bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics
Authors: Carlson Rebecca J. , Patten J.J. , Stefanakis George , Soong Brian Y. , Radhakrishnan Adityanarayanan , Singh Avtar , Thakur Naveen , Amarasinghe Gaya K. , Hacohen Nir , Basler Christopher F. , Leung Daisy , Uhler Caroline , Davey Robert A. , Blainey Paul C. 
Published: April 2024

AbstractEbola virus (EBOV) is a high-consequence filovirus that gives rise to frequent epidemics with high case fatality rates and few therapeutic options. Here, we applied image-based screening of a genome-wide CRISPR library to systematically identify host cell regulators of Ebola virus infection in 39,085,093 million single cells. Measuring viral RNA and protein levels together with their localization in cells identified over 998 related host factors and provided detailed information about the role of each gene across the virus replication cycle. We trained a deep learning model on single-cell images to associate each host factor with predicted replication steps, and confirmed the predicted relationship for select host factors. Among the findings, we showed that the mitochondrial complex III subunit UQCRB is a post-entry regulator of Ebola virus RNA replication, and demonstrated that UQCRB inhibition with a small molecule reduced overall Ebola virus infection with an IC50 of 5 μM. Using a random forest model, we also identified perturbations that reduced infection by disrupting the equilibrium between viral RNA and protein. One such protein, STRAP, is a spliceosome-associated factor that was found to be closely associated with VP35, a viral protein required for RNA processing. Loss of STRAP expression resulted in a reduction in full-length viral genome production and subsequent production of non-infectious virus particles. Overall, the data produced in this genome-wide high-content single-cell screen and secondary screens in additional cell lines and related filoviruses (MARV and SUDV) revealed new insights about the role of host factors in virus replication and potential new targets for therapeutic intervention.
In vivoproperties of Arabidopsis FCA condensates involved in RNA 3’ processing
Authors: Jang Geng-Jen , Payne-Dwyer Alex L. , Maple Robert , Wu Zhe , Liu Fuquan , Lopez Sergio G. , Wang Yanning , Fang Xiaofeng , Leake Mark C. , Dean Caroline 
Published: April 2024

AbstractOur understanding of the functional requirements underpinning biomolecular condensationin vivois still relatively poor. The Arabidopsis RNA binding protein FCA is found in liquid-like nuclear condensates that function in transcription termination, promoting proximal polyadenylation at many targets in the Arabidopsis genome. To further understand the properties of these condensatesin vivowe used single particle tracking experiments on FCA reporters stably expressed at endogenous levels in plant nuclei. These revealed FCA forms a core oligomer of ∼4 molecules that multimerizes into higher-order particles. This assembles into macromolecular condensates through the function of the coiled-coil protein FLL2, which is genetically required for FCA function. FLL2 predominately co-localizes with FCA in larger sized condensates. A missense mutation in the FCA RRM domain, also genetically required for FCA function, reduced both average FCA particle and condensate size but did not perturb the core oligomer. Our work points to a modular structure for FCA condensates involving multimerization of core oligomers that assemble into functional macromolecular condensates via associated RNA and FLL2 interactions.
Automated microscopic measurement of fibrinaloid microclots and their degradation by nattokinase, the main natto protease
Authors: Grixti Justine M. , Theron Chrispian W. , Salcedo-Sora J. Enrique , Pretorius Etheresia , Kell Douglas B. 
Published: April 2024

AbstractNattokinase, from the Japanese fermented food natto, is a protease with fibrinolytic activity that can thus degrade conventional blood clots. In some cases, however, including in Long COVID, fibrinogen can polymerise into an anomalous amyloid form to create clots that are resistant to normal fibrinolysis and that we refer to as fibrinaloid microclots. These can be detected with the fluorogenic stain thioflavin T. We describe an automated microscopic technique for the quantification of fibrinaloid microclot formation, which also allows the kinetics of their formation and aggregation to be recorded. We also here show that recombinant nattokinase is effective at degrading the fibrinaloid microclotsin vitro. This adds to the otherwise largely anecdotal evidence, that we review, that nattokinase might be anticipated to have value as part of therapeutic treatments for individuals with Long COVID and related disorders that involve fibrinaloid microclots.
Associations between structural brain changes and blood neurofilament light chain protein in treatment-resistant schizophrenia
Authors: Cilia Brandon-Joe , Eratne Dhamidhu , Wannan Cassandra , Malpas Charles , Janelidze Shorena , Hansson Oskar , Everall Ian , Bousman Chad , Thomas Naveen , Santillo Alexander F , Velakoulis Dennis , Pantelis Christos 
Published: April 2024

