bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome and variant analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene
Authors: Yokoi Norihide , Adachi Naoki , Hirokoji Tomoki , Nakano Kenta , Yoshihara Minako , Shigenaka Saki , Urakawa Ryuya , Taniguchi Yukio , Yoshida Yusaku , Yokose Shigeo , Suyama Mikita , Okamura Tadashi 
Published: September 2024

AbstractWe have recently established the Zucker fatty diabetes mellitus (ZFDM) rat as a novel model of obese type 2 diabetes (T2D), originating from the obese Zucker fatty (ZF) rat harboring a missense mutation in the leptin receptor gene. Pathogenesis of dysfunction of the pancreatic islets and genetic factors of T2D in ZFDM rats remain unknown. Here, we perform comparative transcriptome and variant analyses of the pancreatic islets between the two strains. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identify a nonsense mutation, c.409C>T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. Interestingly, we find that theLcn2mutation is distributed widely in rat species, such as commonly used DA and F344 strains. We examine theLcn2mutation as a strong candidate gene for T2D in ZFDM rats by using genome editing of ZFDM rats in which the nonsense mutation is replaced with a wild-type nucleotide. We find that the genome editing well works but also observe that there is no significant difference in the development of T2D between genome-edited and original ZFDM rats. Finally, we perform a genetic linkage analysis by using backcross progeny between ZF and ZFDM rats and confirm that theLcn2mutation exhibits no significant association with the onset of T2D. Our data indicate that several rat strains would serve asLcn2deficient models, contributing to elucidate pathophysiological roles of Lcn2 in a wide variety of phenotypes.
Metastatic tumor cells in bone marrow differ from paired neuroblastoma tumor and contain subsets with therapy-resistant characteristics
Authors: Hochheuser Caroline , Boltjes Arjan , Keller Kaylee M. , Tol Simon , van de Mheen Marieke , Pita Barros Carolina , van Gestel-Fadaie Zeinab , van Kuilenburg André B. P. , van Hooff Sander , Voermans Carlijn , Molenaar Jan J. , Tytgat Godelieve A. M. , Timmerman Ilse 
Published: September 2024

AbstractBone marrow (BM) is a common site for solid tumor metastasis, often causing poor outcome. Here, we define the characteristics of BM-disseminated tumor cells (DTCs) using neuroblastoma as a model. We combined single-cell RNA-sequencing (scRNA-seq) and cell-surface protein analysis using 7 paired BM and primary tumor (PT) samples and found that DTCs contain a higher percentage of cycling cells and higher expression of neurodevelopmental genes compared to corresponding PT cells. In 6 patients, the copy number variation profile differed between PT cells and DTCs, indicating spatial heterogeneity. Within the BM, we detected dormant DTCs with potentially reduced chemosensitivity; this population contained cells expressing low levels of the immunotherapeutic antigen GD2 and increased NGFR expression. In conclusion, we characterized DTCs that are particularly challenging to target, offering new avenues for developing therapeutic strategies designed to target all subpopulations within the highly complex metastatic site, thereby preventing the development of drug-resistant clones.
Molecular rotors provide insight into the mechanism of formation and conversion ofα-synuclein aggregates
Authors: Allerton Siân C. , Kuimova Marina K. , Aprile Francesco A. 
Published: September 2024

ABSTRACTα-Synuclein is an intrinsically disordered protein that forms amyloids in Parkinson’s disease. Currently, detection methods predominantly report on the formation of mature amyloids but have poor sensitivity to the early-stage, toxic oligomers. Molecular rotors are fluorophores that sense changes in the viscosity of their local environment. Here, we monitorα-synuclein oligomer formation using the fluorescence lifetime of molecular rotors. We detect oligomer formation and conversion into amyloids forwild typeand twoα-synuclein variants; the pathological mutant A30P and ΔPα-synuclein, which lacks a master regulator region of aggregation (residues 36-42). We report that A30Pα-synuclein shows a similar rate of oligomer formation compared towild type α-synuclein, whereas ΔPα-synuclein shows delayed oligomer formation. Additionally, both variants demonstrate a slower conversion of oligomers to amyloids. Our method provides a quantitative approach to unveiling the complex mechanism ofα-synuclein aggregation which is key to understanding the pathology of Parkinson’s disease.
Loss of Neurofibromin Induces Inflammatory Macrophage Phenotypic Switch and Retinal Neovascularization via GLUT1 Activation
Authors: Zaidi Yusra , Tritz Rebekah , Zaidi Nida , Nabi Faisal , Zaidi Syed Adeel H. , Morsy Abdelhakim , Harris Valerie , Racine Rilee , Hudson Farlyn Z. , Bordan Zsuzsanna , Kennard Simone , Batori Robert , Huo Yuqing , Csanyi Gabor , Belin de Chantemèle Eric J. , Lei Kecheng , Boulis Nicholas M. , Fulton David J. , Khan Rizwan Hasan , Caldwell Ruth B. , Stansfield Brian K. 
Published: September 2024

