bluuebunny/crossref_metadata_2025 huggingface dataset:
A solid beta-sheet structure is formed at the surface of FUS liquid droplets during aging
Authors: Emmanouilidis Leonidas , Bartalucci Ettore , Kan Yelena , Ijavi Mahdiye , Pérez Maria Escura , Afanasyev Pavel , Boehringer Daniel , Zehnder Johannes , Parekh Sapun H. , Bonn Mischa , Michaels Thomas C. T. , Wiegand Thomas , Allain Frédéric H.-T.
Published: June 2023

Insights into liquid droplet formation via liquid-liquid phase separation and the subsequent liquid-to-solid phase transition are important for understanding cell dynamics, as well as a number of neurodegenerative disorders. We report here, using the example of the FUsed in Sarcoma (FUS) protein, an investigation of the liquid droplet maturation process combining solution- and solid-state NMR spectroscopy, Raman spectroscopy, and light and electron microscopies. Our study reveals that the surface of the droplets plays a critical role in this process. Indeed, when comparing a biphasic sample, in which liquid droplets are stabilized in an agarose matrix, with a pure monophasic condensed phase sample, we find that the liquid-droplet maturation kinetics is faster in the biphasic FUS sample, owing to the larger surface-to-volume ratio. In addition, using Raman spectroscopy, we observe structural differences upon liquid-droplet maturation between the inside and the surface of liquid droplets, which is of β-sheet content as revealed by solid-state NMR. This is detected very early on and increases over time. In agreement with these observations, a solid crust-like shell is visually seen by microaspiration experiments. After several months, electron microscopy reveals that the matured FUS droplets have converted into solid linear fibrils distinct from the fibril core of seeded fibrils reported previously, as arginine side-chains from the arginine-and-glycine-rich domain (RGG) motif are partially rigidified, highlighting the participation of this motif in the liquid-to-solid transition. In presence of RNA, this aging process is not taking place.
An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence inC. elegans
Authors: Fryer Emily , Guha Sujay , Rogel-Hernandez Lucero E. , Logan-Garbisch Theresa , Farah Hodan , Rezaei Ehsan , Mollhoff Iris N. , Nekimken Adam L. , Xu Angela , Seyahi Lara Selin , Fechner Sylvia , Druckmann Shaul , Clandinin Thomas R. , Rhee Seung Y. , Goodman Miriam B.
Published: June 2023

Throughout history, humans have relied on plants as a source of medication, flavoring, and food. Plants synthesize large chemical libraries and release many of these compounds into the rhizosphere and atmosphere where they affect animal and microbe behavior. To survive, nematodes must have evolved the sensory capacity to distinguish plant-made small molecules (SMs) that are harmful and must be avoided from those that are beneficial and should be sought. This ability to classify chemical cues as a function of their value is fundamental to olfaction, and represents a capacity shared by many animals, including humans. Here, we present an efficient platform based on multi-well plates, liquid handling instrumentation, inexpensive optical scanners, and bespoke software that can efficiently determine the valence (attraction or repulsion) of single SMs in the model nematode,Caenorhabditis elegans. Using this integrated hardware-wetware-software platform, we screened 90 plant SMs and identified 37 that attracted or repelled wild-type animals, but had no effect on mutants defective in chemosensory transduction. Genetic dissection indicates that for at least 10 of these SMs, response valence emerges from the integration of opposing signals, arguing that olfactory valence is often determined by integrating chemosensory signals over multiple lines of information. This study establishes thatC. elegansis an effective discovery engine for determining chemotaxis valence and for identifying natural products detected by the chemosensory nervous system.
DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma
Authors: Ma Rosanna K. , Tsai Pei-Yin , Farghli Alaa R. , Shumway Alexandria , Kanke Matt , Gordan John D. , Gujral Taranjit S. , Vakili Khashayar , Nukaya Manabu , Noetzli Leila , Ronnekleiv-Kelly Sean , Broom Wendy , Barrow Joeva , Sethupathy Praveen
Published: June 2023

Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogeneDNAJB1-PRKACA(DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based andin vivomodels of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

Highlights

Fibrolamellar carcinoma (FLC) is a lethal liver cancer lacking effective therapeutic options. Ma et al. demonstrate that primate-specific RNA LINC00473 is enriched in tumor epithelial cells and functions to promote FLC growth and dysregulate cellular energetics, unveiling an important mechanism downstream of the fusion oncogene, DNAJB1-PRKACA, in FLC pathogenesis.

In Brief

LINC00473 is consistently elevated in primary FLC tumor tissue from different patient cohorts and in multiple disease models.

DP fusion, the signature oncoprotein of FLC, drives LINC00473 expression.

LINC00473 promotes FLC growth via anti-apoptotic function.

LINC00473 modulates FLC energetics by promoting glycolysis and altering mitochondrial fitness.

