bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centrosome Migration and Apical Membrane Formation in Polarized Epithelial Cells: Insights from the MDCK Cyst Model
Authors: Wang Po-Kai , Lin Keng-Hui , Tang Tang K. 
Published: June 2024

AbstractPolarization is crucial for the proper functioning of epithelial cells. Early polarization features include the trafficking and enrichment of polarity molecules to form the apical membrane (AM) or cell-cell junctions, as well as the apical positioning of the centrosome. However, the dependencies among polarity molecules, AM formation, and centrosome positioning remain poorly understood. In conventional Matrigel-cultured epithelial cells,de novopolarization can occur when a single cell divides. At the exit of mitosis, centrosomes move to the location where the apical membrane will form, raising the question of the role of the centrosome in epithelial polarization. We perturb centrosomes and polarity regulators in Matrigel-cultured cells and also manipulate polarity direction in non-conventional culture to examine the relationship between polarity features. Surprisingly, the centrosome is not essential for AM formation but promotes formation efficiency. The polarity regulator Par3, rather than the trafficking of AM components, affects centrosome positioning. In non-conventional cultures, the centrosome migration is opposite to that of the AM direction, and Par3 exhibits a different pattern from Matrigel culture. Taken together, our work shows that polarity indicated by centrosome position is not universal and elucidates the upstream-downstream relationship between centrosome positioning and other polarization features, providing insights into epithelial polarization.Impact statementSingle-cell observations refute the expectation that centrosome positioning is a critical factor in the polarization of epithelial cells, while showing that proper centrosome positioning enhances the efficiency of cell polarization.
Dynamics in the Intact fd Bacteriophage Revealed by Pseudo 3D REDOR-Based Magic Angle Spinning NMR
Authors: Lusky Orr Simon , Sherer Dvir , Goldbourt Amir 
Published: June 2024

AbstractThe development of robust NMR methodologies to probe dynamics on the atomic scale is vital to elucidate the close relations between structure, motion, and function in biological systems. Here we present an automated protocol to measure, using magic-angle spinning NMR, the effective13C-15N dipolar coupling constants between multiple spin pairs simultaneously with high accuracy. We use the experimental dipolar coupling constants to quantify the order parameters of multiple C-N bonds in the thousands of identical copies of the coat protein in intact fd-Y21M filamentous bacteriophage virus, and describe its overall dynamics on the sub-millisecond time scale. The method is based on combining three pseudo three-dimensional NMR experiments, where a rotational echo double resonance (REDOR) dephasing block, designed to measure internuclear distances, is combined with three complementary13C-13C mixing schemes: dipolar-assisted rotational resonance, through-bond transfer-based double quantum / single quantum correlation, and radio-frequency driven recoupling. These mixing schemes result in highly resolved carbon spectra with correlations that are created by different transfer mechanisms.We show that the helical part of the coat protein undergoes a uniform small (∼30°) amplitude motion, while the N-terminus is highly flexible. In addition, our results suggest that the reduced mobility of lysine sidechains at the C-terminus are a signature of binding to the single stranded DNA.
Hierarchical global and local auxin signals coordinate cellular interdigitation inArabidopsis
Authors: Pérez-Henríquez Patricio , Li Hongjiang , Zhou Xiang , Pan Xue , Lin Wenwei , Tang Wenxin , Nagawa Shingo , Lin Deshu , Xu Tongda , Michniewicz Marta , Prigge Michael J. , Strader Lucia C. , Estelle Mark , Hayashi Ken-ichiro , Friml Jiří , Qi Linlin , Liu Zhongchi , Van Norman Jaimie , Yang Zhenbiao 
Published: June 2024