AbstractPersons with neurofibromatosis type 1 (NF1), a tumor predisposition syndrome, are largely protected from diabetes and exhibit evidence of enhanced glucose metabolism, which is replicated in mice harboringNf1mutations. A hallmark of NF1-associated neurofibromas and sarcomas is the high density of inflammatory macrophages and targeting macrophages appears efficacious in models of NF1. Inflammatory macrophages rely on glycolysis to rapidly generate ATP; thus, identifying whether neurofibromin, the protein encoded by theNF1gene, controls glucose uptake and/or glycolysis in macrophages is therapeutically compelling. Using neurofibromin-deficient macrophages and macrophage-specificNf1knockout mice, we demonstrate that neurofibromin complexes with glucose transporter 1 (GLUT1) to restrain its activity and that loss of neurofibromin permits Akt2 to facilitate GLUT1 translocation to the membrane in macrophages. In turn, glucose internalization and glycolysis are highly up regulated and provoke putative reparative (M2) macrophages to undergo inflammatory phenotypic switch. Inflammatory M1 macrophages and inflammatory-like M2 macrophages invest the perivascular stroma of tumors and induce pathologic angiogenesis in mice harboring macrophage-specificNf1deletion. These studies identify a clear mechanism for the enhanced glycolysis and low risk for diabetes observed in persons with NF1 and provide a novel therapeutic target for manifestations of NF1.
Isotonic and minimally invasive optical clearing media for live cell imagingex vivoandin vivo
Authors: Inagaki Shigenori , Nakagawa-Tamagawa Nao , Huynh Nathan , Kambe Yuki , Yagasaki Rei , Manita Satoshi , Fujimoto Satoshi , Noda Takahiro , Mori Misato , Teranishi Aki , Takeshima Hikari , Naitou Yuki , Yokoyama Tatsushi , Sakamoto Masayuki , Hayashi Katsuhiko , Kitamura Kazuo , Tagawa Yoshiaki , Okuda Satoru , Sato Tatsuo K. , Imai Takeshi 
Published: September 2024

AbstractTissue clearing has been widely used for fluorescence imaging of fixed tissues, but not for live tissues due to its toxicity. Here we develop minimally invasive optical clearing media for fluorescence imaging of live mammalian tissues. Light scattering is minimized by adding spherical polymers with low osmolarity to the extracellular medium. A clearing medium containing bovine serum albumin (SeeDB-Live) is minimally invasive to live cells, allowing for structural and functional imaging of live tissues, such as spheroids, organoids, acute brain slices, and the mouse brainin vivo. SeeDB-Live minimally affects the electrophysiological properties and sensory responses of neurons. We demonstrate its utility for widefield imaging of subcellular voltage dynamics, such as backpropagating action potentials, in acute brain slices. We also utilize SeeDB-Live for widefield voltage imaging of dozens of dendritesin vivo, demonstrating population dynamics. Thus, SeeDB-Live expands the scale and modalities of fluorescence imaging of live mammalian tissues.
CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 Å resolution. A comparison with mammalian and avian F-actin
Authors: Stevenson Sarah R. , Tzokov Svetomir B. , Lahiri Indrajit , Ayscough Kathryn R. , Bullough Per A. 
Published: September 2024

