bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines
Authors: Reinschmidt Andrew , Solano Luis , Chavez Yonny , Hulsy William Drew , Nikolaidis Nikolas 
Published: December 2024

AbstractThe cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical “Receptor Ligand Activity” pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying more uniquely expressed genes and elevated expression levels (fold changes) of shared genes under stress conditions. Validation by qPCR confirmed the activation of key genes within the “Receptor Ligand Activity” pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.
Cytoplasmic expression of the cell cycle regulator cyclin D1 in radial glial progenitor cells modulates brain cortex development
Authors: Pedraza Neus , Rocandio Daniel , Monserrat Maria Ventura , Zammou Bahira , Ortiz-Brugués Ariadna , Marfull-Oromí Pau , Chauhan Disha , Encinas Mario , Dolcet Xavier , Espinet Carme , Ferrezuelo Francisco , Garí Eloi , Egea Joaquim 
Published: December 2024

AbstractDuring nervous system development, the interplay between cell cycle regulation and neurogenesis is fundamental to achieve the correct timing for neuronal differentiation. However, the molecular players regulating this transition are poorly understood. Among these, the cell-cycle regulatory cyclins and their cyclin-dependent kinases (Cdks) play a pivotal role. In the present work we uncover an unknown function of cyclin D1 (Ccnd1) during cortex development which is independent of cell cycle regulation and that relies on its cytoplasmic localization and membrane association. We show that Ccnd1 is localized in the cytoplasm of the radial glial process (RGP) of neuron progenitors in different regions of the developing brain, including the cortex. Cytoplasmic Ccnd1 is enriched at the distal tip of the RGP, adjacent to the meningeal basement membrane, and overlaps with β1-integrin at the plasma membrane.CCND1knock-out animals show an abnormal cortical layering in which the distribution of Tbr2+ and Ctip2+ cells are affected without displaying proliferation defects. This is consistent with a cytoplasmic function of Ccnd1 as overexpression by in utero electroporation of a dominant negative Ccnd1, unable to activate Cdks, and targeted to the cytoplasmic membranes, reproduces some of these Tbr2 and Ctip2 defects. Finally, we provide evidence that cytoplasmic Ccnd1 affects neuron morphology and that it is required for the proper detachment of the RGP from the meningeal basement membrane by a mechanism involving the phosphorylation of the integrin effector protein paxillin. Hence, we propose that Ccnd1 has an important cytoplasmic function for cortical development independently of cell cycle regulation.Significant StatementA key developmental step during nervous system formation is the transition from proliferating progenitors to postmitotic neurons. However, the molecular mechanisms regulating this process are not fully understood. Cyclin D1 (Ccnd1) is a canonical regulator of cell cycle in the cell nucleus. Surprisingly, we show that Ccnd1 is also located in the radial glial process of neuron progenitors and associated to the plasma membrane in different regions of the developing mouse brain. We uncover a novel function for this cytoplasmic Ccnd1 and show that it is required for proper cortical layering, independent of cell cycle regulation. Mechanistically, we provide evidence that this function is mediated by the integrin effector paxillin. We propose therefore that cytoplasmic Ccnd1 is important for cortex development independent of cell cycle regulation.
Gene network architecture, mutation and selection collectively drive developmental pattern evolvability and predictability
Authors: Booth Harry , Hadjivasiliou Z. 
Published: December 2024

AbstractMuch of the striking diversity of life on earth arises from mutations in conserved regulatory elements that govern reduced modules of Gene Regulatory Networks (GRNs). Although the mechanistic basis by which GRNs orchestrate cellular responses and tissue patterning during development is well understood, their evolutionary dynamics remain less clear. In this study, we probe how key evolutionary forces such as mutation, selection and historical contingency interact with GRN architecture to drive the diversification of developmental mechanisms and patterns. We introduce a novel high-throughput theoretical framework for GRN-driven pattern evolution to produce a comprehensive dataset of evolutionary trajectories. Utilizing computational and machine learning methods, we interpret this data within an evolutionary context. Our results elucidate the interplay between mutational and ecological influences and network architecture, revealing how historical contingencies affect the evolvability of GRNs and the predictability of their evolutionary outcomes. This work echoes recent synthetic and laboratory evolution experiments as well as comparative studies, providing a mechanistic basis for their interpretation. Our framework offers a powerful and adaptable platform for the investigation of GRN-drive pattern evolution, that links physical constraints that emerge from genetic architecture to evolutionary change and diversification.
Circadian PERIOD proteins sculpt the mammalian alternative splicing landscape
Authors: Chikhaoui L , Mamgain K , Seki M , Blanco C , Sassolas F , Folco E , Sery D , Suzuki Y , Ananthasubramaniam B , Padmanabhan K 
Published: December 2024