AbstractThe development of multicellular tissues requires both local and global coordination of cell polarization, however, the mechanisms underlying their interplay are poorly understood. In Arabidopsis, leaf epidermal pavement cells (PC) develop a puzzle-piece shape locally coordinated through apoplastic auxin signaling. Here we show auxin also globally coordinates interdigitation by activating the TIR1/AFB-dependent nuclear signaling pathway. This pathway promotes a transient maximum of auxin at the cotyledon tip, which then moves across the leaf activating local PC polarization, as demonstrated by locally uncaged auxin globally rescuing defects intir1;afb1;afb2;afb4;afb5mutant but not intmk1;tmk2;tmk3;tmk4mutants. Our findings show that hierarchically integrated global and local auxin signaling systems, which respectively depend on TIR1/AFB-dependent gene transcription in the nucleus and TMK-mediated rapid activation of ROP GTPases at the cell surface, control PC interdigitation patterns in Arabidopsis cotyledons, revealing a mechanism for coordinating a local cellular process with the development of whole tissues.
High throughput cell mechanotyping of cell response to cytoskeletal modulations using a microfluidic cell deformation system
Authors: Smith Ian M. , Ursitti Jeanine A. , Majeti Pranav , Givpoor Nikka , Stemberger Megan B. , Hengen Autumn , Banerjee Shohini , Stains Joseph , Martin Stuart S. , Ward Christopher , Stroka Kimberly M. 
Published: June 2024

ABSTRACTCellular mechanical properties influence cellular functions across pathological and physiological systems. The observation of these mechanical properties is limited in part by methods with a low throughput of acquisition or with low accessibility. To overcome these limitations, we have designed, developed, validated, and optimized a microfluidic cellular deformation system (MCDS) capable of mechanotyping suspended cells on a population level at a high throughput rate of ∼300 cells pers second. The MCDS provides researchers with a viable method for efficiently quantifying cellular mechanical properties towards defining prognostic implications of mechanical changes in pathology or screening drugs to modulate cytoskeletal integrity.
VPS34-IN1 inhibits cap-mediated translation and synergizes with STING to drive type-I IFN expression in human plasmacytoid DCs
Authors: Antas Paulo , Machado Mariana D. , Leite-Pinheiro Fátima , Barros Daniela , Ramalhinho Carlota , Mendes Andreia , Ferreira Beatriz H. , Carvoeiro Daniela , Reverendo Marisa , Duarte Iola F. , Narita Miwako , Su Bing , Argüello Rafael J. , Nal Beatrice , Pierre Philippe , Almeida Catarina R. , Gatti Evelina 
Published: June 2024

AbstractInhibition of the phosphatidylinositol kinase vacuolar protein sorting 34 (VPS34) with the pharmacological compound VPS34-IN1 has a range of effects on the dynamics of endosomes. While VPS34 inhibition has been suggested as a potential therapeutic approach for treating certain cancers, our findings indicate that it has minimal cytotoxic effects on leukemic blastic plasmacytoid dendritic cell neoplasms (BPDCN). VPS34-IN1, however, interferes with plasmacytoid dendritic cells (pDCs) function by blocking the recruitment of serum and glucocorticoid-regulated kinase 3 (SGK3) to endosomes, which is shown to be necessary for Toll-like receptor 7 (TLR7) signaling. In a contrasting parallel, VPS34-IN1 triggers the activation of the stimulator of interferon genes (STING) and significantly enhances pDCs’ response to the STING agonist 2’3’-cyclic guanosine monophosphate-adenosine monophosphate (2’3’-cGAMP). This cooperative action with VPS34-IN1 leads to strongly increased expression of type-I interferons (IFNs), associated with an alteration of STING degradation and importantly, inhibition of cap-mediated mRNA translation. Inhibition of protein synthesis by VPS34-IN1 appears to be central to this synergy with STING activation, notably by compromising the expression of IFIT1/ISG56, a negative regulator of innate signaling. Thus, despite their limited toxicity towards different cancer lines, inhibitors targeting VPS34 and SGK3 may present promising compounds for controlling the expression of type-I IFNs in response to various microbial stimuli and pathological contexts.One-sentence summaryPharmacological inhibition of VPS34 affects multiple signaling pathways downstream of innate immunity receptors and consequently can inhibit or potentiate type-I Interferon induction according to the danger or microbial stimuli received by plasmacytoid DCs.
Ensemblex: an accuracy-weighted ensemble genetic demultiplexing framework for population-scale scRNAseq sample pooling
Authors: Fiorini Michael R. , Amiri Saeid , Dilliott Allison A. , Ohki Cristine M. Yde , Smigielski Lukasz , Walitza Susanne , Fon Edward A. , Grünblatt Edna , Thomas Rhalena A. , Farhan Sali M.K. 
Published: June 2024

