bluuebunny/crossref_metadata_2025_split huggingface dataset:
The neutrophil-to-lymphocyte ratio, as an emerging marker, is an important indicator predicting spontaneous reperfusion and clinical prognosis in patients with ST-segment elevation myocardial infarction
Authors: Li Bing , Zhang Mingyou , Zhang Yaoting , Zheng Yang , Cai He 
Published: March 2023

AbstractBackgroundNeutrophil to lymphocyte ratio (NLR) has emerged as a new inflammation marker, which plays a major role in plaque instability, rupture, and erosion, and facilitates its progression, leading to acute myocardial infarction. The study aims to explore the role of NLR in predicting spontaneous reperfusion (SR) and prognosis in patients with ST-segment elevation myocardial infarction (STEMI).MethodsThis was a retrospective analysis including 506 STEMI patients undergoing primary percutaneous coronary intervention treatment, who were divided into two groups according to the thrombolysis in myocardial infarction (TIMI) flow: SR group (69 patients, initial TIMI flow 3) and No-SR group (437 patients, initial TIMI flow 0-2).ResultsThe incidence of SR was 13.6%. SR group was associated with a remarkably lower level of NLR [5.14 (2.97, 7.02) vs. 8.03 (4.54, 10.92), P<0.001], more proportions of final TIMI 3 flow (98.6% vs. 91.5%, P < 0.05), lower incidence of congestive heart failure (8.7% vs. 18.5%, P < 0.05), and significantly better outcomes. Using multivariate logistic regression analysis, NLR (OR: 0.799, 95% CI: 0.730-0.874, P < 0.001) and fasting blood glucose were the independent predictors of SR. On multivariate Cox regression analysis, NLR (HR: 1.035, 95% CI: 1.001-1.071, P < 0.05) was the independent predictor of MACEs during follow-up.ConclusionsNLR had the ability in predicting SR in STEMI patients and SR flow was associated with a favorable outcome. We also revealed an association between NLR and increased risk of MACEs during follow-up.Clinical PerspectiveWhat Is New?The incidence of spontaneous reperfusion was 13.6%. Patients with spontaneous reperfusion had a remarkably low level of NLR [5.14 (2.97, 7.02) versus 8.03 (4.54, 10.92), P<0.001], more proportions of final TIMI 3 flow (98.6% versus 91.5%, P < 0.05), lower incidence of congestive heart failure (8.7% versus 18.5%, P < 0.05), and favorable outcomes.NLR was not only an independent predictor of spontaneous reperfusion, but also was the independent predictor of major adverse cardiac events during follow-up (HR: 1.035, 95% CI: 1.001-1.071, P < 0.05) in patients with ST-segment elevation myocardial infarction.What Are the Clinical Implications?The level of neutrophil to lymphocyte ratio in patients with ST-segment elevation myocardial infarction is associated with low occurrence of spontaneous reperfusion and adverse outcomes, although, the patients received primary percutaneous coronary intervention.Neutrophil to lymphocyte ratio the plays a major role in the risk classification of patients with ST-segment elevation myocardial infarction.
ACRC/GCNA is an essential protease for the repair of DNA-protein crosslinks during vertebrate development
Authors: Otten Cecile , Supina-Pavic Christine , Kutnjak Marin , Anticevic Ivan , Medved Vanna , Popovic Marta 
Published: March 2023

SummaryDNA-protein crosslinks (DPCs) are frequent DNA lesions associated with cancer, neurodegeneration and premature aging. These bulky lesions are an obstacle to all DNA transactions, but the mechanisms of DPC repair (DPCR) at the organism level are largely unknown. Because proteases play a central role in DPCR, we investigate the function of the putative protease ACRC/GCNA (ACidic Repeat Containing/Germ Cell Nuclear Antigen) which has recently been linked to DPCR, in a zebrafish model. Using a newly created fish line with a mutation in the protease core, we show for the first time that the proteolytic function of Acrc is critical for DPCR during early vertebrate development and that Acrc deficiency leads to DPC accumulation and embryonic death. We also show that Sprt domain rather than IDR domain of Acrc is essential and that Sprtn protease cannot compensate for the absence of Acrc. We identified histone H3-DPC as a novel Acrc substrate.
Traction Force and Mechanosensing can be Functionally Distinguished Through the Use of Specific Domains of the Calpain Small Subunit
Authors: Hao Bingqing , Beningo Karen A. 
Published: March 2023