AbstractMammalian circadian oscillators are driven by a transcription-translation feedback loop where CLOCK:BMAL1 activity is repressed by the PER:CRY complex. While transcriptional regulation by PER is well established, the role of circadian feedback in co- and post- transcriptional processes remains unclear. Here, we used Nanopore long-read direct RNA sequencing (dRNAseq) and quantitative mass spectrometry (qMS) to uncover a critical function of PERs in alternative splicing (AS) regulation in the liver. Our expanded long-read transcriptome revealed significant changes in rhythmic expression of annotated transcripts, novel isoforms of known genes, and previously unannotated genes, with widespread perturbations in Per1-/-;Per2-/-(PerKO) livers. Rhythmic AS events were restricted to a distinct subset of transcripts, and splicing entropy - a metric of AS complexity - displayed oscillations in only a limited number of pathways, primarily those associated with glucose homeostasis and cellular responses to insulin. In PerKO livers, however, we detected increased isoform complexity and altered splicing entropy across a broad range of pathways linked to cell growth, morphogenesis, ER-associated degradation (ERAD), insulin response and histone methylation. Biochemical analyses and qMS data indicate that these changes are not due to mis-expression of splicing factors, but rather stem from altered nuclear abundance and chromatin retention of a few Serine-Arginine-rich splicing factors (SRSFs). In particular, SRSF3 acts proximal to the core-clock by defining both the period and amplitude of cellular rhythms. Our findings highlight a critical role for PER proteins in shaping the circadian liver proteome by integrating rhythmic transcription with the regulation of a complex and dynamic splicing landscape.
Pharmacophore design and ensemble-docking as approach to screening a large-scale database for identification of potential inhibitors of APH(3')-IIIa ofEnterococcus faecalis
Authors: Velez Luis Alfredo , Arteaga Sandra Denisse 
Published: December 2024

AbstractFighting nosocomial infections represents one of the main difficulties in medical treatment units around the world. Among the bacteria with the greatest potential to cause these complications isEnterococcus faecalis, mainly due to the expression of aminoglycoside-modifying enzymes. In the approach adopted in this work, pharmacophore modeling followed by ensemble-docking were carried out to select potential inhibitors against the nucleotide binding site of EfAPH(3')-IIIa. The most promising ligands are all nucleotide analogues (ZINC000828691112, ZINC000029546074 and ZINC000062624753) and showed good toxicological and pharmacokinetic profiles and the ability to interact with key amino acids such as MET26, SER27 and TYR42. Taken together, these preliminary results show that nucleotide analogues may represent a promising structure for interacting with the EfAPH(3')-IIIa nucleotide-binding pocket. Further analysis will be conducted.
Diversity of motility patterns in benthic diatoms
Authors: Bondoc-Naumovitz Karen Grace , Crosato Emanuele , Wan Kirsty Y. 
Published: December 2024

