bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacological Activation of NO-Sensitive Guanylyl Cyclase Ameliorates Obesity-Induced Arterial Stiffness
Authors: Budbazar Enkhjargal , Balmes Aylin , Elliott Danielle , Tintin Lisette Peres , Kopp Timo , Feil Susanne , Feil Robert , Schäffer Tilman E. , Seta Francesca 
Published: February 2025

ABSTRACTObjectiveArterial stiffness, or loss of elastic compliance in large arteries, is an independent precursor of cardiovascular disease (CVD)1and dementia2. Akin to anti-hypertensive and lipid-lowering drugs, arterial de-stiffening therapies could be beneficial at decreasing CVD risk. We previously discovered that enhanced cytoskeletal actin polymerization in vascular smooth muscle cells (VSMCs) contributes to increased arterial stiffness3. In aortas and VSMCs, we previously found that decreased NO-sensitive guanylyl cyclase (NO-GC), the NO receptor which synthesizes cGMP, caused downregulation of cGMP-dependent protein kinase I (cGKI) and of its target vasodilator-stimulated phosphoprotein (pVASPS239), leading to increased cytoskeletal actin polymerization3. In the current study, we tested whether activating NO-GC with an NO-GC activator (cinaciguat) modulates pVASPS239and cytoskeletal actin polymerization in VSMCs, thereby preventing obesity-induced arterial stiffness.Approach & ResultsCinaciguat administration (5 mg/kg) to high fat, high sucrose diet (HFHS)-fed mice, our established model of arterial stiffness4, (1) decreased pulse wave velocity, thein vivoindex of arterial stiffness, without affecting blood pressure, (2) increased aortic pVASPS239levels, and (3) decreased the ratio of filamentous (F) to globular (G) actin, compared to vehicle administration. In cultured VSMCs, cinaciguat (10 μmol/L) increased pVASPS239levels and decreased the F/G actin ratio at baseline and after stimulation with the cytokine tumor necrosis factor α (TNFα), used to mimic the inflammatory milieu of HFHS aortas. These effects were abrogated in aortas and VSMCs from mice with smooth muscle-specific cGKI deletion (cGKISMKO), while being mimicked by a cell-permeable cGMP analog (8-Br-cGMP, 1 μmol/L), which also decreased VSMC stiffnessin vitro.ConclusionsCollectively, our data strongly support the notion that pharmacological NO-GC activation would be beneficial in decreasing obesity-associated arterial stiffness by decreasing VSMC cytoskeletal actin hyper-polymerization. If translated to humans, NO-GC activators could become a viable approach to clinically treat arterial stiffness, which remains an unmet medical need.
The interactome of the Bakers’ yeast peroxiredoxin Tsa1 implicates it in the redox regulation of intermediary metabolism, glycolysis and zinc homeostasis
Authors: MacDiarmid Colin W. , Taggart Janet , Wang Yirong , Vashisht Ajay , Qing Xin , Wohlschlegel James A. , Eide David J. 
Published: February 2025

ABSTRACTZinc (Zn) is an essential nutrient supporting a range of critical processes. In the yeastSaccharomyces cerevisiae, Zn deficiency induces a transcriptional response mediated by the Zap1 activator, which controls a regulon of ∼80 genes. A subset support zinc homeostasis by promoting zinc uptake and its distribution between compartments, while the remainder mediate an “adaptive response” to enhance fitness of zinc deficient cells. The peroxiredoxin Tsa1 is a Zap1-regulated adaptive factor essential for the growth of Zn deficient cells. Tsa1 can function as an antioxidant peroxidase, protein chaperone, or redox sensor: the latter activity oxidizes associated proteins via a redox relay mechanism. We previously reported that in Zn deficient cells, Tsa1 inhibits pyruvate kinase (Pyk1) to conserve phosphoenolpyruvate for aromatic amino acid synthesis. However, this regulation makes a relatively minor contribution to fitness in low zinc, suggesting that Tsa1 targets other pathways important to adaptation. Consistent with this model, the redox sensor function of Tsa1 was essential for growth of ZnD cells. Using an MBP-tagged version of Tsa1, we identified a redox-sensitive non-covalent interaction with Pyk1, and applied this system to identify multiple novel interacting partners. This interactome implicates Tsa1 in the regulation of critical processes including many Zn-dependent metabolic pathways. Interestingly, Zap1 was a preferred Tsa1 target, as Tsa1 strongly promoted the oxidation of Zap1 activation domain 2, and was essential for full Zap1 activity. Our findings reveal a novel posttranslational response to Zn deficiency, overlain on and interconnected with the Zap1-mediated transcriptional response.Graphical abstractIn ZnD cells, Tsa1 mediates metabolic adaptation by regulation of glycolytic enzymes Pyk1 and Fba1, and supports activity of the Zap1 transcriptional activator via oxidation of the AD2 domain.
Disruption of the mRNA m6A writer complex triggers autoimmunity in Arabidopsis
Authors: Metheringham Carey L , Srivastava Anjil K , Thorpe Peter , Maji Ankita , Parker Matthew T , Barton Geoffrey J , Simpson Gordon G 
Published: February 2025

