bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opposing roles of resident and infiltrating immune cells in the defence againstLegionella longbeachaevia IL-18R/IFN-γ/ROS axis
Authors: Oberkircher Lara M. , Scheiding Victoria M. , Rafeld H. Linda , Hanssen Eric , Hansen Jan N. , Fleischmann Markus J. , Kessler Nina , Pitsch David , Wachten Dagmar , Kastenmüller Wolfgang , Brown Andrew S. , Hartland Elizabeth L. , van Driel Ian R. , Ng Garrett Z. , Garbi Natalio 
Published: February 2024

AbstractThe immune response againstLegionella longbeachae, a causative agent of the often-fatal Legionnaires’ pneumonia, is poorly understood. Here we investigated the specific roles of tissue-resident alveolar macrophages (AM) and infiltrating phagocytes during infection with this pathogen. AM were the predominant cell type that phagocytosed bacteria o day after infection. Three and five days after infection, AM numbers were greatly reduced while there was an influx of neutrophils and later monocyte-derived cells (MC) into lung tissue. AM carried greater numbers of viableL. longbeachaethan neutrophils and MC, which correlated with a higher capacity ofL. longbeachaeto translocate bacterial effector proteins required for bacterial replication into the AM cytosol. Cell ablation experiments demonstrated that AM promoted infection whereas neutrophils and MC were required for efficient bacterial clearance. IL-18 was important for IFN-γ production by IL-18R+NK cells and T cells which, in turn, stimulated ROS-mediated bactericidal activity in neutrophils resulting in restriction ofL. longbeachaeinfection. Ciliated epithelial cells also expressed IL-18R but did not play a role in IL-18-mediatedL. longbeachaeclearance. Our results have identified opposing innate functions of tissue-resident and infiltrating immune cells duringL. longbeachaeinfection that may be manipulated to improve protective responses.HighlightsAM serve as a replicative niche and promoteL. longbeachaeinfection.Infiltrating neutrophils and MC killL. longbeachae.IFN-γ from IL-18R+NK and T cells stimulates ROS and bacterial clearance.
Programmable RNA writing with trans-splicing
Authors: Schmitt-Ulms Cian , Kayabolen Alisan , Manero-Carranza Marcos , Zhou Nathan , Donnelly Keira , Nuccio Sabrina Pia , Kato Kazuki , Nishimasu Hiroshi , Gootenberg Jonathan S. , Abudayyeh Omar O. 
Published: February 2024

AbstractRNA editing offers the opportunity to introduce either stable or transient modifications to nucleic acid sequence without permanent off-target effects, but installation of arbitrary edits into the transcriptome is currently infeasible. Here, we describe Programmable RNA Editing & Cleavage for Insertion, Substitution, and Erasure (PRECISE), a versatile RNA editing method for writing RNA of arbitrary length and sequence into existing pre-mRNAs via 5′ or 3′ trans-splicing. In trans-splicing, an exogenous template is introduced to compete with the endogenous pre-mRNA, allowing for replacement of upstream or downstream exon sequence. Using Cas7-11 cleavage of pre-mRNAs to bias towards editing outcomes, we boost the efficiency of RNA trans-splicing by 10–100 fold, achieving editing rates between 5–50% and 85% on endogenous and reporter transcripts, respectively, while maintaining high-fidelity. We demonstrate PRECISE editing across 11 distinct endogenous transcripts of widely varying expression levels, showcasing more than 50 types of edits, including all 12 possible transversions and transitions, insertions ranging from 1 to 1,863 nucleotides, and deletions. We show high efficiency replacement of exon 4 of MECP2, addressing most mutations that drive the Rett Syndrome; editing of SHANK3 transcripts, a gene involved in Autism; and replacement of exon 1 of HTT, removing the hallmark repeat expansions of Huntington′s disease. Whole transcriptome sequencing reveals the high precision of PRECISE editing and lack of off-target trans-splicing activity. Furthermore, we combine payload engineering and ribozymes for protein-free, high-efficiency trans-splicing, with demonstrated efficiency in editing HTT exon 1 via AAV delivery. We show that the high activity of PRECISE editing enables editing in non-dividing neurons and patient-derived Huntington’s disease fibroblasts. PRECISE editing markedly broadens the scope of genetic editing, is straightforward to deliver over existing gene editing tools like prime editing, lacks permanent off-targets, and can enable any type of genetic edit large or small, including edits not otherwise possible with existing RNA base editors, widening the spectrum of addressable diseases.
Microtubules ensure transport of vegetative nuclei and sperm cells by fine-tuning their home positions
Authors: Motomura Kazuki , Tsuchi Haruna , Komojiri Marin , Matsumoto Ayumi , Sugi Naoya , Susaki Daichi , Takeda Atsushi , Kinoshita Tetsu , Maruyama Daisuke 
Published: February 2024

