bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Modeling of Effects ofPKP2Gene Therapy on Ventricular Conduction Properties in Arrhythmogenic Cardiomyopathy
Authors: Ostini Alessio , Kléber André G. , Rudy Yoram , Saffitz Jeffrey E. , Kucera Jan P. 
Published: December 2024

AbstractBackgroundPatients with arrhythmogenic cardiomyopathy (ACM) due to pathogenic variants inPKP2, the gene for the desmosomal protein plakophilin-2, are being enrolled in gene therapy trials designed to replace the defective allele via adeno-associated viral (AAV) transduction of cardiac myocytes. Evidence from experimental systems and patients indicates that ventricular myocytes inPKP2ACM have greatly reduced electrical coupling at gap junctions and reduced Na+current density. In previous AAV gene therapy trials, <50% of ventricular myocytes have generally been transduced.MethodsWe used established computational models of ventricular cell electrophysiology to define the effects of varying levels of successful gene therapy on conduction in patients withPKP2ACM. Conduction velocity and development of conduction block were analyzed in tissue constructs composed of cells with levels of electrical coupling and Na+current density observed in experimental studies.ResultsWe observed a non-linear relationship between conduction velocity and the proportion of transduced cells. Conduction velocity increased only modestly when up to 40% of myocytes were transduced. Conduction block did not occur in tissue constructs with moderate levels of uncoupling (0.10 or 0.15 of normal) as this degree of coupling was sufficient to allow electrotonic current to pass through diseased cells. Thus, low levels of transduction, likely to occur in phase 1 clinical trials, do not appear to pose a major safety concern. However, our models did not incorporate potential effects of fibrosis and immune signaling, both of which will presumably be present inPKP2ACM patients undergoing gene therapy.ConclusionsThe extent of successful ventricular myocyte transduction anticipated to be achieved inPKP2AAV gene therapy trials will likely not restore conduction velocity to levels sufficient to decrease risk of reentrant arrhythmias.What is Known-Patients with arrhythmogenic cardiomyopathy due to pathogenic variants inPKP2(the gene for the desmosomal protein plakophilin-2) are now being enrolled in gene therapy trials.-Experimental and clinical observations indicate that patients with arrhythmogenic cardiomyopathy have slow ventricular conduction with a propensity to conduction block due to source-sink mismatch.-<50% of ventricular myocytes are usually transduced after adeno-associated viral gene therapy.What the Study Adds-At anticipated levels of successful transduction of ventricular myocytes, little change in conduction velocity will be achieved in patients with arrhythmogenic cardiomyopathy due to variants inPKP2.-Higher levels of transduction could produce conditions that increase risk of conduction block, especially in the presence of areas of non-conducting fibrofatty scar tissue.
Cnot4 heterozygosity attenuates high fat diet-induced obesity in mice and impairs PPARγ-mediated adipocyte differentiation
Authors: Yamaguchi Tomokazu , Hoshizaki Midori , Imai Yumiko , Yamamoto Tadashi , Kuba Keiji 
Published: December 2024

AbstractAdipocyte differentiation is crucial for formation and expansion of white adipose tissue and is also associated with the pathologies of obesity. CNOT4 is an E3 ubiquitin ligase and also contains RNA binding domain. In mammals CNOT4 has been suggested to interact with CCR4-NOT complex, a major executor of mRNA poly(A) shortening. While several subunits within the CCR4-NOT complex were shown to be involved in obesity and energy metabolism, the roles of CNOT4 in obesity remain unexplored. In this study, we generated and analyzed Cnot4 knockout mice and found that Cnot4 heterozygous (Cnot4 Het) mice exhibit resistance to high fat diet-induced obesity, including significant reduction in adipose tissue mass and hepatic lipid depots. However, Cnot4 Het did not affect mRNA expression of metabolic genes as well as serum lipid levels or glucose tolerance. Mechanistically, Cnot4 Het fibroblasts significantly reduced the capability of differentiation into adipocytes and down-regulated adipogenic gene expression compared to wild type fibroblasts. Heterozygous deletion of Cnot4 down-regulated the transcriptional activity of PPARγ, thereby suppressing up-regulation of adipocyte marker gene expression in response to rosiglitazone, a PPARγ agonist. These results suggest that CNOT4 mediates adipocyte differentiation during formation and growth of adipose tissue partly through positively regulating transcriptional activity of PPARγ.
Optogenetic inhibition quenches the integration of sensory input in the cortex
Authors: Manuel Ambrosone , Elena Montagni , Francesco Resta , Lorenzo Curti , Guido Mannaioni , Alessio Masi , Saverio Pavone Francesco , Anna Letizia Allegra Mascaro 
Published: December 2024