AbstractDiatoms, a highly successful group of photosynthetic algae, contribute to a quarter of global primary production. Many species are motile, despite having no appendages and a completely rigid cell body. Cells move to seek out nutrients, locate mating partners, and undergo vertical migration. To explore the natural diversity of diatom motility, we perform a comparative study across five common biofilm-forming species. Combining morphological measurements with high-resolution cell tracking, we establish how gliding movements relate to the morphology of the raphe – a specialised slit in the cell wall responsible for motility generation. Our detailed analyses reveal that cells exhibit a rich but species-dependent phenotype, switching stochastically between four stereotyped motility states. We model this behaviour and use stochastic simulations to predict how heterogeneity in microscale navigation patterns leads to differences in long-time diffusivity and dispersal. In a representative species, we extend these findings to quantify diatom gliding in complex, naturalistic 3D environments, suggesting that cells may exploit these distinct motility signatures to achieve niche segregation in nature.
Wide-field optical redox imaging with leading-edge detection for assessment of patient-derived cancer organoids
Authors: Gillette Amani , Udgata Shirsa , Schmitz Alexa E. , Stoecker Jordan E. , Deming Dustin , Skala Melissa 
Published: December 2024

AbstractPatient-derived cancer organoids (PDCOs) are a valuable model to recapitulate human disease in culture with important implications for drug development. However, current methods for assessing PDCOs are limited. Label-free imaging methods are a promising tool to measure organoid level heterogeneity and rapidly screen drug response in PDCOs. The aim of this study was to assess and predict PDCO response to treatments based on mutational profiles using label-free wide-field optical redox imaging (WF ORI). WF ORI provides organoid-level measurements of treatment response without labels or additional reagents by measuring the autofluorescence intensity of the metabolic co-enzymes NAD(P)H and FAD. The optical redox ratio is defined as the fluorescence intensity of [NAD(P)H / NAD(P)H +FAD] which measures the oxidation-reduction state of PDCOs. We have implemented WF ORI and developed novel leading-edge analysis tools to maximize the sensitivity and reproducibility of treatment response measurements in colorectal PDCOs. Leading-edge analysis improves sensitivity to redox changes in treated PDCOs (GΔ = 1.462 vs GΔ = 1.233). Additionally, WF ORI resolves FOLFOX treatment effects across all PDCOs better than two-photon ORI, with ∼7X increase in effect size (GΔ = 1.462 vs GΔ = 0.189). WF ORI distinguishes metabolic differences based on driver mutations in CRC PDCOs identifyingKRAS+PIK3CAdouble mutant PDCOs vs wildtype PDCOs with 80% accuracy and can identify treatment resistant mutations in mixed PDCO cultures (GΔ = 1.39). Overall, WF ORI enables rapid, sensitive, and reproducible measurements of treatment response and heterogeneity in colorectal PDCOs that will impact patient management, clinical trials, and preclinical drug development.Statement of SignificanceLabel-free wide-field optical redox imaging of patient-derived cancer organoids enables rapid, sensitive, and reproducible measurements of treatment response and heterogeneity that will impact patient management, clinical trials, and preclinical drug development.
A Witches’ Broom Phytoplasma effector induces stunting by stabilizing a bHLH transcription factor in plants
Authors: Yang Shuang , Lovelace Amelia , Yuan Yi , Nie Haizhen , Chen Weikai , Gao Yi , Bo Wenhao , Nagel Dawn H , Pang Xiaoming , Ma Wenbo 
Published: December 2024

SummaryPhytoplasmas are specialized phloem-limited bacteria that cause diseases on various crops resulting in significant agricultural losses. This research focuses on the jujube Witches’ Broom (JWB) phytoplasma and investigates the host-manipulating activity of the effector SJP39.We found that SJP39 directly interacts with the plant transcription factor bHLH87 in the nuclei. SJP39 stabilizes the bHLH87 homologs inA. thalianaand jujube, leading to growth defects in the plants.Transcriptomic analysis indicates that SJP39 affects the gibberellin (GA) pathway in jujube. We further demonstrate that ZjbHLH87 regulates GA signalling as a negative regulator and SJP39 enhances this regulation.The research offers important insights into the pathogenesis of JWB disease and identified SJP39 as a virulence factor that can contribute to the growth defects caused by JWB phytoplasma infection. These findings open new opportunities to manage JWB and other phytoplasma diseases.
Uncovering Ancient DNA in Petroleum: Insights into Earth’s Hidden Life Events and Geological History
Authors: Zhao Wan-Qian , Guo Zhan-Yong , Guo Yu-Qi , Li Mei-Jun , Cao Gang-Qiang , Tian Zeng-Yuan , Chai Ran , Qiu Li-You , Zeng Jin-Hua , Zhang Xin-Ge , Qin Tian-Cang , Yang Jin-Yu , Chen Ming-Jie , Song Mei-Rong , Liang Fei , Geng Jun-Hui , Zhou Chun-Yan , Zhang Shu-Jie , Zhao Li-Juan 
Published: December 2024