Abstract Figure
A novel phenylpropanoid methyl esterase enables catabolism of aromatic compounds that inhibit biological nitrification
Authors: Wilson Andrew , Fossen Elise Van , Shrestha Ritu , Trotter Valentine , Poirier Brenton , Frank Andrew , Nelson William , Kim Young-Mo , Deutschbauer Adam , Egbert Robert , Elmore Joshua R.
Published: June 2023

Agriculture is the largest source of greenhouse gases (GHG) production. Conversion of nitrogen fertilizers into more reduced forms by microbes through a process known as biological nitrification drives GHG production, enhances proliferation of toxic algal blooms, and increases cost of crop production. Some plants reduce biological nitrification in soils by exuding a diverse array of biological nitrification inhibitors (BNIs) that inhibit the ammonium oxidizing microbes responsible for nitrification. Applying synthetic biology to enhance and transfer BNI production into food and bioenergy crops is a promising approach to reduce nitrification but the success of this strategy is contingent upon improving our limited understanding of BNIs mechanisms-of-action and degradation in the soil. We addressed this gap by investigating the previously unknown metabolic route through which a prominent class of aromatic BNIs known as phenylpropanoid methyl esters (PPMEs) are catabolized. While neither transcriptomics (RNAseq) or high-throughput functional genomics (RB-TnSeq) methods reduced the genetic search space for pathway discovery into a tenable number of genes, the combination of narrowed the search space to a collection of 4 proteins of unknown function. Using genetic and biochemical analyses we found that two previously uncharacterized enzymes, including a novel phenylpropanoid methyl esterase, funnel PPMEs into an established phenylpropanoid catabolism pathway. Transfer of these two enzymes into bacteria capable of using other phenylpropanoids use of PPMEs as carbon sources. This work both provided insight into BNI catabolism and is the first step towards development of modelin vivoplant-microbe systems for studying BNI mechanisms under well controlled conditions.
Mapping the genomic landscape of multidrug resistance inPlasmodium falciparumand its impact on parasite fitness
Authors: Mok Sachel , Yeo Tomas , Hong Davin , Shears Melanie J. , Ross Leila S. , Ward Kurt E. , Dhingra Satish K. , Kanai Mariko , Bridgford Jessica L. , Tripathi Abhai K. , Mlambo Godfree , Burkhard Anna Y. , Fairhurst Kate J. , Gil-Iturbe Eva , Park Heekuk , Rozenberg Felix D. , Kim Jonathan , Mancia Filippo , Quick Matthias , Uhlemann Anne-Catrin , Sinnis Photini , Fidock David A.
Published: June 2023

Drug-resistantPlasmodium falciparumparasites have swept across Southeast Asia and now threaten Africa. By implementing aP. falciparumgenetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mappedk13as the central mediator of ART resistance and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
Negative feedback on Retinoic Acid by Brachyury guides gastruloid symmetry-breaking
Authors: Hennessy Meagan J. , Fulton Timothy , Turner David A. , Steventon Ben
Published: June 2023

Establishment of the vertebrate body plan requires a combination of extra-embryonic signalling to establish morphogen gradients, and an underlying self-assembly mechanism that contributes to pattern regulation and robustness. Gastruloids are aggregates of mouse embryonic stem cells that break morphological symmetry and polariseBrachyury(Bra) expression in the absence of extra-embryonic signals. However, the mechanism by which symmetry breaking occurs is not yet known. During gastrulation and body axis elongation, retinoic acid (RA) andCyp26a1are polarised along the anteroposterior axis, and this is critical for balancing the decision of cells to self-renew or differentiate. We found that symmetry-breaking in gastruloids is coincident with the separation ofAldh1a2andCyp26a1expression, and that feedback fromBrais critical for maintaining polarisedCyp26a1gene expression in the gastruloid posterior region. Furthermore, we reveal a short temporal window where RA signalling can negatively influence bothBraandCyp26a1expression. These observations lead us to suggest a mechanism of how initial gastruloid patterning, subsequent elongation, and evolving network topologies can create defined boundaries of RA signalling that permits proper axial patterning and gastruloid growth.
Silk Road Revealed: Mechanism of silk fibre formation inBombyx mori
Authors: Moreno-Tortolero R.O. , Luo Y. , Parmeggiani F. , Skaer N. , Walker R. , Serpell L. , Holland C. , Davis S.A.
Published: June 2023

The transition of silk fibroin from liquid to solid is fundamental to silk-fibre production and key to the superior materials properties of native silks. Here we discover that the fibroin heavy chain from the silkworm mothBombyx morifolds into a novel β-solenoid structure, where the N-terminal domain (NTD) promotes higher-order oligomerization driven by pH reduction. These findings elucidate the complex rheological behaviour of silk and the liquid crystalline textures within the silk gland. We also find that NTD undergoes hydrolysis during standard regeneration, explaining differences between native and regenerated silk feedstocks. Overall, this study establishes a fibroin heavy chain fold, which could be relevant for other similar proteins, and explains mechanistically its liquid-to-solid transition, driven by pH reduction and stress.

