ≤3 and ≤4 [Lower and Upper Severe Disability, respectively], and DRS ≥12 [Severe Disability]) in identifying subjects with functional dependency at 1 year. We compared dataderived optimal cut-points on these scales to a novel DRS-based marker of dependency, the DRSDepend.

Main Outcome and Measure

Total FIM score < 80 (FIM-dependency) at 1 year.

Results

Of 18,486 TBIMS participants, 1,483 with DoC on arrival to inpatient rehabilitation met inclusion criteria (mean [SD] age=38 [18] years; 76% male). The sensitivity of GOSE cut-points of ≤3 and ≤4 for identifying FIM-dependency were 97% and 98%, but specificities were 73% and 51%, respectively. The sensitivity of the DRS cut-point of ≥12 was 60%, but specificity was 100%. The DRSDependhad a sensitivity of 83% and a specificity of 94% for classifying FIM-dependency, with a greater AUROC than the data-derived optimal GOSE (≤3, p=0.01) and DRS (≥10, p=0.008) cut-points.

Conclusions and Relevance

Commonly-used GOSE and DRS cut-points have limited sensitivity or specificity for identifying functional dependency. The DRSDependidentifies FIM-dependency more accurately than GOSE and DRS cut-points, but requires further validation.
SARS-CoV-2 Omicron symptomatic infections in previously infected or vaccinated South African healthcare workers
Authors: Nunes Marta C. , Sibanda Sthembile , Baillie Vicky L. , Kwatra Gaurav , Aguas Ricardo , Madhi Shabir A. ,   the Wits VIDA HCW Study Group
Published: February 2022

We investigated Omicron infections among healthcare workers (HCW) presenting with symptoms of SARS-CoV-2 infection and evaluated the protective effect of vaccination or prior infection.

Between 24th November and 31st December 2021, HCW in Johannesburg, South Africa, were tested for SARS-CoV-2 infection by Nucleic Acid Amplification Test (NAAT). Blood samples collected either at the symptomatic visit or within 3-months prior, were tested for spike protein immunoglobulin G (IgG).

Overall, 433 symptomatic HCW were included in the analysis, with 190 (43.9%) having an Omicron infection; 69 (16.7%) were unvaccinated and 270 (62.4%) received a single dose of Ad26.COV.2 vaccine. There was no difference in the odds of identifying Omicron between unvaccinated and Ad26.COV.2 vaccinated HCW (adjusted odds ratio [aOR] 0.81, 95% confidence interval [CI]: 0.46, 1.43). One-hundred and fifty-four (35.3%) HCW had at least one SARS-CoV-2 NAAT-confirmed prior infection; these had lower odds of Omicron infection compared with those without past infection (aOR 0.55, 95%CI: 0.36, 0.84). Anti-spike IgG concentration of 1549 binding antibody unit/mL was suggestive of significant reduction in the risk of symptomatic Omicron infection.

We found high reinfection and vaccine breakthrough infection rates with the Omicron variant among HCW. Prior infection and high anti-spike IgG concentration were protective against Omicron infection.
Epigenetic clock acceleration is linked to age-at-onset of idiopathic and LRRK2 Parkinson’s disease
Authors: Tang Xuelin , Gonzalez-Latapi Paulina , Marras Connie , Visanji Naomi P. , Yang Wanli , Sato Christine , Lang Anthony E. , Rogaeva Ekaterina , Zhang Ming
Published: February 2022