AbstractBackground and HypothesisAround 30% of people with schizophrenia are refractory to antipsychotic treatment (treatment-resistant schizophrenia; TRS). While abnormal structural neuroimaging findings, in particular volume and thickness reductions, are often observed in schizophrenia, it is anticipated that biomarkers of neuronal injury like neurofilament light chain protein (NfL) can improve our understanding of the pathological basis underlying schizophrenia. The current study aimed to determine whether people with TRS demonstrate different associations between plasma NfL levels and regional cortical thickness reductions compared with controls.Study DesignMeasurements of plasma NfL and cortical thickness were obtained from 39 individuals with TRS, and 43 healthy controls. T1-weighted magnetic resonance imaging sequences were obtained and processed via FreeSurfer. General linear mixed models adjusting for age and weight were estimated to determine whether the interaction between diagnostic group and plasma NfL level predicted lower cortical thickness across frontotemporal structures and the insula.Study Results.Significant (false discovery rate corrected) cortical thinning of the left (p= 0.001,η2p= 0.104) and right (p< 0.001,η2= 0.167) insula was associated with higher levels of plasma NfL in TRS, but not in healthy controls.Conclusions.The association between regional thickness reduction of the insula bilaterally and plasma NfL may reflect a neurodegenerative process during the course of TRS. The findings of the present study suggest that some level of cortical degeneration localised to the bilateral insula may exist in people with TRS, which is not observed in the normal population.
Transcriptome landscape of high and low responders to an inactivated COVID-19 vaccine after 4 months using single-cell sequencing
Authors: Zhu Zhongyi , Huang Yaling , Sun Jiatong , Li Meirong , Chen Yong , Zhang Lei , Huang Fubaoqian , Liu Chuanyu , Chen Weijun , Ma Jinmin 
Published: April 2024

AbstractBackgroundVariability in antibody responses among individuals following vaccination is a universal phenomenon. Single-cell transcriptomics offers a potential avenue to understand the underlying mechanisms of these variations and improve our ability to evaluate and predict vaccine effectiveness.ObjectiveThis study aimed to explore the potential of single-cell transcriptomic data in understanding the variability of antibody responses post-vaccination and its correlation with transcriptomic changes.MethodsBlood samples were collected from 124 individuals on day 21 post COVID-19 vaccination. These samples were categorized based on antibody titers (high, medium, low). On day 135, PBMCs from 27 donors underwent single-cell RNA sequencing to depict the transcriptome atlas.ResultsDifferentially expressed genes (DEGs) affecting antibody expression in various cell types were identified. We found that innate immunity, B cell, and T cell population each had a small set of common DEGs (MT-CO1, HLA-DQA2, FOSB, TXNIP, and JUN), and Macrophages and Th1 cells exhibited the largest number of DEGs. Pathway analysis highlighted the dominant role of the innate immune cell population in antibody differences among populations, with a significant impact from the interferon pathway. Furthermore, protein complexes analysis revealed that alterations in the ribosome complex, primarily regulated by DC cells, may play a crucial role in regulating antibody differences. Combining these findings with previous research we proposed a potential regulatory mechanism model of DC cells on B cell antibody production.ConclusionWhile direct prediction of specific antibody levels using single-cell transcriptomic data remains technically and data-wise challenging, our study demonstrated the vast potential of single-cell transcriptomics in understanding the mechanisms underlying antibody responses induced by vaccines.
Negative selection allows human primary fibroblasts to tolerate high somatic mutation loads induced by N-ethyl-N-nitrosourea
Authors: Heid Johanna , Cutler Ronald , Sun Shixiang , Lee Moonsook , Maslov Alexander Y. , Dong Xiao , Sidoli Simone , Vijg Jan 
Published: April 2024

SummarySingle-cell sequencing has shown that thousands of mutations accumulate with age in most human tissues. While there is ample evidence that some mutations can clonally amplify and lead to disease, the total burden of mutations a cell tolerates without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts to multiple, low doses of N-ethyl-N-nitrosourea (ENU) and analyzed somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain ∼60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate. We provide evidence that such high levels of mutations are only tolerated through negative selection against variants in gene coding regions, and in sequences associated with genetic pathways for maintaining basic cellular function and growth. Since most tissues in adults are non-dividing, these results suggest that somatic mutations in the absence of negative selection may have functionally adverse effects.
Comparative genomics of macaques and integrated insights into genetic variation and population history
Authors: Zhang Shilong , Xu Ning , Fu Lianting , Yang Xiangyu , Li Yamei , Yang Zikun , Feng Yu , Ma Kaiyue , Jiang Xinrui , Han Junmin , Hu Ruixing , Zhang Lu , de Gennaro Luciana , Ryabov Fedor , Meng Dan , He Yaoxi , Wu Dongya , Yang Chentao , Paparella Annalisa , Mao Yuxiang , Bian Xinyan , Lu Yong , Antonacci Francesca , Ventura Mario , Shepelev Valery A. , Miga Karen H. , Alexandrov Ivan A. , Logsdon Glennis A. , Phillippy Adam M. , Su Bing , Zhang Guojie , Eichler Evan E. , Lu Qing , Shi Yongyong , Sun Qiang , Mao Yafei 
Published: April 2024