AbstractCell migration is a fundamental process pertaining to many critical physiological events. The ability to form and release adhesion structures is necessary for cell migration. The Calpain family of cysteine proteases are known to target adhesion proteins as their substrates and modulate adhesion dynamics. The two best studied Calpains, Calpain 1 and Calpain 2 form catalytically active holoenzymes through heterodimerization with a common non-catalytic regulatory small subunit known as Calpain 4. In previous studies, we determined that calpains are important in the production of traction forces and in the sensing of localized mechanical stimulation from the external environment. We found that perturbation of either Calpain 1 or 2 had no effect on the generation of traction forces. However, traction forces were weak when Calpain 4 was silenced. On the other hand, silencing of Calpain 1, 2, or 4 resulted in deficient sensing of external mechanical stimuli. These results together suggest that Calpain 4 functions independent of the catalytic large subunits in the generation of traction forces but functions together with either catalytic subunit in sensing external mechanical stimuli. The small subunit Calpain 4 contains 268 a.a. and is composed of 2 domains, the N-terminal domain V and C-terminal domain VI. Domain VI is a calmodulinlike domain containing five consecutive EF-hand motifs, of which the fifth one heterodimerizes with a large subunit. Moreover, domain V contains the common sequence GTAMRILGGVI that suggests cell membrane interactions. Given these attributes of domain V and VI of Calpain 4, we speculated that an individual domain might provide the functional properties for either traction or sensing. Therefore, each domain was cloned and expressed individually inCapn4−/−cells and assayed for traction and sensing. Results revealed that over-expression of domain V was sufficient to rescue the traction forces defect inCapn4−/−cells while overexpression of domain VI did not rescue the traction force. Consistent with our hypothesis, overexpression of domain VI rescued the sensing defect inCapn4−/−cells while overexpression of domain V had no effect. These results suggest that individual domains of Calpain 4 do indeed function independently to regulate either traction force or the sensing of external stimuli. We speculate that membrane association of Calpain 4 is required for the regulation of traction force and its association with a catalytic subunit is necessary for mechanosensing.
Functional analysis of flavivirus replicase by deep mutational scanning of dengue NS5
Authors: Suphatrakul Amporn , Posiri Pratsaneeyaporn , Srisuk Nittaya , Nantachokchawapan Rapirat , Onnome Suppachoke , Mongkolsapaya Juthathip , Siridechadilok Bunpote 
Published: March 2023

AbstractFlavivirus NS5 is multi-functional viral protein that play critical roles in virus replication, evolution, and immune antagonism against the hosts. Its error-prone replicase activity copies viral RNA for progeny virus particles and shapes virus evolution. Its methyltransferase activity and STAT2-targeting activity compromise type-I interferon signalling, dampening protective immune response during infection. It interacts with several host factors to shape the host-cell environment for virus replication. Thus, NS5 represents a critical target for both vaccine and antiviral drug development. Here, we performed deep mutational scanning (DMS) on the NS5 of dengue virus serotype 2 in mammalian cells. In combination with available structural and biochemical data, the comprehensive single amino-acid mutational data corroborated key residues and interactions involved in enzymatic functions of the replicase and suggested potential plasticity in NS5 guanylyl transferase. Strikingly, we identified that a set of strictly conserved residues in the motifs lining the replicase active site could tolerate mutations, suggesting additional roles of the priming loop in viral RNA synthesis and possible strategies to modulate the error rate of viral replicase activity through active-site engineering. Our DMS dataset and NS5 libraries could provide a framework and a resource to investigate molecular, evolutionary, and immunological aspects of NS5 functions, with relevance to vaccine and antiviral drug development.
Temporal landscape and translational regulation of A-to-I editing in mouse retina development
Authors: Yang Ludong , Yi Liang , Yang Jiaqi , Zhang Rui , Xie Zhi , Wang Hongwei 
Published: March 2023

