bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gentle rhodamines for live-cell fluorescence microscopy
Authors: Liu Tianyan , Kompa Julian , Ling Jing , Lardon Nicolas , Zhang Yuan , Chen Jingting , Reymond Luc , Chen Peng , Tran Mai , Yang Zhongtian , Zhang Haolin , Liu Yitong , Pitsch Stefan , Zou Peng , Wang Lu , Johnsson Kai , Chen Zhixing 
Published: February 2024

AbstractRhodamines have been continuously optimized in brightness, biocompatibility, and colors to fulfill the demands of modern bioimaging. However, the problem of phototoxicity caused by the excited fluorophore under long-term illumination has been largely neglected, hampering their use in time-lapse imaging. Here we introduce cyclooctatetraene (COT) conjugated rhodamines that span the visible spectrum and exhibit significantly reduced phototoxicity. We identified a general strategy for the generation of Gentle Rhodamines, which preserved their outstanding spectroscopic properties and cell permeability while showing an efficient reduction of singlet-oxygen formation and diminished cellular photodamage. Paradoxically, their photobleaching kinetics do not go hand in hand with reduced phototoxicity. By combining COT-conjugated spirocyclization motifs with targeting moieties, these gentle rhodamines compose a toolkit for time-lapse imaging of mitochondria, DNA, and actin and synergize with covalent and exchangeable HaloTag labeling of cellular proteins with less photodamage than their commonly used precursors. Taken together, the Gentle Rhodamines generally offer alleviated phototoxicity and allow advanced video recording applications, including voltage imaging.
S-nitrosylation of EZH2 at C329 and C700 interplay with PRC2 complex assembly, methyltransferase activity, and EZH2 stability to regulate endothelial functions
Authors: Sakhuja Ashima , Katakia Yash T , Tripathi Shailesh Mani , Bhattacharyya Ritobrata , Thakkar Niyati Pandya , Ramakrishnan S , Chakraborty Srinjoy , Thakar Sumukh , Sundriyal Sandeep , Chowdhury Shibasish , Majumder Syamantak 
Published: February 2024

ABSTRACTNitric oxide (NO), a versatile bio-active molecule modulates cellular function through diverse mechanisms including S-nitrosylation of proteins. However, the role of this post-translational modification in regulating epigenetic pathways was very limitedly explored. Herein, we report that NO causes S-nitrosylation of selected cysteine residues of EZH2 in endothelial cells (EC) resulting in SUZ12 dissociation from EZH2 bound PRC2 complex, reduced methyltransferase activity, and diminished nuclear localization eventually hampering its stability. We detected a significant reduction in H3K27me3 upon exposure to NO as contributed by the early dissociation of SUZ12 from the PRC2 complex. Longer exposure to NO donors caused EZH2 cytosolic translocation, its ubiquitination, and further degradation primarily through the autophagosome-lysosome pathway. Throughin silicoS-nitrosylation prediction analysis and site-directed mutagenesis assay, we identified three cysteine residues namely at locations 260, 329, and 700 in EZH2 and further determined that S-nitrosylation of cysteine 329 induced EZH2 instability while S-nitrosylation of cysteine 700 abrogated EZH2’s catalytic activity. A double mutant of EZH2 containing mutations at Cysteine 329 and 700 remained undeterred to NO exposure. Furthermore, reinforcing H3K27me3 in NO exposed EC through the use of an inhibitor of H3K27me3 demethylase, we confirmed a significant contribution of the EZH2-H3K27me3 axis in defining NO-mediated regulation of endothelial gene expression and migration. Molecular dynamics simulation study revealed SUZ12’s inability in efficiently binding to the SAL domain of EZH2 upon S-nitrosylation of C329 and C700. Taken together, our study for the first-time reports that S-nitrosylation dependent regulation of EZH2 and its associated PRC2 complex –influences endothelial homeostasis.
Trackoscope: A Low-Cost, Open, Autonomous Tracking Microscope for Long-Term Observations of Microscale Organisms
Authors: Soneji Priya , Challita Elio J. , Bhamla M. Saad 
Published: February 2024