ABSTRACTThe crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g.,CYP2C76andEHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g.,PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g.,FOLH1andPIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g.,STAB1,SEMA3F, andHOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.
Arabidopsis ubiquitin ligase PUB41 is a positive regulator of the ABA response
Authors: Sharma Avinash , Goldfarb Shalev , Raveh Dina , Bar-Zvi Dudy 
Published: April 2024

AbstractSeed germination is a highly controlled developmental process. Prevention of early germination is essential to avoid germination at a time that is not likely to allow the completion of the plant life cycle before entering unfavorable seasons. The plant hormone ABA is the key regulator of seed dormancy and inhibition of germination. ABA is also involved in the plant response to drought. Here we report on the involvement of AtPUB41, a U-BOX E3 ubiquitin ligase fromArabidopsis thaliana, in regulating ABA signaling, seed dormancy, germination, and drought resilience.AtPUB41is expressed in most plant vegetative and reproductive tissues. AtPUB41 protein is localized in the cytosol and nucleus.pub41T-DNA insertion mutants display reduced seed dormancy, and their germination is less inhibited by exogenous ABA than seeds of wild-type plants.pub41mutant plants are also hypersensitive to drought. ABA inducesAtPUB41promoter activity and steady-state mRNA levels in the roots. Our data suggest thatAtPUB41is a positive regulator of ABA signaling.Main ConclusionArabidopsis ubiquitin ligase PUB41 is induced by ABA and acts as a positive regulator of ABA signaling by modulating seed dormancy, germination, and drought resilience.
Unveiling Ageing-Associated and Caloric Restriction-Associated Changes in miRNA Expression in Rat Skeletal Muscle and the Mechanisms Mediating their Effects on Muscle Cell Function
Authors: Altab Gulum , Merry Brian J. , Beckett Charles W. , Raina Priyanka , Soriano-Arroquia Ana , Zhang Bruce , Vasilaki Aphrodite , Goljanek-Whysall Katarzyna , de Magalhães João Pedro 
Published: April 2024

AbstractThe mechanisms underlying skeletal muscle ageing, whilst poorly understood, are thought to involve dysregulated micro (mi)RNA expression. Using young and aged rat skeletal muscle tissue, we applied high-throughput RNA sequencing to comprehensively study alterations in miRNA expression occurring with age, as well as the impact of caloric restriction (CR) on these changes. Furthermore, the function of the proteins targeted by these age- and CR-associated miRNAs was ascertained.Numerous known and novel age-associated miRNAs were identified of which CR normalised 45.5% to youthful levels. Our results suggested miRNAs upregulated with age to downregulated proteins involved in muscle tissue development and metabolism, as well as longevity pathways, such as AMPK and autophagy. Furthermore, our results found miRNAs downregulated with age to upregulate pro-inflammatory proteins, particularly those involved in innate immunity and the complement and coagulation cascades. Interestingly, CR was particularly effective at normalising miRNAs upregulated with age, rescuing their associated protein coding genes but was less effective at rescuing anti-inflammatory miRNAs downregulated with age.Lastly, the effects of a specific miRNA, miR-96-5p, identified by our analysis to be upregulated with age, were studied in culture C2C12 myoblasts. We demonstrated miR-96-5p to decrease cell viability and markers of mitochondrial biogenesis, myogenic differentiation and autophagy. Overall, our results provide useful information regarding how miRNA expression changes in skeletal muscle, as well as the consequences of these changes and how they are ameliorated by CR.
The BLM-TOP3A-RMI1-RMI2 proximity map reveals that RAD54L2 suppresses sister chromatid exchanges
Authors: Ho Jung Jennifer , Cheng Edith , Wong Cassandra J. , St-Germain Jonathan R. , Dunham Wade H. , Raught Brian , Gingras Anne-Claude , Brown Grant W. 
Published: April 2024