ABSTRACTThe significance of A-to-I RNA editing in neurological development is widely recognized, however, its influence on retina development remains to be thoroughly understood. In this study, we aimed to characterize the temporal landscape of A-to-I editing in mouse retina development using total RNA-seq and Ribosome profiling, with a specific emphasis on its effect on gene translation. Our findings revealed that the editing underwent plastic changes and distinct editing contents facilitated stage-specific functions. Further analysis showed a dynamic interplay between A-to-I editing and alternative splicing, with A-to-I editing having a significant impact on splicing efficiency and increasing the quantity of splicing events. A-to-I editing held the potential of enhancing the translatome’s diversity, but this came at the expense of reduced translational efficiency. When coupled with splicing, it could produce a coordinated regulatory effect on translatome dynamics. Overall, our study presents a temporally resolved atlas of A-to-I editing, connecting its dynamic changes with the regulatory impact on splicing and translation.
How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-formTrypanosoma bruceicell
Authors: Nascimento Janaina F. , Souza Rodolpho O. O. , Alencar Mayke B. , Marsiccobetre Sabrina , Murillo Ana M. , Damasceno Flávia S. , Girard Richard B. M. M. , Marchese Letícia , Luévano-Martinez Luis A. , Achjian Renan W. , Haanstra Jurgen R. , Michels Paul A. M. , Silber Ariel M. 
Published: March 2023

AbstractATP hydrolysis is required for the synthesis, transport and polymerization of monomers for macromolecules as well as for the assembly of the latter into cellular structures. Other cellular processes not directly related to synthesis of biomass, such as maintenance of membrane potential and cellular shape, also require ATP. The unicellular flagellated parasiteTrypanosoma bruceihas a complex digenetic life cycle. The primary energy source for this parasite in its bloodstream form (BSF) is glucose, which is abundant in the host’s bloodstream. Here, we made a detailed estimation of the energy budget during the BSF cell cycle. As glycolysis is the source of most produced ATP, we calculated that a single parasite produces 6×1011molecules of ATP/cell cycle. Biomass production accounts for ∼62% of the total energy budget, with translation being the most expensive process. Flagellar motility, variant surface glycoprotein recycling, transport and maintenance of transmembrane potential account for less than 30% of the consumed ATP. Finally, there is still ∼9% available in the budget that is being used for other cellular processes of unknown cost. These data put a new perspective on the assumptions about the relative energetic weight of the processes a BSF trypanosome undergoes during its cell cycle.Abstract ImportanceCells use ATP as the main energy currency for the synthesis, organization and maintenance of their macromolecules and cellular structures, in order to stay alive and proliferate. For this purpose, ATP is produced from external nutrients, and is spent by cells in the many processes that are necessary for maintenance and building up new cells. Despite its relevance and the impressive quantity of biological data available, very little is known about how much ATP is required for maintaining and duplicating a cell. In this paper, we present a calculation on how much of the ATP produced by catabolism of the nutrient glucose is used to energize the different processes known to occur during the cell cycle of the infective form of the trypanosomatid parasite that causes human sleeping sickness, the bloodstream form ofTrypanosoma brucei.
Naturally-acquired and Vaccine-induced Human Monoclonal Antibodies toPlasmodium vivaxDuffy Binding Protein Inhibit Invasion ofPlasmodium knowlesi(PvDBPOR) Transgenic Parasites
Authors: Watson Quentin D. , Carias Lenore L. , Malachin Alyssa , Redinger Karli R. , Bosch Jürgen , Bardelli Martino , Moon Robert W. , Draper Simon J. , Zimmerman Peter A. , King Christopher L. 
Published: March 2023

