bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulsed stimuli entrain p53 to synchronize single cells and modulate cell-fate determination
Authors: Venkatachalapathy Harish , Yang Zhilin , Azarin Samira M. , Sarkar Casim A. , Batchelor Eric 
Published: October 2023

AbstractEntrainment to an external stimulus enables a synchronized oscillatory response across a population of cells, increasing coherent responses by reducing cell-to-cell heterogeneity. It is unclear whether the property of entrainability extends to systems where responses are intrinsic to the individual cell, rather than dependent on coherence across a population of cells. Using a combination of mathematical modeling, time-lapse fluorescence microscopy, and single-cell tracking, we demonstrated that p53 oscillations triggered by DNA double-strand breaks (DSBs) can be entrained with a periodic damage stimulus, despite such synchrony not known to function in effective DNA damage responses. Surprisingly, p53 oscillations were experimentally entrained over a wider range of DSB frequencies than predicted by an established computational model for the system. We determined that recapitulating the increased range of entrainment frequencies required, non-intuitively, a less robust oscillator and wider steady-state valley on the energy landscape. Further, we show that p53 entrainment can lead to altered expression dynamics of downstream targets responsible for cell fate in a manner dependent on target mRNA stability. Overall, this study demonstrates that entrainment can occur in a biological oscillator despite the apparent lack of an evolutionary advantage conferred through synchronized responses and highlights the potential of externally entraining p53 dynamics to reduce cellular variability and synchronize cell-fate responses for therapeutic outcomes.
Sensitive detection of chloroplast movements through changes in leaf cross-polarized reflectance
Authors: Hermanowicz Paweł , Giza Aleksandra , Łabuz Justyna 
Published: October 2023

AbstractWe present a sensitive method for non-contact detection of chloroplast movements in leaves and other photosynthetic tissues, based on changes in the magnitude of cross-polarized reflectance of the leaf. We created a custom optical set-up and dedicated software for measurements of changes in red light reflectance during irradiation with blue light, known to trigger chloroplast relocations. Experiments onArabidopsis thalianawild type and several mutants with disrupted chloroplast movements showed that the chloroplast avoidance response, induced by high blue light, led to a substantial increase in diffuse reflectance of unpolarized red light. The effects of the accumulation response in low blue light were the opposite. The specular reflectance of the leaf was unaffected by the chloroplast positioning. To further improve the specificity of the detection, we examined the effects of chloroplast relocations on the leaf reflectance of a linearly polarized incident beam. The greatest relative change associated with chloroplast movements was observed when the planes of polarization of the incident and detected beams were perpendicular. This suggests that the chloroplast positioning affects the magnitude of depolarization of light. We applied the developed approach to examine chloroplast relocations in four angiosperm species collected in the field. In particular, the method allowed us to detect the chloroplast avoidance response in the green stems of bilberry before bud break. Such samples are not amenable to transmittance-based detection.Significance statementDespite the importance of chloroplast movements for the optimization of photosynthetic efficiency and biomass production, high throughput reflectance-based methods are not routinely used for their detection. Strong dependence of the amount of specularly reflected light reaching the detector on the leaf orientation may lead to a substantial error in chloroplast relocation measurements. We show that the assessment of chloroplast responses through polarized reflectance reduces systematic errors due to the leaf movements and improves the sensitivity of detection. This opens a possibility of non-invasive, non-contact detection of chloroplast relocations using existing instrumentation for remote sensing of agriculturally relevant crop traits.
Emerging role of oncogenic β-catenin in exosome biogenesis as a driver of immune escape in hepatocellular carcinoma
Authors: Dantzer Camille , Vaché Justine , Brunel Aude , Mahouche Isabelle , Raymond Anne-Aurélie , Dupuy Jean-William , Petrel Melina , Bioulac-Sage Paulette , Perrais David , Dugot-Senant Nathalie , Verdier Mireille , Bessette Barbara , Billottet Clotilde , Moreau Violaine 
Published: October 2023