One sentence summary

This study redefines the molecular structure of fibroin heavy chain and its role in the transition from solution to fibre.
Imaging membrane damage in ferroptosis and necrosis by wash-free fluorogenic chemical probes
Authors: Mauker Philipp , Beckmann Daniela , Kitowski Annabel , Heise Constanze , Wientjens Chantal , Davidson Andrew J. , Wood Will , Wilhelm Christoph , Thorn-Seshold Julia , Misgeld Thomas , Kerschensteiner Martin , Thorn-Seshold Oliver
Published: June 2023

Selectively labelling cells with damaged membranes is needed in contexts as simple as identifying dead cells in culture, or as complex as imaging membrane barrier functionalityin vivo. The commonly used dyes are permanently coloured/fluorescent dyes that are simply excluded by intact membranes, but to achieve good image contrast therefore requires removing their extracellular signal by washing or background subtraction, which are not possiblein vivo. Here, we develop fluorogenic probes which sensitively and selectively reveal damaged cells, without needing washing steps since their fluorescence turns on from near-zero background. From a set of novel fluorogenic probes impermeabilised by sulfonations along different vectors, we identify a specific disulfonated fluorogenic scaffold that enters cells only upon membrane damage, where it is enzymatically activated to mark them. The esterase probeiPS-FS2is a reliable tool to reveal live cells that have been permeabilised by biological, biochemical, or physical membrane damage; and it can be used in multicolour microscopy. We confirm the modularity of this approach by also adapting it for redox-unmasked cell-excluded probes with improved hydrolytic stability. This scaffold-based design thus provides tools for wash-freein vivoimaging of membrane damage, which is relevant across many pathologies. The insightss gained from these probes should also be translatable to damage-targeted prodrugs, for selective therapy of membrane-compromised cells.

Abstract Figure
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity
Authors: Mout Rubul , Bretherton Ross C. , Decarreau Justin , Lee Sangmin , Edman Natasha I. , Ahlrichs Maggie , Hsia Yang , Sahtoe Danny D. , Ueda George , Gregorio Nicole , Sharma Alee , Schulman Rebecca , DeForest Cole A. , Baker David
Published: June 2023

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency ofde novoprotein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment and molecular dynamics (MD) simulation, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in non-Newtonian biomaterials exhibiting fluid-like properties under rest and low shear, but shear-stiffening solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and showviafluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly, in correlation with matching formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

Significance

Protein-based hydrogels have many applications in cellular engineering and medicine. Most genetically encodable protein hydrogels are made from naturally harvested proteins or protein-polymer hybrid constructs. Here we describede novoprotein hydrogels and systematically investigate the impact of microscopic properties of the building blocks (e.g., supramolecular interaction, valencies, geometries, flexibility) on the resultant macroscopic gel mechanics, both intra-and extracellularly. Thesede novosupramolecular protein assemblies, whose properties can be tuned from solid gels to non-Newtonian fluids, provide expanded opportunities for applications in synthetic biology and medicine.
Gel-assisted mass spectrometry imaging
Authors: Chan Yat Ho , Pathmasiri Koralege C. , Pierre-Jacques Dominick , Cologna Stephanie M. , Gao Ruixuan
Published: June 2023

Compatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method’s physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.
Discovery of hypercompact epigenetic modulators for persistent CRISPR-mediated gene activation
Authors: Carosso Giovanni A. , Yeo Robin W. , Gainous T. Blair , Jawaid M. Zaki , Yang Xiao , Kim James Y.S. , Jadhav Kavita , Juan-Sing Nina , Boregowda Siddaraju V. , Cutillas Vincent , Qi Lei Stanley , l’Hortet Alexandra Collin de , Daley Timothy P. , Hart Daniel O.
Published: June 2023

Programmable epigenetic modulators provide a powerful toolkit for controlling gene expression in novel therapeutic applications, but recent discovery efforts have primarily selected for potency of effect rather than contextual robustness or durability thereof. Current CRISPR-based tools are further limited by large cargo sizes that impede clinical delivery and, in gene activation contexts, by brief activity windows that preclude transient, single-dose strategies such as lipid nanoparticle (LNP) delivery. To address these limitations, we perform high-throughput screening to discover novel classes of transcriptional modulators derived from thousands of human, viral, and archaeal proteomes. We identify high-potency activators capable of mitotically stable gene activation in a multitude of cellular contexts and leverage machine learning models to rationally engineer variants with improved activities. In liver and T-cells, novel hypercompact activators (64 to 98 amino acids) derived from vIRF2 core domain (vCD) achieve superior potency and durable activation lasting weeks beyond the current large activators (∼five-fold larger). In a humanized mouse model, we target a human hypercholesterolemia susceptibility gene and achieve activation persisting five weeks after a single dose by LNP delivery. Our discovery pipeline provides a predictive rubric for the development of contextually robust, potent, and persistent activators of compact size, broadly advancing the therapeutic potential of epigenetic gene activation.
Disordered regions and folded modules in CAF-1 promote histone deposition inS. pombe
Authors: Ouasti Fouad , Audin Maxime , Freon Karine , Quivy Jean-Pierre , Tachekort Mehdi , Cesard Elizabeth , Thureau Aurélien , Ropars Virginie , Varela Paloma F. , Moal Gwenaelle , Amadou Ibrahim Soumana , Uryga Aleksandra , Legrand Pierre , Andreani Jessica , Guerois Raphael , Almouzni Geneviève , Lambert Sarah , Ochsenbein Francoise
Published: June 2023

