bluuebunny/crossref_metadata_2025_split huggingface dataset:
The proteomic landscape of proteotoxic stress in a fibrogenic liver disease
Authors: Rosenberger Florian A. , Mädler Sophia C. , Holtz Thorhauge Katrine , Steigerwald Sophia , Fromme Malin , Lebedev Mikhail , Weiss Caroline A. M. , Oeller Marc , Wahle Maria , Zwiebel Maximilian , Schmacke Niklas A. , Detlefsen Sönke , Boor Peter , Kaserman Joseph , Wilson Andrew , Fabián Ondřej , Fraňková Soňa , Krag Aleksander A. , Strnad Pavel , Mann Matthias 
Published: November 2024

AbstractProtein misfolding diseases, including alpha-1 antitrypsin deficiency (AATD), pose significant health challenges, with their cellular progression still poorly understood1–3. We utilize spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudo-time across fibrosis stages. We achieve unprecedented proteome depth of up to 3,800 proteins from a third of a single cell in formalin-fixed, paraffin-embedded (FFPE) tissue. This dataset revealed a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show alpha-1 antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with AI-guided image-based phenotyping across multiple disease stages, revealing a terminal hepatocyte state characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10/TRAIL expression. This phenotype may represent a critical disease progression stage. Our study offers novel insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.
HIRA-SETDB1-H3K9me3 axis regulate chromatin architecture in chronic myeloid leukemia cells
Authors: Shirude Mayur Balkrishna , Devarajan Anjali , Dutta Debasree 
Published: November 2024

AbstractHistone cell cycle regulator A (HIRA) confers chromatin accessibility and regulates developmental hematopoiesis. But whether HIRA displays similar role in leukemia, a condition caused by abnormalities during hematopoiesis, remain elusive. Here we show that HIRA interact with heterochromatin cluster in Chronic Myeloid Leukemia, K562, cells. FRAP, FLIM-FRET and ATAC-sequencing analysis revealed increased chromatin compaction, altered spatial distribution of chromatin towards nuclear periphery and loss in chromatin accessibility at the promoter and gene bodies upon downregulation of HIRA in K562 cells. Enhanced chromatin compaction was attributed to increased histone H3K9me3 level mediated by histone methyltransferase SETDB1. Incorporation of histone H3.3 within theSETDB1promoter inHIRA-knockdown cells induced SETDB1 expression. HIRA-SETDB1-H3K9me3 axis regulate the chromatin architecture in CML cells leading to inhibition of proliferation while induction in differentiation. We anticipate that the exploration of this axis would introduce new paradigm in understanding and targeting molecules that could influence CML disease progression.
TET2-mediated epigenetic modification promotes stress senescence of pancreatic β cells in type 2 diabetes mellitus
Authors: Cai Weijuan , Song Qingqing , Mo Xiaoqing , Li Huaqian , Song Yuling , Yin Liang 
Published: November 2024

AbstractEpigenetic modification plays a key role in β cell senescence. In the regulation of gene expression, there is a complex and close relationship between DNA methylation and histone modification. In order to explore its specific mechanism in T2DM β cell senescence, we used postbisulfite aptamer labeling of genome-wide bisulfite-SEQ, chromatin immunocoprecipitation-SEQ, RNA-SEQ, CRISPR/Cas9 TETs knockout, RNA interference, TET2 inhibitors, lentiviral overexpression, and gene knockout mouse models. Our study found that demethylase TET2 was localized in the islets of mice, and the expression level increased with age. TET2 knockout in pancreatic β cells can hypermethylate PTEN, up-regulate MOF and enrich H4K16ac, and reduce the level of aging markers. This study confirmed that TET2-mediated PTEN DNA methylation can promote a new mechanism of β cell senescence by regulating H4K16ac, providing a new molecular mechanism and therapeutic target for T2DM β cell senescence therapy.
Mitochondrial efficiency determines Crabtree effect across yeasts
Authors: Battjes Julius , Grigaitis Pranas , Hoving Milou , Visser Thomas D. , Stampfl Karina , Miguel Gabriela A. , van Heerden Johan , Andersen Jesper K. , Bruggeman Frank J. , Teusink Bas 
Published: November 2024