ABSTRACTDistinguishing self from non-self is crucial to direct immune responses against pathogens. Unmodified RNAs stimulate human innate immunity, but RNA modifications suppress this response. mRNA m6A modification is essential forArabidopsis thalianaviability. However, the molecular basis of the impact of mRNA m6A depletion is poorly understood. Here, we show that disruption of the Arabidopsis mRNA m6A writer complex triggers autoimmunity. Most gene expression changes in m6A writer complexvir-1mutants grown at 17°C are explained by defence gene activation and are suppressed at 27°C, consistent with the established temperature sensitivity of Arabidopsis immunity. Accordingly, we found enhanced pathogen resistance and increased premature cell death invir-1mutants at 17°C but not 27°C. Global temperature-sensitive mRNA poly(A) tail length changes accompany these phenotypes. Our results demonstrate that autoimmunity is a major phenotype of mRNA m6A writer complex mutants, which has important implications for interpreting this modification’s role. Furthermore, we open the broader question of whether unmodified RNA triggers immune signalling in plants.
A genetic signature predicts aggressive paraganglioma sensitivity to dual PI3K-CDK4/6 inhibition therapy
Authors: Karna Bhargavi , Gentile Federica , Gulde Sebastian , Martino Daniela De , Maurer Julian , Ganesan Katyayni , Wang Katharina , Bechmann Nicole , Rapizzi Elena , Robledo Mercedes , Arroba Ester , Herzig Stephan , Nölting Svenja , Mohr Hermine , Pellegata Natalia S. 
Published: February 2025

AbstractEffective medical therapies for metastatic paraganglioma (mPPGL) are currently lacking, leading to dismal prognosis. Building on our knowledge of molecular mechanisms driving PPGL progression, we assessed the therapeutic potential of targeting two critical processes: PI3K signaling and cell cycle regulation. The efficacy of buparlisib (PI3Ki) and ribociclib (CDK4/6i), individually and combined, was assessedin vitrousing PPGL cell lines, rat– and patient-derived primary cells, andin vivousing PPGL cells-derived mouse xenografts. The combination therapy demonstrated superior antitumor activity compared to single agents, particularlyin vivo. Mechanistically, the efficacy of the combination therapy was associated to the downregulation of FOXM1-controlled genes implicated in mitotic spindle assembly and chromosomal segregation, leading to mitotic catastrophe. Data mining and qRT-PCR showed this genetic signature to be upregulated in human mPPGLs. This suggests that aggressive PPGLs exhibit heightened vulnerability to dual PI3K and CDK4/6 inhibition, offering a promising therapeutic avenue for these challenging cancers.
Seek-a-Seq: Optical detection of target nucleic acids with attomolar sensitivity
Authors: Das Anand Kant , Saj Alam , Gan Hin Hark , Gunsalus Kristin C. , Shubeita George T. 
Published: February 2025

AbstractWe introduce Seek-a-Seq, an enzyme-free, PCR amplification-free, optical method to detect microbial nucleic acids based on fluorescent readout of hybridization between target sequences and complementary probes immobilized on the surface of customized sample chambers. We demonstrate the ability to detect ultralow concentration (~ 1 attomolar) of short target DNA and synthetic SARS-CoV-2 RNA with ease and specificity. Seek-a-Seq can enormously reduce costs, accelerate diagnostic workflows, and outperform existing enzyme-dependent methods.
Fabrication & Characterization of Hyaluronic Acid/Eucalyptus Hydrogels Loaded with PLGA Nanoparticles with Methotrexate as an Injectable Therapy for Rheumatoid Arthritis
Authors: Castilla-Bolanos Maria Alejandra , Duenas Mariana , Bustamante Laura , Castillo Samuel 
Published: February 2025