AbstractThe pollen tube plays a pivotal role in double fertilization by delivering sperm cells (SCs) to the ovule. InArabidopsis thaliana, a pair of SCs tightly connects with the vegetative nucleus (VN) to form the male germ unit (MGU), which is located in the apical region during pollen-tube growth, keeping the VN ahead of the SCs. MGU transport relies on independent motility of VN and SC pairs. However, the complexity of this dual motive force has hindered our understanding of MGU behavior, including its positioning and nuclear order. We usedArabidopsismutants or transgenic plants that produced semi-motile MGUs with aberrant VNs or SCs to analyze the positioning of VN or SCs after stochastically disconnecting the MGU. In pollen tubes with an immotile SC pair, the VN was ∼70 μm away from the tip, whereas in pollen tubes with an immotile VN, the SC pair was ∼100 μm away from the tip, implying that the VN and SCs have independent home positions. The position of MGU moved forward owing to the loss of the microtubule-destabilizing kinesinKINESIN-13A. Conversely, microtubule depolymerization by oryzalin treatment or introducing mutations inTUBULIN BETA 4(TUB4) deregulated the position of the MGU and shifted its position backward. In addition,tub4plants exhibited reduced fertility. These data indicate a significant role of microtubules in stable MGU positioning to ensure reproductive success.
Trait prediction through computational intelligence and machine learning applied to soybean (Glycine max) breeding in shaded environments
Authors: da Silva Júnior Antônio Carlos , Costa Weverton Gomes da , Guimarães Amanda Gonçalves , de Melo Moura Waldênia , Bhering Leonardo Lopes , Cruz Cosme Damião , Batista Renata Oliveira , dos Santos Jose Barbosa , Campos Wellington Ferreira , Evaristo Anderson Barbosa 
Published: February 2024

ABSTRACTThis study aims to identify more relevant predictors traits, considering different prediction approaches in soybean under different shading levels in the field, using methodologies based on artificial intelligence and machine learning. The experiments were carried out under different shading levels in a greenhouse and in the field, using sixteen cultivars. We have evaluated grain yield, which was used as a response trait, and 22 other attributes as explanatory traits. Three levels of shading were used to restrict photosynthetically active radiation (RPAR): 0%, 25%, and 48%. At full sun level (0% RPAR), the traits that presented better predictive performances using a multilayer perceptron were specific leaf area, plant height and number of pods. In the three levels of shading, the plant height trait exhibited the best performance for the radial base function network. Plant height showed the best predictive efficiency for grain yield at 25% and 48% RPAR, for all machine learning methodologies. Computational intelligence and machine learning methodologies have proven to be efficient in predicting soybean grain yield, regardless of shading level.
Heterologous expression and characterization of mutant cellulase from indigenous strain of Aspergillus niger
Authors: Ahmad Waqas , Zafar Muddassar , Anwar Zahid , Mehmood Ashraf Naeem , Ahmad Saira 
Published: February 2024