ABSTRACTImmune checkpoint inhibitors have produced encouraging results in cancer patients. However, the majority of β-catenin-mutated tumors have been described as lacking immune infiltrates and resistant to immunotherapy. The mechanisms by which oncogenic β-catenin affects immune surveillance remain unclear. Herein, we highlighted the involvement of β-catenin in the regulation of the exosomal pathway and, by extension, in immune/cancer cell communication in hepatocellular carcinoma (HCC). We showed that mutated β-catenin represses expression ofSDC4andRAB27A, two main actors in exosome biogenesis, in both liver cancer cell lines and HCC patient samples. Using nanoparticle tracking analysis and live-cell imaging, we further demonstrated that activated β-catenin represses exosome release. Then, we demonstrated in 3D spheroid models that activation of β-catenin promotes a decrease in immune cell infiltration through a defect in exosome secretion. Taken together, our results provide the first evidence that oncogenic β-catenin plays a key role in exosome biogenesis. Our study gives new insight into the impact of β-catenin mutations on tumor microenvironment remodeling, which could lead to the development of new strategies to enhance immunotherapeutic response.
Analysis of uveal melanoma scRNA sequencing data identifies neoplastic-immune hybrid cells that exhibit metastatic potential
Authors: Anderson Ashley N. , Conley Patrick , Klocke Christopher D. , Sengupta Sidharth K. , Robinson Trinity L. , Fan Yichen , Jones Jocelyn A. , Gibbs Summer L. , Skalet Alison H. , Wu Guanming , Wong Melissa H. 
Published: October 2023

AbstractUveal melanoma (UM) is the most common non-cutaneous melanoma and is an intraocular malignancy that affects nearly 7,000 individuals per year worldwide. Of these, nearly 50% will progress to metastatic disease for which there are currently no effective therapies. Despite advances in the molecular profiling and metastatic stratification of class 1 and 2 UM tumors, little is known regarding the underlying biology of UM metastasis. Our group has identified a disseminated tumor cell population characterized by co-expression of immune and melanoma proteins, (circulating hybrid cells (CHCs), in patients with UM. Compared to circulating tumor cells, CHCs are detected at an increased prevalence in peripheral blood and can be used as a non-invasive biomarker to predict metastatic progression. To identify mechanisms underlying enhanced hybrid cell dissemination we sought to identify hybrid cells within a primary UM single cell RNA-seq dataset. Using rigorous doublet discrimination approaches, we identified UM hybrids and evaluated their gene expression, predicted ligand-receptor status, and cell-cell communication state in relation to other melanoma and immune cells within the primary tumor. We identified several genes and pathways upregulated in hybrid cells, including those involved in enhancing cell motility and cytoskeleton rearrangement, evading immune detection, and altering cellular metabolism. In addition, we identified that hybrid cells express ligand-receptor signaling pathways implicated in promoting cancer metastasis including IGF1-IGFR1, GAS6-AXL, LGALS9-P4HB, APP-CD74 and CXCL12-CXCR4. These results contribute to our understanding of tumor progression and interactions between tumor cells and immune cells in the UM microenvironment that may promote metastasis.
Measuring mtDNA turnover, synthesis, and supercoiling via selective bromodeoxyuridine incorporation
Authors: Deng Jingti , Mohan Armaan , Shutt Timothy E 
Published: October 2023

AbstractIncreasing work on mitochondria is focused on the dynamic aspects of this organelle, a key part of which is regulation of the mitochondrial genome (mtDNA). Here we describe a protocol that selectively incorporates bromodeoxyuridine into mtDNA for the measurement of mtDNA turnover, synthesis or supercoiling via an adapted immunoblot and Southern blot protocol. For complete use and execution of this protocol see Al Khatib et al.1,2and Lei et al.3
Co-transcriptional translation amplifies mRNA noise inEscherichia coli
Authors: Yang Sora , Park Soojin , Son Jung Bae , Kim Seunghyeon , Yi Soojung , Bu Gayun , Lee Nam Ki 
Published: October 2023