Genome and epigenome integrity in eukaryotes depends on the proper coupling of histone deposition with DNA synthesis. This process relies on the evolutionary conserved histone chaperone CAF-1 for which the links between structure and functions are still a puzzle. While studies of theS. cerevisiaeCAF-1 complex enabled to propose a model for the histone deposition mechanism, we still lack a framework to demonstrate its generality and in particular, how its interaction with the polymerase accessory factor PCNA is operating. Here, we reconstituted a completeSpCAF-1 from fission yeast. We characterized its dynamic structure using NMR, SAXS and molecular modeling together within vitroandin vivofunctional studies on rationally designed interaction mutants. Importantly, we identify the unfolded nature of the acidic domain which folds up when binding to histones. We also show how the long KER helix mediates DNA binding and stimulatesSpCAF-1 association with PCNA. Our study highlights how the organization of CAF-1 comprising both disordered regions and folded modules enables the dynamics of multiple interactions to promote synthesis-coupled histone deposition essential for its DNA replication, heterochromatin maintenance, and genome stability functions.
Temporal composition of the cervicovaginal microbiome associates with hrHPV infection outcomes in a longitudinal study
Authors: Molina Mariano A. , Leenders William P. J. , Huynen Martijn A. , Melchers Willem J. G. , Andralojc Karolina M.
Published: June 2023

Persistent infections with high-risk human papillomavirus (hrHPV) can cause cervical squamous intraepithelial lesions (SIL) that may progress to cancer. The cervicovaginal microbiome (CVM) correlates with SIL, but the temporal composition of the CVM after hrHPV infections has not been fully clarified. To determine the association between the CVM composition and infection outcome, we applied high-resolution microbiome profiling using the circular probes-based RNA sequencing technology on a longitudinal cohort of cervical smears obtained from 141 hrHPV DNA-positive women with normal cytology at first visit, of whom 51 were diagnosed by cytology with SIL six months later. Here we show that women with a microbial community characterized by low diversity and highLactobacillus crispatusabundance exhibit low risk to SIL development at both visits, while women with a microbial community characterized by high diversity andLactobacillusdepletion at first visit have a higher risk of developing SIL. At the level of individual species we observed that an increased abundance forGardnerella vaginalisandAtopobium vaginaeassociate with SIL outcomes at both visits. These species together withDialister micraerophilusshowed a moderate discriminatory power for hrHPV infection progression. Our results suggest that the CVM can potentially be used as a biomarker for cervical disease and SIL development after hrHPV infection diagnosis with implications on cervical cancer prevention strategies and treatment of SIL.
Beyond antibiotic resistance: thewhiB7transcription factor coordinates an adaptive response to alanine starvation in mycobacteria
Authors: Poulton Nicholas C. , DeJesus Michael A. , Munsamy-Govender Vanisha , Roberts Cameron G. , Azadian Zachary A. , Bosch Barbara , Lin Karl Matthew , Li Shuqi , Rock Jeremy M.
Published: June 2023

Pathogenic mycobacteria are a significant cause of morbidity and mortality worldwide. These bacteria are highly intrinsically drug resistant, making infections challenging to treat. The conservedwhiB7stress response is a key contributor to mycobacterial intrinsic drug resistance. Although we have a comprehensive structural and biochemical understanding of WhiB7, the complex set of signals that activatewhiB7expression remain less clear. It is believed thatwhiB7expression is triggered by translational stalling in an upstream open reading frame (uORF) within thewhiB75’ leader, leading to antitermination and transcription into the downstreamwhiB7ORF. To define the signals that activatewhiB7, we employed a genome-wide CRISPRi epistasis screen and identified a diverse set of 150 mycobacterial genes whose inhibition results in constitutivewhiB7activation. Many of these genes encode amino acid biosynthetic enzymes, tRNAs, and tRNA synthetases, consistent with the proposed mechanism forwhiB7activation by translational stalling in the uORF. We show that the ability of thewhiB75’ regulatory region to sense amino acid starvation is determined by the coding sequence of the uORF. The uORF shows considerable sequence variation among different mycobacterial species, but it is universally and specifically enriched for alanine. Providing a potential rationalization for this enrichment, we find that while deprivation of many amino acids can activatewhiB7expression,whiB7specifically coordinates an adaptive response to alanine starvation by engaging in a feedback loop with the alanine biosynthetic enzyme,aspC. Our results provide a holistic understanding of the biological pathways that influencewhiB7activation and reveal an extended role for thewhiB7pathway in mycobacterial physiology, beyond its canonical function in antibiotic resistance. These results have important implications for the design of combination drug treatments to avoidwhiB7activation, as well as help explain the conservation of this stress response across a wide range of pathogenic and environmental mycobacteria.
RewiringSaccharomyces cerevisiaemetabolism for optimised Taxol® precursors production
Authors: Nowrouzi Behnaz , Torres-Montero Pablo , Kerkhoven Eduard J. , Martínez José L. , Rios-Solis Leonardo
Published: June 2023