AbstractHomologous recombination is a largely error-free DNA repair mechanism conserved across all domains of life and is essential for the maintenance of genome integrity. Not only are the mutations in homologous recombination repair genes probable cancer drivers, some also cause genetic disorders. In particular, mutations in the Bloom (BLM) helicase cause Bloom Syndrome, a rare autosomal recessive disorder characterized by increased sister chromatid exchanges and predisposition to a variety of cancers. The pathology of Bloom Syndrome stems from the impaired activity of the BLM-TOP3A-RMI1-RMI2 (BTRR) complex which suppresses crossover recombination to prevent potentially deleterious genome rearrangements. We provide a comprehensive BTRR proximity interactome, revealing proteins that suppress crossover recombination. We find that RAD54L2, a SNF2-family protein, physically interacts with BLM and suppresses sister chromatid exchanges. RAD54L2 is important for recruitment of BLM to chromatin and requires an intact ATPase domain to promote non-crossover recombination. Thus, the BTRR proximity map identifies a regulator of recombination.
Study of the hepatotoxicity of trans-coric acid isolated fromScutellaria baicalensisinin vivoexperiments
Authors: Mikhailovna Fedorova Anastasia , Dmitrievna Vesnina Anna , Sergeevna Milentyeva Irina , Yuryevich Prosekov Alexander 
Published: April 2024

AbstractBiologically active supplements (BAS) based on plant material, possessing a wide range of beneficial properties (antioxidant, anti-inflammatory, antimicrobial, etc.), are becoming increasingly popular worldwide. Such supplements are readily available and can be used without consulting a healthcare professional. Consequently, the extent of their use is underestimated by doctors. Plant hepatotoxicity is not uncommon, but the frequency and manifestation are not sufficiently characterized. This study is dedicated to investigating the hepatotoxicity of trans-coric acid isolated from the root culture ofScutellaria baicalensisinin vivoexperiments. This work aims to evaluate the hepatotoxicity of trans-coric acid on male rats at doses of 50.0 and 100.0 mg/kg. During the experiment, it was found that trans-coric acid, isolated from the root culture extract ofScutellaria baicalensis, does not induce hepatotoxicity in the presented doses in model animals with 14-day intragastric administration. Thus, this study demonstrates that trans-coric acid can be safely used as a component of BAS for the prevention of chronic diseases, thereby promoting healthy aging.
Modulation of photosystem II heterogeneity and stomatal functioning contribute to sustaining photochemistry and photoprotection in mangroves exposed to a cold wave
Authors: Sebastian John Sunoj. V. , Mathur Sonal , Elsheery Nabil. I. , Yan Li , Lambers Hans , Short Aidan. W. , Wee Alison. K.S. , Jajoo Anjana , Aritsara Amy Ny Aina , Kajita Tadashi , Cao Kun-Fang 
Published: April 2024

AbstractCold waves restrict the distribution of mangroves. This study examined the contribution of PSII heterogeneity and stomatal functioning to sustaining photochemistry and photoprotection in mangroves during a cold wave. We exposed eight populations of Kandelia obovata (cold-tolerant) and, Bruguiera gymnorhiza (cold-susceptible) from different latitudes to 27/20°C (favorable) and 10/3°C (chilling; simulated cold wave) day and night temperatures. Multiple trait responses imply that cold waves affected K. obovata the least. Significant changes in chlorophyll fluorescence transients (photosystem II [PSII]) with a slight decrease in the redox status of P700 (photosystem I [PSI]) imply a greater impact of a cold wave on PSII. During the cold wave, photochemical efficiency of PSII, efficiency of the water-splitting complex, light absorptance, stomatal pore area, cyclic electron flow, nonphotochemical quenching, and number of active PSIIα and PSII QB reducing centers decreased, while light transmittance, night respiration, and inactive PSII QB nonreducing, PSIIβ, and γ centers increased in both species. The population of K. obovata from the coldest latitudinal site (Fujian, China) was least affected by cold wave due to local evolutionary adaptations. Modulation of PSII heterogeneity and stomatal functioning is important to sustaining photochemistry and photoprotection in mangroves to cope with cold waves.HighlightsPSII heterogeneity and stomatal functioning support mangroves to cope with cold waves.Local evolutionary adaptations promote the cold tolerance of mangrove populations.
Breakdown insensitive acceleration regime in a metamaterial accelerating structure
Authors: Merenich Dillon , Leung Brendan , Rijal Gaurab , Lu Xueying , Doran Scott , Chen Gongxiaohui , Liu Wanming , Jing Chunguang , Power John , Whiteford Charles , Wisniewski Eric 
Published: April 2024

A new regime in radiofrequency (rf) breakdown, named the breakdown insensitive acceleration regime (BIAR), was observed in an 11.7 GHz metamaterial structure for wakefield acceleration driven by rf pulses with a duration of a few nanoseconds. In the BIAR, rf breakdown occurs without interrupting potential beam acceleration, resulting in greater resilience to breakdown. We have investigated the possibility that BIAR can support higher gradients by characterizing the breakdown in a high-power test. The peak gradient reached 190  MV/m when the structure was powered by 6 ns long rf pulses with 115 MW peak power. The short rf pulses were extracted from 65 MeV electron bunch trains with a total charge of up to 210 nC. This work has revealed the benefits of short-pulse acceleration by characterizing rf breakdown in the previously unexplored parameter space.

Published by the American Physical Society
2024