ABSTRACTSignificanceMany fundamental processes of brain computation, such as sensory perception and motor control, heavily rely on the mesoscopic dynamics of activity across the cerebral cortex. Manipulating mesoscale activity and observing its effects across multiple brain regions is crucial for understanding the causal link between cortical dynamics and behavior.ObjectiveThe goal of this study was to develop a novel all-optical system that allows inhibition of excitatory neurons while simultaneously monitoring cortical responses at arbitrary sites across the entire dorsal cortex of mice.MethodsWe combined wide-field imaging and optogenetics to create a mesoscale all-optical approach, enabling simultaneous monitoring and manipulation of cortical activity using light. Intravenous injection of two PHP.eB AAVs enabled the whole-brain co-expression of the red-shifted calcium indicator jRCaMP1b and the inhibitory actuator stGtACR2, with stable expression over several weeks. This system was calibrated, and the effects of inhibition on sensory responses were tested.ResultsIncreasing laser power progressively reduced spontaneous activity at the site of irradiation. A single 5-second pulse on the barrel field cortex significantly decreased the amplitude of sensory-evoked responses, not only in the stimulated region but across the entire stimulated hemisphere.ConclusionsThis novel all-optical system enables targeted inhibition while concurrently monitoring mesoscale cortical activity. It provides insights into the dynamics of cortical circuits and offers a milestone for investigating the causal links between neuronal activity and behavior. Future research can use this tool to address sensory responsiveness impairments in neurological and neuropsychiatric disorders.
Multimodal normative modeling in Alzheimer’s Disease with introspective variational autoencoders
Authors: Kumar Sayantan , Qiu Peijie , Yang Braden , Bani Abdalla , Payne Philip R.O , Sotiras Aristeidis 
Published: December 2024

AbstractNormative models in neuroimaging learn patterns of healthy brain distributions to identify deviations in disease subjects, such as those with Alzheimer’s Disease (AD). This study addresses two key limitations of variational autoencoder (VAE)-based normative models: (1) VAEs often struggle to accurately model healthy control distributions, resulting in high reconstruction errors and false positives, and (2) traditional multimodal aggregation methods, like Product-of-Experts (PoE) and Mixture-of-Experts (MoE), can produce uninformative latent representations. To overcome these challenges, we developed a multimodal introspective VAE that enhances normative modeling by achieving more precise representations of healthy anatomy in both the latent space and reconstructions. Additionally, we implemented a Mixture-of-Product-of-Experts (MOPOE) approach, leveraging the strengths of PoE and MoE to efficiently aggregate multimodal information and improve abnormality detection in the latent space. Using multimodal neuroimaging biomarkers from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset, our proposed multimodal introspective VAE demonstrated superior reconstruction of healthy controls and outperformed baseline methods in detecting outliers. Deviations calculated in the aggregated latent space effectively integrated complementary information from multiple modalities, leading to higher likelihood ratios. The model exhibited strong performance in Out-of-Distribution (OOD) detection, achieving clear separation between control and disease cohorts. Additionally, Z-score deviations in specific latent dimensions were mapped to feature-space abnormalities, enabling interpretable identification of brain regions associated with AD pathology.
Targeted KRASG12Vdegradation elicits efficient and durable lung adenocarcinoma regressionin vivo
Authors: Martín Alberto , García-Pérez Inés M. , José Sonia San , Rojo Pep , Riego-Mejías Carlos , Teodosio Cristina , Barbosa Bárbara MG. , Sánchez-Zarzalejo Carolina , Folch-I-Casanovas Ignasi , Caballol Antonia Odena , Jarió Sònia , Entrialgo Rodrigo , Nokin Marie-Julie , Loa Diana , Guruceaga Elizabeth , Attolini Camille Stephan-Otto , Ambrogio Chiara , Villanueva Alberto , Vicent Silvestre , Riera Antoni , Santamaría David , Mayor-Ruiz Cristina 
Published: December 2024

