bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linear ubiquitination at damaged lysosomes induces local NF-κB activation and controls cell survival
Authors: Zein Laura , Dietrich Marvin , Balta Denise , Bader Verian , Scheuer Christoph , Zellner Suzanne , Weinelt Nadine , Vandrey Julia , Mari Muriel C. , Behrends Christian , Zunke Friederike , Winklhofer Konstanze F. , van Wijk Sjoerd J. L. 
Published: October 2023

AbstractLysosomes are the major cellular organelles responsible for nutrient recycling and degradation of cellular material. Maintenance of lysosomal integrity is essential for cellular homeostasis and lysosomal membrane permeabilization (LMP), induced by lysosomotrophic agents, sensitizes towards cell death. Damaged lysosomes are repaired or degraded via lysophagy, during which glycans, exposed on ruptured lysosomal membranes, are recognized by galectins leading to K48- and K63-linked poly-ubiquitination (poly-Ub) of lysosomal proteins followed by recruitment of the autophagic machinery and degradation. Linear (M1) poly-Ub, catalyzed by the E3 ligase linear ubiquitin chain assembly complex (LUBAC) and removed by the OTU domain-containing deubiquitinase with linear linkage specificity (OTULIN) exerts important functions in immune signaling and cell survival, but the role of M1 poly-Ub in lysosomal homeostasis remains largely unexplored. Here, we demonstrate that damaged lysosomes are decorated with M1 poly-Ub in a LUBAC-, OTULIN- and K63-dependent manner. LMP-induced M1 poly-Ub at damaged lysosomes contributes to lysosome degradation, recruits nuclear factor κ-B (NF-κB) essential modulator (NEMO) and locally activates inhibitor of NF-ĸB kinase (IKK) to trigger NF-κB activation in a K63 poly-Ub-dependent manner. Inhibition of lysosomal degradation enhances LMP- and OTULIN-dependent cell death, indicating pro-survival functions of LMP and potentially lysophagy. Finally, we demonstrate that M1 poly-Ub occurs at L-leucyl-leucine methyl ester (LLOMe)-damaged lysosomes in primary mouse neurons and induced pluripotent stem cell (iPSC)-derived primary human dopaminergic neurons. Together, our results reveal novel functions of M1 poly-Ub during lysosomal homeostasis, LMP and degradation of damaged lysosomes, with important implications for NF-κB signaling, inflammation and cell death.
Encoding extracellular modification of artificial cell membranes using engineered self-translocating proteins
Authors: Harjung Alexander , Fracassi Alessandro , Devaraj Neal 
Published: October 2023

AbstractA common method of generating artificial cells is to encapsulate protein expression systems within lipid vesicles. However, to communicate with the external environment, protein translocation across lipid membranes must take place. In living cells, protein transport across membranes is achieved with the aid of complex translocase systems which are difficult to reconstitute into artificial cells. Thus, there is need for simple mechanisms by which proteins can be encoded and expressed inside synthetic compartments yet still be externally displayed. Here we present a genetically encodable membrane functionalization system based on mutants of pore-forming proteins. We show that the membrane translocating loop of α-hemolysin can be engineered to translocate functional peptides up to 52 amino acids across lipid membranes. Engineered hemolysins can be used for genetically programming artificial cells to display interacting peptide pairs, enabling their assembly into artificial tissue-like structures capable of signal transduction.
MPSeqM, a tool combining multiplex PCR and high-throughput sequencing to study the polymorphism of eightLeptosphaeria maculansavirulence genes and its application to field surveys in France
Authors: Gautier Angélique , Laval Valérie , Balesdent Marie-Hélène 
Published: October 2023