ABSTRACTThe Duffy antigen receptor for chemokines (DARC) expressed on erythrocytes is central toPlasmodium vivax(Pv) invasion of reticulocytes. Pv expresses a Duffy binding protein (PvDBP) on merozoites, a DARC ligand, and their protein-protein interaction is central to vivax blood stage malaria. Here we compared the functional activity of humAbs derived from naturally exposed and vaccinated individuals for the first time using easily culturedP. knowlesi(Pk) that had been genetically modified to replace its endogenous PkDBP orthologue with PvDBP to create a transgenic parasite, PkPvDBPOR. This transgenic parasite requires DARC to invade human erythrocytes but is not reticulocyte restricted. Using this model, we evaluated the invasion inhibition potential of 12 humAbs (9 naturally acquired; 3 vaccine-induced) targeting PvDBP individually and in combinations using growth inhibition assays (GIAs). The PvDBP-specific humAbs demonstrated 70-100% inhibition of PkPvDBPOR invasion with the IC50values ranging from 51 to 338 μg/mL for the 9 naturally acquired (NA) humAbs and 33 to 99 μg/ml for the 3 vaccine-induced (VI) humAbs. To evaluate antagonistic, additive, or synergistic effects, six pairwise combinations were performed using select humAbs. Of these combinations tested, one NA/NA (099100/094083) combination demonstrated relatively strong additive inhibition between 10-100 μg/mL; all combinations of NA and VI humAbs showed additive inhibition at concentrations below 25 μg/mL and antagonism at higher concentrations. None of the humAb combinations showed synergy. This PkPvDBPOR model system enables efficient assessment of NA and VI humAbs individually and in combination.IMPORTANCEGiven the importance of Duffy blood group antigen andP. vivaxDuffy binding protein (PvDBP) interaction leading to blood stage vivax malaria, development of vaccines or therapeutic human monoclonal antibodies (humAbs) targeting PvDBP are key strategies for treating and controlling Pv. TheP. knowlesi-based PkPvDBPOR transgenic model system enables efficient assessment of NA and VI humAbs individually and in combination. As such, this model could prioritize specific humAb combinations ahead of clinical trials of these reagents.
Adhesion-based capture stabilizes nascent microvilli at epithelial cell junctions
Authors: Cencer Caroline S. , Silverman Jennifer B. , Meenderink Leslie M. , Krystofiak Evan S. , Millis Bryan A. , Tyska Matthew J. 
Published: March 2023

SUMMARYDifferentiated transporting epithelial cells present an extensive apical array of microvilli – a “brush border” – where neighboring microvilli are linked together by intermicrovillar adhesion complexes (IMACs) composed of protocadherins CDHR2 and CDHR5. Although loss-of-function studies provide strong evidence that IMAC function is needed to build a mature brush border, how the IMAC contributes to the stabilization and accumulation of nascent microvilli remains unclear. We found that, early in differentiation, the apical surface exhibits a marginal accumulation of microvilli, characterized by higher packing density relative to medial regions of the surface. While medial microvilli are highly dynamic and sample multiple orientations over time, marginal protrusions exhibit constrained motion and maintain a vertical orientation. Unexpectedly, we found that marginal microvilli span the junctional space and contact protrusions on neighboring cells, mediated by complexes of CDHR2/CDHR5. FRAP analysis indicated that thesetransjunctionalIMACs are highly stable relative to adhesion complexes between medial microvilli, which explains the restricted motion of protrusions in the marginal zone. Finally, long-term live imaging revealed that the accumulation of microvilli at cell margins consistently leads to accumulation in medial regions of the cell. Collectively, our findings suggest that nascent microvilli are stabilized by a capture mechanism that is localized to cell margins and enabled by the transjunctional formation of IMACs. These results inform our understanding of how apical specializations are assembled in diverse epithelial systems.
The syntax-meter interface in spoken language and music: Same, different, or individually variable?
Authors: Harding Eleanor E. , Sammler Daniela , Kotz Sonja A. 
Published: March 2023