AbstractThe current study highlights the effect of mutagenesis on endoglucanase B activity of indigenous strain ofAspergillus nigerand its heterologous expression studies in thepET28a+vector. The physical and chemical mutagens were employed to incorporate mutations inA. niger. For determination of mutations, mRNA was isolated followed by cDNA synthesis and cellulase gene was amplified, purified and sequenced both from native and mutantA. niger.On comparison of gene sequences, it was observed that 5 nucleotide base pairs have been replaced in the mutant cellulase. The mutant recombinant enzyme showed 4.5 times higher activity (428.5 µmol/mL/min) as compared to activity of native enzyme (94 µmol/mL/min). The mutant gene was further investigated using Phyre2 and I-Tesser tools which exhibited 71% structural homology with Endoglucanase B ofThermoascus aurantiacus. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent accessible surface area (SASA), radius of gyration (Rg) and hydrogen bonds analysis were carried at 35 °C and 50 °C to explore the integrity of structure of recombinant mutant endoglucanase B which corresponded to its optimal temperature. Hydrogen bonds analysis showed more stability of recombinant mutant endoglucanase B as compared to native enzyme. Both native and mutant endoglucanase B genes were expressed inpET 28a+and purified with nickel affinity chromatography. Theoretical masses determined through ExPaSy Protparam were found 38.7 and 38.5 kDa for native and mutant enzymes, respectively. The optimal pH and temperature values for the mutant were 5.0 and 50 °C while for native these were found 4.0 and 35 °C, respectively. On reacting with carboxy methyl cellulose (CMC) as substrate, the mutant enzyme exhibited less Km(0.452 mg/mL) and more Vmax(50.25 µmol/ml/min) as compared to native having 0.534 mg/mL as Kmand 38.76 µmol/ml/min as Vmax. Among metal ions, Mg2+showed maximum inducing effect (200 %) on cellulase activity at 50 mM concentration followed by Ca2+(140%) at 100 mM concentration. Hence, expression of a recombinant mutant cellulase fromA. nigersignificantly enhanced its cellulytic potential which could be employed for further industrial applications at pilot scale.
SPRITE: improving spatial gene expression imputation with gene and cell networks
Authors: Sun Eric D. , Ma Rong , Zou James 
Published: February 2024

AbstractSpatially resolved single-cell transcriptomics have provided unprecedented insights into gene expressionin situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution are generally limited to the measurement of a small number of genes. To address this limitation, several algorithms have been developed to impute or predict the expression of additional genes that were not present in the measured gene panel. Current algorithms do not leverage the rich spatial and gene relational information in spatial transcriptomics. To improve spatial gene expression predictions, we introduce SPRITE (Spatial Propagation and Reinforcement of Imputed Transcript Expression) as a meta-algorithm that processes predictions obtained from existing methods by propagating information across gene correlation networks and spatial neighborhood graphs. SPRITE improves spatial gene expression predictions across multiple spatial transcriptomics datasets. Furthermore, SPRITE predicted spatial gene expression leads to improved clustering, visualization, and classification of cells. SPRITE is available as a software package and can be used in spatial transcriptomics data analysis to improve inferences based on predicted gene expression.
The lncRNAMalat1is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons
Authors: Xiao Wen , Halabi Reem , Lin Chia-Ho , Nazim Mohammad , Yeom Kyu-Hyeon , Black Douglas L 
Published: February 2024

AbstractSynaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion ofMalat1RNA redistributes to the cytoplasm. Depletion ofMalat1from neurons stimulated expression of particular pre- and post-synaptic proteins, implicatingMalat1in their regulation. NeuronalMalat1is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region ofMalat1containing short open reading frames. The upstream-most reading frame (M1) of theMalat1locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate thatMalat1serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
IL-3-driven T cell-basophil crosstalk enhances anti-tumor immunity
Authors: Wei Jian , Mayberry Colleen L. , Lv Xiaoting , Hu Fangyan , Sears John D. , Khan Taushif , Logan Natalie A. , Wilson John J. , Chaussabel Damien , Chang Chih-Hao 
Published: February 2024