Saccharomyces cerevisiaehas been recognised as a convenient host for the production of early precursors to the Taxol® anticancer drug. Recent studies have highlighted the harmful impact of oxidative stress as a result of the activity of Taxol® first cytochrome P450-reductase enzymes (Taxusspp. CYP725A4-POR). Here, we evolved a new oxidative stress-tolerant yeast strain on galactose, which led to a three-fold higher titre of the CYP725A4 enzyme substrate, taxadiene. We comprehensively analysed the performance of the evolved and parent strain in galactose-limited chemostat cultures before and during oxidative stress induction. Integrating the transcriptomics and metabolite profiling data in an enzyme-constrained genome scale model enabled a more accurate prediction of changes that occurred to biological pathways as a response to/consequence of evolution and oxidative stress. The analyses showed a better performance of the evolved strain with improved respiration and reduced overflow metabolites production. The strain was robust to re-introduction of the oxidative stress, potentially due to the cross-protection mechanism, which contributed to likely better heme, flavin and NADPH availability for an optimal expression ofCYP725A4andPORin yeast. The increased level of taxadiene production has potentially occurred due to the antioxidant properties of taxadiene or as a mechanism to overcome the toxicity of geranylgeranyl diphosphate, the precursor to taxadiene synthase.

Highlights

The antioxidant properties of taxadiene promotes its production inSaccharomyces cerevisiae

S. cerevisiaeALE on H2O2and galactose regulates Flavin, iron and NADPH metabolism as well as carbon and protein recycling pathways through cross-protection and anticipation mechanisms

Abstract Figure

Figure 1.

Graphical abstract of the study.

Figure was created with BioRender.com.
Genetic determinants of virulence and extensive drug resistance inPseudomonas aeruginosaPPA14 isolated from eggplant rhizosphere
Authors: Ambreetha Sakthivel , Parshatd Govindasamy , Castellanos Christian , Narasimhan Giri , Balachandar Dananjeyan , Cickovski Trevor , Mathee Kalai
Published: June 2023

Pseudomonas aeruginosais one of the Priority Level I critical pathogens that are least sensitive to antibiotics and can cause fatal hospital-acquired infections. This bacterium is predominantly present in the agricultural ecosystem. However, there are very limited studies on health threats associated withP. aeruginosastrains flourishing in edible plants. Previously, we isolated and characterized 18P. aeruginosastrains from vegetable plants directly harvested from the farms. In the current work, it has been hypothesized that plant-associatedP. aeruginosaharbors genetic determinants for virulence and resistance. To test this hypothesis,in vitroresistome profiles of the plant-associatedP. aeruginosastrains were assessed based on the Kirby-Bauer disk diffusion method. Hierarchical clustering analysis was done to identify the plant-associated strains that are phenotypically similar to clinical isolates. An eggplant-associated strain, PPA14, that exhibited high virulence and extensivein vitroresistance against eight antibiotic classes was selected for complete genome analyses. The PPA14 genome was sequenced using the Solexa-Illumina and Oxford-Nanopore platforms, assembled, and annotated. The presence of virulence-related and antibiotic resistance (ABR) genes were predicted using the ABRicate tool and validated based on standard reference databases such as VFDB, NCBI AMRFinderPlus, MEGARes, CARD, and ResFinder. IslandViewer4 tool was used to predict the genes acquired through horizontal gene transfer. Additionally, comparative analyses of all the plant-associated and environmentalP. aeruginosagenomes characterized so far were done using the Roary tool. The PPA14 genome size was 6.72 Mbp, encoding 6315 open reading frames. The genome harbored 49 ABR genes, including those coding for multiple families of efflux pumps that collectively confer resistance against 11 antibiotic classes. In addition, we detected 225 virulence-related genes, 83 genomic islands, and 235 unique genes in the PPA14 genome. Over 4% of the PPA14 genome is devoted to conferring virulence and extensive drug resistance. Our report highlights the health threat associated with an eggplant-associatedP. aeruginosa.
CISD3 is required for Complex I function, mitochondrial integrity, and skeletal muscle maintenance
Authors: Marjault Henri-Baptiste , Karmi Ola , Rowland Linda , Nguyen Thi Thao , Grant DeAna , Manrique-Acevedo Camila , Nechushtai Rachel , Mittler Ron
Published: June 2023