SUMMARYThe core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerises into filaments (F-actin). Budding yeast possesses a single actin which shares 87-89% sequence identity with vertebrate actin isoforms. Previous structural studies indicate very close overlap of main-chain backbones. Intriguingly however, substitution of yeastACT1with vertebrate β-cytoplasmic actin severely disrupts cell function and substitution with a skeletal muscle isoform is lethal. Here we report a 2.5 Å structure of budding yeast F-actin. Previously unresolved side-chain information now highlights four main differences in the comparison of yeast and vertebrate ADP F-actins: a more open nucleotide binding pocket; a more solvent exposed C-terminus; a rearrangement of intersubunit binding interactions in the vicinity of the D-loop and changes in the hydrogen bonding network in the vicinity of histidine 73 (yeast actin) and methyl-histidine 73 (vertebrate actin).
Differential restriction of chikungunya virus in primary human cardiac endothelial cells occurs at multiple steps in the viral life cycle
Authors: Spector Sophie N. , Noval Maria G. , Stapleford Kenneth A. 
Published: September 2024

AbstractArthropod-borne viruses (arboviruses) constitute a significant ongoing public health threat, as the mechanisms of pathogenesis remain incompletely understood. Cardiovascular symptomatology is emerging as an important manifestation of arboviral infection. We have recently studied the cardiac tropism and mechanisms implicated in cardiac damage in mice for the alphavirus chikungunya virus (CHIKV), and we therefore sought to evaluate the cardiac tropism of other emerging alphaviruses and arboviruses. Using human primary cardiac cells, we found that arboviruses from diverse viral families were able to replicate within these cells. Interestingly, we noted that while the closely related alphavirus Mayaro virus (MAYV) could replicate to high titers in primary human cardiac microvascular endothelial cells, pulmonary, and brain endothelial cells, the Indian Ocean Lineage of CHIKV (CHIKV-IOL) was completely restricted in all endothelial cells tested. Upon further investigation, we discovered that this restriction occurs at both entry and egress stages. Additionally, we observed that compared to CHIKV, MAYV may antagonize or evade the innate immune response more efficiently in human cardiac endothelial cells to increase infection. Overall, this study explores the tropism of arboviruses in human primary cardiac cells and characterizes the strain-specific restriction of CHIKV-IOL in human endothelial cells. Further work is needed to understand how the differential restriction of alphaviruses in human endothelial cells impacts pathogenesis in a living model, as well as the specific host factors responsible.Author SummaryMosquito-borne viruses, such as those within the alphavirus genus, are an ongoing concern to human health globally. While we have recently begun to explore the mechanisms of CHIKV-induced pathology in the heart, little is known about other arboviruses and alphaviruses related to CHIKV. Here, we identified that multiple cardiac cell types are susceptible to infection by several arboviruses important to public health. Specifically, we noted differences in how two related viruses, CHIKV and MAYV, infect endothelial cells from multiple origins. This work highlights the potential for other emerging arboviruses, in addition to CHIKV, to directly infect cardiac tissue. Moreover, it emphasizes the ability for MAYV, an emerging virus that is less studied, to infect various endothelial cell types to high titers, suggesting the need for further research on MAYV pathogenesis. Finally, this research identifies differences in infection between individual strains of CHIKV, suggesting a finely tuned mechanism of restriction in endothelial cells that can be further explored, as well as the need to study use different viral strains for future alphavirus research.
Toxoplasma gondiitranscription factor AP2XII-8: a key regulator of G1 phase progression and parasite division
Authors: Shi Yuehong , Yang Qiang , He Yue , Song Xingju , Hu Dandan 
Published: September 2024

AbstractThe apicomplexan parasiteToxoplasma gondiican infect humans and virtually all warm-blooded animals worldwide, posing a significant threat to public health and being of veterinary importance. Acute infections are characterized by the fast replication of tachyzoites inside host cells. During this fast amplification process, gene expression is highly regulated by a series of regulatory networks. The G1 phase, which is usually conserved across species, is responsible for preparing the materials necessary for the next replicating cell cycle; however, few regulators have been identified at this stage. Here, we functionally characterized the C/G1 phase-expressed ApiAP2 transcription factor, TgAP2XII-8, inT. gondiitachyzoites. Conditional knockdown of TgAP2XII-8 leads to significant growth defects and asexual division disorders. Additionally, parasite cell cycle progression was disrupted following TgAP2XII-8 depletion, characterized by G1 phase arrest. RNA-seq and CUT&Tag experiments revealed that TgAP2XII-8 acts as an activator of ribosomal proteins expressed in the G1 phase. Moreover, TgAP2XII-8 binds to a specific DNA motif ([T/C]GCATGCA), which is abundant and conserved in the intergenic region of several other apicomplexans, possibly suggesting a broad and conserved role for this ApiAP2 in the Phylum of Apicomplexa. Our study reveals that TgAP2XII-8 acts as a critical C/G1 phase regulator, orchestrating the cell cycle inT. gondiitachyzoites. This study contributes to a broader understanding of the complexity of the parasite’s cell cycle and its key regulators.
gsQTL: Associating genetic risk variants with gene sets by exploiting their shared variability
Authors: Bouland Gerard A. , Tesi Niccolò , Mahfouz Ahmed , Reinders Marcel J.T. 
Published: September 2024