ABSTRACTCytotoxic T lymphocytes (CTLs) are pivotal in combating cancer, yet their efficacy is often hindered by the immunosuppressive tumor microenvironment, resulting in exhaustion. This study investigates the role of interleukin (IL)-3 in orchestrating anti-tumor immunity through CTL modulation. Intratumoral CTLs undergo a progressive decline in IL-3 production, which is correlated with impaired cytotoxic function. Augmenting IL-3, through intraperitoneal administration, IL-3-expressing melanoma cells, or IL-3-engineered CD8+T cells, confers protection against tumor progression, concomitant with increased CTL activity. CTLs are critical in this therapeutic efficacy as IL-3 demonstrates no impact on tumor growth in RAG1 knockout mice or following CD8+T cell-depletion. Rather than acting directly, CTL-derived IL-3 exerts its influence on basophils, synergistically amplifying anti-tumor immunity within CTLs. Introducing IL-3-activated basophils retards tumor progression, whereas basophil depletion diminishes the effectiveness of IL-3 supplementation. Furthermore, IL-3 prompts basophils to produce IL-4, which subsequently elevates IFN-γ production and viability of CTLs. Notably, the importance of basophil-derived IL-4 is evident from the absent benefits in IL-3-supplementated, IL-4 knockout tumor-bearing mice. Overall, this research unveils IL-3-mediated CTL-basophil crosstalk in regulating anti-tumor immunity and offers the prospect of harnessing IL-3 sustenance as a promising approach for optimizing and enhancing cancer immunotherapy.Significance StatementThis study elucidates the critical role of IL-3 in orchestrating anti-tumor immunity, particularly within the context of CTLs and melanoma growth. It reveals a progressive decline in CTL-derived IL-3 during tumor progression, correlated with CTL exhaustion—a formidable barrier in cancer immunotherapy. Intriguingly, augmentation of IL-3, achieved through diverse means, effectively impedes tumor progression by enhancing CTL activity. This research unveils a novel mechanism: IL-3-mediated crosstalk between CTLs and IL-4-producing basophils, resulting in the rejuvenation of CTLs and amplifying their anti-tumor ability. These insights hold promise for the advancement and optimization of cancer immunotherapeutic strategies, deepening our comprehension of CTL dynamics within the tumor microenvironment, and advancing our ability to combat cancer effectively.
Bilateral regulation of EGFR activity and local PI dynamics observed with superresolution microscopy
Authors: Abe Mitsuhiro , Yanagawa Masataka , Hiroshima Michio , Kobayashi Toshihide , Sako Yasushi 
Published: February 2024

AbstractAnionic lipid molecules, including phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), are implicated in the regulation of epidermal growth factor receptor (EGFR). However, the role of the spatiotemporal dynamics of PI(4,5)P2in the regulation of EGFR activity in living cells is not fully understood, as it is difficult to visualize the local lipid domains around EGFR. In this study, both EGFR and PI(4,5)P2nanodomains in the plasma membrane were visualized using super-resolution single-molecule microscopy. The EGFR and PI(4,5)P2nanodomains aggregated before stimulation with epidermal growth factor (EGF) through transient visits of EGFR to the PI(4,5)P2nanodomains. The degree of coaggregation decreased after EGF stimulation and depended on phospholipase Cγ, the EGFR effector hydrolyzing PI(4,5)P2. Artificial reduction in the PI(4,5)P2content of the plasma membrane reduced both the dimerization and autophosphorylation of EGFR after stimulation with EGF. Inhibition of PI(4,5)P2hydrolysis after EGF stimulation decreased phosphorylation of EGFR-Thr654. Thus, EGFR kinase activity and the density of PI(4,5)P2around EGFR molecules were found to be mutually regulated.
Reconstructing microvascular network skeletons from 3D images: what is the ground truth?
Authors: Walsh Claire , Berg Maxime , West Hannah , Holroyd Natalie A. , Walker-Samuel Simon , Shipley Rebecca J. 
Published: February 2024

ABSTRACTStructural changes to microvascular networks are increasingly highlighted as markers of pathogenesis in a wide range of disease, e.g. Alzheimer’s disease, vascular dementia and tumour growth. This has motivated the development of dedicated 3D imaging techniques, alongside the creation of computational modelling frameworks capable of using 3D reconstructed networks to simulate functional behaviours such as blood flow or transport processes. Extraction of 3D networks from imaging data broadly consists of two image processing steps: segmentation followed by skeletonisation. Much research effort has been devoted to segmentation field, and there are standard and widely-applied methodologies for creating and assessing gold standards or ground truths produced by manual annotation or automated algorithms.The Skeletonisation field, however, lacks widely applied, simple to compute metrics for the validation or optimisation of the numerous algorithms that exist to extract skeletons from binary images. This is particularly problematic as 3D imaging datasets increase in size and visual inspection becomes an insufficient validation approach. In this work, we first demonstrate the extent of the problem by applying 4 widely-used skeletonisation algorithms to 3 different imaging datasets. In doing so we show significant variability between reconstructed skeletons of the same segmented imaging dataset. Moreover, we show that such a structural variability propagates to simulated metrics such as blood flow. To mitigate this variability we introduce a new, fast and easy to compute super-metric that compares the volume, connectivity, medialness, correct bifurcation point identification and homology of the reconstructed skeletons to the original segmented data. We then show that such a metric can be used to select the best performing skeletonisation algorithm for a given dataset, as well as to optimize its parameters. Finally, we demonstrate that the super-metric can also be used to quickly identify how a particular skeletonisation algorithm could be improved, becoming a powerful tool in understanding the complex implication of small structural changes in a network.
Memory’s gatekeeper: the role of PFC in the encoding of familiar events
Authors: Guerreiro Inês C. , Clopath Claudia 
Published: February 2024