Mitochondria play a central role in muscle metabolism and function. In skeletal muscles, a unique family of iron-sulfur proteins, termed CISD proteins, support mitochondrial function. The abundance of these proteins declines with aging leading to muscle degeneration. Although the function of the outer mitochondrial proteins CISD1 and CISD2 has been defined, the role of the inner mitochondrial protein CISD3, is currently unknown. Here we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne Muscular Dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscle mitochondria, and that CISD3 interacts with, and donates its clusters to, Complex I respiratory chain subunit NDUFV2. These findings reveal that CISD3 is important for supporting the biogenesis and function of Complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact muscle degeneration syndromes, aging, and related conditions.
Sialylation of EGFR by ST6GAL1 induces receptor activation and modulates trafficking dynamics
Authors: Ankenbauer Katherine E. , Rao Tejeshwar C. , Mattheyses Alexa L. , Bellis Susan L.
Published: June 2023

Aberrant glycosylation is a hallmark of a cancer cell. One prevalent alteration is an enrichment in α2,6-linked sialylation of N-glycosylated proteins, a modification directed by the ST6GAL1 sialyltransferase. ST6GAL1 is upregulated in many malignancies including ovarian cancer. Prior studies have shown that the addition of α2,6 sialic acid to the Epidermal Growth Factor Receptor (EGFR) activates this receptor, although the mechanism was largely unknown. To investigate the role of ST6GAL1 in EGFR activation, ST6GAL1 was overexpressed in the OV4 ovarian cancer line, which lacks endogenous ST6GAL1, or knocked down in the OVCAR-3 and OVCAR-5 ovarian cancer lines, which have robust ST6GAL1 expression. Cells with high expression of ST6GAL1 displayed increased activation of EGFR and its downstream signaling targets, AKT and NFκB. Using biochemical and microscopy approaches, including Total Internal Reflection Fluorescence (TIRF) microscopy, we determined that the α2,6 sialylation of EGFR promoted its dimerization and higher order oligomerization. Additionally, ST6GAL1 activity was found to modulate EGFR trafficking dynamics following EGF-induced receptor activation. Specifically, EGFR sialylation enhanced receptor recycling to the cell surface following activation while simultaneously inhibiting lysosomal degradation. 3D widefield deconvolution microscopy confirmed that in cells with high ST6GAL1 expression, EGFR exhibited greater co-localization with Rab11 recycling endosomes and reduced co-localization with LAMP1-positive lysosomes. Collectively, our findings highlight a novel mechanism by which α2,6 sialylation promotes EGFR signaling by facilitating receptor oligomerization and recycling.
Rewiring capsule production by CRISPRi-based genetic oscillators demonstrates a functional role of phenotypic variation in pneumococcal-host interactions
Authors: Rueff Anne-Stéphanie , Raaphorst Renske van , Aggarwal Surya , Santos-Moreno Javier , Laloux Géraldine , Schaerli Yolanda , Weiser Jeffrey N. , Veening Jan-Willem
Published: June 2023

Phenotypic variation is the phenomenon in which clonal cells display different traits even under identical environmental conditions. This plasticity is thought to be important for processes including bacterial virulence1–8, but direct evidence for its relevance is often lacking. For instance, variation in capsule production in the human pathogenStreptococcus pneumoniaehas been linked to different clinical outcomes9–14, but the exact relationship between variation and pathogenesis is not well understood due to complex natural regulation15–20. In this study, we used synthetic oscillatory gene regulatory networks (GRNs) based on CRISPR interference together with live cell microscopy and cell tracking within microfluidics devices to mimic and test the biological function of bacterial phenotypic variation. We provide a universally applicable approach for engineering intricate GRNs using only two components: dCas9 and extended sgRNAs (ext-sgRNAs). Our findings demonstrate that variation in capsule production is beneficial for pneumococcal fitness in traits associated with pathogenesis providing conclusive evidence for this longstanding question.
Actin and microtubules position stress granules
Authors: Böddeker Thomas J. , Rusch Anja , Leeners Keno , Murrell Michael P. , Dufresne Eric R.
Published: June 2023

Membraneless organelles, composed of protein and nucleic acids, alter the biochemical and physical landscape of the cell. While specific membraneless organelles are found in stereotypical locations, little is known about the physical mechanisms that guide their positioning. Here, we investigate how stress granules, a type of cytoplasmic membraneless organelle, establish their stereotypical perinuclear positioning. We find that actin and microtubules play complementary roles. Lamellar actin confines stress granules, and its retrograde flow drives them toward the cell center. Microtubules, in turn, adhere to stress granules through capillary interactions, which tend to concentrate stress granules in micro-tubule rich regions near the nucleus. Similar physical mechanisms are likely to play a role in the positioning of other membraneless organelles.
Filament structure and subcellular organization of the bacterial intermediate filament-like protein crescentin
Authors: Liu Yue , van den Ent Fusinita , Löwe Jan
Published: June 2023

