bluuebunny/crossref_metadata_2025_split huggingface dataset:
ACSL4 activity drives TNBC metastasis by positively regulating Histone H3 Acetylation mediated SNAIL expression
Authors: Sinha Abhipsa , Saini Krishan Kumar , Tripathi Kiran , Khan Muqtada Ali , Satrusal Saumya Ranjan , Verma Ayushi , Mandal Biswajit , Rai Priyanka , Meena Sanjeev , Nengroo Mushtaq Ahmad , Singh Manish Pratap , Bhushan Namratha Shashi , Vasudevan Madavan , Singhai Atin , Singh Kulranjan , Mishra Anand Kumar , Datta Dipak 
Published: October 2023

AbstractTriple-Negative Breast Cancer (TNBC) has profound unmet medical need globally for its devastating clinical outcome associated with rapid metastasis and lack of targeted therapies. Recently, lipid metabolic reprogramming has emerged as a major driver of breast cancer metastasis. Here, we unveil a strong association between the heightened expression of fatty acid metabolic enzyme, acyl-CoA synthetase 4 (ACSL4) and TNBC, which is primarily attributed by the selective absence of progesterone receptor (PR). Loss of ACSL4 function, either through genetic ablation or pharmacological inhibition significantly reduces metastatic potential of TNBC. Global transcriptome analysis reveals that ACSL4 activity markedly influences the gene expression pattern associated with TNBC migration. Mechanistically, ACSL4 alters fatty acid oxidation (FAO) and cellular acetyl-CoA levels, leading to the hyper-acetylation of particularly H3K27Ac and H3K9Ac marks resulting in overexpression of SNAIL during the course of TNBC metastatic spread to lymph node and lungs. Further, human TNBC metastasis exhibits positive correlation between ACSL4 and SNAIL expression. Altogether, our findings provide new molecular insights regarding the intricate interplay between metabolic alterations and epigenetic modifications, intertwined to orchestrate TNBC metastasis and posit a rational understanding for the development of ACSL4 inhibitors as a targeted therapy against TNBC.
Polinton-like Viruses Associated with Entomopoxviruses Provide Insight into Replicon Evolution
Authors: Barth Zachary K. , Hicklin Ian , Thézé Julien , Takatsuka Jun , Nakai Madoka , Herniou Elisabeth A. , Brown Anne M. , Aylward Frank O. 
Published: October 2023

AbstractPolinton-like viruses (PLVs) are a diverse group of small integrative dsDNA viruses that infect diverse eukaryotic hosts. Many PLVs are hypothesized to parasitize viruses in the phylumNucleocytoviricotafor their own propagation and spread. Here we analyze the genomes of novel PLVs associated with the occlusion bodies of entomopoxvirus (EV) infections of two separate lepidopteran hosts. The presence of these elements within EV occlusion bodies suggests that they are the first known hyperparasites of poxviruses. We find that these PLVs belong to two distinct lineages that are highly diverged from known PLVs. These PLVs possess mosaic genomes, and some essential genes share homology with mobile genes within EVs. Based on this homology and observed PLV mosaicism, we propose a mechanism to explain the turnover of PLV replication and integration genes.
T cells Use Focal Adhesions to Pull Themselves Through Confined Environments
Authors: Caillier Alexia , Oleksyn David , Fowell Deborah J. , Miller Jim , Oakes Patrick W. 
Published: October 2023

Immune cells are highly dynamic and able to migrate through environments with diverse biochemical and mechanical composition. Their migration has classically been defined as amoeboid under the assumption that it is integrin-independent. Here we show that activated primary Th1 T cells require both confinement and extracellular matrix protein to migrate efficiently. This migration is mediated through small and dynamic focal adhesions that are composed of the same proteins associated with canonical mesenchymal focal adhesions, such as integrins, talin, and vinculin. These focal adhesions, furthermore, localize to sites of contractile traction stresses, enabling T cells to pull themselves through confined spaces. Finally, we show that Th1 T cell preferentially follows tracks of other T cells, suggesting that these adhesions are modifying the extracellular matrix to provide additional environmental guidance cues. These results demonstrate not only that the boundaries between amoeboid and mesenchymal migration modes are ambiguous, but that integrin-mediated adhesions play a key role in T cell motility.Graphical Abstract
Electrophysiological characterisation of iPSC-derived human β-like cells and anSLC30A8disease model
Authors: Jaffredo Manon , Krentz Nicole A. J. , Champon Benoite , Duff Claire E. , Nawaz Sameena , Beer Nicola , Honore Christian , Clark Anne , Rorsman Patrik , Lang Jochen , Gloyn Anna L. , Raoux Matthieu , Hastoy Benoit 
Published: October 2023