AbstractMultiplexing samples from distinct individuals prior to sequencing is a promising step toward achieving population-scale single-cell RNA sequencing by reducing the restrictive costs of the technology. Individual genetic demultiplexing tools resolve the donor-of-origin identity of pooled cells using natural genetic variation but present diminished accuracy on highly multiplexed experiments, impeding the analytic potential of the dataset. In response, we introduce Ensemblex: an accuracy-weighted, ensemble genetic demultiplexing framework that integrates four distinct algorithms to identify the most probable subject labels. Using computationally and experimentally pooled samples, we demonstrate Ensemblex’s superior accuracy and illustrate the implications of robust demultiplexing on biological analyses.
Single-cell based integrative analysis of transcriptomics and genetics reveals robust associations and complexities for inflammatory diseases
Authors: Townsend Hope , Rosenberger Kaylee , Vanderlinden Lauren , Inamo Jun , Zhang Fan 
Published: June 2024

AbstractBackgroundUnderstanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.MethodsWe present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases.First, we applied and compared the results of two recent algorithms, based on networks (scGWAS) or single-cell disease scores (scDRS), according to accuracy/sensitivity and interpretability (M. J. Zhang et al. 2022; Jia et al. 2022). While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,1,73 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC) (F. Zhang et al. 2023; Ishigaki et al. 2022; Smillie et al. 2019; de Lange et al. 2017).Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools’ resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas.Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.ResultsWe first found that single-cell based tool scDRS called superior numbers of supported cell states, like MERTK+ myeloid cells in RA, which were overlooked by network-based scGWAS. While scGWAS was advantageous for gene exploration, scDRS captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5’ scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn’s disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.
Association of demographic factors with acute mountain sickness: a retrospective study in Litang
Authors: Zhao Haitong , Wang Hao , Wang Chao , Li Lifen , Zhang Xuan , Chen Ling , Ni Guohua , Yan Hui , Chen Lei , Luo Fengming 
Published: June 2024

AbstractObjectiveAcute mountain sickness (AMS) is a common clinical syndrome in high altitude areas, but the role of demographic factors in AMS has not been well-illucidated. This study aims to describe the relationship between demographic factors and AMS in Litang, one of the highest-altitude town in the world.MethodsDemographic data of patients diagnosed with AMS from January 2022 to December 2023 were collected from the information management system of Litang County People’s Hospital, including gender, age, onset time, ethnicity, current residence and its altitude. Descriptive statistical methods were used to describe these factors.Results7,290 AMS patients were included, among which 62.37% (4,547/7,290) were male and 37.63% (2,743/7,290) were female; 90.41% (6,591/7,290) were non-Tibetan, and 9.59% (699/7,290) were Tibetan; the age group 20-29 had the highest number of patients (2,422, 39.08%), and the incidence of AMS generally decreased with age; the proportion of AMS occurring from May to August reached 51.99% (3,790/7,290); the percentage from lower altitude areas was 79.05% (4,333/7,150).ConclusionsThese data from Litang suggest higher incidence of AMS may be detected in males, non-Tibetans, young people, summer time and residents from lower altitude. Special attention should be paid to these demographic factors for preventing the occurrence of AMS.
Whole exome-seq and RNA-seq data reveal unique neoantigen profiles in Kenyan breast cancer patients
Authors: Wagutu Godfrey , Gitau John , Mwangi Kennedy , Murithi Mary , Melly Elias , Harris Alexandra R. , Sayed Shahin , Ambs Stefan , Makokha Francis 
Published: June 2024