AbstractTo investigate the functional significance of genetic risk loci identified through genome-wide association studies (GWASs), genetic loci are linked to genes based on their capacity to account for variation in gene expression, resulting in expression quantitative trait loci (eQTL). Following this, gene set analyses are commonly used to gain insights into functionality. However, the efficacy of this approach is hampered by small effect sizes and the burden of multiple testing. We propose an alternative approach: instead of examining the cumulative associations of individual genes within a gene set, we consider the collective variation of the entire gene set. We introduce the concept of gene set QTL (gsQTL), and show it to be more adept at identifying links between genetic risk variants and specific gene sets. Notably, gsQTL experiences less susceptibility to inflation or deflation of significant enrichments compared with conventional methods. Furthermore, we demonstrate the broader applicability of shared variability within gene sets. This is evident in scenarios such as the coordinated regulation of genes by a transcription factor or coordinated differential expression.
Preventive Effects of Pomegranate Seed Oil on Transient Middle Cerebral Artery Occlusion via the Keap1/Nrf2/NQO1 Pathway in the rats Cortex
Authors: Li Dongyang , Zhang Chaoying , Luo Qi , Li Man , Tian Meiqi , Jiao Hanyi , Xi Xiangwen , Weng Qifang 
Published: September 2024

AbstractIschemic stroke remains a pressing challenge that needs to be solved. Energy metabolic failure is a critical factor contributing to mitochondrial dysfunction and oxidative stress in the pathogenesis of brain ischemia, leading to the generation of excessive reactive oxygen species. Pomegranate seed oil (PSO) exhibits antioxidant properties; however, its protective effects against cerebral ischemia/reperfusion injury and the underlying mechanisms remain unclear. In this study, a transient middle cerebral artery occlusion (tMCAO) rat model was employed to simulate cerebral ischemia/reperfusion injury. We investigated the mechanisms by which different concentrations of PSO modulate oxidative damage caused by cerebral ischemia/reperfusion injury through the Keap1/Nrf2/NQO1 pathway in cortex. SD male rats were randomly divided into four groups: Control, tMCAO+NaCl, tMCAO+LO (low concentration of PSO), tMCAO+MO (medium concentration of PSO), and tMCAO+HO (high concentration of PSO). Our findings suggest that low concentration of PSO exerts neuroprotective effects by activating Nrf2 and NQO1, thereby reducing oxidative stress. Furthermore, LO significantly improved neurological scores and reduced neuronal edema. Additionally, the results demonstrated an increase in superoxide dismutase (SOD) levels and a decrease in malondialdehyde (MDA) levels. In contrast, MO and HO exhibited suboptimal effects. To sum up, these results indicate that PSO activates neuroprotective pathways against oxidative stress following cerebral ischemia/reperfusion injury via the Keap1/Nrf2/NQO1 pathway, providing novel insights into potential preventive therapies for cerebral ischemia/reperfusion.
Production of bioactive structural motifs from wheat arabinoxylan via colonic fermentation and enzymatic catalysis: evidence of interaction with toll-like receptors fromin vitro, in silicoand functional analysis
Authors: de A Guerreiro Caroline , Andrade Leandro AD , Fraga Layanne N , Marques Tatiana M , Prado Samira BR , Brummer Robert J , Nascimento João Roberto O , Castro-Alves Victor 
Published: September 2024