AbstractThis study employed nanoparticle affinity bead technology to isolate DNA from petroleum. The research identified 3,159,020 DNA sequences from petroleum extracts (pDNA), primarily from environmental DNA (eDNA). The study demonstrates how oil captures a vast array of eDNA through molecular exchanges with its surroundings, including the fragments from ancient periods (paeDNA) and more recent times (preDNA). An academically rigorous “mega screening method” was established to identify these fragments, revealing significant loss of the most originalin situDNA (oriDNA). Interestingly, the persistence of paeDNA provides valuable ecological and evolutionary insights that surpass traditional fossils. Petroleum, regarded as newly discovered fossils, reveals Earth’s hidden history by uncovering the ancient existence of marine species, ancestral birds, and unclassified species of ancient hominids. Additionally, the study sheds light on the tracks of locally extinct animals, including yaks, turkeys, and kiwi birds. Notably, these ancient DNA (aDNA) fragments do not exhibit signs of “deamination”, contradicting Pääbo’s standards for ancient,in situDNA authenticity. The study also highlights significant geological events, such as marine invasions during the Paleocene epoch. This work has the potential to revolutionize both petroleum geology and paleontology.
Generalists in a Specialist World: Vibrio-Phages with Broad Host Range
Authors: Bernard Charles , Labreuche Yannick , Diarra Carine , Daszkowski Pauline , Cahier Karine , Goudenège David , Lamarche Martin G. , Whitfield Gregory , Lang Manon , Valencia Jeffrey , Groseille Justine , Piel Damien , Brun Yves V. , Rocha Eduardo P.C. , Le Roux Frédérique 
Published: December 2024

ABSTRACTThe host range of a bacteriophage—the diversity of hosts it can infect—is central to understanding phage ecology and applications. While most well-characterized phages have narrow host ranges, broad-host-range phages represent an intriguing component of marine ecosystems. The genetic and evolutionary mechanisms driving their generalism remain poorly understood. In this study, we analyzed Schizotequatroviruses and theirVibrio crassostreaehosts, collected from an oyster farm. Schizotequatroviruses exhibit broad host ranges, large genomes (~252 kbp) encoding 26 tRNAs, and conserved genomic organization interspersed with recombination hotspots. These recombination events, particularly in regions encoding receptor-binding proteins and antidefense systems, highlight their adaptability to host resistance. Notably, some lineages demonstrated receptor-switching between OmpK and LamB, showcasing their evolutionary flexibility. Despite their broad host range, Schizotequatroviruses were rare in the environment. Their scarcity could not be attributed to burst size, which was comparable to other phagesin vitro, but may result from ecological constraints or fitness trade-offs, such as their preference for targeting generalist vibrios in seawater rather than the patho-phylotypes selected in oyster farms. Our findings clarify the genetic and ecological trade-offs shaping Schizotequatrovirus generalism and provide a foundation for future phage applications in aquaculture and beyond.
Cigarette smoke induces PPP1R15A via oxidative stress to modulate inflammatory cytokine production by bronchial epithelial cells
Authors: Amatngalim Gimano D. , van der Does Anne M. , Zarcone Maria C. , Malzer Elke , Bradley Jayson , Belvisi Maria G. , Birrell Mark , van Schadewijk Annemarie , Hiemstra Pieter S. , Marciniak Stefan J. 
Published: December 2024