AbstractLeptosphaeria maculansis a fungal pathogen causing stem canker of oilseed rape (Brassica napus). The disease is mainly controlled by the deployment of varieties with major resistance genes (Rlm).Rlmgenes can rapidly become ineffective following the selection of virulent isolates of the fungus, i.e. with deletions or mutations in the corresponding avirulence genes (AvrLm). Reasoned and durable management ofRlmgenes relies on the detection and monitoring of virulent isolates in field populations. Based on previous knowledge ofAvrLmgene polymorphism, we developed a tool combining multiplex PCR and Illumina sequencing to characterise allelic variants for eightAvrLmgenes in fieldL. maculanspopulations.We tested the method on DNA pools of 71 characterisedL. maculansisolates and of leaf spots from 32L. maculansisolates. After multiplex-PCR and sequencing with MiSeq technology, reads were mapped on an in-houseAvrLmsequence database. Data were filtered using thresholds defined from control samples included in each run. Proportions of each allelic variant per gene, including deletions, perfectly correlated with expected ones. The method was then applied to around 1300 symptoms (42 pools of mainly 32 leaf spots) from nineB. napusfields. The proportions of virulent isolates estimated by sequencing leaf spot pools perfectly correlated with those estimated by pathotyping. In addition, the proportions of allelic variants determined at the national scale also correlated with those previously determined following individual sequencing ofAvrLmgenes in a representative collection of isolates. Finally, the method also allowed us to detect still undescribed and rare allelic variants. Despite the diversity of mechanisms generating virulent isolates and the gene-dependant diversity ofAvrLmgene polymorphism, the method proved suitable for large-scale and regular monitoring ofL. maculanspopulations, which will make it possible to choose effectiveRlmgenes and to detect resistance breakdowns at early stages.
Deciphering Cancer Genomes with GenomeSpy: A Grammar-Based Visualization Toolkit
Authors: Lavikka Kari , Oikkonen Jaana , Li Yilin , Muranen Taru , Micoli Giulia , Marchi Giovanni , Lahtinen Alexandra , Huhtinen Kaisa , Lehtonen Rainer , Hietanen Sakari , Hynninen Johanna , Virtanen Anni , Hautaniemi Sampsa 
Published: October 2023

AbstractBackgroundVisualization is an indispensable facet of genomic data analysis. Despite the abundance of specialized visualization tools, there remains a distinct need for tailored solutions. However, their implementation typically requires extensive programming expertise from bioinformaticians and software developers, especially when building interactive applications. Toolkits based on visualization grammars offer a more accessible, declarative way to author new visualizations. Nevertheless, current grammar-based solutions fall short in adequately supporting the interactive analysis of large data sets with extensive sample collections, a pivotal task often encountered in cancer research.ResultsWe present GenomeSpy, a grammar-based toolkit for authoring tailored, interactive visualizations for genomic data analysis. Users can implement new visualization designs with little effort by using combinatorial building blocks that are put together with a declarative language. These fully customizable visualizations can be embedded in web pages or end-user-oriented applications. The toolkit also includes a fully customizable but user-friendly application for analyzing sample collections, which may comprise genomic and clinical data. Findings can be bookmarked and shared as links that incorporate provenance information. A distinctive element of GenomeSpy’s architecture is its effective use of the graphics processing unit (GPU) in all rendering. GPU usage enables a high frame rate and smoothly animated interactions, such as navigation within a genome. We demonstrate the utility of GenomeSpy by characterizing the genomic landscape of 753 ovarian cancer samples from patients in the DECIDER clinical trial. Our results expand the understanding of the genomic architecture in ovarian cancer, particularly the diversity of chromosomal instability. We also show how GenomeSpy enabled the discovery of clinically actionable genomic aberrations.ConclusionsGenomeSpy is a visualization toolkit applicable to a wide range of tasks pertinent to genome analysis. It offers high flexibility and exceptional performance in interactive analysis. The toolkit is open source with an MIT license, implemented in JavaScript, and available athttps://genomespy.app/.
Fine-tuning FAM161A gene augmentation therapy to restore retinal function
Authors: Arsenijevic Yvan , Chang Ning , Mercey Olivier , Fersioui Younes El , Koskiniemi-Kuendig Hanna , Joubert Caroline , Bemelmans Alexis-Pierre , Rivolta Carlo , Banin Eyal , Sharon Dror , Guichard Paul , Hamel Virginie , Kostic Corinne 
Published: October 2023