AbstractUnder excess glucose conditions, many yeasts switch from high-yield respiratory metabolism to low-yield fermentation, a phenomenon called the Crabtree effect in yeast, or the Warburg effect in mammalian cells. Cellular constraints and limited resources are generally believed to govern the metabolic strategies of cells to adapt to environmental conditions, but which constraints drive this switch is still under debate. Here we study the Crabtree-negative, fully respiratory yeastPichia kluyveriand compare it to the Crabtree-positive yeastSaccharomyces cerevisiaefrom a resource allocation perspective. By integrating quantitative physiology and proteomics into whole-cell proteome-constrained models, we find that the Crabtree effect is determined by the composition and catalytic efficiency of the electron transport chain. We find that the subsequent proteome efficiency of respiration versus fermentation varies between these species. The variation in parameters and composition of the respiratory machinery likely reflects the evolutionary and ecological history of these yeast species. This study advances our understanding of the role of proteome constraints and proteome efficiency in governing cellular metabolism of yeasts, and that of eukaryotic cells at large.
AInsectID Version 1.1: an Insect Species Identification Software Based on the Transfer Learning of Deep Convolutional Neural Networks
Authors: Sadia Haleema , Alam Parvez 
Published: November 2024

ABSTRACTAInsectID Version 1.11, is a GUI operable open-source insect species identification, color processing2and image analysis software. The software has a current database of 150 insects and integrates Artificial Intelligence (AI) approaches to streamline the process of species identification, with a focus on addressing the prediction challenges posed by insect mimics. This paper presents the methods of algorithmic development, coupled to rigorous machine training used to enable high levels of validation accuracy. Our work integrates the transfer learning of prominent convolutional neural network (CNN) architectures, including VGG16, GoogLeNet, InceptionV3, MobileNetV2, ResNet50, and ResNet101. Here, we employ both fine tuning and hyperparameter optimization approaches to improve prediction performance. After extensive computational experimentation, ResNet101 is evidenced as being the most effective CNN model, achieving a validation accuracy of 99.65%. The dataset utilized for training AInsectID is sourced from the National Museum of Scotland (NMS), the Natural History Museum (NHM) London and open source insect species datasets from Zenodo (CERN’s Data Center), ensuring a diverse and comprehensive collection of insect species.
Amphiphile-engineered DNA adjuvants stimulate strong type I IFN production in lymph nodes via cytosolic danger-sensing to induce potent cellular and humoral immunity in mice and non-human primates
Authors: Steinbuck Martin P. , Seenappa Lochana M. , Zhan Wei , Palmer Erica , Jakubowski Aniela , Cabana-Puig Xavier , Jung Mimi M. , McNeil Lisa K. , Haqq Christopher M. , Fitzgerald Katherine A. , DeMuth Peter C. 
Published: November 2024

ABSTRACTAdjuvants are immuno-activators capable of shaping the magnitude and quality of antigen-specific immune responses induced by subunit immunization. Presently, there is an acute need for effective adjuvants that safely induce durable and balanced humoral and cellular responses; the latter being indispensable for protection against intracellular pathogens and cancer. Here, we iteratively optimized a novel class of Amphiphile (AMP)-modified, immunostimulatory DNA-adjuvants designed for targeted delivery to lymph nodes and enhanced stimulation of cytosolic danger-sensing pathways to generate strong adaptive immunity. AMP-DNA adjuvants induced potent IFN-I-driven inflammatory environments in mouse and NHP lymph nodes that were dependent on TBK1 signaling, leading to significantly enhanced cytokine secretion by polyfunctional CD8+and CD4+T cells in multiple tissues, and strongly elevated TH1-associated and neutralizing antibody responses, without toxicity. These results demonstrate that AMP-engineering enables lymph node-targeted DNA-adjuvants to uniquely activate cytosolic immune-signaling to generate robust adaptive responses crucial for vaccine efficacy.
Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function
Authors: Barker Andi V. , Carlson Kara B. , Wcisel Dustin J. , De Allende Ian Birchler , Braasch Ingo , Fisk Michael , Dornburg Alex , Yoder Jeffrey A. 
Published: November 2024

AbstractHolosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes. However, the immune repertoire of holosteans remains relatively unexplored. Here, we investigate the evolution of PSMB8, a core component of the immunoproteasome responsible for cleaving intracellular proteins into peptides for presentation by MHC class I molecules. We identify two holostean PSMB8 types—S type and K type—that are unique among vertebrates. These types likely cause significant biochemical changes to the S1 binding pocket involved in antigen cleavage which could result in the presentation of novel peptides by MHC class I. Integrating comparative analyses across major ray-finned fish lineages demonstrates that bowfins and gars independently evolved the PSMB8 S type within separate PSMB8 paralog lineages, while the PSMB8-K type is an evolutionary novelty found only in gars. Our results provide new perspectives into PSMB8 haplotypes and their role in peptide antigen processing, offering unique insights into the molecular evolution of the vertebrate immunity and antigen presentation.
Androgen receptor interactions provide insight into steroid mediated metabolic shifts in endocrine resistant breast cancer
Authors: Bleach Rachel , Bozkurt Emir , Sheehan Katherine , Shirran Sally , Xin Jingqi , Agbana Stephanie , Ola Mihaela , Young Leonie , O’Reilly Michael W , Prehn Jochen HM , McIlroy Marie 
Published: November 2024

AbstractPurposeAromatase Inhibitors (AI) are standard therapy for hormone receptor positive breast cancers in post-menopausal patients. Disease recurrence is common and previous studies suggest that the altered steroid environment may be a driver of resistance. Using label-free mass-spectrometry we explored the unique androgen receptor (AR) interactome that supervenes in AI resistant breast cancer and the associated hyperandrogenic environment.Experimental DesignAR expression was evaluated in a primary breast cancer tissue-microarray (n=875) with nuclear and cytoplasmic localization quantified. Liquid-chromatography tandem mass-spectrometry (LC-MS/MS) analysis was utilized to identify proteins interacting with the AR in models of AI-resistance. Validation was carried out by co-immunoprecipitation and co-localisation studies. Live-cell imaging, Seahorse MitoStress Assays and flow cytometry were used to quantify changes in mitochondria and cell metabolism arising in models of AI-resistance.ResultsUtilising digital pathology we detected that abundant cytoplasmic AR protein was associated with poor survival only in the post-menopausal cohort, and most significantly, in the therapy-refractory Luminal B subtype (p=0.0085). Models of AI-resistance and androgen excess highlight diffuse AR localisation throughout the cytoplasm and nucleus accompanied by increased mitochondrial mass and membrane potential, and increased oxidative phosphorylation and glycolysis. Exploration of the AR protein interactome identified G3BP1, SLIRP, and IGFBP5 as AR protein partners which are associated with stress, adaptive metabolic response and estrogen receptor repression.ConclusionsThe findings of this study highlight the prognostic potential of cytoplasmic AR immunoreactivity in specific breast cancer subtypes and uncover novel extra-nuclear AR protein interactions that may mediate metabolic adaptations during the development of endocrine-resistance.
High-throughput development and characterization of new functional nanobodies for gene regulation and epigenetic control in human cells
Authors: Wan Jun , Thurm Abby R. , Allen Sage J. , Ludwig Connor H. , Patel Aayan N. , Bintu Lacramioara 
Published: November 2024

AbstractControlling gene expression and chromatin state via the recruitment of transcriptional effector proteins to specific genetic loci has advanced the potential of mammalian synthetic biology, but is still hindered by the challenge of delivering large chromatin regulators. Here, we develop a new method for generating small nanobodies against human chromatin regulators that can repress or activate gene expression. We start with a large and diverse nanobody library and perform enrichment against chromatin regulatory complexes using yeast display, followed by high-throughput pooled selection for transcriptional control when recruited to a reporter in human cells. This workflow allows us to efficiently select tens of functional nanobodies that can act as transcriptional repressors or activators in human cells.
Freedom of speech predicts animal welfare protection across the globe
Authors: Montalcini Camille M. , Crowther Thomas W. 
Published: November 2024

