bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs
Authors: Han Alvin X. , Hannay Emma , Carmona Sergio , Rodriguez Bill , Nichols Brooke E. , Russell Colin A. 
Published: October 2022

AbstractOral antivirals have the potential to reduce the public health burden of COVID-19. However, now that we have exited the emergency phase of the COVID-19 pandemic, declining SARS-CoV-2 clinical testing rates (average testing rates = ≪10 tests/100,000 people/day in low- and-middle income countries; <100 tests/100,000 people/day in high-income countries; September 2023) make the development of effective test-and-treat programs challenging. We used an agent-based model to investigate how testing rates and strategies affect the use and effectiveness of oral antiviral test-to-treat programs in four country archetypes of different income levels and demographies. We find that in the post-emergency phase of the pandemic, in countries where low testing rates are driven by limited testing capacity, significant population-level impact of test-and-treat programs can only be achieved by both increasing testing rates and prioritizing individuals with greater risk of severe disease. However, for all countries, significant reductions in severe cases with antivirals are only possible if testing rates were substantially increased with high willingness of people to seek testing. Comparing the potential population-level reductions in severe disease outcomes of test-to-treat programs and vaccination shows that test-and-treat strategies are likely substantially more resource intensive requiring very high levels of testing (>>100 tests/100,000 people/day) and antiviral use suggesting that vaccination should be a higher priority.
Non-Small Cell Lung Cancer Patients Treated with Anti-PD1 Immunotherapy Show Distinct Microbial Signatures and Metabolic Pathways According to Clinical Outcomes
Authors: Dora David , Ligeti Balazs , Kovacs Tamas , Revisnyei Peter , Galffy Gabriella , Dulka Edit , Krizsán Dániel , Kalcsevszki Regina , Megyesfalvi Zsolt , Dome Balazs , Weiss Glenn J. , Lohinai Zoltan 
Published: October 2022

ABSTRACTBackgroundClinical outcomes of immune checkpoint inhibitor (ICI)-treated non-small cell lung cancer (NSCLC) patients might be associated with the gut metagenome.MethodsSixty-two Caucasian advanced-stage NSCLC patients treated with anti-PD1 immunotherapy were included. Gut bacterial signatures were evaluated by metagenomic sequencing and correlated with progression-free survival (PFS), PD-L1 expression defined by immunohistochemistry, and other clinicopathological parameters. The predictive role of PFS-related key bacteria was confirmed with multivariate statistical models and validated on an additional patient cohort (n=60). The functional microbial signature of distinct patient groups were determined by analyzing metabolic pathways. A random forest (RF) machine learning algorithm was used to assess the predictive power of taxonomic and metabolic microbial signatures.ResultsAlpha-diversity showed no significant difference in any comparison. However, there was a significant difference in beta-diversity between patients with long- (>6 months) vs. short (≤6 months) PFS and between chemotherapy (CHT)-treated vs. CHT-naive cases. Short PFS was associated with increased abundance of Firmicutes (F) and Actinobacteria phyla, whereas elevated abundance of Euryarcheota was specific for low-PD-L1 expression. F/Bacteroides (F/B) ratio was significantly increased in patients with short PFS. Multivariate analysis revealed an association between Alistipes shahii, Alistipes finegoldii, Barnesiella visceriola, and long PFS. In contrast, Streptococcus salivarius, Streptococcus vestibularis, and Bifidobacterium breve were associated with short PFS. Taxonomic profiles performed superiorly in predicting PFS (AUC=0.74), while metabolic pathways including Amino Acid Synthesis and Fermentation were better predictors of PD-L1 expression (AUC=0.87).ConclusionThe specific metagenomic features of the gut microbiome including bacterial taxonomy and metabolic pathways are suggestive of ICI efficacy and PD-L1 expression in NSCLC patients.
Integrative genetic analysis identifies FLVCR1 as an essential component of choline transport in mammals
Authors: Kenny Timothy C. , Khan Artem , Son Yeeun , Yue Lishu , Heissel Søren , Gamazon Eric R. , Alwaseem Hanan , Hite Richard , Birsoy Kıvanç 
Published: October 2022