Parkinson’s disease is a clinically and genetically heterogeneous movement disorder with highly variable age-at-onset. DNA methylation (DNAm) age is an epigenetic clock that could reflect biological aging. Studies of DNAm-age acceleration (difference between DNAm-age and chronological age) are pertinent to neurodegenerative diseases (e.g., Parkinson’s disease), for which aging is the strongest risk-factor. We assessed DNAm-age in idiopathic Parkinson’s disease (n=96) and a longitudinal LRRK2 cohort at four time-points over a 3-year period (n=220), including manifesting (n=91) and non-manifesting (n=129) G2019S-carriers. A highly variable age-at-onset was observed in both the idiopathic cohort (26-77 years) and manifesting G2019S-carriers (39-79 years). Increased DNAm-age acceleration was significantly associated with younger onset in idiopathic and LRRK2-related Parkinson’s disease, suggesting that every 5-year increase in DNAm-age acceleration is linked to about 6-year earlier onset. At an individual level, DNAm-age acceleration remained steady over a 3-year period for most G2019S-carriers, indicating that it might serve as a stable biomarker of biological aging. Future studies should evaluate the stability of DNAm-age acceleration over longer time-periods, especially for phenoconverters from non-manifesting to manifesting subjects. In conclusion, DNAm-age acceleration is linked to disease onset, and could be used in disease-modifying clinical trials of prodromal Parkinson’s disease.
Human Cerebral Spheroids Undergo Activity Dependent Changes In Cellular Composition And Microrna Expression
Authors: Parmentier Thomas , James Fiona , Hewitson Elizabeth , Bailey Craig , Werry Nicholas , Sheridan Steve D. , Perlis Roy H. , Perreault Melissa , Gaitero Luis , Lalonde Jasmin , LaMarre Jonathan
Published: February 2022

Activity-induced neurogenesis has been extensively studied in rodents but the lack of ante mortem accessibility to human brain at the cellular and molecular levels limits studies of the process in humans. Using cerebral spheroids derived from human induced pluripotent stem cells (iPSCs), we investigated the effects of increased neuronal activity on neurogenesis. Our studies demonstrate that increasing neuronal activity with 4-aminopyridine in 3-month-old cerebral spheroids is associated with increases in the numbers of new neurons and decreases in the population of new glial cells. We also observed a significant decrease in the expression of miR-135a, which has previously been shown to be decreased in exercise-induced neurogenesis. Predicted targets of miR-135a include key participants in the SMAD2/3 and BDNF pathways. Together, our results suggest that iPSC-derived cerebral spheroids are an attractive model to study some aspects of activity-induced neurogenesis.
metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists
Authors: Vaulot Daniel , Hung Sim Clarence Wei , Ong Denise , Teo Bryan , Biwer Charlie , Jamy Mahwash , dos Santos Adriana Lopes
Published: February 2022

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities, and an increasing number of environmental datasets are being published. Although unprocessed sequence files are often publicly available, processed data, i.e. sequences clustered as operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) are rarely at hand in a comparable format. This hampers comparative studies between different environments and datasets, for example examining the biogeographical patterns of specific groups/species, as well analysing the micro-genetic diversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2, contains 41 datasets corresponding to more than 4,000 samples and 73,000 ASVs. The database is accessible through both a web-based interface (https://shiny.metapr2.org) and as an R package, and should prove very useful to all researchers working on protist diversity in a variety of systems.
Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3-D Collagen Matrices
Authors: Shahhosseini Melika , Beshay Peter E. , Akbari Ehsan , Avendano Alex , Song Jonathan W. , Castro Carlos E.
Published: February 2022

The interactions of cells with signaling molecules present in their local microenvironment maintain cell proliferation, differentiation, and spatial organization, and mediate progression of diseases such as metabolic disorders and cancer. Real-time monitoring of the interactions between cells and their extracellular ligands in a 3-D microenvironment can inform detection and understanding of cell processes and development of effective therapeutic agents. DNA-origami technology allows for the design and fabrication of biocompatible and 3-D functional nanodevices via molecular self-assembly for various applications including molecular sensing. Here, we report a robust method to monitor live cell interactions with molecules in their surrounding environment in a 3-D tissue model using a microfluidic device. We used a DNA origami Cell Sensing Platform (CSP) to detect two specific nucleic acid sequences on the membrane of B cells and dendritic cells. We further demonstrated real-time detection of biomolecules with the DNA sensing platform on the surface of dendritic cells in a 3-D microfluidic tissue model. Our results establish the integration of live cells with membranes engineered with DNA nanodevices into microfluidic chips as a highly capable biosensor approach to investigate subcellular interactions in physiologically relevant 3-D environments under controlled biomolecular transport.
Genome-microbiome interplay provides insight into the determinants of the human blood metabolome
Authors: Diener Christian , Dai Chengzhen L. , Wilmanski Tomasz , Baloni Priyanka , Smith Brett , Rappaport Noa , Hood Leroy , Magis Andrew T. , Gibbons Sean M.
Published: February 2022