AbstractIt is well known that dietary fibers (DF) from plant-source foods can induce beneficial health effects through their physicochemical properties and utilization by the gut microbiota during fermentation, which is mainly explored with a focus on changes in the gut microbiota profile and the production of microbial-derived metabolites. Here, we characterized structural motifs (i.e., oligomers) produced during DF breakdown upon colonic fermentation and explored their interaction with toll-like receptors (TLRs) present on the surface of human intestinal and immune system cells. Firstly, a source of wheat arabinoxylan (WAX) was subjected toin vitrosimulation of human colonic fermentation, followed by characterization and quantification of WAX structural motifs to explore their dynamics throughout fermentation. The identified structural motifs were further produced through enzymatic catalysis of WAX using carbohydrate-active enzymes and fractionated into six well-defined fractions of arabinoxylans and linear xylans. These fractions of structural motifs were then tested for interaction with TLR2 and TLR4 using a reporter cell assay. Results revealed structure-dependent effects, primarily with inhibition of TLR2 and activation of TLR4 depending on the degree of polymerization and branching of WAX structural motifs. The role of the fine structure of WAX structural motifs was confirmed by molecular docking, which revealed that minor structural changes substantially influence the interaction between structural motifs and TLRs. The results fromin vitroandin silicostudies also support the hypothesis that the direct effects of oligomers and polysaccharides on cell receptors are likely the result of complex interactions involving multiple cell surface receptors. Finally, in addition to highlighting that direct effects of structural motifs might play an important role in the overall effects of DF, this work suggests that enzymatic-tailoring design of DF can be a potential tool for producing functional ingredients with specific effects on human health.
A high-speed OLED monitor for precise stimulation in vision, eye-tracking, and EEG research
Authors: Dimigen Olaf , Stein Arne 
Published: September 2024

ABSTRACTThe recent introduction of organic light-emitting diode (OLED) monitors with refresh rates of 240 Hz or more opens new possibilities for their use as precise stimulation devices in vision research, experimental psychology, and electrophysiology. These affordable high-speed monitors, targeted at video gamers, promise several advantages over the cathode ray tube (CRT) and liquid crystal display (LCD) monitors commonly used in these fields. Unlike LCDs, OLED displays have self-emitting pixels that can show true black, resulting in superior contrast ratios, a broad color gamut, and good viewing angles. More importantly, the latest gaming OLEDs promise excellent timing properties with minimal input lags and rapid transition times. However, OLED technology also has potential drawbacks, notably Auto-Brightness Limiting (ABL) behavior, where the local luminance of a stimulus can change with the number of currently illuminated pixels. This study characterized a 240 Hz OLED monitor, the ASUS PG27AQDM, in terms of its timing properties, spatial uniformity, viewing angles, warm-up times, and ABL behavior. We also compared its responses to those of CRTs and LCDs. Results confirm the monitor’s excellent temporal properties with CRT-like transition times (around 0.3 ms), wide viewing angles, and decent spatial uniformity. Additionally, we found that ABL could be prevented with appropriate settings. We illustrate the monitor’s benefits in two time-critical paradigms: Rapid “invisible” flicker stimulation and the gaze-contingent presentation of stimuli during eye movements. Ourfindings suggest that the newest gaming OLEDs are precise and cost-effective stimulation devices for visual experiments that have several key advantages over CRTs and LCDs.
Identification of a fungal antibacterial endopeptidase that modulates immune responses
Authors: Machata Silke , Bertsche Ute , Hoffmann Franziska , Fattal Zaher M. , Kage Franziska , Flak Michal , Iliou Alexander N. J. , Hillmann Falk , von Eggeling Ferdinand , Slevogt Hortense , Brakhage Axel A. , Jacobsen Ilse D. 
Published: September 2024

AbstractAspergillus fumigatusis a saprophytic fungus dwelling in soil and on decaying plant material, but also an opportunistic pathogen in immunocompromised patients. In its environmental niche,A. fumigatusfaces competition from other microorganisms including bacteria. Here, we describe the discovery of the first secreted antibacterial protein inA. fumigatus. We identified a secreted fungal endopeptidase, designated CwhA, that cleaves peptidoglycan of Gram-positive bacteria at specific residues within the peptidoglycan stem peptide. Cleavage leads to bacterial lysis and the release of peptidoglycan cleavage products. Expression ofcwhAis induced by the presence of bacteria. Furthermore, CwhA is highly abundant in murine lungs during invasive pulmonary aspergillosis and peptidoglycan cleavage products generated by CwhA stimulate cytokine production of human immune cells. Although CwhA does not affect human cells directly, this novel player in fungal-bacterial interactions could affectA. fumigatusinfections by inhibiting Gram-positive bacteria in its vicinity, and modulating the immune system.