AbstractCigarette smoke is the principal cause of chronic obstructive pulmonary disease (COPD) in western societies. It induces pulmonary inflammation and activates multiple stress signaling pathways in bronchial epithelial cells, including the integrated stress response (ISR). The ISR is triggered by phosphorylation of the translation initiation factor eIF2α in response to a variety of insults and is functionally antagonised by the eIF2α phosphatase subunit PPP1R15A. Deletion of PPP1R15A exaggerates the ISR and in many models protects against a cellular stress. However, loss of PPP1R15A was recently shown to exaggerate pulmonary fibrosis in bleomycin-challenged mice. We therefore wished to understand the role of PPP1R15A in the pulmonary response to cigarette smoke, which can cause both COPD and pulmonary fibrosis. Whole cigarette smoke rapidly activated the ISR in mucociliary differentiated human primary bronchial epithelial cells with those from COPD patients exhibiting higher levels of ISR. Acute exposure to cigarette smoke condensate induced a pro-inflammatory cytokine response accompanied by PPP1R15A expression. In this model, PPP1R15A induction was independent of eIF2α phosphorylation but was suppressed by antioxidants suggesting a response to oxidative stress. In vivo studies in mice revealed that PPP1R15A deficiency enhanced the secretion of proinflammatory cytokines in mice, suggesting a regulatory role for PPP1R15A in modulating the inflammatory response to smoke. Taken together, these data suggest that PPP1R15A is induced by cigarette smoke by an ISR-independent oxidative stress mechanism and ameliorates the pro-inflammatory cytokine response to cigarette smoke.
ISCO: Intelligent Framework for Accurate Segmentation and Comparative Analysis of Organoids
Authors: Zhou Jian , Fu Zihao , Ni Xiaoying , Luo Qi , Yang Gen 
Published: December 2024

AbstractOrganoids are self-organizing 3D cell clusters that closely mimic the structure and function of in vivo tissues and organs. Quantifying organoid morphology is critical for advancing our understanding of organ development, drug discovery, and toxicity assessment. Recent advances in microscopy have provided powerful tools to capture detailed morphological features of organoids, yet manual image analysis remains labor-intensive and time-consuming. In response, we present a comprehensive microscopy-based analysis pipeline that utilizes SegmentAnything 2.1 to accurately segment individual organoids. Additionally, we introduce a suite of morphological features—including perimeter, area, radius, non-smoothness, and non-circularity—that enable researchers to quantitatively and automatically analyze organoid structures. To further standardize organoid analysis across the field, Intelligent segmentation and comparison of organoids(ISCO), an intelligent AI-driven open-source algorithm, is developed with the aim of establishing a comprehensive toolset for organoid characterization.
Design of multi-echelon multi-fruit supply chain network considering multi-compartment reefer trucks to ensure food security
Authors: Yuvaraj M. , Jothi Basu R. , Prabhu B.V. , Boppana Satish Babu , Ganesh Kumar C. 
Published: December 2024

PurposeThe four pillars of food security are availability, accessibility, utilization and stability. In order to facilitate food security, an attempt is made to design a fruit supply chain network (FSCN) considering multi-compartment reefer trucks (MCRT) to reduce total supply chain costs. This in turn increases affordability, decreases food loss and increases availability, which further helps in improving food security.Design/methodology/approachA mixed integer non-linear programming (MNILP) model is developed to minimize the overall cost considering MCRT and the same is solved by a heuristic approach. A real-world case study is conducted to test the robustness of the model.FindingsThere is a considerable cost saving with the new proposed model (MCRT). The number of trucks used is drastically reduced when the dedicated truck is replaced with MCRT. Overall, the design of the FSCN not only improves food security by lowering the total supply chain cost but also shows a high impact on sustainability. Since the proposed model is a mathematical formulation, the same model can be applied to other perishable commodities like vegetables.Research limitations/implicationsThe proposed FSCN still requires more intermediaries to be added for more practicality. The model will be suitable for emerging markets mainly because the food supply chain sector is not completely organized.Originality/valueThis study is one of the initial studies in the context of facility location and FSCN optimization, specifically focusing on the inclusion of capacitated DCs. This study has the potential to assist supply chain managers in achieving sustainability by optimizing location decisions, inventory levels and movement between facilities. This study provides a valuable contribution towards the sustainable development goal of zero hunger (food security) by increasing affordability for low-income people.