Variation in the blood metabolome is intimately related to human health. Prior work has shown that host genetics and gut microbiome composition, combined, explain sizable, but orthogonal, components of the overall variance in blood metabolomic profiles. However, few details are known about the interplay between genetics and the microbiome in explaining variation on a metabolite-by-metabolite level. Here, we performed analyses of variance for each of the 945 blood metabolites that were robustly detected across a cohort of 2,049 individuals, while controlling for a number of relevant covariates, like sex, age, and genetic ancestry. Over 60% of the detected blood metabolites were significantly associated with either host genetics or the gut microbiome, with more than half of these associations driven solely by the microbiome and around 30% under hybrid genetic-microbiome control. The variances explained by genetics and the microbiome for each metabolite were indeed largely additive, although subtle, but significant, non-additivity was detected. We found that interaction effects, where a metabolitemicrobe association was specific to a particular genetic background, were quite common, albeit with modest effect sizes. The outputs of our integrated genetic-microbiome regression models provide novel biological insights into the processes governing the composition of the blood metabolome. For example, we found that unconjugated secondary bile acids were solely associated with the microbiome, while their conjugated forms were under strong host genetic control. Overall, our results reveal which components of the blood metabolome are under strong genetic control, which are more dependent on gut microbiome composition, and which are dependent upon both. This knowledge will help to guide targeted interventions designed to alter the composition of the blood metabolome.
Dopamine transporter and synaptic vesicle sorting defects initiate auxilin-linked Parkinson’s disease
Authors: Vidyadhara D J , Somayaji Mahalakshmi , Wade Nigel , Yücel Betül , Zhao Helen , Shashaank N , Ribaudo Joseph , Gupta Jyoti , Lam TuKiet T. , Sames Dalibor , Greene Lois E. , Sulzer David L. , Chandra Sreeganga S.
Published: February 2022

Auxilin participates in the uncoating of clathrin-coated vesicles (CCVs), thereby facilitating synaptic vesicle (SV) regeneration at presynaptic sites. Auxilin (DNAJC6/PARK19) loss-of- function mutations cause early-onset Parkinson’s disease (PD). Here, we utilized auxilin-knockout (KO) mice to elucidate the mechanisms through which auxilin deficiency and clathrin-uncoating deficits lead to PD. We demonstrate that auxilin KO mice display the cardinal features of PD, including progressive motor deficits, α-synuclein pathology, nigral dopaminergic loss, and neuroinflammation. Through unbiased proteomic and neurochemical analyses, we demonstrate that dopamine homeostasis is disrupted in auxilin KO brains, including via slower dopamine reuptake kinetics in vivo, an effect associated with dopamine transporter misrouting into axonal membrane deformities in the dorsal striatum. We also show that elevated macroautophagy and defective SV protein sorting contribute to ineffective dopamine sequestration and homeostasis, ultimately leading to neurodegeneration. This study advances our knowledge of how presynaptic endocytosis deficits lead to dopaminergic vulnerability and pathogenesis of PD.
Genetic and genomic analysis of oxygen consumption in mice
Authors: Ogawa Shinichiro , Darhan Hongyu , Suzuki Keiichi
Published: February 2022

We estimated genetic parameters of oxygen consumption (OC), OC per metabolic body weight (OCMBW), and body weight at three through eight weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental, and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. For OC, estimated direct heritability was moderate (0.32) and estimated maternal heritability and proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance were very low (both <0.03), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes by performing pool-seq using pooled DNA samples from mice in high and low OC lines and selective signature detection. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binging proteins (Ndufa12, Sdhc, Atp10b, etc.),Prr16encoding Largen protein,Cry1encoding a key component of the circadian core oscillator, and so on. The results could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement and therefore feed efficiency.
Idiosyncratic fitness costs of ampicillin-resistant mutants derived from a long-term experiment with Escherichia coli
Authors: Jordan Jalin A. , Lenski Richard E. , Card Kyle J.
Published: February 2022

