bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensing endogenous RNA in living human cells using a CRISPR-activated protease
Authors: Blumenstock Katja , Hoch Alexander , Hinterlang Leo D. , Fandrey Caroline I. , Schneberger Niels , Hagelueken Gregor , Schmid-Burgk Jonathan L. 
Published: July 2024

ABSTRACTMost techniques used to detect specific mRNAs in eukaryotic cells require to extract nucleic acids and thereby kill the cells. A programmable sensor for monitoring endogenous transcripts in living cells, in contrast, would enable to enrich living cells based on a specific transcription or splicing event, and studying these cells by live microscopy or sequencing methods requiring intact cells. We have engineered CRISPR-READ, a live cell RNA detector based on the CRISPR-associated Lon protease CalpL and a cA4-producing Type III CRISPR system. Upon RNA-programmable RNA sensing, CRISPR-READ produces an orthogonal second messenger, which leads to the cleavage of a dual FRET / localization reporter compatible with FACS sorting and live microscopy. Using this genetically encoded sensing circuit as a readout for a genome-wide CRISPR perturbation screen, we identified an extended Type-I interferon signaling cascade; RNA-Seq on sensor-sorted cells enabled unbiased identification of correlated stochasticity in gene expression across single cells.
Endomucin regulates the endothelial cytoskeleton independent of VEGF
Authors: Moon Jean , Chaudhary Suman , Martinez Lorena Rodriguez , Hu Zhengping , D’Amore Patricia A. 
Published: July 2024

AbstractThe endothelial glycocalyx, lining the apical surface of the endothelium, is involved in a host of vascular processes. The layer contains a network of membrane-bound proteoglycans and glycoproteins. One such glycoprotein is endomucin (EMCN), which our lab has revealed is a modulator of VEGFR2 function. Intravitreal injection of siEMCN into the eyes of P5 mice impairs vascular development. In vitro silencing of EMCN suppresses VEGF-induced proliferation and migration. Signaling pathways that drive cell migration converge on cytoskeletal remodeling. By coupling co-immunoprecipitation with liquid chromatography/mass spectrometry, we identified interactions between EMCN, and proteins associated with actin cytoskeleton organization. The aim of the study was to investigate the influence of EMCN on cytoskeleton dynamics in angiogenesis. EMCN depletion resulted in reduction of F-actin levels, whereas overexpression of EMCN induced membrane protrusions in cells that were rich in stress fibers. The reorganization of the actin filaments did not depend on VEGFR2 signaling, suggesting that EMCN is a potential connection between the cytoskeleton and the glycocalyx.
Temporal dynamics analysis reveals that concurrent working memory load eliminates the Stroop effect through disrupting stimulus-response mapping
Authors: Li Yafen , Lin Yixuan , Li Qing , Chen Yongqiang , Li Zhifang , Chen Antao 
Published: July 2024

AbstractConcurrent verbal working memory task can eliminate the color-word Stroop effect. Previous research, based on specific and limited resources, suggested that the disappearance of the conflict effect was due to the memory information preempting the resources for distractors. However, it remains unclear which particular stage of Stroop conflict processing is influenced by working memory loads. In this study, electroencephalography (EEG) recordings with event-related potential (ERP) analyses, time-frequency analyses, multivariate pattern analyses (MVPA), and representational similarity analyses (RSA) were applied to provide an in-depth investigation of the aforementioned issue. Subjects were required to complete the single task (the classical manual color-word Stroop task) and the dual task (the Sternberg working memory task combined with the Stroop task), respectively. Behaviorally, the results indicated that the Stroop effect was eliminated in the dual-task condition. The EEG results showed that the concurrent working memory task did not modulate the P1, N450, and alpha bands. However, it modulated the sustained potential (SP), late theta (740-820 ms), and beta (920-1040 ms) power, showing no difference between congruent and incongruent trials in the dual-task condition but significant difference in the single-task condition. Importantly, the RSA results revealed that the neural activation pattern of the late theta was similar to the response interaction pattern. Together, these findings implied that concurrent working memory task eliminated the Stroop effect through disrupting stimulus-response mapping.
Microbial metabolomics’ latest SICRIT: Soft ionization by Chemical Reaction in-Transfer mass spectrometry
Authors: McAtamney Allyson , Ferranti Allison , Ludvik Denise A. , Yildiz Fitnat H. , Mandel Mark J. , Hayward Taylor , Sanchez Laura M. 
Published: July 2024