The coiled coil protein crescentin is required for the crescent shape of the freshwater bacteriumCaulobacter crescentus(vibrioides). Crescentin forms a filamentous structure on the inner, concave side of the curved cells. It shares features with eukaryotic intermediate filament (IF) proteins, such as its ability to form filamentsin vitro, the protein’s length, sequence comparisons and the presence of a coiled coil discontinuity called the “stutter”. Here, we have used electron cryomicroscopy (cryo-EM) to determine the structure of the full-length protein and its filament, exploiting a crescentin-specific nanobody. The filament is formed by two strands, related by two-fold symmetry that each consist of two dimers, resulting in an octameric assembly. Crescentin subunits form longitudinal contacts head-to-head and tail-to-tail, making the entire filament non-polar. Usingin vivosite-directed cysteine crosslinking we demonstrated that contacts observed in thein vitrofilament structure exist in cells. Electron cryotomography (cryo-ET) of cells expressing crescentin showed filaments on the concave side of the curved cells, close to the inner membrane, where they form a band. Comparison of our crescentin filament structure with current models of IF proteins and their filaments revealed similar coiled coil dimer formation as well as an absence of overall polarity. IF proteins form head-to-tail longitudinal contacts in contrast to crescentin and hence several inter-dimer contacts in IFs have no equivalents in crescentin filaments. Our work supports the idea that intermediate filament-like proteins achieve their shared polymerization and mechanical properties through a variety of filament architectures.

SIGNIFICANCE STATEMENT

Crescentin is a coiled coil protein that is required for the crescent cell shape of bacteria such asCaulobacter crescentus. Crescentin shares biochemical and cytoskeletal properties with intermediate filament (IF) proteins, which form the third major class of cytoskeletal proteins in eukaryotes. To better understand the relationship between crescentin and IF proteins, and the filaments they form, we have determined the three-dimensional structure of crescentin filaments by cryo-EM. This revealed the full-length structure of the parallel coiled coil dimer of crescentin and how dimers come together laterally and longitudinally, to form a non-polar, octameric filament. Differences in filament architecture highlight the versatility of intermediate filament-like proteins across the tree of life.
The cost of foreign ownership: Voluntary sustainability reporting and financial performance in an emerging economy
Authors: Liou Ru-Shiun , Ting Pi-Hui , Chen Ying-Yu
Published: June 2023

Purpose

Many emerging economy firms are under foreign owners' pressure to embrace the challenges of addressing corporate social responsibility (CSR) and consider adopting sustainability initiatives. However, it is not clear how foreign ownership plays a role to enable or inhibit these emerging economy firms from translating sustainability initiatives into improved financial performance. Utilizing neo-institutional theory, the authors argue that emerging economy firms that voluntarily report sustainability gain legitimacy in the eyes of shareholders and improve stock market performance. However, emerging economy firms may not have the resources to reconcile the internal stakeholders' various legitimacy requirements to promote sustainability practices, resulting in a negative association with accounting performance. Foreign ownership attenuates the relationship between sustainability reporting and firm performance due to the different legitimacy requirements in foreign markets.

Design/methodology/approach

To test the study’s hypotheses, the authors collected and analyzed a large sample of publicly listed firms between 2010 and 2016 in Taiwan where the types of foreign ownership include foreign trust funds, foreign financial institutions and other foreign legal entities. Regression analyses were conducted to investigate whether the firms that report their sustainable practices have better financial performance, including stock market performance and accounting performance. Additionally, a three-step procedure was employed to address the endogeneity issue with a binary explanatory variable.

Findings

The positive stock market reaction to the emerging economy firms' voluntary sustainability reporting supports legitimacy gained among investors. By contrast, sustainability reporting has a negative association with accounting performance due to the difficulty of reconciling different legitimacy requirements among various stakeholders in emerging economies. Further, foreign ownership, particularly the trust fund, exhibits a negative moderating effect on the relationship between sustainability reporting in aligning corporate practices with sustainable development goals (SDGs) and the company's stock market performance.

Originality/value

By examining the less tested contingent role played by foreign ownership in the emerging economy firms' sustainability reporting, the authors provide insights into the influence exerted by different types of foreign ownership on firms' financial performances beyond previous studies that focus on family ownership, state ownership, or managerial ownership in emerging economies. The findings shed light on corporate sustainability strategy and foreign direct investment policies for an emerging economy.
Phlebitis in Takayasu arteritis: A case‐based literature review
Authors: Dang Xin , Zhu Qingqing , Zou Yuzhen , Han Yongmei
Published: June 2023