AbstractiPSC-derived human β-like cells (BLC) hold promise for both therapy and disease modelling, but their generation remains challenging and their functional analyses beyond transcriptomic and morphological assessments remain limited. Here, we validate an approach using multicellular and single cell electrophysiological tools to evaluate BLCs functions. The Multi-Electrode Arrays (MEAs) measuring the extracellular electrical activity revealed that BLCs are electrically coupled, produce slow potential (SP) signals like primary β-cells that are closely linked to insulin secretion. We also used high-resolution single-cell patch-clamp measurements to capture the exocytotic properties, and characterize voltage-gated sodium and calcium currents. These were comparable to those in primary β and EndoC-βH1 cells. The KATPchannel conductance is greater than in human primary β cells which may account for the limited glucose responsiveness observed with MEA. We used MEAs to study the impact of the type 2 diabetes protectiveSLC30A8allele (p.Lys34Serfs*50) and found that BLCs with this allele have stronger electrical coupling. Our data suggest that with an adapted approach BLCs from pioneer protocol can be used to evaluate the functional impact of genetic variants on β-cell function and coupling.Article highlightsWhy did we undertake this study?iPSC-derived beta like cells (BLCs) from pioneering protocols are known for variable β-cell functionality and mixed cell populations which greatly limits downstream functional assessment. To overcome this challenge, we used electrophysiological tools to provide a detailed functional assessment of BLCs. We then wanted to apply this approach to identify additional functional differences from BLCs carrying a protective Type 2 DiabetesSLC30A8allele.What is the specific question(s) we wanted to answer?Can an electrophysiological approach provide detailed functional characterisation of iPSC-derived BLCs? Is this approach sensitive enough to capture functional differences resulting fromSLC30A8loss of function (lof)?What did we find?We found that BLCs generated from pioneer protocol shared electrophysiological features with human pancreatic β-cells, and that a T2D-protectiveSLC30A8lof allele improves the electrical coupling activity of human β-cells.What are the implications of our findings?Our findings validate the use of intra- and extra-cellular electrophysiology to assess and monitor the functions of BLCs. Our approach opens the perspective of using MEAs to live-monitor the differentiation quality of iPSC-derived BLCs and to determine the functional consequences of diabetes-associated variants.
VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes
Authors: Copeland Conner J. , Roddy Jack W. , Schmidt Amelia K. , Secor Patrick R. , Wheeler Travis J. 
Published: October 2023

ABSTRACTBacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster, and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’ primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072Pseudomonasspp. genomes. VIBES software is available athttps://github.com/TravisWheelerLab/VIBES.
Universal conditions for establish continuous cell cultures in ray-finned fishes
Authors: Cardoso Adauto Lima , Nascimento Oliveira Jordana Inácio , Climaco João Pedro Silva , Venturelli Natália Bortholazzi , Moreira Camila do Nascimento , Martins Cesar 
Published: October 2023

AbstractRay-finned fishes represent the most diverse vertebrate lineage and show extensive variations in physiology, ways of life and adaptations to marine and freshwater environments. Actinopterygii are largely exploited for human consumption and several species have been established as biological models. The in vitro culture of cells is fundamental for several fields of biological research, being an alternative for studies that use animals, since it mimics the cellular homogeneity of the original organisms beyond the advantage of reducing the variability of responses observed under in vivo conditions. In the case of fish cell cultures, besides being an important biomedical tool, they can offer important contributions to aquaculture and fish conservation. Hundreds of fish cell lines have been established using specific methods for each cell type and species. Here we describe an optimized protocol for obtaining cell cultures from the caudal fin of a wide range of ray-finned fishes including marine and freshwater species. The proliferative potential of these cultures makes them useful for several applications and the minimally invasive feature of this protocol makes it suitable for use in conservation plans.
Disulfiram reduces atherosclerosis and enhances efferocytosis, autophagy, and atheroprotective gut microbiota in hyperlipidemic mice
Authors: Traughber C. Alicia , Timinski Kara , Prince Ashutosh , Bhandari Nilam , Neupane Kalash , Khan Mariam R , Opoku Esther , Opoku Emmanuel , Brubaker Gregory , Nageshwar Kanuri , Ertugral Elif G. , Naggareddy Prabha , Kothapalli Chandrasekhar R. , Smith Jonathan D. , Gulshan Kailash 
Published: October 2023