AbstractRheumatoid arthritis is an autoimmune disease that affects about 250,000 Colombians, 82% of whom are women. Current treatments include disease-modifying antirheumatic drugs (DMARDs), such as methotrexate (MTX), analgesics and physiotherapy. The most common DMARD is MTX, which binds to plasma proteins with low efficiency (50%) and has a half-life of 6 hours. Due to its limitations when administered orally, nanoparticles (NPs) have been proposed to overcome these limitations. NPs support the release of therapeutic molecules, minimizing side effects and increasing the bioavailability of the drug in a controlled administration. NPs synthesized from biodegradable polymers, such as polyglycolic lactic acid (PLGA), are convenient for drug delivery due to their high biocompatibility and ability to bind DMARDs such as MTX. PLGA NPs loaded with MTX (MTX-PLGA-NPs) have reduced the presence of proinflammatory factors such as IL-10 and TGF-β, suggesting their potential as anti-inflammatory therapies for arthritis. Therefore, this study aims to develop MTX-PLGA-NPs in bioactive and biocompatible hyaluronic acid-eucalyptus (GelHA-E) hydrogels to preserve their stability and delay their degradation. PLGA-NPs were synthesized with an average hydrodynamic diameter of 200 nm, the 1237 cm-1 band found in FITR indicated the successful covalent conjugation with MTX; the mass loss of only 1% in GelHA-E indicated the thermogravimetric stability of the biomaterial and the low hemolytic and platelet aggregation percentage confirmed the biocompatibility of the biomaterial as a potential localized, anti-inflammatory, and injectable treatment for rheumatoid arthritis.
Leishmania amazonensisinfection induces IL1β-dependent hyperalgesia, while dampening mechanical allodynia in C57BL/6 mice
Authors: Perez Gustavo G. , de Lima Emanuelle V. , Antonio Leticia S. , Vidal Eduardo Matheus M. , Christoff Raissa R. , Paiva Milla B. , Gonçalves Antônio José S. , Duarte Marcia Pereira O. , Bellio Maria , Silva Robson Coutinho , da Costa Robson , Figueiredo Rodrigo T. , Clarke Julia R. , Guedes Herbert L. 
Published: February 2025

AbstractLeishmaniases are neglected diseases causing significant deaths and disabilities. In Brazil, the most prevalent form is cutaneous leishmaniasis, characterized by painless lesions despite intense inflammation and ulceration. While BALB/c mice models exhibit hypersensitization to inflammatory stimuli, C57BL/6 mice better mimic human-like lesion progression and nociceptive responses. This study aimed to investigate the mechanisms underlying nociceptive changes in cutaneous leishmaniasis using the C57BL/6 model. Following infection withL. amazonensis, behavioral and nociceptive tests revealed unaltered mechanical nociception and motor capacity, though thermal hypersensitivity emerged during the chronic phase. Elevated IL-1β production in the lesions and upregulation of TRPV1 in dorsal root ganglia (DRG) neurons were detected via ELISA and qPCR. Mice deficient in IL-1β-related proteins or receptors exhibited higher thermal nociception thresholds, highlighting IL-1β’s role in heat hypersensitization during late infection stages. Microscopy of chronic lesions revealed tissue deformities, indicating desensitization to mechanical and inflammatory stimuli due to nerve terminal alterations and fibroplasia from regenerative processes. Conversely, thermal hypersensitivity in chronic phases was driven by IL-1β effects on thermal nociceptive neurons in the DRG. These findings suggest that IL-1β and TRPV1 contribute to thermal hypersensitivity, while structural changes in lesions underlie mechanical desensitization. This model provides insights into the complex nociceptive mechanisms of cutaneous leishmaniasis.
BENDER DB: a database of protein binding sites across neglected disease proteomes
Authors: Paiva Vinícius A. , Pires Douglas E. V. , Bressan Gustavo C. , Izidoro Sandro C. , Silveira Sabrina A. 
Published: February 2025