AbstractConsiderable debate surrounds syntactic processing similarities in language and music. Yet few studies have investigated how syntax interacts with meter considering that metrical regularity varies across domains. Furthermore, there are reports on individual differences in syntactic and metrical structure processing in music and language. Thus, a direct comparison of individual variation in syntax and meter processing across domains is warranted. In a behavioral (Experiment 1) and EEG study (Experiment 2), participants engaged in syntactic processing tasks with sentence- and melody stimuli that were more or less metrically regular, and followed a preferred or non-preferred (but correct) syntactic structure. We further employed a range of cognitive diagnostic tests, parametrically indexed verbal- and musical abilities using a principal component analysis, and correlated cognitive factors with the behavioral and ERP results (Experiment 3). Based on previous results in the language domain, we expected that a regular meter would facilitate the syntactic integration of non-preferred syntax. While syntactic discrimination was better in regular than irregular meter conditions in both domains (Experiment 1), a P600 effect indicated different integration costs during the processing of syntactic complexities in the two domains (Experiment 2). Metrical regularity altered the P600 response to preferred syntax in language while it modulated non-preferred syntax processing in music. Moreover, experimental results yielded within-domain individual differences, and identified continuous metrics of musical ability more beneficial than grouping musicians or non-musicians (Experiment 3). These combined results suggest that the meter-syntax interface differs uniquely in how it forms syntactic preferences in language and music.
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions
Authors: Chen Ziyuan , Seman Melissa , Farhat Ali , Fyodorova Yekaterina , Biswas Saikat , Levashkevich Alexander , Freddolino P. Lydia , Biteen Julie S. , Ragunathan Kaushik 
Published: March 2023

ABSTRACTVisualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and each of their binding partners based on which we inferred their most likely interaction sites. Our results indicate that H3K9me promotes specific complex formation between HP1 proteins and their interactors in a spatially restricted manner, while attenuating their ability to form off-chromatin complexes. As opposed to being an inert platform or scaffold to direct HP1 binding, our studies propose a novel function for H3K9me as an active participant in enhancing HP1-associated complex formation in living cells.
Label-free proteomic comparison reveals ciliary and non-ciliary phenotypes of IFT-A mutants
Authors: Leggere Janelle C. , Hibbard Jaime V.K. , Papoulas Ophelia , Lee Chanjae , Pearson Chad G. , Marcotte Edward M. , Wallingford John B. 
Published: March 2023

AbstractDIFFRAC is a powerful method for systematically comparing proteome content and organization between samples in a high-throughput manner. By subjecting control and experimental protein extracts to native chromatography and quantifying the contents of each fraction using mass spectrometry, it enables the quantitative detection of alterations to protein complexes and abundances. Here, we applied DIFFRAC to investigate the consequences of genetic loss of Ift122, a subunit of the intraflagellar transport-A (IFT-A) protein complex that plays a vital role in the formation and function of cilia and flagella, on the proteome ofTetrahymena thermophila. A single DIFFRAC experiment was sufficient to detect changes in protein behavior that mirrored known effects of IFT-A loss and revealed new biology. We uncovered several novel IFT-A-regulated proteins, which we validated through live imaging inXenopusmulticiliated cells, shedding new light on both the ciliary and non-ciliary functions of IFT-A. Our findings underscore the robustness of DIFFRAC for revealing proteomic changes in response to genetic or biochemical perturbation.
The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types
Authors: Wernig-Zorc Sara , Schwartz Uwe , Martínez Paulina , Inalef Josefa , Pavicic Francisca , Ehrenfeld Pamela , Längst Gernot , Maldonado Rodrigo 
Published: March 2023

SummaryChromatin-associated long non-coding RNAs (lncRNAs) have been shown to define chromatin density, regulate gene expression, and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA modulation, little data is showing the direct effects of lncRNA on regulatory elements (REs) that drive gene expression. Here we explored the molecular mechanism of the chromatin-interacting lncRNA, MALAT1, through RNA- and ATAC-seq, using HeLa cells as a model system. Time-resolved MALAT1 knock-down assays revealed its direct regulation of a limited number of protein-coding genes. Loss of MALAT1 resulted in a substantial loss of chromatin accessibility downstream of theNR4A1gene, associated with its down-regulation. CRISPR-i assays revealed that this region corresponds to a new downstream RE. Next, using TCGA data, we identified a direct correlation between the expression of NR4A1 and the accessibility of the downstream RE in breast cancer. The molecular mechanism was validated on estrogen receptor (ER) positive breast cancer cells (MCF7) and Pancreatic Duct Epithelioid Carcinoma (PANC1) cells, not showing this effect according to TCGA data. Indeed, MALAT1 regulates the expression of NR4A1 in a cell type-specific manner by changing the accessibility of the downstream RE. MALAT1 exhibits a molecular mechanism that fine-tunes the expression of cancer drivers, like NR4A1, in ER-positive breast cancer cells, but not in other cell types.