AbstractThe welfare of captive and wild animals is closely tied to human health, nutrition, and environmental wellbeing. Yet, until now, the global determinants of animal welfare remain unclear, as we lack quantitative global data on animal treatment. Here, by collapsing 13 indicators of animal welfare legislation across 50 major animal product-producing countries, we identify two key dimensions reflecting ‘animal welfare protection’ and ‘responsible consumption and production’. While high-income countries with lower dependence on agriculture may have more opportunity to focus on animal welfare, our analysis suggests that the level social freedoms of citizens can dramatically overwhelms this economic signal. We find that the ‘voice and accountability’ of citizens ultimately determines the extent of animal welfare protection, explaining 58% of the variation across the globe. Irrespective of environmental or economic conditions, structures that enhance political freedoms, civil liberties, and citizen participation in governance may provide the necessary foundation for developing legislation to promote animal welfare protection.
Control of electromechanical waves in engineered tissue of human iPSC-cardiomyocytes using a Halbach array and magnetic nanoparticles
Authors: Pozo Maria R. , Heinson Yuli W. , Chua Christianne J. , Entcheva Emilia 
Published: November 2024

AbstractThe Halbach array, originally developed for particle accelerators, is a compact arrangement of permanent magnets to create well-defined magnetic fields without heating. Here, we demonstrate its use for modulating the speed of electromechanical waves in cardiac syncytia of human stem cell-derived cardiomyocytes. At 40-50 mT magnetic field strength, a cylindrical dipolar Halbach array boosted the conduction velocity, CV, of excitation in a directional manner by up to 25% when the magnetic field was co-aligned with the electromechanical wave (but not when perpendicular to it). To observe the effects, a short-term incubation of the cardiac cell constructs with non-targeted magnetic nanoparticles, mNPs, was sufficient. This increased CV anisotropy, and the effects were most pronounced at slower pacing rates. Instantaneous formation and re-arrangement of elongated mNP clusters upon magnetic field rotation was seen, thus creating dynamic structural anisotropy that may have contributed to the directional CV effects. This approach may be useful for anti-arrhythmic control of cardiac waves.One sentence summaryA Halbach array of permanent magnets can modulate the speed of excitation waves in human cardiac cell assemblies with magnetic nanoparticles.
Squirrel: Reconstructing semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments
Authors: Holtgrefe Niels , Huber Katharina T. , van Iersel Leo , Jones Mark , Martin Samuel , Moulton Vincent 
Published: November 2024

AbstractPhylogenetic networks model the evolutionary history of taxa while allowing for reticulate events such as hybridization and horizontal gene transfer. As is the case for phylogenetic trees, it is often not possible to infer the root location of such a network directly from biological data for several evolutionary models. Hence, we consider semi-directed (phylogenetic) networks: partially directed graphs without a root in which the directed edges represent reticulate evolutionary events. By specifying a known outgroup, the rooted topology can be recovered from such networks. We introduce the algorithm Squirrel(Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks) which constructs a semi-directed level-1 network from a full set of quarnets (four-leaf semi-directed networks). Our method also includes a heuristic to construct such a quarnet set directly from sequence alignments. To build a network from quarnets, Squirrelfirst builds a tree, after which it repeatedly solves the TravellingSalesmanProblem(TSP) to replace each high-degree vertex by a cycle. We demonstrate Squirrel’s performance on randomly generated networks and on real sequence data sets, the largest of which contains 29 aligned sequences close to 1.7 Mpb long. The resulting networks are obtained on a standard laptop within a few minutes. Lastly, we prove that Squirrelis combinatorially consistent: given a full set of quarnets coming from a triangle-free semi-directed level-1 network, it is guaranteed to reconstruct the original network. Squirrelis implemented in Python, has an easy-to-use graphical user-interface that takes sequence alignments or quarnets as input, and is freely available athttps://github.com/nholtgrefe/squirrel.
Modelling DNA replication fork stability and collapse using chromatin fiber analysis and the R-ODD-BLOBS program
Authors: Cheng Kerenza , Aliar Kazeera , Manshaei Roozbeh , Mazalek Ali , Sabatinos Sarah A 
Published: November 2024