AbstractIdentifying binding sites is crucial for expanding our knowledge of various biological processes, supporting drug discovery, and repositioning strategies, particularly in the early research phases of target hopping. This is especially important for neglected diseases, which predominantly impact vulnerable populations in developing regions. To address this, we created BENDER DB, a database designed to map predicted protein binding sites within the proteomes of pathogens associated with neglected diseases. Utilizing AlphaFold-predicted structures, BENDER DB integrates results from five leading binding site prediction tools, resulting in over one million binding sites across over 100,000 proteins from 10 different proteomes. BENDER DB offers unique features, such as integrating multiple predictors, interactive visualization tools, and comprehensive graphical representations, allowing for a detailed visual comparative analysis of different prediction methods and the predicted binding sites. We combined the computational approaches to offer a consensus of binding site predictions, leveraging the strengths of multiple techniques. Additionally, we introduce BENDER AI, a meta-predictor that combines the outputs of the predictors to provide a unified binding site classification. BENDER AI outperformed all individual methods in 4 out of 5 evaluated metrics. Specifically, it achieved an MCC of 0.64 and an AUC of 0.89, surpassing the highest MCC of 0.63 and the highest AUC of 0.84 obtained by individual predictors, demonstrating strong performance and effectiveness in supporting binding site prediction. By consolidating these results, BENDER DB enables detailed comparative analyses of prediction methods and integrates interactive visualization tools to provide users with an intuitive platform for binding site exploration. The database aims to accelerate drug discovery efforts, particularly in underdeveloped regions, by providing a robust and detailed resource for studying protein binding sites. BENDER DB is available athttps://benderdb.ufv.br.
Gonococcal polarization dynamics during adaptation to low oxygen levels
Authors: Schiefer Paul , Maier Berenike 
Published: February 2025

ABSTRACTNeisseria gonorrhoeaecan switch between aerobic and microaerophilic lifestyles, but little is known about the dynamics of this transition. In particular, switching from respiration to partial denitrification is likely to affect the electrophysiology of these bacteria. Here, we use a Nernstian dye to measure the membrane potential of single planktonic cells while they continuously consume the oxygen in the growth medium. We show that cells undergo a characteristic pattern of transient depolarization followed by transient hyperpolarization at a critical oxygen concentration, reminiscent of the response to sudden changes in membrane voltage driven by gated ion-channels. Subsequently, the cells depolarize strongly to a near-constant membrane potential. In the presence of nitrite, the cells repolarize after a delay and the repolarization depends on the oxygen-dependent regulatorfnrrequired for denitrification. The temporal behaviour of planktonic cells explains the complex spatio-temporal polarization pattern of the colonies formed byN. gonorrhoeae. This sexually transmitted human pathogen experiences different growth environments during transmission. Our results are an important step towards understanding how electrophysiology adapts to changing environments.
Long-Term Functional Rescue of Trauma-Induced Vision Loss by a Novel, Small Molecule TrkB Activator
Authors: Modgil Shweta , Walker Christopher L. , Chrenek Micah A. , Grossniklaus Hans E. , McDonald Frank E. , Iuvone P. Michael 
Published: February 2025

AbstractBrain-derived neurotrophic factor (BDNF) signaling through the tropomyosin-related kinase B (TrkB) receptor promotes neuronal growth and survival following an injury. However, its short half-life and pleiotropic effects limit the clinical use of BDNF as a therapy in neurodegenerative disorders. Identification of novel and selective TrkB activators may ameliorate the damage caused to retinal neurons during eye-related injuries, and may reduce adverse visual outcomes associated with visual trauma. We previously described a selective TrkB agonist, N-[2-(5-hydroxy-1H-indol-3-yl) ethyl]-2-oxopiperidine-3-carboxamide (HIOC), that reduces the decline in visual function in a mouse model of ocular trauma (1). Using the lead optimization approach, we subsequently synthesized a fluoropyridine analog of HIOC, 2-fluoro-N-(2-(5-hydroxy-1H-indol-3-yl) ethyl) nicotinamide (HIFN), which also successfully activates TrkB. HIFN is a more potent TrkB activator than the parent compound, HIOC. Further, treatment with HIFN demonstrated neuroprotection in an animal model of overpressure ocular blast injury, ameliorating blast-related visual functional decline. Mice treated with HIFN had better visual acuity, contrast sensitivity, and retinal function supported by enhanced survival of retinal ganglion cells compared to vehicle-treated animals. Moreover, HIFN exhibited better protective effects than HIOC. The therapeutic effects of HIFN were attributed to TrkB activation, as blocking the receptor with a selective receptor antagonist (ANA-12) abrogated the neuroprotection. Together, our results identify HIFN, a novel TrkB receptor activator, as a strategy for decreasing retinal degeneration and progressive vision loss associated with traumatic ocular injury. In addition, this compound may have broader applications treating other diseases with altered TrkB activity.
Machine Learning-Based Model for Behavioral Analysis in Rodents: Application to the Forced Swim Test
Authors: Della Valle Andrea , De Carlo Sara , Sonsini Gregorio , Pilati Sebastiano , Perali Andrea , Ubaldi Massimo , Ciccocioppo Roberto 
Published: February 2025