Takayasu arteritis (TAK) is the main type of large vessel arteritis in young adults, which mainly affects the aorta and its main branches, leading to clinical manifestations such as syncope, intermittent limb claudication, hypertension, and abdominal pain. Among them, venous involvement is rarely reported. Here we show a case of TAK presenting as phlebitis. This was a 27‐year‐old woman, who initially admitted to our hospital with myalgia of the upper and lower extremities and night sweats. She was diagnosed as TAK according to the 1990 American College of Rheumatology TAK criteria. Surprisingly, vascular ultrasonography revealed wall thickening as indicated by macaroni sign of the multiple veins. TAK phlebitis appeared at the active phase, while disappearing rapidly at remission. Phlebitis might have a close relationship with disease activity. By retrospective study in our department, the estimated incidence rate of phlebitis might be 9.1% in TAK. With the literature review, it revealed that phlebitis might be an ignored manifestation in active TAK. However, due to the smaller sample size, it should be noted that a direct cause‐effect relationship cannot be established.
Prenatal detection of major congenital malformations in a cohort of 19 367 Danish fetuses with a complete follow‐up six months after birth
Authors: Hjort‐Pedersen Karina , Olesen Annette Wind , Garne Ester , Sperling Lene
Published: June 2023

Introduction

To investigate the performance of the second‐trimester ultrasound scan regarding ultrasound‐detectable congenital malformations in a Danish region. The study sample was population‐based, with 6 months of postnatal follow‐up. Hospital records and autopsy reports were reviewed in each case to validate the prenatal ultrasound diagnosis.

Material and methods

This population‐based cohort study included all fetuses (n = 19.367) alive at the second‐trimester scan in four hospitals in a Danish region. The final diagnosis of the malformations was based on hospital records during the 6‐month postnatal follow‐up. In case of termination or stillbirth, the result from the autopsy report was used to validate the prenatal ultrasound diagnosis.

Results

The detection rate of congenital malformations in the prenatal screening program was 69%, where 18% was detected on the first‐trimester scan and 51% on the second‐trimester scan. Another 8% was detected in the third trimester. Specificity was 99.9%. The positive predictive value of the screening program was 94.5%, and the negative predictive value was 99.5%. The overall prevalence of malformations was 16.8 per 1000 fetuses, most frequently in the heart and the urinary tract.

Conclusions

This study shows that the national screening program for congenital malformations can detect many severe malformations and is an effective screening test for malformations.
Left atrial strain predicts improvement in left atrial functions of severe rheumatic mitral stenoses undergoing successful percutaneous transmitral commissurotomy
Authors: Sharma Prabhat , Garg Salil , Malani Susheel Kumar
Published: June 2023

Aims

Chronic rheumatic heart disease (RHD) is prevalent in India. The mitral valve in isolation or combination with the aortic or tricuspid valve is involved in 31.6% and 52.8% of chronic RHD patients, respectively. The left atrium (LA) functions as a reservoir during the cardiac cycle. Therefore, the LA enlargement leads to longitudinal lengthening, measured as a positive strain, permitting the measurement of the longitudinal strain of LA. This study aimed to assess the LA functions using peak atrial longitudinal strain (PALS) in patients with severe rheumatic mitral stenoses (MS) in sinus rhythm who underwent successful percutaneous transvenous mitral commissurotomy (PTMC).

Material and Methods

We recruited 56 patients with severe rheumatic MS for the study, of which 06 PTMC procedures were considered unsuccessful. So, 50 patients of chronic severe rheumatic MS in sinus rhythm undergoing PTMC were enrolled in a tertiary care centre of the Armed Forces from August 2017 to May 2019. Patients included in the study were not consecutive, and patients with atrial fibrillation (AF) were excluded.

Results

PALS improved post‑PTMC (P < .001) in this study, effectively concluding that PALS is impaired in patients with severe symptomatic MS and is acutely enhanced after treatment.

Conclusions

PALS is a good indicator of LA function and may predict the success of PTMC on the rheumatic mitral valve.
Acceptance of preventive home visits by nurses – The user perspective
Authors: Blotenberg Britta , Seeling Stefanie , Büscher Andreas
Published: June 2023

Objective

The aim of this study was to investigate acceptance of preventive home visits (PHVs) for older adults in rural Germany.

Design

Qualitative descriptive approach.

Sample

We investigated the personal, individual perspective of adults aged 65 to 85, who were not yet eligible for benefits from the long‐term care insurance, were able to understand and speak German, and who lived in the municipality under study.

Measurements

Fifteen semi‐structured interviews were conducted between 02/2019 and 08/2020. They were transcribed, coded using MAXQDA, and content analyzed. Ethical approval was obtained.

Results

The acceptance of PHVs was extremely high and characterized by five main effects: very close relationship with the nurse, well‐being, empowerment, satisfaction, ambivalence. Participants wish to receive PHVs in the future and would recommend it to others. Even those with a healthy or health‐promoting lifestyle are thankful to be able to refer to the counselling sessions if life circumstances should deteriorate. Those who became care‐dependent wish to continue and perceive it as a valuable addition to their care.

Conclusion

From the participants’ point of view, this low‐threshold counselling‐and‐support approach should be maintained in the future. PHVs can support health and independence in older adults and therefore prevent them from becoming care‐dependent.