AbstractCells and microorganisms are motile, yet the stationary nature of conventional microscopes impedes comprehensive, long-term behavioral and biomechanical analysis. The limitations are twofold: a narrow focus permits high-resolution imaging but sacrifices the broader context of organism behavior, while a wider focus compromises microscopic detail. This trade-off is especially problematic when investigating rapidly motile ciliates, which often have to be confined to small volumes between coverslips affecting their natural behavior. To address this challenge, we introduceTrackoscope, a 2-axis autonomous tracking microscope designed to follow swimming organisms ranging from 10µmto 2mmacross a 325cm2area (equivalent to an A5 sheet) for extended durations—ranging from hours to days—at high resolution. UtilizingTrackoscope, we captured a diverse array of behaviors, from the air-water swimming locomotion ofAmoebato bacterial hunting dynamics inActinosphaerium, walking gait inTardigrada, and binary fission in motileBlepharisma.Trackoscopeis a cost-effective solution well-suited for diverse settings, from high school labs to resource-constrained research environments. Its capability to capture diverse behaviors in larger, more realistic ecosystems extends our understanding of the physics of living systems. The low-cost, open architecture democratizes scientific discovery, offering a dynamic window into the lives of previously inaccessible small aquatic organisms.
Identification of early-stage liver fibrosis by modifications in the interstitial space diffusive microenvironment using fluorescent single-walled carbon nanotubes
Authors: Lee Antony , Simon Apolline A. , Boyreau Adeline , Allain-Courtois Nathalie , Lambert Benjamin , Pradère Jean-Philippe , Saltel Fredéric , Cognet Laurent 
Published: February 2024

AbstractDuring liver fibrosis, recurrent hepatic injuries lead to accumulation of collagen and other extracellular matrix components in the interstitial space, ultimately disrupting liver functions. Early stages of liver fibrosis may be reversible, but opportunities for diagnosis at these stages are currently limited. Here, we show that the alterations of the interstitial space associated with fibrosis can be probed by tracking individual fluorescent single-walled carbon nanotubes (SWCNTs) diffusing in that space. In a mouse model of early liver fibrosis, we find that nanotubes generally explore elongated areas, whose length decrease as the disease progresses even in regions where histopathological examination does not reveal fibrosis yet. Furthermore, this decrease in nanotube mobility is a purely geometrical effect, as the instantaneous nanotube diffusivity stays unmodified. This work establishes the promise of SWCNTs both for the diagnosis of liver fibrosis at an early stage, and for more in-depth studies of the biophysical effects of the disease.
Bayesian Modelling Approaches for Breath-Hold Induced Cerebrovascular Reactivity
Authors: Hayes Genevieve , Bulte Daniel P. , Moia Stefano , Craig Martin , Chappell Michael , Uruñuela Eneko , Sparks Sierra , Caballero-Gaudes César , Pinto Joana 
Published: February 2024

AbstractCerebrovascular reactivity (CVR) reflects the ability of blood vessels to dilate and constrict in response to a vasoactive stimulus and is an important indicator of cerebrovascular health. CVR can be mapped non-invasively with functional magnetic resonance imaging (fMRI) based on blood oxygen level-dependent (BOLD) contrast in combination with a breath-hold (BH) task. There are several ways to analyse this type of data and retrieve individual CVR amplitude and timing information. The most common approach involves employing a time-shifted general linear model with the measured end-tidal carbon dioxide signal as a regressor of interest. In this work, we introduce a novel method for CVR mapping based on a variational Bayesian approach. We analysed BOLD fMRI data from six participants that performed a BH task in ten different sessions each, and computed the corresponding CVR amplitude and delay maps for each session/subject. No statistically significant differences were observed between the modelling approaches in the CVR delay and amplitude maps in grey matter. Notably, the largest difference between methods was apparent in the case of low CVR amplitude, attributed to how each method addressed noisy voxels, particularly in white matter and cerebral spinal fluid. Both approaches showed highly reproducible CVR amplitude maps where between-subject variability was significantly larger than between-session variability. Furthermore, our results illustrated that the Bayesian approach is more computationally efficient, and future implementations could incorporate more complex noise models, non-linear fitting, and physiologically meaningful information into the model in the form of priors. This work demonstrates the utility of variational Bayesian modelling for CVR mapping and highlights its potential for characterising BOLD fMRI dynamics in the study of cerebrovascular health and its application to clinical settings.
Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species
Authors: Daigle Austin , Johri Parul 
Published: February 2024