AbstractTheoretical models conventionally portray the consolidation of memories as a slow process that unfolds during sleep. According to the classical Complementary Learning Systems (CLS) theory (as presented in J. McClelland et al., 1995), the hippocampus (HPC) rapidly changes its connectivity during wakefulness to encode ongoing events and create memory ensembles that are later transferred to the prefrontal cortex (PFC) during sleep. However, recent experimental studies challenge this notion by showing that new information consistent with prior knowledge can be rapidly consolidated in PFC during wakefulness, and that PFC lesions disrupt the encoding of familiar events in the HPC. These results challenge the widely accepted view that consolidation is a slow process that unfolds during sleep and highlight the role of PFC during the initial stages of memory encoding. The contributions of the PFC to memory encoding have therefore largely been overlooked. Moreover, most theoretical frameworks assume random and uncorrelated patterns representing memories, disregarding the correlations between our experiences. To address this shortcomings, we developed a HPC-PFC network model that simulates interactions between the HPC and PFC during the encoding of a memory (awake stage), and subsequent consolidation (sleeping stage) to examine the contributions of each region to the consolidation of novel and familiar memories. Our results show that the PFC network uses stored memory “schemas” consolidated during previous experiences to identify inputs that evoke familiar patterns of activity, quickly integrated it in its network, and gate which components are encoded in the HPC. More specifically, the PFC uses GABAergic long-range projections to inhibit HPC neurons representing input components correlated with a previously stored memory “schema”, eliciting sparse hippocampal activity during exposure to familiar events, as it has been experimentally observed.
MicroRNAs and mRNA Regulatory Network of Parenchymal Hematoma after Endovascular Mechanical Reperfusion for Acute Ischemic Stroke in Rat
Authors: Zhuang Jin-Kun , Huang Zhong-Run , Qin Wang , Li Chang-Luo , Li Qi , Xiang Chun , Tuo Yong-Hua , Liu Zhong , Chen Qian-Yu , Shi Zhong-Song 
Published: February 2024

AbstractHemorrhagic transformation after endovascular thrombectomy predicts poor outcomes in acute ischemic stroke with large vessel occlusion. The roles of microRNAs in the pathogenesis of parenchymal hematoma (PH) are still unclear. This study aims to investigate the microRNA and mRNA regulatory network associated with PH after mechanical reperfusion in the animal stroke model and oxygen-glucose deprivation/reoxygenation (OGD/R) model. Twenty-five microRNAs were assessed in the reperfusion-induced hemorrhage model in rats with hyperglycemic conditions receiving 5-hour middle cerebral artery occlusion. Thirteen down-regulated microRNAs (miRNA-29a-5p, miRNA-29c-3p, miRNA-126a-5p, miRNA-132-3p, miRNA-136-3p, miRNA-142-3p, miRNA-153-5p, miRNA-218a-5p, miRNA-219a-2-3p, miRNA-369-5p, miRNA-376a-5p, miRNA-376b-5p, miRNA-383-5p) and one up-regulated microRNA (miRNA-195-3p) were found in rat peri-infarct with PH. Ten of these 14 PH-related microRNAs were significantly differentially expressed in at least two of five models of neuron, astrocyte, microglia, BMEC, and pericyte after OGD/R, consistent with the animal model results. Thirty-one predicted hub target genes were significantly differentially expressed in rat peri-infarct with PH. Forty-nine microRNA-mRNA regulatory axes of PH were revealed, which were related to the mechanisms of oxidative stress, apoptosis, immune, and inflammation. Simultaneously differentially expressed microRNAs and related genes in several cells of the neurovascular unit may serve as valuable targets for PH after endovascular thrombectomy in acute ischemic stroke.