AbstractThe Forced Swim Test (FST) is a widely used preclinical model for assessing antidepressant efficacy, studying stress response, and evaluating depressive-like behaviours in rodents. Over the last 10 years, more than 5,500 scientific articles reporting the use of the FST have been published. Despite its widespread use, the FST behaviours are still manually scored, resulting in a labor-intensive and time-consuming process that is prone to human bias and variability. Despite eliminating some biases, existing automated systems are costly and typically only able to distinguish between immobility and active behaviours. Therefore, they are often unable to accurately differentiate the major subtypes of movement patterns, such as swimming and climbing. To address these limitations, we propose a novel approach based on machine learning (ML) using a three-dimensional residual convolutional neural network (3D RCNN) that processes video pixels directly, capturing the spatiotemporal dynamics of rodent behaviour. Our ML model was validated against manual scoring in rats treated with fluoxetine and desipramine, two antidepressants known to induce distinct behavioural patterns. The ML model successfully differentiated among swimming, climbing, and immobility behaviours, demonstrating its potential as a standardized and unbiased tool for automatized behavioural analysis in the FST. Subsequently, we successfully validated our model by testing its ability to distinguish between drugs that predominantly evoke climbing (i.e., amitriptyline), those that preferentially facilitate swimming (i.e., paroxetine), and those that evoke both in a more balanced manner (i.e., venlafaxine). This approach represents a significant advancement in preclinical research, providing a more accurate and efficient method to analyze forced swimming data in rodents. We anticipate that due to its adaptability, in addition to the FST, the model could be applied to various behavioural tests in laboratory animals.
BRCA1-A and LIG4 complexes mediate ecDNA biogenesis and cancer drug resistance
Authors: Chung Oliver W. , Yao Shun , Yang Fu , Wang Ling , Cerda-Smith Christian , Hutchinson Haley M. , Wood Kris C. , Su Weijia , Khasraw Mustafa , Zou Lee , Ramsden Dale A. , Zhang ZZ Zhao 
Published: February 2025

SUMMARYExtrachromosomal circular DNA (ecDNA) are commonly produced within the nucleus to drive genome dynamics and heterogeneity, enabling cancer cell evolution and adaptation. However, the mechanisms underlying ecDNA biogenesis remain poorly understood. Here using genome-wide CRISPR screening in human cells, we identified the BRCA1-A and the LIG4 complexes mediate ecDNA production. Following DNA fragmentation, the upstream BRCA1-A complex protects DNA ends from excessive resection, promoting end-joining for circularization. Conversely, the MRN complex, which mediates end resection and thus antagonizes the BRCA1-A complex, suppresses ecDNA formation. Downstream, LIG4 conservatively catalyzes ecDNA production inDrosophilaand mammals, with patient tumor ecDNA harboring junctions marked by LIG4 activity. Notably, disrupting LIG4 or BRCA1-A in cancer cells impairs ecDNA-mediated adaptation, hindering resistance to both chemotherapy and targeted therapies. Together, our study reveals the roles of the LIG4 and BRCA1-A complexes in ecDNA biogenesis, and uncovers new therapeutic targets to block ecDNA-mediated adaptation for cancer treatment.
Tumor Treating Fields inhibit cell proliferation and promote immunogenic cell death in biliary tract cancer cells
Authors: Yue Ying , Wang Yingying , Yao Min , Suo Yuanzhen 
Published: February 2025

ABSTRACTTumor Treating Fields (TTFields) are low-intensity, intermediate-frequency alternating electric fields that exert antimitotic effects on cancer cells. This study evaluated the in vitro efficacy of TTFields on biliary tract cancer (BTC) cell lines HCCC-9810 and RBE, investigating their sensitivity to TTFields across varying frequencies and electric field intensities. The results demonstrated that a frequency of 150 kHz induced the most pronounced cytotoxic effects, significantly impairing clonogenicity and migratory capacity while inducing abnormal mitotic processes. Furthermore, TTFields treatment triggered a marked upregulation of immunogenic cell death (ICD) biomarkers, including enhanced surface exposure of calreticulin (CRT) and increased extracellular release of high mobility group box 1 (HMGB1) and ATP. These findings indicate that TTFields represent a promising therapeutic approach for BTC, not only by suppressing tumor proliferation but also by enhancing ICD.