AbstractThe variability in mRNA expression among isogenic cells exposed to identical environments is inherent. This variability originates from the inherent stochasticity of all processes underlying transcription. Although transcription and translation can occur simultaneously on the same mRNA molecule in bacteria, it is not well understood whether and how co-transcriptional translation contributes to variability in mRNA expression. Here, we studied the contribution of co-transcriptional translation to mRNA noise inE. colicells. Using a transcription system physically decoupled from translation, we investigated the effect of ribosome binding to mRNA transcripts on variability in mRNA expression. We found that the propagation of RNAP noise to the mRNA level was increased by ribosome binding, leading to larger variations in the mRNA levels. We further demonstrated that ribosome binding increased the transcription initiation rate, resulting in the promoter becoming susceptible to RNAP noise. Co-transcriptional translation amplified transcriptional noise and modulated transcriptional bursting kinetics in bacterial cells.
Development of neural circuits for social motion perception in schooling fish
Authors: Zada David , Schulze Lisanne , Yu Jo-Hsien , Tarabishi Princess , Napoli Julia L , Lovett-Barron Matthew 
Published: October 2023

AbstractMany animals move in groups, where collective behavior emerges from the interactions amongst individuals. These social interactions produce the coordinated movements of bird flocks and fish schools, but little is known about their developmental emergence and neurobiological foundations. By characterizing the visually-based schooling behavior of the micro glassfishDanionella cerebrum, here we found that social development progresses sequentially, with animals first acquiring the ability to aggregate, followed by postural alignment with social partners. This social maturation was accompanied by the development of neural populations in the midbrain and forebrain that were preferentially driven by visual stimuli that resemble the shape and movements of schooling fish. The development of these neural circuits enables the social coordination required for collective movement.One-Sentence SummaryThe collective behavior of schooling fish emerges with the development of neural populations selective to social motion.
Analysis of the peptide helicity using an ensemble spectroscopic model with re-calibrated parameters
Authors: Zavrtanik Uroš , Lah Jurij , Hadži San 
Published: October 2023

AbstractThe α-helix is the fundamental building block of protein structure. Understanding the physical principles that determine how a specific amino acid sequence defines helicity is a key step towards elucidating the sequence-structure relationship. An established method for quantitation of helix content using circular dichroism (CD) relies on the linear spectroscopic model. In this model, the helix length-correction is not applied to each ensemble conformer individually, rather an average value is assumed for all conformers. Here we assess the validity of this approximation and introduce a more physically realistic ensemble-based analysis of the CD signal. We find that the linear model tends to underestimate peptide helicity, with the difference depending on the ensemble composition. Using a CD dataset covering a broad range of helicities, we re-calibrate spectroscopic parameters (helix and coil baselines) and determine helix-coil parameters for a set of alanine-rich peptides. Our results show that the ensemble model can leverage the small spectroscopic differences between peptide conformers, enabling it to extract more information from the experimental data. We show that some previously poorly-defined quantities, such as helix nucleation constant and heat capacity change associated with helix folding, can be reliably determined using ensemble model. Overall, the presented ensemble-based treatment of the CD signal, together with the re-calibrated values of the spectroscopic baseline parameters, provides a coherent framework for the analysis of the peptide helix content.Abstract Figure
Discovery of a novel inhibitor of macropinocytosis with antiviral activity
Authors: Porebski Bartlomiej , Christ Wanda , Corman Alba , Haraldsson Martin , Barz Myriam , Lidemalm Louise , Häggblad Maria , Ilmain Juliana , Wright Shane C. , Murga Matilde , Shlegel Jan , Sezgin Erdinc , Bhabha Gira , Lauschke Volker M , Lafarga Miguel , Klingström Jonas , Huhn Daniela , Fernandez-Capetillo Oscar 
Published: October 2023

SUMMARYSeveral viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a new molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using High-Throughput Microscopy, where we identified new chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as Monkeypox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present a new molecule that inhibits viral entry via the endocytic route, offering a new alternative to prevent viral infection.
Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations
Authors: Wang Tong , Coshic Kush , Badiee Mohsen , Aksimentiev Aleksei , Pollack Lois , Leung Anthony K. L. 
Published: October 2023