AbstractMicrobial metabolomics studies are a common approach to identifying microbial strains that have a capacity to produce new chemistries bothin vitroandin situ. A limitation to applying microbial metabolomics to the discovery of new chemical entities is the rediscovery of known compounds, or “known unknowns.” One contributing factor to this rediscovery is the majority of laboratories use one ionization source–electrospray ionization (ESI)–to conduct metabolomics studies. Although ESI is an efficient, widely adopted ionization method, its widespread use may contribute to the re-identification of known metabolites. Here, we present the use of a dielectric barrier discharge ionization (DBDI) for microbial metabolomics applications through the use of soft ionization chemical reaction in-transfer (SICRIT). Additionally, we compared SICRIT to ESI using two differentVibriospecies–Vibrio fischeri,a symbiotic marine bacterium, andVibrio cholerae, a pathogenic bacterium. Overall, we found that the SICRIT source ionizes a different set of metabolites than ESI, and it has the ability to ionize lipids more efficiently than ESI in positive mode. This work highlights the value of using more than one ionization source for the detection of metabolites.
STK19 is a transcription-coupled repair factor that participates in UVSSA ubiquitination and TFIIH loading
Authors: Tan Yuanqing , Gao Meng , Huang Yanchao , Zhan Delin , Wu Sizhong , An Jiao , Zhang Xiping , Hu Jinchuan 
Published: July 2024

AbstractTranscription-coupled repair (TCR) is the major pathway to remove transcription-blocking lesions. Although discovered for nearly 40 years, the mechanism and critical players of mammalian TCR remain unclear. STK19 is a factor affecting cell survival and recovery of RNA synthesis in response to DNA damage, however, whether it is a necessary component for TCR is unknown. Here we demonstrated that STK19 is essential for human TCR. Mechanistically, STK19 is recruited to damage sites through direct interaction with CSA. It can also interact with RNA polymerase IIin vitro. Once recruited, STK19 plays an important role in UVSSA ubiquitination which is needed for TCR. STK19 also promotes TCR independent of UVSSA ubiquitination by stimulating TFIIH recruitment through its direct interaction with TFIIH. In summary, our results suggest that STK19 is a key factor of human TCR that links CSA, UVSSA ubiquitination and TFIIH loading, shedding light on the molecular mechanisms of TCR.
Systemic Review of Health Disparities in Access and Delivery of Care for Geriatric Diseases in the United States
Authors: Thomas Mony , Hussein Muhammad R , Utterman Sonia , Jushua Jackline 
Published: July 2024

AbstractBackgroundThe U.S. population continues to age, and the identification of disparities in geriatric care -so that they may be understood and solutions addressed - is ever more critical. A systematic review is presented on current disparities found in access to care for geriatric diseases as well as in the delivery of care within the United States.MethodsA comprehensive search for the available literature from 2010 to 2024 was carried out through the PubMed, CINAHL, and Scopus databases in peer-reviewed journals. Studies that focused on disparities in access and provision of geriatric care for adults aged 65 years and above within the U.S. health system were included in this study. The Joanna Briggs Institute critical appraisal tools were used in the quality appraisal of studies included.ResultsOf the total number of 5,218 studies that were identified initially, 132 studies were eligible for inclusion. Our analysis uncovered continued inequity in geriatric care across racial, ethnic, socioeconomic, and geographic lines. Findings include: (1) low rates of early diagnosis and delayed treatment of dementia and Alzheimer’s among minority seniors, who were found to be 2.3 times more likely for African Americans and 1.9 times more likely for Hispanics than their white counterparts; (2) inability to access high-level geriatric care in regions outside of metropolitan areas, where it was identified that older adults had to commute, on average, 3.2 times farther to the nearest provider; (3) socioeconomic factors found to present obstacles to home health and long-term care, with seniors from a lower income bracket 1.8 times more likely to be placed in a poor-quality nursing home; and (4) disparities in the quality of end-of-life care for elders of lower socioeconomic status, with African Americans and Hispanics being respectively 38% and 51% less likely to use hospice care.ConclusionThis review has demonstrated that important and persistent disparities exist in the availability and delivery of geriatric care in the United States. Of the 132 studies, 34 directed their efforts toward reducing interventions to have such disparities with salutary results coming from culturally tailored community-based approaches. Multipronged interventions that include policy revision, workforce development, and community-based initiatives hold promise for reducing these disparities. This should be an area of focus for future targeted interventions, which should, therefore, be evaluated for effectiveness in reducing disparities in health outcomes for all older adults.
Do amyloid cerebral deposits influence the long-term post-stroke cognitive outcome? The IDEA3 study
Authors: Godefroy Olivier , Trinchard Niels , Marchal Etienne , Lamy Chantal , Canaple Sandrine , Meyer Marc-Etienne , Roussel Martine , Wollenweber Frank A ,   the IDEA3 study group
Published: July 2024