ABSTRACTGenome-wide association studies (GWAS) of serum metabolites have the potential to uncover genes that influence human metabolism. Here, we combined an integrative genetic analysis associating serum metabolites to membrane transporters with a coessentiality map of metabolic genes. This analysis revealed a connection between feline leukemia virus subgroup C cellular receptor 1 (FLVCR1) - a plasma membrane protein - and phosphocholine, a downstream metabolite of choline metabolism. Loss of FLVCR1 in human cells and in mice strongly impairs choline metabolism due to a block in choline import. Consistently, CRISPR-based genetic screens identified several components of the membrane phospholipid machinery as synthetic lethal with FLVCR1 loss. Finally, cells lacking FLVCR1 exhibit mitochondrial defects and upregulate the integrated stress response (ISR) through heme regulated inhibitors kinase (HRI). Altogether, these findings identify FLVCR1 as a universal mediator of choline transport in mammals and provide a platform to discover substrates for unknown metabolite transporters.
Three components of human brain gene expression reflect normative developmental programmes with specific links to neurodevelopmental disorders
Authors: Dear Richard , Wagstyl Konrad , Seidlitz Jakob , Markello Ross D. , Arnatkevičiūtė Aurina , Anderson Kevin M. , Bethlehem Richard A.I. ,   Lifespan Brain Chart Consortium, Raznahan Armin , Bullmore Edward T. , Vértes Petra E. 
Published: October 2022

AbstractHuman brain organisation emerges from the coordinated transcription of thousands of genes, and the first principal component (C1) of spatial whole genome expression was shown to reflect cortical hierarchy. Here, optimised processing of the Allen Human Brain Atlas revealed two new components of brain transcription, C2 and C3, which were distinctively enriched for neuronal, metabolic and immune processes, cell-types and cytoarchitecture, and genetic variants associated with intelligence. Using additional datasets (PsychENCODE, Allen Cell Atlas, and BrainSpan), we found that C1-C3 represent generalisable transcriptional programmes that are coordinated within cells, and differentially phased during foetal and postnatal development. Autism spectrum disorder and schizophrenia were specifically associated with C1/C2 and C3, respectively, across neuroimaging, gene expression, and genome-wide association studies. Evidence converged especially in support of C3 as a normative transcriptional programme for adolescent brain development, which can lead to atypical supragranular brain connectivity in people at high genetic risk for schizophrenia.
Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution
Authors: Zhao Lihua , Fonseca Alejandro , Meschichi Anis , Sicard Adrien , Rosa Stefanie 
Published: October 2022

ABSTRACTMulticellular organisms result from complex developmental processes largely orchestrated through the quantitative spatiotemporal regulation of gene expression. Yet, obtaining absolute counts of mRNAs at a 3-dimensional resolution remains challenging, especially in plants, due to high levels of tissue autofluorescence that prevent the detection of diffraction-limited fluorescent spots. In situ hybridization methods based on amplification cycles have recently emerged, but they are laborious and often lead to quantification biases. In this article, we present a simple method based on single molecule RNA fluorescence in situ hybridization (smFISH) to visualize and count the number of mRNA molecules in several intact plant tissues. In addition, with the use of fluorescent protein reporters, our method also enables simultaneous detection of mRNA and protein quantity, as well as subcellular distribution, in single cells. With this method, research in plants can now fully explore the benefits of the quantitative analysis of transcription and protein levels at cellular and subcellular resolution in plant tissues.
eCRUIS captures RNA-protein interaction in vitro and in vivo
Authors: Zhang Ziheng , Zhang Yuanbing , Liu Ji-Long 
Published: October 2022

ABSTRACTAs an information bridge between DNA and protein, RNA regulates cellular processes and gene expression in a variety of ways. From synthesis to degradation, RNA is associated with a series of RNA-binding proteins. Therefore, it is very important to develop innovative methods to study the interaction between RNA and protein. Previously, we developed an RNA-centric method, called CRISPR-based RNA-United Interacting System (CRUIS), to capture RNA-protein interaction in cells. On this basis, here we develop an enhanced CRUIS (eCRUIS) by combining the power of dCas13d and the engineered promiscuous ligase TurboID. The new version allows us to label RNA-binding proteins on the target RNA within 30 minutes, which may be used in vivo. By introducing bait-assay with exogenous RNA, we confirm that eCRUIS can effectively label RNA-binding proteins on bait RNA in a short time. eCRUIS provides a wider range of in vitro and in vivo applications.
High-resolution structure of a microtubule-like tube composed of FtsZ–monobody complexes
Authors: Fujita Junso , Amesaka Hiroshi , Yoshizawa Takuya , Kuroda Natsuko , Kamimura Natsuki , Hara Mizuho , Inoue Tsuyoshi , Namba Keiichi , Tanaka Shun-ichi , Matsumura Hiroyoshi 
Published: October 2022