Antibiotic resistance is a growing concern that has prompted a renewed focus on drug discovery, stewardship, and evolutionary studies of the patterns and processes that underlie this phenomenon. A resistant strain’s competitive fitness relative to its sensitive counterparts in the absence of drug can impact its spread and persistence in both clinical and community settings. In a prior study, we examined the fitness of tetracycline-resistant clones that evolved from five different Escherichia coli genotypes, which had diverged during a long-term evolution experiment. In this study, we build on that work to examine whether ampicillin-resistant mutants are also less fit in the absence of the drug than their sensitive parents, and whether the cost of resistance is constant or variable among independently derived lines. Like the tetracycline-resistant lines, the ampicillin-resistant mutants were often less fit than their sensitive parents, with significant variation in the fitness costs among the mutants. This variation was not associated with the level of resistance conferred by the mutations, nor did it vary across the different parental backgrounds. In our earlier study, some of the variation in fitness costs associated with tetracycline resistance was explained by the effects of different mutations affecting the same cellular pathway and even the same gene. In contrast, the variance among the ampicillin-resistant mutants was associated with different sets of target genes. About half of the resistant clones suffered large fitness deficits, and their mutations impacted major outer-membrane proteins or subunits of RNA polymerases. The other mutants experienced little or no fitness costs and with, one exception, they had mutations affecting other genes and functions. Our findings underscore the importance of comparative studies on the evolution of antibiotic resistance, and they highlight the nuanced processes that shape these phenotypes.
The AAA+ ATPase RavA and its binding partner ViaA modulate E. coli aminoglycoside sensitivity through interaction with the inner membrane
Authors: Felix Jan , Bumba Ladislav , Liesche Clarissa , Fraudeau Angelique , Rébeillé Fabrice , El Khoury Jessica Y. , Huard Karine , Gallet Benoit , Moriscot Christine , Kleman Jean-Philippe , Duhoo Yoan , Jessop Matthew , Kandiah Eaazhisai , Barras Frédéric , Jouhet Juliette , Gutsche Irina
Published: February 2022

Enteric bacteria have to adapt to environmental stresses in the human gastrointestinal tract such as acid and nutrient stress, oxygen limitation and exposure to antibiotics. Membrane lipid composition has recently emerged as a key factor for stress adaptation. The E. coli ravA-viaA operon is essential for aminoglycoside bactericidal activity under anaerobiosis but its mechanism of action is unclear. Here we characterise the VWA domain-protein ViaA and its interaction with the AAA+ ATPase RavA, and find that both proteins localise at the inner cell membrane. We demonstrate that RavA and ViaA target specific phospholipids and subsequently identify their lipid-binding sites. We further show that mutations abolishing interaction with lipids restore induced changes in cell membrane morphology and lipid composition. Finally we reveal that these mutations render E. coli gentamicin-resistant under fumarate respiration conditions. Our work thus uncovers a ravA-viaA-based pathway which is mobilised in response to antibiotics under anaerobiosis and has a major impact on cell membrane regulation.
Non-essential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress
Authors: Babosan Anamaria , Fruchard Louna , Krin Evelyne , Carvalho André , Mazel Didier , Baharoglu Zeynep
Published: February 2022

Antimicrobial resistance (AMR) develops as a major problem in infectious diseases treatment. While antibiotic resistance mechanisms are usually studied using lethal antibiotic doses, lower doses allowing bacterial growth are now considered as factors influencing the development and selection of resistance. Based on high throughput transposon insertion sequencing (TN-seq) in V. cholerae, we have undertaken the phenotypic characterization of 23 transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications deletion mutants, for which growth is globally not affected in the absence of stress. We uncover a specific involvement of different RNA modification genes in the response to aminoglycosides (tobramycin (TOB), gentamicin (GEN)), fluoroquinolones (ciprofloxacin (CIP)), β-lactams (carbenicillin (CRB)), chloramphenicol (CM) and trimethoprim (TRM). Our results identify t/rRNA modification genes, not previously associated to any antibiotic resistance phenotype, as important factors affecting the bacterial response to sub-MIC antibiotics from different families. This suggests differential translation and codon decoding as critical factors involved in the bacterial response to stress.
Apremilast prevents blistering in human epidermis by stabilization of keratinocyte adhesion in pemphigus
Authors: Sigmund Anna M. , Winkler Markus , Engelmayer Sophia , Egu Desalegn T. , Kugelmann Daniela , Radeva Mariya Y. , Bayerbach Franziska C. , Kotschi Stefan , Yeruva Sunil , Schmidt Enno , Yazdi Amir S. , Ghoreschi Kamran , Vielmuth Franziska , Waschke Jens
Published: February 2022