ABSTRACTThe accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill- Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, when inferring the distribution of selection coefficients, there is an overestimation of nearly neutral and strongly deleterious mutations and an underestimation of mildly deleterious mutations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.
CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data
Authors: Simon Franck , Comes Maria Colomba , Tocci Tiziana , Dupuis Louise , Cabeli Vincent , Lagrange Nikita , Mencattini Arianna , Parrini Maria Carla , Martinelli Eugenio , Isambert Hervé 
Published: February 2024

AbstractLive-cell microscopy routinely provides massive amount of time-lapse images of complex cellular systems under various physiological or therapeutic conditions. However, this wealth of data remains difficult to interpret in terms of causal effects. Here, we describe CausalXtract, a flexible computational pipeline that discovers causal and possibly time-lagged effects from morphodynamic features and cell-cell interactions in live-cell imaging data. CausalXtract methodology combines network-based and information-based frameworks, which is shown to discover causal effects overlooked by classical Granger and Schreiber causality approaches. We showcase the use of CausalXtract to uncover novel causal effects in a tumor-on-chip cellular ecosystem under therapeutically relevant conditions. In particular, we find that cancer associated fibroblasts directly inhibit cancer cell apoptosis, independently from anti-cancer treatment. CausalXtract uncovers also multiple antagonistic effects at different time delays. Hence, CausalXtract provides a unique computational tool to interpret live-cell imaging data for a range of fundamental and translational research applications.
Crypt and Villus Enterochromaffin Cells are Distinct Stress Sensors in the Gut
Authors: Touhara Kouki K. , Rossen Nathan D. , Deng Fei , Chu Tifany , Harrington Andrea M. , Garcia Caraballo Sonia , Brizuela Mariana , O’Donnell Tracey , Cil Onur , Brierley Stuart M. , Li Yulong , Julius David 
Published: February 2024

AbstractThe crypt-villus structure of the small intestine serves as an essential protective barrier, with its integrity monitored by the gut’s sensory system. Enterochromaffin (EC) cells, which are rare sensory epithelial cells that release serotonin (5-HT), surveil the mucosal environment and signal both within and outside the gut. However, it remains unclear whether EC cells in intestinal crypts and villi respond to different stimuli and elicit distinct responses. In this study, we introduce a new reporter mouse model to observe the release and propagation of serotonin in live intestines. Using this system, we show that crypt EC cells exhibit two modes of serotonin release: transient receptor potential A1 (TRPA1)-dependent tonic serotonin release that controls basal ionic secretion, and irritant-evoked serotonin release that activates gut sensory neurons. Furthermore, we find that a thick protective mucus layer prevents TRPA1 receptors on crypt EC cells from responding to luminal irritants such as reactive electrophiles; if this mucus layer is compromised, then crypt EC cells become susceptible to activation by luminal irritants. On the other hand, villus EC cells detect oxidative stress through TRPM2 channels and co-release serotonin and ATP to activate nearby gut sensory fibers. Our work highlights the physiological importance of intestinal architecture and differential TRP channel expression in sensing noxious stimuli that elicit nausea and/or pain sensations in the gut.
Inhibition of ULK1/2 and KRASG12Ccontrols tumor growth in preclinical models of lung cancer
Authors: Ghazi Phaedra C. , O’Toole Kayla T. , Srinivas Boggaram Sanjana , Scherzer Michael T. , Silvis Mark R. , Zhang Yun , Bogdan Madhumita , Smith Bryan D. , Lozano Guillermina , Flynn Daniel L. , Snyder Eric L. , Kinsey Conan G. , McMahon Martin 
Published: February 2024