ABSTRACTBackgroundThe immune response against tumors relies on distinguishing between self and non-self, the basis of cancer immunotherapy. Neoantigens from somatic mutations are central to many immunotherapeutic strategies and understanding their landscape in breast cancer is crucial for targeted interventions. We aimed to profile neoantigens in Kenyan breast cancer patients using genomic DNA and total RNA from paired tumor and adjacent non-cancerous tissue samples of 23 patients.MethodsWe sequenced the genome-wide exome (WES) and RNA, from which somatic mutations were identified and their expression quantified, respectively. Neoantigen prediction focused on human leukocyte antigens (HLA) crucial to cancer, HLA type I. HLA alleles were predicted from WES data covering the adjacent non-cancerous tissue samples, identifying four alleles that were present in at least 50% of the patients. Neoantigens were deemed potentially immunogenic if their predicted median IC50 binding scores were ≤500nM and were expressed [transcripts per million (TPM) >1] in tumor samples.ResultsAn average of 1465 neoantigens covering 10260 genes had ≤500nM median IC50 binding score and >1 TPM in the 23 patients and their presence significantly correlated with the somatic mutations (R2=0.570,P=0.001). Assessing 58 genes reported in the catalog of somatic mutations in cancer (COSMIC, v99) to be commonly mutated in breast cancer, 44 (76%) produced >2 neoantigens among the 23 patients, with a mean of 10.5 ranging from 2 to 93. For the 44 genes, a total of 477 putative neoantigens were identified, predominantly derived from missense mutations (88%), indels (6%), and frameshift mutations (6%). Notably, 78% of the putative breast cancer neoantigens were patient-specific. HLA-C*06:01 allele was associated with the majority of neoantigens (194), followed by HLA-A*30:01 (131), HLA-A*02:01 (103), and HLA-B*58:01 (49). Among the genes of interest that produced putative neoantigens wereMUC17,TTN,MUC16,AKAP9,NEB,RP1L1,CDH23,PCDHB10,BRCA2,TP53,TG, andRB1.ConclusionsThe unique neoantigen profiles in our patient group highlight the potential of immunotherapy in personalized breast cancer treatment as well as potential biomarkers for prognosis. The unique mutations producing these neoantigens, compared to other populations, provide an opportunity for validation in a much larger sample cohort.
The effect of circulating neutralizing antibodies on the replication of SARS-CoV-2 variants following post-vaccination infections
Authors: Garcia-Knight Miguel A. , Kelly J. Daniel , Lu Scott , Tassetto Michel , Goldberg Sarah A. , Zhang Amethyst , Pineda-Ramirez Jesus , Anglin Khamal , Davidson Michelle C. , Chen Jessica Y. , Fortes-Cobby Maya , Park Sara , Martinez Ana , So Matthew , Donovan Aidan , Viswanathan Badri , Richardson Eugene T. , McIlwain David R. , Gaudilliere Brice , Rutishauser Rachel L. , Chenna Ahmed , Petropoulos Christos , Wrin Terri , Deeks Steve G. , Abedi Glen R. , Saydah Sharon , Martin Jeffrey N. , Briggs-Hagen Melissa , Midgley Claire M. , Peluso Michael J. , Andino Raul 
Published: June 2024