ABSTRACTIn 15 years, inherited retinal diseases have seen gene therapy as a springboard to hope. Many preclinical investigations focused on vectors with maximal gene expression capabilities. But despite an efficient gene transfer, little physiological improvement was noted for certain ciliopathies. FAM161A is an essential protein for the structure of photoreceptor connecting cilium (CC). In the absence of FAM161A, cilia disorganize resulting in outersegment collapses and vision impairment. Within the human retina,FAM161Aproduces two isoforms: the long with exon 4, and the short, lacking it. To restore CC inFam161a-deficient mice, we compared AAV vectors with different promoter activities, doses, and human isoforms injected subretinally in 14-daysFam161atm1b/tm1bmice, shortly after the onset of cilium disorganization. All vectors improved cell survival, but only combining both isoforms using the weak FCBR1-F0.4 promoter allowed precise FAM161A expression in the CC and enhanced retinal function.Our study onFAM161Agene replacement for RP28, a rod-cone-related disease, underscores the critical need for precise therapeutic gene regulation, appropriate vector dosing and delivery of both isoforms. Fine tuning of therapeutic gene expression, tailored to disease traits, is crucial for restoring retinal function. This precision is pivotal for secure gene therapy involving structural proteins like FAM161A.
Co-transcriptional production of programmable RNA condensates and synthetic organelles
Authors: Fabrini Giacomo , Farag Nada , Nuccio Sabrina Pia , Li Shiyi , Stewart Jaimie M. , Tang Anli A. , McCoy Reece , Owens Róisín M. , Rothemund Paul W. K. , Franco Elisa , Di Antonio Marco , Di Michele Lorenzo 
Published: October 2023

AbstractCondensation of RNA and proteins is central to cellular functions, and the ability to program it would be valuable in synthetic biology and synthetic cell science. Here we introduce a modular platform for engineering synthetic RNA condensates from tailor-made, branched RNA nanostructures that fold and assemble co-transcriptionally. Up to three orthogonal condensates can form simultaneously and selectively accumulate guest molecules. The RNA condensates can be expressed within synthetic cells to produce membrane-less organelles with controlled number, size, morphology and composition, and that display the ability to selectively capture proteins. Thein situexpression of programmable RNA condensates could underpin spatial organisation of functionalities in both biological and synthetic cells.
Synergistic, Multi-level Understanding of Psychedelics: Three Systematic Reviews and Meta-analyses of Their Pharmacology, Neuroimaging and Phenomenology
Authors: Shinozuka Kenneth , Jerotic Katarina , Mediano Pedro , Zhao Alex T. , Preller Katrin H. , Carhart-Harris Robin , Kringelbach Morten L. 
Published: October 2023

AbstractSerotonergic psychedelics induce altered states of consciousness and have shown potential for treating a variety of neuropsychiatric disorders, including depression and addiction. Yet their modes of action are not fully understood. Here, we provide a novel, synergistic understanding of psychedelics arising from systematic reviews and meta-analyses of three hierarchical levels of analysis: 1) subjective experience (phenomenology), 2) neuroimaging and 3) molecular pharmacology. Phenomenologically, medium and high doses of LSD yield significantly higher ratings of visionary restructuralisation than psilocybin on the 5-dimensional Altered States of Consciousness Scale. Our neuroimaging results reveal that, in general, psychedelics significantly strengthen between-network functional connectivity (FC) while significantly diminishing within-network FC. Pharmacologically, LSD induces significantly more inositol phosphate formation at the 5-HT2Areceptor than DMT and psilocin, yet there are no significant between-drug differences in the selectivity of psychedelics for the 5-HT2A, 5-HT2C, or D2receptors, relative to the 5-HT1Areceptor. Our meta-analyses link DMT, LSD, and psilocybin to specific neural fingerprints at each level of analysis. The results show a highly non-linear relationship between these fingerprints. Overall, our analysis highlighted the high heterogeneity and risk of bias in the literature. This suggests an urgent need for standardising experimental procedures and analysis techniques, as well as for more research on the emergence between different levels of psychedelic effects.
Single cell expression and chromatin access of theToxoplasma gondiilytic cycle identifies AP2XII-8 as an essential pivotal controller of a ribosome regulon
Authors: Lou Jingjing , Rezvani Yasaman , Arriojas Argenis , Degras David , Keroack Caroline D. , Duraisingh Manoj T. , Zarringhalam Kourosh , Gubbels Marc-Jan 
Published: October 2023