AbstractBackgroundAlthough the presence of amyloid deposits is associated with a more severe cognitive status in stroke patients at baseline, its influence on the subsequent cognitive outcome has not been extensively assessed. The primary objective of the present study of the IDEA3 cohort was to determine the influence of amyloid PET status on the 5-year cognitive outcome.MethodsThe 91 stroke patients (ischemic stroke: 89%; hemorrhagic stroke: 11%) with florbetapir PET data at baseline (positive: n=14) underwent comprehensive clinical and cognitive assessments for 5 years after the PET scan.ResultsA survival analysis (mean post-stroke follow-up: 80.4 ±27 months) showed that the incidence of dementia was higher in the PET-positive patients (OR=5.89, 95% CI: 1.24-22.7, p=0.02), as was the incidence of cognitive impairment (OR=10, 95% CI: 1.9-52.3, p=0.003). A Cox regression analysis showed that the association between amyloid status and the incidences of dementia (p=0.006) and CI (p=0.04) was still significant after adjustment for age. Considering the overall prevalence at last follow-up in the whole study population (n=91 patients), PET positivity was associated with an elevated risk of post-stroke cognitive impairment (OR=6.25, 95%CI: 1.77-22, p=0.002) or dementia (OR= 6, 95%CI: 1.76-20.5, p=0.002). The final Rankin score did not differ according to PET status (p=0.3).ConclusionsOur results demonstrated the major impact of amyloid deposition on the stroke outcome and emphasized the need for comprehensive etiologic work-up in patients with post-stroke cognitive impairment.Clinical Trial RegistrationNCT 02813434
Multidrug-resistant organism bloodstream infections in solid organ transplant recipients and impact on mortality: a systematic review
Authors: Liu Alice , Dennis Adelaide , Fariha Zarin , Pai Mangalore Rekha , Macesic Nenad 
Published: July 2024

AbstractBackgroundBloodstream infections (BSI) cause significant morbidity and mortality in solid organ transplant (SOT) recipients. There are few data regarding the contribution of multidrug-resistant organisms (MDROs) to these infections.ObjectivesWe evaluated the resistance-percentage of MDRO BSIs in SOT recipients and assessed associated mortality.MethodsA systematic reviewData sourcesMEDLINE and Embase databases up to January 2024.Study eligibility criteriaStudies of adult SOT recipients that quantify MDRO BSI resistance-percentage and/or associated crude mortality. MDROs studied were carbapenem-resistant Enterobacterales (CRE),Acinetobacter baumannii(CRAB) andPseudomonas aeruginosa(CRPA), third-generation-cephalosporin-resistant Enterobacterales (3GCR-E), methicillin-resistantStaphylococcus aureus(MRSA) and vancomycin-resistantEnterococcus faecium(VRE).ParticipantsAdult SOT recipients with a microbiologically confirmed BSI.InterventionsNot applicable.Risk of bias assessmentNewcastle Ottawa Scale.Methods of data synthesisMDRO BSI resistance-percentage and mortality outcomes were reported as median (IQR) and crude mortality (%), respectively.ResultsOf 945 studies identified, 52 were included. Most were retrospective (41/52) and/or single centre (37/52), and liver transplantation was the most studied SOT type (22/52). High resistance-percentages of BSIs were noted, ranging from 13.6% CRE for Enterobacterales to 59.2% CRAB forAcinetobacter baumannii. Resistance-percentage trends decreased over time, but these changes were not statistically significant. Asia had highest resistance-percentages for MRSA (86.2% [IQR 77.3-94.6%]), 3GCR-E (59.5% [IQR 40.5-66.7%]) and CRE (35.7% [IQR 8.3-63.1%]). North America had highest VRE resistance-percentages (77.7% [IQR 54.6-94.7%]). Crude mortality was 15.4-82.4% and was consistently higher than non-MDRO BSIs.ConclusionsMDRO BSIs resistance-percentages were high for all pathogens studied (IQR 24.6-69.4%) but there was geographical and temporal heterogeneity. MDRO BSIs were associated with high mortality in SOT recipients. Microbiological and clinical data in this vulnerable population were incomplete, highlighting the need for robust international multi-centre studies.
A conjugative plasmid exploits flagella rotation as a cue to facilitate its transfer
Authors: Bhattacharya Saurabh , Bejerano-Sagie Michal , Ravins Miriam , Zeroni Liat , Kaur Prabhjot , Gopu Venkadesaperumal , Rosenshine Ilan , Ben-Yehuda Sigal 
Published: July 2024