AbstractPyroptosis executor Gasdermin (GsdmD) promotes atherosclerosis in mice and humans. Disulfiram (DSF) was recently shown to potently inhibit GsdmD, but the in-vivo efficacy and mechanism of DSF’s anti-atherosclerotic activity is yet to be explored. We used human/mouse macrophages and a hyperlipidemic mouse model of atherosclerosis to determine DSF anti-atherosclerotic efficacy and mechanism. DSF-fed hyperlipidemic apoE-/-mice showed significantly reduced IL-1β release upon in-vivo Nlrp3 inflammasome assembly and showed smaller atherosclerotic lesions (∼27% and 29% reduction in males and females, respectively). The necrotic core area was also smaller (∼50% and 46% reduction in DSF-fed males and females, respectively). DSF induced autophagy in macrophages, hepatocytes/liver, and in atherosclerotic plaques. DSF modulated other atheroprotective pathways such as efferocytosis, phagocytosis, and gut microbiota. DSF-treated macrophages showed enhanced phagocytosis/efferocytosis, with a mechanism being a marked increase in cell-surface expression of efferocytic receptor MerTK. Atomic-force microscopy analysis revealed altered biophysical membrane properties of DSF treated macrophages, showing increased ordered-state of the plasma membrane and increased adhesion strength. Furthermore, the 16sRNA sequencing of DSF-fed hyperlipidemic mice showed highly significant enrichment in atheroprotective gut microbiotaAkkermansiaand a reduction in atherogenicRomboutsiaspecies. Taken together, our data shows that DSF can simultaneously modulate multiple atheroprotective pathways, and thus may serve as novel adjuvant therapeutic to treat atherosclerosis.
The landscape of genomic structural variation in Indigenous Australians
Authors: Reis Andre L.M. , Rapadas Melissa , Hammond Jillian M. , Gamaarachchi Hasindu , Stevanovski Igor , Kumaheri Meutia Ayuputeri , Chintalaphani Sanjog R. , Dissanayake Duminda S.B. , Siggs Owen M. , Hewitt Alex W. , Llamas Bastien , Brown Alex , Baynam Gareth , Mann Graham J. , Hermes Azure ,   The National Centre for Indigenous Genomics, Patel Hardip R. , Deveson Ira W. 
Published: October 2023

ABSTRACTIndigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference databases. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp;n=136,797) and structural variants (SVs; ≥50bp;n=159,912), the majority of which are composed of tandem repeat or interspersed mobile element sequences (90%) and have not been previously annotated (73%). A large fraction of SVs appear to be exclusive to Indigenous Australians (>30%) and the majority of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions, diversity and evolutionary trajectories of genomic structural variation within and beyond Australia.
TheAspergillus fumigatus maiAgene contributes to cell wall homeostasis and fungal virulence
Authors: Guruceaga X , Perez-Cuesta U , Martin-Vicente A , Pelegri-Martinez E , Thorn H , Cendon-Sanchez S , Xie J , Nywening A , Ramirez-Garcia A , Fortwendel JR , Rementeria A 
Published: October 2023

AbstractIn this study, two distinctin vitroinfection models ofAspergillus fumigatus, using murine macrophages (RAW264.7) and human lung epithelial cells (A549), were employed to identify the genes important for fungal adaptation during infection. Transcriptomic analyses of co-incubatedAspergillusuncovered 140 fungal genes up-regulated in common between both models that, when compared with a previously publishedin vivotranscriptomic study, allowed the identification of 13 genes consistently up-regulated in all three infection conditions. Among them, themaiAgene, responsible for a critical step in the L-phenylalanine degradation pathway, was identified. Disruption ofmaiAresulted in a mutant strain unable to complete the Phe degradation pathway, leading to an excessive production of pyomelanin when this amino acid served as the sole carbon source. Moreover, the disruption mutant exhibited noticeable cell wall abnormalities, with reduced levels of β-glucans within the cell wall. themaiA-1mutant strain induced reduced inflammation in primary macrophages and displayed significantly lower virulence in a neutropenic mouse model of infection. This is the first study linking theA. fumigatus maiAgene to fungal cell wall homeostasis and virulence.
Recombinant biosensors for multiplex and super-resolution imaging of phosphoinositides
Authors: Maib Hannes , Adarska Petia , Hunton Robert , Vines James , Strutt David , Bottanelli Francesca , Murray David H. 
Published: October 2023