AbstractSequential lytic cycles driven by cascading transcriptional waves underlie pathogenesis in the apicomplexan parasiteToxoplasma gondii. This parasite’s unique division by internal budding, short cell cycle, and jumbled up classically defined cell cycle stages have restrained in-depth transcriptional program analysis. Here, unbiased transcriptome and chromatin accessibility maps throughout the lytic cell cycle were established at the single cell level. Correlated pseudo-timeline assemblies of expression and chromatin profiles mapped transcriptional versus chromatin level transition points promoting the cell division cycle. Sequential clustering analysis identified putatively functionally related gene groups facilitating parasite division. Promoter DNA motif mapping revealed patterns of combinatorial regulation. Pseudo-time trajectory analysis revealed transcriptional bursts at different cell cycle points. The dominant burst in G1 was driven by transcription factor AP2XII-8, which engages TGCATGCG/A and TATAAGCCG motifs, and promoted the expression of a regulon encoding 40 ribosomal proteins. Overall, the study provides integrated, multi-level insights into apicomplexan transcriptional regulation.
“The Translesion Polymerase Pol Y1 is a Constitutive Component of theB. subtilisReplication Machinery”
Authors: Marrin McKayla E. , Foster Michael R. , Santana Chloe M. , Choi Yoonhee , Jassal Avtar S. , Rancic Sarah J. , Greenwald Carolyn R. , Drucker Madeline N. , Thrall Elizabeth S. 
Published: October 2023

AbstractUnrepaired DNA damage encountered by the cellular replication machinery can stall DNA replication, ultimately leading to cell death. In the DNA damage tolerance pathway translesion synthesis (TLS), replication stalling is alleviated by the recruitment of specialized polymerases to synthesize short stretches of DNA near a lesion. Although TLS promotes cell survival, most TLS polymerases are low fidelity and must be tightly regulated to avoid harmful mutagenesis. The gram-negative bacteriumEscherichia colihas served as the model organism for studies of the molecular mechanisms of bacterial TLS. However, it is poorly understood whether these same mechanisms apply to other bacteria. Here, we use in vivo single-molecule fluorescence microscopy to investigate the TLS polymerase Pol Y1 in the model gram-positive bacteriumBacillus subtilis. We find significant differences in the localization and dynamics of Pol Y1 in comparison to itsE. colihomolog, Pol IV. Notably, Pol Y1 is constitutively enriched at or near sites of replication in the absence of DNA damage through interactions with the DnaN clamp; in contrast, Pol IV has been shown to be selectively enriched only upon replication stalling. These results suggest key differences in the roles and mechanisms of regulation of TLS polymerases across different bacterial species.
A green alternative to fragrant agarwood sesquiterpenoid production
Authors: Gutiérrez Sergio , Overmans Sebastian , Wellman Gordon B. , Samaras Vasilios G. , Oviedo Claudia , Gede Martin , Szekely Gyorgy , Lauersen Kyle J. 
Published: October 2023

AbstractCertain endangered Thymelaeaceous trees are major sources of the fragrant and highly valued resinous agarwood, comprised of hundreds of oxygenated sesquiterpenoids (STPs). Despite growing pressure on natural agarwood sources, the chemical complexity of STPs severely limits synthetic production. Here, we catalogued the chemical diversity in 58 agarwood samples by two-dimensional gas chromatography–mass spectrometry and partially recreated complex STP mixtures through synthetic biology. We improved STP yields in the unicellular algaChlamydomonas reinhardtiiby combinatorial engineering to biosynthesise nine macrocyclic STP backbones found in agarwood. A bioprocess following green-chemistry principles was developed that exploits ‘milking’ of STPs without cell lysis, solvent–solvent STP extraction, solvent–STP nanofiltration, and bulk STP oxy-functionalisation to obtain terpene mixtures like those of agarwood. This process occurs with total solvent recycling and enables continuous production. Our synthetic-biology approach offers a sustainable alternative to harvesting agarwood trees to obtain mixtures of complex, fragrant, oxygenated STPs.
Commentary on Pang et al. (2023) Nature
Authors: Patil Kaustubh R. , Jung Kyesam , Eickhoff Simon B. 
Published: October 2023