AbstractConjugation-mediated DNA delivery is the primary mode for antibiotic resistance spread; yet, molecular mechanisms regulating the process remain largely unexplored. While conjugative plasmids typically rely on solid surfaces to facilitate donor-to-recipient proximity, the pLS20 conjugative plasmid, prevalent among Gram-positiveBacillusspp., uniquely requires fluid environments to motivate its transfer. Here we unveiled that pLS20, carried byB. subtilis, induces adhesin-promoted multicellular clustering, which can accommodate various species, offering a stable platform for DNA delivery in liquid milieu. We further discovered that induction of pLS20 promoters, governing crucial conjugative genes, hinges on the presence of donor cell flagella, the major bacterial motility organelle. Moreover, pLS20 regulatory circuit is strategically integrated into a mechanosensing signal transduction pathway responsive to flagella rotation, harnessing propelled flagella to activate conjugation genes exclusively during the host motile phase. This flagella-conjugation coupling strategy, provides the plasmid with the benefit of disseminating into remote destinations, infiltrating new niches.
A development-specific POLX essential for programmed genome rearrangement inParamecium tetraurelia
Authors: Verron Baptiste , Arnaiz Olivier , Zangarelli Coralie , Mathy Nathalie , Bétermier Mireille , Bischerour Julien 
Published: July 2024

ABSTRACTDuring the sexual cycle, programmed genome rearrangement (PGR) inParamecium tetraureliainvolves the non-homologous end joining (NHEJ) DNA repair pathway to eliminate specific germinal Internal Eliminated Sequences (IESs) from the newly developing somatic nucleus. In addition to the core NHEJ factors Ku70/80 and Xrcc4/Lig4, additional enzymes are required to process the 4-base 5’-protruding ends generated following DNA cleavage at IES boundaries, prior to their ligation. Here, we report that PolX (a,b,c,d), fourP. tetraureliadistant orthologs of the human Polλ DNA polymerase, are involved in repair of IES excision junctions. During rearrangements, PolX-depleted cells accumulate genome-wide errors, such as unrepaired double-strand breaks, 1-nucleotide deletions and IES retention. Although all PolX paralogs can process DNA ends, two of them (PolXa&b) are induced during PGR and have acquired tight nuclear anchoring properties through their N-terminal region, which contains a predicted BRCT domain. Finally, we show that PolXa accumulates in nuclear foci together with other NHEJ proteins and the Dicer-like enzyme Dcl5, which is involved in the biogenesis of IES-specific small RNAs. We propose that these “DNA repair foci” correspond to the sites where IES concatemers, a by-product of IES excision, are ligated together to produce the precursors of iesRNAs.
Shape that matters: Yolk geometry spatially modulates developing vascular networks within chick chorioallantoic membrane
Authors: Padmanaban Prasanna , Wanders Dirk , Katovich Oryan Karni , Salehi-Nik Nasim , Levenberg Shulamit , Rouwkema Jeroen 
Published: July 2024