ABSTRACTWe describe the anatomy of replication forks by comparing the lengths of synthesized BrdU-labelled DNA in wild-type,mrc1Δandcds1Δ Schizoasaccharomyces pombe. We correlated Rad51 and Cdc45 proteins relative to their positions on the fork, replicated tract, or unreplicated regions. We did this using chromatin spread pixel intensity data that was analyzed using our program: R-ODD-BLOBS. Graphs on the lengths of BrdU tract, and proteins, as well as the percentage of Rad51 and Cdc45 colocalization, were created by the program. These results were compared to the literature. The BrdU lengths detected matched current literature; cds1Δ was the longest at 8.6 px, wild-type was 7.5 px, and mrc1Δ was the shortest at 5.1 px. When colocalization of rad 51 around the fork was explored, we found that mrc1Δ uniquely had 22% more colocalization than wt at the unreplicated region of a fork. This suggests that HR was potentially detected at the forks of mrc1Δ. In this study, we summarize the usefulness of R-ODD-BLOBS in aiding in analyzing chromatin spread data which provides data on the lengths and protein colocalization and starts to paint a picture of the anatomy of a fork.SIGNIFICANCE STATEMENT- The dynamics of a replication fork are important to maintaining genome stability, however, current methods create an average bulk data that can conceal the heterogeneity of forks.- This pipeline involving chromatin spread fiber, and data analysis using R-ODD-BLOBS establishes a single-molecule approach to a dynamic problem that can determine patterns like differences in synthesized DNA between conditions, and determine colocalization of proteins at different regions on chromatin, while systematically determining parameters- This pipeline shows and quantifies patterns found in chromatin spread fibers, while maintaining the option to average out data or individually look at them
Insight Into the Molecular Parameters of PEI Promoting an Efficient Gene Delivery into Cells
Authors: Montaño González Paulina Alejandra , Tranchimand Sylvain , Rochedy Manon , Leroyer Patricia , Chapel Jean-Paul , Chevance Soizic , Schatz Christophe , Gauffre Fabienne , Loyer Pascal , Bravo Anaya Lourdes Mónica 
Published: November 2024

AbstractThe development of natural or synthetic polycations able to interact with nucleic acids and condense them into nanoparticles known as polyplexes, faces several unresolved challenges at the cellular level. Key issues include the intracellular trafficking of polyplexes, the endosomal escape and the release of nucleic acids into the cytosol, which are considered major bottlenecks for efficient protein expression. Here, we aim at gaining fundamental insights into the stability of polyplexes in biological media and their uptake and intracellular trafficking, while correlating data of the expression of reporter protein with both the molecular characteristics of various poly(ethylenimines) (PEI) and the physicochemical characteristics of PEI/peGFP-C3 polyplexes. For this, we chosen four samples of PEI, selected as a model polycation, with different molecular weights (Mw = 0.8, 20, 25 and 60 kg/mol) and structures (linear and branched). We found that thein vitroandin vivostability of PEI/peGFP-C3 polyplexes, their cell internalization and transfection efficiency is dependent on the variation of polycation Mw and structure, as well as the intrinsic properties of polyplexes, such as the charge ratio (R=[N+]/[P−]). A relation between the percentage of positive cells to green fluorescent protein (GFP) and the amount of internalized nucleic acid (cyanine 5-peGFP-C3) allowed revealing the molecular characteristics of PEI promoting both higher both cell internalization and GFP expression on HEK293T cells. In the long term, the outcome of this work will be to propose guidelines to help design more effective, and less cytotoxic non-viral gene carriers with a great potential for new therapeutic applications.