AbstractPhosphoinositides are a small family of phospholipids, acting as signalling hubs and key regulators of cellular function. Detecting their subcellular distribution is crucial to gain insights into membrane organisation and is most commonly done by over-expression of biosensors. However, this leads to perturbations of phosphoinositide signalling and is challenging in systems that cannot be transfected. Here, we present a toolkit for the reliable, fast, multiplex, and super-resolution detection of all 8 phosphoinositides using a unifying staining approach for fixed cells and tissue, based on recombinant biosensors with self-labelling SNAP tags. These recombinant biosensors are highly specific, and reliably visualise the subcellular distributions of phosphoinositides across scales, ranging from 2D or 3D cell culture toDrosophilatissue. Using stimulated emission depletion (STED) microscopy, we reveal the nanoscale organisation of PI(3)P on endosomes and PI(4)P on the Golgi and confirm the preservation of subcellular membranes. Multiplex staining enables the investigation of phosphoinositide conversions and reveals an unexpected presence of residual PI(3,5)P2positive membranes in swollen lysosomes following PIKfyve inhibition. This approach enables the versatile, high-resolution visualisation of multiple phosphoinositide species in an unprecedented manner.
Adaptive capacity of a DNA polymerase clamp-loader ATPase complex
Authors: Subramanian Subu , Zhang Weilin , Nimkar Siddharth , Kamel Mazzin , O’Donnell Michael , Kuriyan John 
Published: October 2023

AbstractThe ability of mutations to facilitate adaptation is central to evolution. To understand how mutations can lead to functional adaptation in a complex molecular machine, we created a defective version of the T4 clamp-loader complex, which is essential for DNA replication. This variant, which is ∼5000-fold less active than the wildtype, was made by replacing the catalytic domains with those from another phage. A directed-evolution experiment revealed that multiple substitutions to a single negatively-charged residue in the chimeric clamp loader – Asp 86 – restore fitness to within ∼20-fold of wildtype. These mutations remove an adventitious electrostatic repulsive interaction between Asp 86 and the sliding clamp. Deep mutagenesis shows that the reduced fitness of the chimeric clamp loader is compensated for by lysine and arginine substitutions of several DNA-proximal residues in the clamp loader or the sliding clamp. Thus, the fitness decrease of the chimeric clamp loader is caused by a reduction in affinity between the clamp loader and the clamp. Our results demonstrate that there is a latent capacity for increasing affinity of the clamp loader for DNA and the sliding clamp, such that even single point mutations can readily compensate for the loss of function due to suboptimal interactions elsewhere.
Regulatory Mimicry of Cyclin-Dependent Kinases by Conserved Herpesvirus Protein Kinases
Authors: Koyanagi Naoto , Hengphasatporn Kowit , Kato Akihisa , Nobe Moeka , Takeshima Kosuke , Maruzuru Yuhei , Maenaka Katsumi , Shigeta Yasuteru , Kawaguchi Yasushi 
Published: October 2023

ABSTRACTHerpesviruses encode conserved protein kinases (CHPKs) that target cellular cyclin-dependent kinase (CDK) phosphorylation sites; thus, they are termed viral CDK-like kinases. Tyrosine 15 in the GxGxxG motifs of CDK1 and CDK2, whose phosphorylation down-regulates their catalytic activities, is conserved in the corresponding motifs of CHPKs. We found that herpes simplex virus 2 (HSV-2) CHPK UL13 mimicked the regulatory mechanism of CDKs. This regulatory mimicry was conserved in CHPKs encoded by herpesviruses subclassified into subfamilies other than HSV-2, suggesting CHPKs have regulatory and functional mimicry with CDKs. Phosphorylation of the corresponding Tyr in HSV-2 UL13 was required for the down-regulation of viral replication and pathogenicity, specifically in the central nervous system of mice, and for efficient viral recurrence in guinea pigs. These data highlight the dual impact of the regulatory mimicry of CDKs by CHPK on the fine-tuned regulation of lytic and latent HSV-2 infectionsin vivo.
Numerical investigation of particle effect on wear characteristic of centrifugal slurry pump based on CFD-DEM coupling
Authors: Shi Xiuwei , Ding Wujian , Xu Chunjie , Xie Fangwei , Tian Zuzhi 
Published: October 2023

PurposeIn the process of conveying the solid–liquid two-phase medium of the centrifugal slurry pump, the wear of the flow-passing parts is an important problem affecting its life and safe operation. Therefore, a numerical investigation on the wear characteristics of the centrifugal slurry pump under different particle conditions was conducted.Design/methodology/approachA solid-liquid two-phase model based on CFD-DEM coupling is established and used to analyze the flow field and the wear characteristics of the flow-passing parts with different particle densities, volume fractions and sizes.FindingsParticle conditions will affect the pump flow field. To analyze the pump wear characteristics, the wear distribution, wear value and cumulative force laws of flow-passing parts under different particle conditions are obtained. In each flow-passing part, with the increase of particle density, volume fraction and size, the wear area is concentrated and the wear depth increases. Under different particle conditions, the wear is mainly on the volute chamber and the blade pressure surface, and the tangential cumulative force of flow-passing parts is much larger than the normal cumulative force.Originality/valueAn accurate model and a coupled simulation method for predicting the wear of the slurry pump are obtained, and the wear characteristic law can provide a reference for the design of the slurry pump to reduce friction.