ABSTRACTMutational activation ofKRASoccurs commonly in lung carcinogenesis and, with the recent FDA approval of covalent inhibitors of KRASG12Csuch as sotorasib or adagrasib, KRAS oncoproteins are important pharmacological targets in non-small cell lung cancer (NSCLC). However, not all KRASG12C-driven NSCLCs respond to these inhibitors, and the emergence of drug resistance in those patients that do respond can be rapid and pleiotropic. Hence, based on a backbone of covalent inhibition of KRASG12C, efforts are underway to develop effective combination therapies. Here we report that inhibition of KRASG12Csignaling increases autophagy in KRASG12Cexpressing lung cancer cells. Moreover, the combination of DCC-3116, a selective ULK1/2 inhibitor, plus sotorasib displays cooperative/synergistic suppression of human KRASG12C-driven lung cancer cell proliferationin vitroand superior tumor controlin vivo. Additionally, in genetically engineered mouse models of KRASG12C-driven NSCLC, inhibition of either KRASG12Cor ULK1/2 decreases tumor burden and increases mouse survival. Consequently, these data suggest that ULK1/2-mediated autophagy is a pharmacologically actionable cytoprotective stress response to inhibition of KRASG12Cin lung cancer.
Single-molecule evidence of Entropic Pulling by Hsp70 chaperones
Authors: Rukes Verena , Rebeaud Mathieu E. , Perrin Louis , De Los Rios Paolo , Cao Chan 
Published: February 2024

AbstractHsp70 chaperones are central components of the cellular network that ensure the structural quality of proteins. Despite their crucial roles in processes as diverse as the prevention of protein aggregation and protein translocation into organelles, their molecular mechanism of action has remained a hotly debated issue. Due to a lack of suitable methods, no experimental data has directly proven any of the models that have been proposed (Power Stroke, Brownian Ratchet, and Entropic Pulling). Recently, nanopores have emerged as a powerful tool to analyze the function of motor enzymes, as well as protein-protein interactions. Here, we used anin vitrosingle-molecule nanopore to mimicin vivotranslocation of proteins, and to investigate the molecular mechanism of Hsp70. Our experiments demonstrate that Hsp70s forcefully extract polypeptide substrates that are trapped inside the pore. The forces they exert are strong at the molecular level, being equivalent to 46 pN over distances of 1 nm, and depend on the size of Hsp70. These findings provide unambiguous evidence supporting the Entropic Pulling mechanism of action of Hsp70s, thus solving a long-standing debate, and proposing a potentially universal principle governing diverse cellular processes. In addition, these results emphasize the utility of biological nanopores for studying protein function at the single-molecule level.
Scrutinizing science to save lives: uncovering flaws in the data linking L-type calcium channels blockers to CRAC channels and heart failure
Authors: Bird Gary S. , Lin Yu-Ping , Tucker Charles J. , Mueller Geoffrey , Shi Min , Padmanabhan Sandosh , Parekh Anant B. 
Published: February 2024