AbstractPang et al. (2023) observe that the geometric eigenmodes, derived from the shape of the cortical surface, are better at reconstructing patterns of both spontaneous and stimulus-evoked activity, when contrasted with three alternative connectome-based models including structural connectome derived eigenmodes. Based on this observation they propose that geometric eigenmodes offer a good model for explaining brain function, noting that “wave dynamics offer a more accurate and parsimonious mechanistic account of macroscale, spontaneous cortical dynamics captured by fMRI”. They then question the prevailing view that brain activity is “localized to focal, spatially isolated clusters” and it is driven by “intricate patterns of anatomical connections”. While the observation that geometric properties fit brain activity well is intriguing, we argue that accepting geometric eigenmodes as a model for brain function risks the logical fallacy of “affirming the consequent”. A representation that effectively describes the underlying geometry is inherently adept at fitting patterns within that geometric space; it does not necessarily shed light on mechanisms of the brain’s functional attributes. To this end, we provide two lines of empirical results: (a) Basic parcel-based representations, which capture localized structures, can reconstruct activity patterns as well. (b) Geometric eigenmodes demonstrate a high flexibility when fit to a range of manipulated patterns, which evokes the danger of overfitting. Based on those results, theoretical considerations, and previous data we argue that more consideration is needed regarding “parsimony, robustness and generality of geometric eigenmodes as a basis set for brain function”. While we recognize the potential role of the brain’s geometry in influencing its dynamics, assertions regarding its efficacy should be weighed against the performance of simpler models, an inherent risk of overfitting and anatomical evidence. Pang et al.1put forth harmonic modes derived from the brain’s geometry as a previously underrecognized model to explain brain-wide dynamics. Their reconstruction framework relies on multiple linear regression to fit brain patterns using a basis set and then calculating Pearson’s correlation between original data and fitted data, both parcellated using an atlas with 180 parcels in each hemisphere2. In addition to the overarching challenge of accepting any model as an actual reflection of the real world3, we here provide empirical results and theoretical arguments that highlight the need for further consideration regarding geometric eigenmodes as a model of macroscale brain activity.
Characterization of a novel mouse model for Fuchs Endothelial Corneal Dystrophy
Authors: Murugan Subashree , de Campos Viviane Souza , Ghag Sachin Anil , Ng Matthew , Shyam Rajalekshmy 
Published: October 2023

AbstractPurposeFuchs Endothelial Corneal Dystrophy (FECD) is a progressive blinding disorder prevalent in 4% of Americans over 40. Corneal transplantation is the standard treatment. Animal models with partial FECD features exist, but a model encompassing all the major disease characteristics is desirable to improve the understanding of the pathogenesis and to identify signaling pathways involved in the disease onset and progression. Such an animal model can be helpful to develop intervention strategies. Here, we developed a mouse model that recapitulates all the features of FECD.MethodLoss of function mutations inSlc4a11and a knock-in mutation inCol8a2(Q455K) are implicated in FECD. Mice with Slc4a11 and Col8a2 mutations in C57BL/6J background were crossed to generate double mutant mice at F2 generation. At five weeks of age, a subset of the animals were fed tamoxifen-enriched chow or standard chow for two weeks, followed by standard chow. Corneal thickness, endothelial cell density, and guttae were measured at 5 (baseline) and 16 weeks of age. Corneas collected from mice at 16 weeks were stained for tight and adherens junctions, and reactive oxygen species. A lactate assay was performed to evaluate the endothelial pump function.ResultsThe double mutant tamoxifen-fed mice showed increased corneal thickness, decreased endothelial cell density, presence of guttae, and elevated stromal lactate levels. The endothelial cells showed altered morphology with disrupted adherens junctions and elevated ROS.ConclusionOverall, this mouse model recapitulates all the important phenotypic features associated with FECD.