Pemphigus vulgaris (PV) is a life-threatening blistering skin disease caused by autoantibodies (PV-IgG) destabilizing desmosomal adhesion. Current therapies focus on suppression of autoantibody formation and thus treatments directly stabilizing keratinocyte adhesion would fulfill an unmet medical need. We here demonstrate that apremilast, a phosphodiesterase 4 inhibitor used e.g. in psoriasis, prevents blistering in PV. Apremilast abrogated PV-IgG-induced loss of keratinocyte cohesion in ex-vivo epidermis and in vitro. This was paralleled by inhibition of keratin retraction and desmosome splitting but affected neither desmoglein (Dsg) depletion nor Dsg3 binding properties.

Apremilast induced phosphorylation of plakoglobin at serine 665 – a mechanisms which is known to stabilize cardiomyocyte cohesion. Interestingly, keratinocytes phospho-deficient at this side showed altered organization of Dsg1, Dsg3 and keratin filaments and impaired adhesion, which was not rescued by apremilast. These data identified a new mechanism of desmosome regulation and propose that apremilast is protective in pemphigus by stabilizing keratinocyte cohesion.
FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells
Authors: Sharma Abhishek , Meer Marco , Dapkunas Arvydas , Ihermann-Hella Anneliis , Kuure Satu , Vainio Seppo , Iber Dagmar , Naillat Florence
Published: February 2022

Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a novel function of FGF8. By combining transgenic mouse models, quantitative imaging assays, and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPCs behaviour to the UB. Chemokinetic effects have been described also for other FGFs and may be relevant more generally for the formation of mesenchymal condensations.
Compressive forces stabilise microtubules in living cells
Authors: Li Yuhui , Kučera Ondřej , Cuvelier Damien , Rutkowski David M. , Deygas Mathieu , Rai Dipti , Pavlovič Tonja , Vicente Filipe Nunes , Piel Matthieu , Giannone Gregory , Vavylonis Dimitrios , Akhmanova Anna , Blanchoin Laurent , Théry Manuel
Published: February 2022

Cell mechano-sensation and adaptation are supported by the actin network. The microtubule network is not considered to be directly sensitive to mechanical forces acting on a cell. However, recent studies on isolated microtubulesin vitrohave shown that bending forces have an impact on their structure, composition and lifespan, suggesting that, in a cellular context, microtubules may react to mechanical forces. We tested this hypothesis in living cells by subjecting them to cycles of compressive forces and found that microtubules became distorted, less dynamic and more stable. This mechano-stabilisation depends on CLASP2, which relocates from the end to the deformed shaft of microtubules. These results demonstrate that microtubules in living cells have mechano-responsive properties that allow them to resist and even counteract the forces to which they are subjected.
A pair of primers facing at the double-strand break site enables to detect NHEJ-mediated indel mutations at a 1-bp resolution
Authors: Ijaz Faryal , Nakazato Ryota , Setou Mitsutoshi , Ikegami Koji
Published: February 2022

The introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are awaited to efficiently screen the frameshift null mutant candidates. Here, we developed a simple genotyping method called DST-PCR (Double-strand break Site-Targeted PCR) using “face-to-face” primers where the 3’ ends of forward and reverse primers face each other at the position between 3-bp and 4-bp upstream of the PAM sequence, which is generally the Cas9-mediated double-strand break site. Generated amplicons are directly subjected to TBE-High-Resolution PAGE, which contains a high concentration of bis-acrylamide, for mutant clones detection with 1-bp resolution. We demonstrate six examples of CRISPR/Cas9-engineered knockout cells, to screen indels to obtain potential KO cell clones utilizing our approach. This method allowed us to detect 1-bp to 2-bp insertion and 1-bp to 4-bp deletion in one or both alleles of mutant cell clones. In addition, this technique also allowed the identification of heterozygous and homozygous biallelic functional KO candidates. Thus, DST-PCR coupled with TBE-High-Resolution PAGE is a simple method for genotyping of the CRISPR/Cas9-engineered cell lines, which can be performed without special equipment and techniques.
High-throughput cryo-EM structure determination of amyloids
Authors: Lövestam Sofia , Scheres Sjors H.W.
Published: February 2022