ABSTRACTRecent drug discovery breakthroughs led to the approval of KRASG12Cinhibitors in lung adenocarcinoma (LUAD). Unfortunately, clinical responses remain limited due to rapid resistance onset. Proteolysis-targeting chimeras (PROTACs) have emerged as promising alternatives to traditional inhibition. However, there is limited mechanistic understanding of KRAS degradationin vivo. Here, we developed a preclinical LUAD mouse model and demonstrated that targeted oncogenic KRAS degradation induces rapid tumor regression. Transcriptional, histological, and immunophenotypic analyses revealed a substantial remodeling of the tumor microenvironment. Notably, disease relapse observed during long-term degrader treatment stems from proteolysis machinery dysregulation, indicating resistance mechanisms distinct from those reported upon KRAS inhibition. Our findings highlight the therapeutic potential of KRAS degradation in LUAD, offering insights into cell-intrinsic and extrinsic mechanisms driving durable antitumor responses and supporting further clinical exploration.SIGNIFICANCEGiven the short duration of the clinical responses to KRAS inhibitors, complementary therapies are a dire medical need. Our preclinical findings endorse KRAS degradation as a therapeutic alternative in LUAD, where cell-intrinsic and extrinsic mechanisms drive tumor regression and durable therapeutic responses.
Future climate and land use change will equally impact global terrestrial vertebrate diversity
Authors: Hari Chantal , Hickler Thomas , Hof Christian , Reyer Christopher P.O. , Vanderkelen Inne , Voskamp Alke , Biber Matthias F. , Fischer Markus , Davin Édouard L. 
Published: December 2024

AbstractAimTerrestrial biodiversity is impacted by both climate and land use change. Yet, future biodiversity projections have rarely considered these two drivers in combination. In this study, we aim to assess the individual and combined impact of future climate and land use change on global terrestrial vertebrate diversity under a “sustainability” (SSP1-RCP2.6) and an “inequality” (SSP4-RCP6.0) scenario.LocationGlobal land, excluding Antarctica.Time period1995, 2080Major taxa studiedAmphibians, birds, and mammals.MethodsWe combined global climate-driven species distribution model (SDM) projections of 13903 vertebrates (amphibians, birds and mammals) with future and present land use projections from the Land Use Harmonization 2 (LUH2) project. We refined the SDM outputs by the habitat requirements of each species using a land use filtering approach. We then analyzed future species richness changes globally, per region and per land-use category and also looked at taxon-specific effects.ResultsUnder both scenarios, decreases in future species richness dominate at low and mid-latitudes with climate and land use change playing an equally important role. Land use change can be either an alleviating (SSP1-RCP2.6) or an exacerbating (SSP4-RCP6.0) factor of climate-induced biodiversity loss. Sub-Saharan Africa is projected to become a high-risk area for future land use-driven biodiversity loss under the “inequality” scenario. Under SSP1-RCP2.6, forested and non-forested land areas increase, while SSP4-RCP6.0 leads to higher rates of deforestation and pasture expansion. Mammals experience the largest climate-driven losses, affecting 56.4% of land area under SSP4-RCP6.0, while amphibians are particularly vulnerable to land use-driven losses, especially under SSP4-RCP6.0.Main conclusionsGenerally, our results suggest that both climate and land use pressures on biodiversity will be highest in lower latitudes which harbor the highest levels of biodiversity.
A simplified two-plasmid system for orthogonal control of mammalian gene expression using light-activated CRISPR effector
Authors: Garimella Shruthi S. , Minami Shiaki A. , Khanchandani Anusha N. , Schaffer Susannah R. , Shah Priya S. 
Published: December 2024