ABSTRACTPoly(ADP-ribose) (PAR), as part of a post-translational modification, serves as a flexible scaffold for noncovalent protein binding. Such binding is influenced by PAR chain length through a mechanism yet to be elucidated. Structural insights have been elusive, partly due to the difficulties associated with synthesizing PAR chains of defined lengths. Here, we employ an integrated approach combining molecular dynamics (MD) simulations with small-angle X-ray scattering (SAXS) experiments, enabling us to identify highly heterogeneous ensembles of PAR conformers at two different, physiologically relevant lengths: PAR15and PAR22. Our findings reveal that numerous factors including backbone conformation, base stacking, and chain length contribute to determining the structural ensembles. We also observe length-dependent compaction of PAR upon the addition of small amounts of Mg2+ions, with the 22-mer exhibiting ADP-ribose bundles formed through local intramolecular coil-to-globule transitions. This study illuminates how such bundling could be instrumental in deciphering the length-dependent action of PAR.GRAPHICAL ABSTRACT
A Phase 2 random, double-blind, placebo-controlled study of the safety and immunogenicity of a recombinant G protein-based respiratory syncytial virus vaccine in healthy older adults
Authors: Zhang Lunan , Zhao Gan , Cheng Xin , Wang Shuo , Wang Jiarong , Huai Xuefen , Xia Yu , Xiao Yanling , Ren Sulin , Zhang Shijie , Wang Bin 
Published: October 2023

ABSTRACTBackgroundRespiratory syncytial virus (RSV) is an important cause of disease in older adults. Vaccines against RSV infections and respiratory diseases are in large market demand. Although there are currently two licensed RSV-based pre-F antigen vaccines available for older adults, no G antigen-based RSV vaccine is authorized. This phase 2 study aimed to evaluate the safety and immunogenicity of a recombinant G protein-based RSV vaccine in this population.MethodsA phase-2 randomized, double-blind, placebo-controlled, dose-ranging study was conducted to evaluate the safety, tolerability and immunogenicity of the BARS13 (rRSV G protein with CsA) when administered by an intramuscular (IM) injection to healthy participants 60 to 80 years old. A total of 125 eligible participants were randomized in a 3:1 ratio (vaccine versus placebo) for Cohorts 1 and 2 and randomized in a 2:1 ratio for Cohort 3 to receive one of the three treatment regimens or placebo.ResultsThe average age was 65.3, and 50.4% (63/125) were men. Until the interim analysis (4 weeks following the last vaccination), no treatment-related SAE occurred. TEAEs did not increase with vaccination dosage or frequency. All adverse effects were mild or moderate, not severe or life-threatening. BARS13 vaccination increased IgG anti-RSV antibody levels in all cohorts, but higher doses and frequency boosted immune responses significantly. The high-dose thrice-administered recipients had serum-specific IgG antibody GMC of 881.0 IU/mL (95% CI: 794.5-1473.4) before the first dose (Week 0), 1116.3 IU/mL (95% CI:990.7-1772.5) 4 weeks after the first dose (Week 4), 1309.4IU/mL (95% CI: 1162.8-2041.5) 4 weeks after the second dose (Week 8), and1359.6 IU/mL (95% CI: 1197.9-2525.7) 4 weeks after the third dose (Week 12). For the low-dose twice-administered recipients, 84% responded at 4 weeks after the first immunization (Week 4) and 83.3% at 4 weeks after the second (Week 8). The high-dose twice-administered recipients had 95.5% response at 4 weeks after the first immunization (Week 4) and 72.2% at 4 weeks after the second (Week 8). At Week 4, 85.7% of high-dose thrice-administered recipients responded, 85.2% at Week 8, and 79.2% at Week 12.ConclusionsThe study demonstrates the safety and tolerability of BARS13 across different dose groups. Adverse reactions were not significantly different among participants receiving varying doses of BARS13. Levels of anti-G antibodies exhibited a dose- and frequency-dependent responses in the older population. The continuous upward trend in antibody concentration up to the interim analysis is promising for the effectiveness of BARS13.
Restoration of normal central pain processing following manual therapy in nonspecific chronic neck pain
Authors: Mata Josu Zabala , Azkue Jon Jatsu , Bialosky Joel E. , Saez Marc , López Estíbaliz Dominguez , Arrieta Maialen Araolaza , Lascurain-Aguirrebeña Ion 
Published: October 2023