AbstractHypertension is estimated to affect almost 1 billion people globally and significantly increases risk of myocardial infarction, heart failure, stroke, retinopathy and kidney disease. One major front line therapy that has been used for over 50 years involves L-type Ca2+channel blockers (LCCBs). One class of LCCBs is the dihydropyridine family, with amlodipine being widely prescribed regardless of gender, race, ethnicity or age. In 2020, Johnson et al.7reported that all LCCBs significantly increased the risk of heart failure, and attributed this effect to non-canonical activation of store-operated Ca2+entry. A major approach on which they based many of their arguments was to measure cytosolic Ca2+using the fluorescent Ca2+indicator dye fura-2. We recently demonstrated that amlodipine is highly fluorescent within cells and overwhelms the fura-2 signal, precluding the use of the indicator dye with amlodipine24. Our meta-analyses and prospective real world study showed that dihydropyridines were not associated with an increase in heart failure, likely explained by the lack of consideration by Johnson et al.7of well-known confounding factors such as age, race, obesity, prior anti-hypertensive treatment or diabetes24. Trebak and colleagues have responded to our paper with a forthright and unwavering defence of their work27. In this paper, we carry out a forensic dissection of Johnson et al.,7and conduct new experiments that address directly points raised by Trebak et al.27. We show that there are major flaws in the design and interpretation of their key experiments, that fura-2 cannot be used with amlodipine, that there are fundamental mathematical misunderstandings and mistakes throughout their study leading to critical calculations on heart failure that are demonstrably wrong, and several of their own results are inconsistent with their interpretation. We therefore believe the study by Johnson et al.7is flawed at many levels and we stand by our conclusions.
Cross-species prediction of transcription factor binding by adversarial training of a novel nucleotide-level deep neural network
Authors: Zhang Qinhu 
Published: February 2024

AbstractCross-species prediction of TF binding remains a major challenge due to the rapid evolutionary turnover of individual TF binding sites, resulting in cross-species predictive performance being consistently worse than within-species performance. In this study, we first propose a novel Nucleotide-Level Deep Neural Network (NLDNN) to predict TF binding within or across species. NLDNN regards the task of TF binding prediction as a nucleotide-level regression task. Beyond predictive performance, we also assess model performance by locating potential TF binding regions, discriminating TF-specific single-nucleotide polymorphisms (SNPs), and identifying causal disease-associated SNPs. Then, we design a dual-path framework for adversarial training of NLDNN to further improve the cross-species prediction performance by pulling the domain space of human and mouse species closer.
Expanding the mutational spectrum ofGCKin Turkish pediatric population
Authors: Topcu Vehap , Buyukyilmaz Gonul , Adiguzel Keziban Toksoy , Boyraz Mehmet 
Published: February 2024

AbstractHeterozygous loss-of-function variants inGCKcause persistent, mildly elevated plasma glucose beginning at birth. Recently, clinical phenotype created by deleterious variants inGCKis called GCK-MODY, although currently registered as “MODY, type 2” (maturity-onset diabetes of the young type 2, MODY2, MIM # 125851) in OMIM. The hyperglycemia of GCK-MODY is a benign and non-progressive condition, usually suspected upon detection of hyperglycemia in adulthood. Medication is not essential, nevertheless, pregnant females may require special attention. Here, we report recurrent and novelGCKvariants detected in 43 pediatric patients who were investigated for hyperglycemia by the referring pediatric endocrinologist. Electronic medical records (EMR) of the patients were collected and reviewed retrospectively. All patients applied to Ankara City Hospital between April 2019 and June 2022.GCKvariants were screened on NovaSeq 6000 next-generation sequencing platform (Illumina). Variants detected inGCKwere checked with recent literature for a proper pathogenicity classification. In 43 patients, 28 distinctGCKvariants were identified. Of these variants, 25 were classified as likely pathogenic/pathogenic variants (c.1342G>A, c.112C>T, c.1178T>C, c.130G>A, c.565A>G, c.208+3A>T, c.349G>C, c.863+5G>A, c.214G>A, c.1292C>A, c.830_831delTG, c.106C>T, c.572G>A, c.107G>C, c.454T>C, c.793G>A, c.645C>A, c.377T>A, c.667G>A, c.46-1G>A, c.149A>C, c.1079C>G, c.401T>C, c.758T>G, c.467_483+6del; NM_000162.5), while remaining 3 variants (c.950A>C, c.186G>T, c.188G>A; NM_000162.5) were classified as variant of uncertain significance. According to the variant effect, missense variants accounted for the majority (71%; 20/28), followed by splice junction (14%; 4/28), premature termination (7%; 2/28), frameshift (4%; 1/28), and synonymous (4%; 1/28) alterations. There were 3 novel variants: c.830_831del, c.377T>A, c.467_483+6del.