AbstractControlling the multiscale organization of vasculature within diverse geometries is essential for shaping tissue-specific and organ-specific architectures. Nevertheless, how geometrical characteristics of surrounding tissues influence vessel morphology and blood flow remains unclear. Where the regulation of vascular organization by mechanical signals associated with fluid flow is well known, this study postulates that the organization of developing vasculature can also be regulated by mechanical signals connected to the confinement and thus the deformation of surrounding tissues. To test the Shape-Induced Vascular Adaptation (SIVA) concept, fertilized chicken egg contents containing developing vasculature were cultured within engineered eggshell platforms of different shapes. Our findings demonstrate that the vascularized chick chorioallantoic membrane (CAM) adapts to the shape of engineered eggshell, long before reaching its boundaries. This adaptation affects the organization of the vascular network within the CAM, affecting parameters such as vessel area, branching, orientation, length, diameter and endpoints. Specifically, we observed that sharp corners in the engineered eggshell led to more elongated vascular structures. To further explore the dynamic nature of this phenomenon, a proof-of-concept experiment was performed using a shape-shifting engineered eggshell that deforms the egg content from circle to square shape. Using this shape-shifting prototype, we observed a direct effect of eggshell deformation on the vessel morphology and flow dynamics in a time-dependent manner. Overall, our exovo experimental platform provides a unique opportunity to study how mechanical stimuli such as shape influence the spatial and temporal organization of developing vascularized tissues. By subjecting these tissues to various static and dynamic conditions, we induced both local and global changes in their organization. This class of perturbation provides us with an additional tool which can be used for shaping vascular organization within developing tissues and to engineer tissues with geometrically tunable vessel structures.
Histone Tetrasome Dynamics Affects Chromatin Transcription
Authors: Shi X. , Fedulova A.S. , Kotova E.Y. , Maluchenko N.V. , Armeev G.A. , Chen Q. , Prasanna C. , Sivkina A.L. , Feofanov A.V. , Kirpichnikov M.P. , Nordensköld L. , Shaytan A. K. , Studitsky V.M. 
Published: July 2024

AbstractDuring various DNA-centered processes in the cell nucleus, the minimal structural units of chromatin organization, nucleosomes, are often transiently converted to hexasomes and tetrasomes missing one or both H2A/H2B histone dimers, respectively. However, the structural and functional properties of the subnucleosomes and their impact on biological processes in the nuclei are poorly understood. Here, using biochemical approaches, molecular dynamics simulations, single-particle Förster resonance energy transfer (spFRET) microscopy and NMR spectroscopy, we have shown that, surprisingly, removal of both dimers from a nucleosome results in much higher mobility of both histones and DNA in the tetrasome. Accordingly, DNase I footprinting shows that DNA-histone interactions in tetrasomes are greatly compromised, resulting in formation of a much lower barrier to transcribing RNA polymerase II than nucleosomes. The data suggest that tetrasomes are remarkably dynamic structures and their formation can strongly affect various biological processes.
Global survey of secondary metabolism inAspergillus nigervia activation of specific transcription factors
Authors: Semper Cameron , Pham Thi Thanh My , Ram Shane , Palys Sylvester , Evdokias Gregory , Ouedraogo Jean-Paul , Moisan Marie-Claude , Geoffrion Nicholas , Reid Ian , Di Falco Marcos , Bailey Zachary , Tsang Adrian , Benoit-Gelber Isabelle , Savchenko Alexei 
Published: July 2024

AbstractGenomics analysis confirmed the status of the filamentous fungi as a rich source of novel secondary metabolites; however, the discovery of these compounds is hampered by the cryptic nature of their biosynthetic pathways under laboratory conditions. Consequently, despite substantial research effort over the past decades, much of the secondary metabolome remains uncharacterized in fungal organisms. Our manual curation of biosynthetic gene clusters (BGCs) in theAspergillus nigerNRRL3 genome revealed that only 13 of 86 BGCs have had their cognate secondary metabolite products confirmed or reliably inferred. We also identified 60 transcription factors associated with cryptic BGCs. To further characterizeA. nigersecondary metabolism, we created a collection of strains each overexpressing a single BGC-associated transcription factor. We analyzed the strain collection using a standardized pipeline where we monitored phenotypic changes and compound production using mass spectrometry. Strains showing evidence of secondary metabolism activation were selected for gene expression analysis. Our approach resulted in the production of multiple potentially novel secondary metabolites and linked a specific BGC to tensidol production inA. niger.More broadly, this study found evidence counter to the existing paradigm of BGC expression controlled by co-localized transcription factors, lending credence to the emerging picture of a complex regulatory network governing fungal secondary metabolism.Significance StatementFungi produce an array of chemically diverse compounds that are routinely found to harbour valuable bioactivity. The products of secondary metabolism, these compounds have been a source of antimicrobials, anti-cancer agents, and other biopharmaceutical compounds termed natural products. Despite their demonstrated economic value, much is still unknown about the biosynthesis, regulation, and identities of these compounds. This study adopted a genome-wide approach to improve our understanding of the regulatory mechanisms that control fungal secondary metabolism, improving our ability to investigate the pathways responsible for natural product production.