AbstractObjectiveto determine if a 4-week manual therapy treatment restores normal functioning of central pain processing mechanisms in non-specific chronic neck pain (NSCNP), as well as the existence of a possible relationship between changes in pain processing mechanisms and clinical outcome.Designcohort study.Methodssixty-three patients with NSCNP received four treatment sessions (once a week) of manual therapy. Pressure pain thresholds (PPTs), conditioned pain modulation (CPM) and temporal summation of pain (TSP) were evaluated at baseline and after treatment completion. Therapy outcome was measured using the Global Rating of Change Scale, the Neck disability Index, intensity of pain during the last 24 hours, Tampa Scale of Kinesiophobia and Pain Catastrophizing Scale.ResultsFollowing treatment, an increased CPM response and attenuated TSP were found, along with amelioration of pain and improved clinical status. PPTs at trapezius muscle on the side of neck pain were increased after therapy, but not those on the contralateral trapezius and tibialis anterior muscles. Only minor associations were found between normalization of TSP/CPM and measures of clinical outcome.ConclusionClinical improvement after manual therapy is accompanied by restoration of CPM and TSP responses to normal levels in NSCNP patients. The existence of only minor associations between changes in central pain processing and clinical outcome suggests multiple mechanisms of action of manual therapy in NSCNP.
Improving treatment precision in head and neck BNCT: delineation of oral and pharyngeal mucosa based on an MRI Atlas for standardized applications
Authors: Hirose Katsumi , Kato Ryohei , Sato Mariko , Ichise Koji , Tanaka Mitsuki , Fujioka Ichitaro , Kawaguchi Hideo , Hatayama Yoshiomi , Aoki Masahiko , Takai Yoshihiro 
Published: October 2023

AbstractBackground and purposeBoron neutron capture therapy (BNCT) has been routinely practiced for treatment of head and neck cancer in Japan. However, differences in contouring the oral and pharyngeal mucosa can lead to discrepancies in treatment. This study aimed to introduce a standardized approach using an MRI-based atlas, aiming to minimize inter-observer error and improve dose precision.Materials and MethodsAn MRI atlas of the head and neck mucosa was developed using water/fat-separated images from a healthy man. Using CT images from three patients, seven radiation oncologists performed contouring of the head and neck mucosa twice over a 3-week period. Contouring was first performed using CT alone, then later using fused T2-weighted images with the mucosal atlas for guidance. Contouring errors were assessed and their impacts on tumor dose were evaluated.ResultsThe introduction of the MRI-based mucosal atlas significantly reduced inter-observer variation in mucosal volume (the coefficient of variation, abbreviated with COV, decreased from 0.61 with CT alone to 0.21 with the MRI atlas; p=0.003). Moreover, the atlas resulted in improved contour homology among observers and reduced variations in tumor dose. For all cases, COVs for maximum, mean, and minimum tumor doses were all below 5%.ConclusionUtilizing an MRI-based mucosal atlas in BNCT contouring can significantly reduce inter-observer variation, improve contour homology, and decrease variations in tumor dose. These findings suggest strong potential for standardizing and enhancing the quality of BNCT for head and neck cancer.
Role of canonical and non-canonical cAMP Sources in CRHR2α-dependent Signaling
Authors: Armando Natalia G. , dos Santos Claro Paula A. , Fuertes Mariana , Arzt Eduardo , Silberstein Susana 
Published: October 2023

AbstractHippocampal neurons exhibit activation of both the conventional transmembrane adenylyl cyclases (tmACs) and the non-canonical soluble adenylyl cyclase (sAC) as sources of cyclic AMP (cAMP). These two cAMP sources play crucial roles in mediating signaling pathways downstream of CRHR1 in neuronal and neuroendocrine contexts. In this study, we investigate the involvement of both cAMP sources in the molecular mechanisms triggered by CRHR2α. Here we provide evidence demonstrating that UCN1 and UCN3 exert a neuritogenic effect on HT22-CRHR2α cells, which is solely dependent on the cAMP pool generated by sAC and PKA activity but independent of ERK1/2 activation. Through the characterization of the effectors implicated in neurite elongation, we found that CREB phosphorylation and c-Fos induction rely on PKA activity and ERK1/2 phosphorylation, underscoring the critical role of signaling pathway regulation. These findings strengthen the concept that localized cAMP microdomains actively participate in the regulation of these signaling processes.