AbstractBackgroundOptogenetic systems use light-responsive proteins to control gene expression with the “flip of a switch”. One such tool is thelightactivatedCRISPReffector (LACE) system. Its ability to regulate gene expression in a tunable, reversible, and spatially resolved manner makes it attractive for many applications. However, LACE relies on delivery of four separate components on individual plasmids, which can limit its use. Here, we optimize LACE to reduce the number of plasmids needed to deliver all four components.ResultsThe two-plasmid LACE (2pLACE) system combines the four components of the original LACE system into two plasmids. Following construction, the behavior of 2pLACE was rigorously tested using optogenetic control of enhanced green fluorescent protein (eGFP) expression as a reporter. We optimized the ratio of the two plasmids, measured activation as a function of light intensity, and determined the frequency of the light to activate the maximum fluorescence. Overall, the 2pLACE system showed a similar dynamic range, tunability, and activation kinetics as the original four plasmid LACE (4pLACE) system. Interestingly, 2pLACE also had less variability in activation signal compared to 4pLACE.ConclusionsThis simplified system for optogenetics will be more amenable to biotechnology applications where variability needs to be minimized. By optimizing the LACE system to use fewer plasmids, 2pLACE becomes a flexible tool in multiple research applications.
PacBio genome assembly ofOlea europaeaL. subsp.europaeacultivars ‘Frantoio’ and ‘Leccino’ reveal main structural differences in key genes related to salt stress
Authors: Sebastiani Luca , Sarfraz Iqra , Francini Alessandra , Celii Mirko , Wing Rod A. , Zuccolo Andrea 
Published: December 2024

AbstractWe present two high-quality genome assemblies forOlea europaeaL. cultivars ‘Frantoio’ and ‘Leccino’ leveraging PacBio HiFi sequencing to achieve approximately 30× genome coverage for each cultivar. The assemblies span 1.18 Gbp and 1.43 Gbp with contig N50 values of 1.78 Mbp and 45.88 Mbp for ‘Frantoio’ and ‘Leccino’ respectively. BUSCO analysis revealed a great genome completeness (∼97.9%), surpassing many of earlierOlea europaeaassemblies and is in par with the most recent one. Repetitive content accounted for ∼67.5% in ‘Frantoio’ and ∼70.8% in ‘Leccino’ with long terminal repeats (LTRs) dominating. Notably, a tandem repeat family, Satellite 1, represented ∼16.9% and ∼8.6% of the ‘Leccino’ and ‘Frantoio’ genomes, respectively. The structural variant (SV) analysis was done with a particular focus on those associated with nine key gene families involved in salinity tolerance and identified cultivar-specific genomic differences, emphasizing the diversity within domesticated olives. This comprehensive analysis provides valuable resources for studying olive genome evolution, domestication, and genetic improvement, underscoring the utility of long-read sequencing for resolving complex genomic features.
StayRose: a photostable StayGold derivative red-shifted by genetic code expansion
Authors: Scott Will , Ivorra-Molla Esther , Akhuli Dipayan , Massam-Wu Teresa , Cook Jonathan , Song Lijiang , Mishima Masanori , Crow Allister , Balasubramanian Mohan K. 
Published: December 2024

ABSTRACTPhotobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engineering, addresses this challenge with its high photostability. There is now focus on producing different colour StayGold derivatives to facilitate concurrent tagging of multiple targets. The unnatural amino acid 3-aminotyrosine has previously been shown to red-shift super folder GFP upon incorporation into its chromophore via genetic code expansion. Here we apply the same strategy to red-shift StayGold through substitution of Tyrosine-58 with 3-aminotyrosine. The resultant red fluorescent protein, StayRose, shows 530 nm excitation and 588 nm emission peaks, shifting from the 497 nm and 504 nm excitation and emission peaks of StayGold. StayRose also retains the favourable photostability of StayGold and can be similarly monomerised using mutations at the dimer interface. A high-resolution crystal structure of StayRose confirms the modified structure of the amino-chromophore within an unperturbed 3D fold. Although reliant on genetic code expansion, StayRose provides an important step towards developing red-shifted StayGold derivatives.
Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples
Authors: Ozirmak Lermi Nejla , Molina Ayala Max , Hernandez Sharia , Lu Wei , Khan Khaja , Serrano Alejandra , Lubo Idania , Hamana Leticia , Tomczak Katarzyna , Barnes Sean , Dou Jinzhuang , Liang Qingnan , Team RTI , Raso Maria Gabriela , Tang Ximing , Jiang Mei , Sanchez-Espiridion Beatriz , Weissferdt Annikka , Heymach John , Zhang Jianjun , Sepesi Boris , Cascone Tina , Tsao Anne , Altan Mehmet , Mehran Reza , Gibbons Don , Wistuba Ignacio , Haymaker Cara , Chen Ken , Solis Soto Luisa M. 
Published: December 2024

AbstractImaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples. In addition to objective assessment of automatic cell segmentation and phenotyping, we performed pixel-resolution manual evaluation of phenotyping to carry out pathologically meaningful comparison between ST platforms. Our study detailed the intricate differences between the ST platforms, revealed the importance of parameters such as tissue age and probe design in determining the data quality, and suggested reliable workflows for accurate spatial profiling and molecular discovery.
Discovery of an on-pathway protein folding intermediate illuminates the kinetic competition between folding and misfolding
Authors: Luan Qing , Clark Patricia L. 
Published: December 2024

AbstractOur current understanding of protein folding is based predominantly on studies of small (<150 aa) proteins that refold reversibly from a chemically denatured state. As protein length increases, the competition between off-pathway misfolding and on-pathway folding likewise increases, creating a more complex energy landscape. Little is known about how intermediates populated during the folding of larger proteins affect navigation of this more complex landscape. Previously, we reported extremely slow folding rates for the 539 aa β-helical passenger domain of pertactin (P.69T), including conditions that favor the formation of a kinetically trapped, off-pathway partially folded state (PFS). The existence of an on-pathway intermediate for P.69T folding was speculated but its characterization remained elusive. In this work, we exploited the extremely slow kinetics of PFS unfolding to develop a double-jump “denaturant challenge” assay. With this assay, we identified a transient unfolding intermediate, PFS*, that adopts a similar structure to PFS, including C-terminal folded structure and a disordered N-terminus, yet unfolds much more quickly than PFS. Additional experiments revealed that PFS* also functions as an on-pathway intermediate for P.69T folding. Collectively, these results support a two-step, C-to-N-terminal model for P.69T folding: folding initiates in the C-terminus with the rate-limiting formation of the transient on-pathway PFS* intermediate, which sits at the junction of the kinetic competition between folding and misfolding. Notably, processive folding from C-to-N-terminus also occurs during C-to-N-terminal translocation of P.69T across the bacterial outer membrane. These results illuminate the crucial role of kinetics when navigating a complex energy landscape for protein folding.
Sub-clustering, marker identification and multi-omics integration influenced by protoplasting in plant scRNA-seq data analysis
Authors: Yao Jie , Shang Nianmin , Chen Hongyu , Hu Yurong , Zhu Qian-Hao , Fan Longjiang , Ye Chuyu , Chu Qinjie 
Published: December 2024

AbstractSingle-cell RNA sequencing (scRNA-seq) technology is a powerful tool for exploring cell heterogeneity and lineage dynamics, revealing complex mechanisms driving tissue function and development. However, plant cell’s rigid cell walls require a protoplasing step, an enzymatic process that can introduce biases. The impact of protoplasting on plant scRNA-seq data remains poorly understood. In this study, we analyzed gene expression patterns from bulk RNA-seq of various plant tissues before and after protoplasting. Cell-type specific protoplasting effects were discovered in different plant tissues. Protoplasting-related biases were found to distort clustering, marker gene identification, and multi-omics integration. By calculating protoplasted scores based on gene expression, we identified and mitigated protoplasting effects, enabling the accurate clustering and annotation of tobacco BY-2 cells and identification of cell-cycle-related genes. Our findings underscore the importance of assessing and correcting for protoplasting biases in plant scRNA-seq data analysis, offering new insights for more accurate data interpretation and biological discovery.