The formation of amyloid filaments is characteristic of various degenerative diseases. Recent breakthroughs in electron cryo-microscopy (cryo-EM) have led to atomic structure determination of multiple amyloid filaments, both of filaments assembled in vitro from recombinant proteins, and of filaments extracted from diseased tissue. These observations revealed that a single protein may adopt multiple different amyloid folds, and that in vitro assembly does not necessarily lead to the same filaments as those observed in disease. In order to develop relevant model systems for disease, and ultimately to better understand the molecular mechanisms of disease, it will be important to determine which factors determine the formation of distinct amyloid folds. High-throughput cryo-EM, in which structure determination becomes a tool rather than a project in itself, will facilitate the screening of large numbers of in vitro assembly conditions. To this end, we describe a new filament picking algorithm based on the Topaz approach, and we outline image processing strategies in Relion that enable atomic structure determination of amyloids within days.
Factors determining teleworking before and during COVID-19: some evidence from Spain and Andalusia
Authors: Caparrós Ruiz Antonio
Published: February 2022

Purpose

This study aims to analyse the inequalities in access to teleworking in Spain. More specifically, the study examines what factors determine remote working in a pre-pandemic period and during the state of alarm (March 2020). Moreover, the study examines whether telecommuting is related to the likelihood of suffering emotional disorders during lockdowns.

Design/methodology/approach

The methodological approach followed to analyse access to teleworking mainly consists of the estimation of ordered response models. Two datasets are used: the first is the Survey on Equipment and Use of Information and Communication Technologies (ICTs) in Households, conducted by the Spanish National Statistics Institute (INE) in the pre-pandemic period (2018). The second is the Social Survey 2020. Habits and Living Conditions of the Andalusian Population during the State of Alarm, conducted by the Institute of Statistics and Cartography of Andalusia (IECA) once the state of alarm was declared in Spain.

Findings

The results obtained indicate that ICT training is a key element in helping to explain the likelihood of working from home. However, some groups of workers might experience difficulties in their transition to teleworking. This could increase labour market segmentation and hinder the transition to the knowledge economy. Moreover, the findings detect that employees working both on the company premises and from home are more likely to suffer emotional disorders.

Originality/value

The paper sheds new empirical evidence on teleworking in Spain and Andalusia, including some novel methodological aspects to estimate the regressors’ effects on the probability of working from home.
The influence of cross-cultural stable and dynamic competencies on expatriate adaptation and outcomes: the case of Taiwan
Authors: Wu Wann-Yih , Bui Tuan Anh , Dao Tuan Cong
Published: February 2022

Purpose

This study investigates the influence of cross-cultural stable and dynamic competencies on expatriate adaptation and outcomes.

Design/methodology/approach

This study surveys 10 expatriates in Taiwan and conducts qualitative analysis based on the newly collected original data.

Findings

The study's results confirm that cross-cultural stable and dynamic competencies improve expatriates' cross-cultural adaptation, enhancing expatriate outcomes in cross-cultural environments.

Originality/value

This study contributes to cross-cultural management research by clarifying the characteristics and action mechanisms of cross-cultural stable competencies (including cultural empathy, emotional stability, social initiative, open-mindedness and flexibility) and cross-cultural dynamic competencies (including relational skills, general self-efficacy and non-ethnocentrism) in the international business context. The study's findings suggest future research directions in the empirical investigation of the antecedents, characteristics and results of cross-cultural competencies, cross-cultural adaptation and expatriate outcomes.
A novel hybrid particle swarm optimization rat search algorithm for parameter estimation of solar PV and fuel cell model
Authors: Singla Manish Kumar , Nijhawan Parag , Oberoi Amandeep Singh
Published: February 2022

Purpose

The purpose of the proposed hybrid method aims to increase population efficiency, and a local search is used to further improve the value of the global best solution. An experimental observation suggests that the model’s statistical outcomes are more aligned with the real-time experimental findings.

Design/methodology/approach

A novel metaheuristic efficient hybrid algorithm, i.e. hybrid particle swarm optimization rat search algorithm, is introduced and applied for parameter extraction of hybrid energy system. This proposed hybrid method rules out the chances of local minima, hence enhancing the precision of the parametric estimation. The parameter extraction and error is calculated for the solar photovoltaic (PV)–fuel cell system using the proposed algorithm.