ABSTRACTThe impact of pre-existing neutralizing antibodies (NAbs) titers on SARS-CoV-2 viral shedding dynamics in post-vaccination infection (PVI) are not well understood. We characterized viral shedding longitudinally in nasal specimens in relation to baseline (pre/peri-infection) serum neutralizing antibody titers in 125 participants infected with distinct SARS-CoV-2 variants. Among 68 participants who had received vaccinations, we quantified the effect of baseline serum NAb titers on maximum viral RNA titers and on the duration of infectivity. Baseline NAb titers were higher and efficiently targeted a broader range of variants in participants who received one or two monovalent ancestral booster vaccinations compared to those with a full primary vaccine series. In participants with Delta variant infections, baseline NAb titers targeting Delta were negatively correlated with maximum viral RNA copies. Per log10increase in baseline NAb IC50, maximum viral load was reduced -2.43 (95% confidence interval [CI] -3.76, -1.11) log10 N copies and days of infectious viral shedding were reduced -2.79 [95% CI: -4.99, -0.60] days. By contrast, in those with Omicron infections (BA.1, BA.2, BA.4 or BA.5 lineages) baseline NAb responses against Omicron lineages did not predict viral outcomes. Our results provide robust estimates of the effect of baseline NAbs on the magnitude and duration of nasal viral replication after PVI (albeit with an unclear effect on transmission) and show how immune escape variants efficiently evade these modulating effects.
tbea: tools for pre- and post-processing in Bayesian evolutionary analyses
Authors: Ballen Gustavo A. , Reinales Sandra 
Published: June 2024

1AbstractEstimating phylogenies in which branch lengths are expressed in units of absolute time is crucial for testing hypotheses in modern evolutionary biology. However, bioinformatic tools to process data from bayesian divergence time estimation analyses are often not easily adaptable, and documenting methodological choices is not a generalized practice.The R package tbea is a toolset to integrate biological, geological and paleontological information to optimize the specification of models, their parameters and prior distributions in divergence times estimation analyses. tbea implements statistical models to (i) better translate time information in dating sources into the specified calibration densities, (ii) improve comparisons between prior and posterior distributions for parameters of interest, (iii) carry out inference on origination times for a collection of posterior distributions, (iv) summarize different distributions into a single one, useful e.g. when building secondary calibrations, and (v) improve the reproducibility of divergence time estimation analyses allowing users to document methodological choices.We illustrate the package functionalities by carrying out two worked examples. One on the phylogenetic relationships and divergence time estimation of South American Saber-Tooth Characins of the family Cynodontidae, and another one on the separation time of drainages East and West of the Andes in South America during the Neogene.It is expected that the tools herein available will be key when estimating events in time from collections of point estimates, as well as the combination of different posterior densities from the same parameter are useful to justifying the selection of secondary calibration points, or discussing the timing of biogeographic events when multiple sources are available.
A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity
Authors: Madhuprakash Jogi , Toghani AmirAli , Contreras Mauricio P. , Posbeyikian Andres , Richardson Jake , Kourelis Jiorgos , Bozkurt Tolga O. , Webster Michael , Kamoun Sophien 
Published: June 2024

AbstractNRCs are essential helper NLR (nucleotide-binding domain and leucine-rich repeat) proteins that execute the immune response triggered by disease resistance proteins, also known as sensor NLRs. The structure of the resting state of NbNRC2 was recently revealed to be a homodimer. However, the sensor-activated state has not yet been elucidated. In this study, we used cryo-EM to determine the structure of sensor-activated NbNRC2, which forms a hexameric inflammasome-like structure known as resistosome. To confirm the functional significance of the hexamer, we mutagenized the interfaces involved in oligomerization and found that mutations in three nucleotide-binding domain interface residues abolish oligomerization and immune signalling. Comparative structural analyses between the resting state NbNRC2 homodimer and the sensor-activated homohexamer revealed significant structural rearrangements before and after activation, providing insights into NLR activation mechanisms. Furthermore, structural comparisons between the NbNRC2 hexamer and previously reported CC-NLR pentameric assemblies revealed features in NbNRC2 that allow for the integration of an additional protomer. We also used the NbNRC2 hexamer structure to assess the recently released AlphaFold 3 for the prediction of activated CC-NLR oligomers. This revealed that AlphaFold 3 allows for high-confidence modelling of the N-terminalα1-helices of NbNRC2 and other CC-NLRs, a region that has proven difficult to fully resolve using structural approaches. Overall, our work sheds light on the structural and biochemical mechanisms underpinning NLR activation and expands our understanding of NLR structural diversity.