Findings

Nonparametric statistical tests are also conducted to indicate the findings of the outcome parameters using various metaheuristic algorithms. The proposed algorithm is better than the rest of the compared algorithms in the study.

Originality/value

The authors proposed a novel algorithm, and this proposed algorithm is implemented on hybrid solar PV and fuel cell-based system for parameter extraction. The nonparametric test results clearly suggest that the proposed algorithm is far more effective for parameter estimation of the test system.
Integration of risk management within the building information modeling (BIM) framework
Authors: Moshtaghian Farzaneh , Noorzai Esmatullah
Published: February 2022

Purpose

This research has been conducted with a view to creating a framework to integrate risk management based on building information modeling (BIM) information.

Design/methodology/approach

In this research, all the information related to the construction of a residential project including 3D, 4D and 5D BIM models and the execution and control phases information was collected, and the risk list was determined for each activity accordingly.

Findings

The present study has suggested a framework for risk management in order to optimize project changes.

Originality/value

The lack of integration between 3D, 4D and 5D modeling besides execution information is a fundamental problem in many projects. The gap between these two groups of information will lead to improper management and late decisions, eventually imposing unforeseen delays and cost overruns. Risk management by the means of adopting a new approach has been addressed in recent studies using new methods, such as BIM and its associated technologies, some of which were mentioned in the review of theoretical literature in this research.
Adoptions of prefabrication in residential sector in China: agent-based policy option exploration
Authors: Du Hua , Han Qi , Sun Jun , Wang Cynthia Changxin
Published: February 2022

Purpose

This study aims to evaluate the effectiveness of different prefabricated construction (PC) policies using a case study in Wuhan, considering the local context.

Design/methodology/approach

The effectiveness of PC policies is falling behind expectations. The main reason lies in an insufficient understanding of the policy impacts. An agent-based model was built by choosing the residential sector in a typical large city of Wuhan, China, as the study case. Different cost reduction scenarios were introduced for investigating the PC policy effectiveness. The proposed model and simulation approach can be used for other cities and generalized to the whole Chinese PC industry with the potential to include more local policies and corresponding data.

Findings

Simulation results show that carbon emission reduction will be between 60,000 and 80,000 tons with policy incentives, nearly double that of the no policy intervention scenario. The target of 30% PC in all new buildings by 2026 in China is achievable with the subsidy policies of linear cost reduction, or cost reduction conforms to the learning curve.

Practical implications

Simulation results of three kinds of policy show that subsidy policy optimization is necessary regarding reducing the level of subsidy needed. The carbon credit policy is not essential since it has little influence on PC development. Implementing the project procurement restriction policy is not recommended if the scale of development of PC is more important than achieving the development target.

Originality/value

This study can help the government and developers make better policy and strategic decisions on PC development and boost the sustainability transition of the construction industry.
Rural access programs in Yemen: delay of international funded road projects
Authors: Alashwal Niyazi , Alashwal Ali
Published: February 2022

Purpose

Road projects are essential for poverty reduction and the socio-economic development of Yemeni people living in rural areas. Rural access programs, which are mainly sponsored by foreign countries and international organisations, are often delayed. The purpose of this paper is to identify the delay factors of rural road projects with a focus on stakeholder-related factors.

Design/methodology/approach

The data was collected using a questionnaire survey from 164 participants representing 7 groups, namely, owner, government, donors, consultants, designers, contractors and beneficiaries. The data was analysed using the partial least squares path modelling (PLS-SEM).

Findings

The results show that the identified factors contribute to 16% of the variance of project delay. Donor and government-related factors have a significant relationship with delay. Further analysis of data using the IPMA procedure in PLS-SEM revealed the top factors contributing to delay, which are project selection criteria imposed by donors, government bureaucracy, decision-making process, weak laws and guidelines that regulate the work of project implementation units, procurement procedures, delay of payment to contractor and delay of transactions.

Originality/value

The timely completion of rural road projects can have a positive impact on the current and future rural access programs aiming to reduce poverty and increase access to health and education services of over 70% of Yemeni people living in rural areas. Such programs will reduce the misfortune of displaced people due to the ongoing war in the country.