AbstractFtsZ, a bacterial tubulin homologue, forms protofilaments and the Z-ring, which acts as a scaffold for accessory proteins during cell division. Although various studies have revealed its molecular mechanisms, the lack of high-resolution solution structures has hindered the understanding of the detailed mechanisms. Here, we developed a monobody (Mb) that binds FtsZs from Escherichia coli and Klebsiella pneumoniae (KpFtsZ) without affecting their GTPase activities. When expressed in E. coli cells, the Mb did not inhibit Z-ring formation but did inhibit cell division. The crystal structures of the KpFtsZ–Mb complexes revealed the epitope, and the cryoEM structure at 2.67 Å resolution showed a double helical tube consisting of two KpFtsZ protofilaments stabilized by the Mb filling interfilament gaps. Our structural analyses highlight the similarity between the microtubule and the FtsZ tube and the importance of the plasticity of FtsZ protofilaments.
Heterogeneous and Surface-Catalyzed Amyloid Aggregation Monitored by Spatially Resolved Fluorescence and Single Molecule Microscopy
Authors: Zhou Xin , Sinkjær Anders Wilgaard , Zhang Min , Pinholt Henrik Dahl , Mørck Nielsen Hanne , Hatzakis Nikos S. , van de Weert Marco , Foderà Vito 
Published: October 2022

ABSTRACTAmyloid aggregation is associated with many diseases and may also occur in therapeutic protein formulations. Addition of co-solutes is a key strategy to modulate the stability of proteins in pharmaceutical formulations and select inhibitors for drug design in the context of diseases. However, the heterogeneous nature of this multi-component system in terms of structures and mechanisms poses a number of challenges for the analysis of the chemical reaction. Combining a spatially resolved fluorescence approach with single molecule microscopy and machine learning approaches, we disentangle the different contributions from multiple species within a single aggregation experiment. Moreover, we link the presence of interfaces to the degree of heterogeneity of the aggregation kinetics and retrieve the rate constants and underlying mechanisms for single aggregation events, providing a general tool for a comprehensive analysis of self-assembly reactions.Table of Contents
Assessing the influence of distinct IVF culture media on human pre-implantation development using single-embryo transcriptomics
Authors: Ducreux Bastien , Barberet Julie , Guilleman Magali , Pérez-Palacios Raquel , Teissandier Aurélie , Bourc’his Déborah , Fauque Patricia 
Published: October 2022

AbstractThe use of Assisted Reproductive Technologies (ART) is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. Particularly, embryos within their first days of development are highly sensitive to their micro-environment. Here, we aimed to determine the impact of culture media composition on gene expression of human preimplantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of post-fertilization culture in different commercially available media, we revealed medium-specific differences in gene expression changes. In particular, we found that culture medium composition can affect the dynamics of expression of developmentally relevant genes at day-2 but the differences were mitigated at the blastocyst stage. This study highlights the ability of embryos conceived in suboptimal in vitro culture media to recover proper transcriptome competency.
Functional genomics of cattle through integration of multi-omics data
Authors: Beiki Hamid , Murdoch Brenda M. , Park Carissa A. , Kern Chandlar , Kontechy Denise , Becker Gabrielle , Rincon Gonzalo , Jiang Honglin , Zhou Huaijun , Thorne Jacob , Koltes James E. , Michal Jennifer J. , Davenport Kimberly , Rijnkels Monique , Ross Pablo J. , Hu Rui , Corum Sarah , McKay Stephanie , Smith Timothy P.L. , Liu Wansheng , Ma Wenzhi , Zhang Xiaohui , Xu Xiaoqing , Han Xuelei , Jiang Zhihua , Hu Zhi-Liang , Reecy James M. 
Published: October 2022

AbstractFunctional annotation of the bovine genome was performed by characterizing the spectrum of RNA transcription using a multi-omics approach, combining long- and short-read transcript sequencing and orthogonal data to identify promoters and enhancers and to determine boundaries of open chromatin. A total number of 171,985 unique transcripts (50% protein-coding) representing 35,150 unique genes (64% protein-coding) were identified across tissues. Among them, 159,033 transcripts (92% of the total) were structurally validated by independent datasets such as PacBio Iso-seq, ONT-seq,de novoassembled transcripts from RNA-seq, or Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive independent data from different technologies such as WTTS-seq, RAMPAGE, ChIP-seq, and ATAC-seq. A large proportion of identified transcripts (69%) were novel, of which 87% were produced by known genes and 13% by novel genes. A median of two 5’ untranslated regions was detected per gene, an increase from Ensembl and NCBI annotations (single). Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as non-coding genes in fetal tissues, but as protein coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 known gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available QTL data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. These validated results show significant improvement over current bovine genome annotations.
A Theory for High-Throughput Genetic Interaction Screening
Authors: McCarthy Madeline E. , Dodd William B. , Lu Xiaoming , Patel Nishi D. , Haskell Charlotte V. , Sanabria Hugo , Blenner Mark A. , Birtwistle Marc R. 
Published: October 2022

AbstractSystematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically-encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single-cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
Imaging of lactate metabolism in retinal Müller cells with a FRET nanosensor
Authors: Calbiague García Víctor , Chen Yiyi , Cádiz Bárbara , Paquet-Durand François , Schmachtenberg Oliver 
Published: October 2022

AbstractMüller cells, the glial cells of the retina, provide metabolic support for photoreceptors and inner retinal neurons, and have been proposed as source of the significant lactate production of this tissue. To better understand the role of lactate in retinal metabolism, we expressed a lactate and a glucose nanosensor in organotypic mouse retinal explants cultured for 14 days, and used FRET imaging in acute vibratome sections of the explants to study metabolite flux in real time. Pharmacological manipulation with specific monocarboxylate transporter (MCT) inhibitors and immunohistochemistry revealed the functional expression of MCT2 and MCT4 in Müller cells. The introduction of nanosensors to measure key metabolites at the cellular level may contribute to a better understanding of heretofore poorly understood issues in retinal metabolism.
Cytoskeletal association of ATP citrate lyase controls the mechanodynamics of macropinocytosis
Authors: Puccini Joseph , Bar-Sagi Dafna 
Published: October 2022

AbstractMacropinocytosis is an actin-dependent mode of non-selective endocytosis that mediates the uptake of extracellular fluid-phase cargoes. It is now well-recognized that tumor cells exploit macropinocytosis to internalize macromolecules that can be catabolized and used to support cell growth and proliferation under nutrient limiting conditions. Therefore, the identification of molecular mechanisms that control macropinocytosis is fundamental to the understanding of the metabolic adaptive landscape of tumor cells. Here we report that the acetyl-CoA producing enzyme, ATP citrate lyase (ACLY), is a key regulator of macropinocytosis and describe a heretofore unappreciated association of ACLY with the actin cytoskeleton. The cytoskeletal tethering of ACLY is required for the spatially-defined acetylation of heterodimeric actin capping protein, which we identify as an essential mediator of the actin remodeling events that drive membrane ruffling and macropinocytosis. Furthermore, we identify a requirement for mitochondrial-derived citrate, an ACLY substrate, for macropinocytosis, and show that mitochondria traffic to cell periphery regions juxtaposed to plasma membrane ruffles. Collectively these findings establish a new mode of metabolite compartmentalization that supports the spatiotemporal modulation of membrane-cytoskeletal interactions required for macropinocytosis by coupling regional acetyl-CoA availability with dynamic protein acetylation.SignificanceThe scavenging of extracellular macromolecules via macropinocytosis is a key adaptive mechanism that supports the metabolic fitness of cancer cells. Although the importance of macropinocytosis for sustaining tumor cell growth under nutrient limiting conditions is well documented, less is known about the molecular mechanisms by which macropinocytosis is regulated. This study describes a previously uncharacterized dependence of macropinocytosis on the compartmentalized generation of acetyl-CoA through the association of ACLY with the actin cytoskeleton. This metabolic channeling process establishes a new mechanistic framework for understanding actin remodeling events that drive macropinocytosis.
Opposing transcription factors MYCL and HEY1 mediate the Notch-dependent airway stem cell fate decision
Authors: Byrnes Lauren E. , Deleon Rachel , Reiter Jeremy F. , Choksi Semil P. 
Published: October 2022

AbstractTissue function depends on the relative proportions of multiple cell types. In the airway, basal stem cells differentiate into both multiciliated and secretory cells, which together protect the lungs from inhaled pathogens and particulates. To define how airway stem cells differentiate, we mapped differentiation trajectories using single-cell mRNA sequencing (scRNA-seq) and identified a transitional intermediate cell state in between basal stem cells and differentiated cells. These intermediate cells induce different gene expression programs that precede differentiation into either multiciliated or secretory cells. For example, we found that within the intermediate cell population, multiciliated cell precursors express Mycl, encoding a MYC-family transcription factor, and secretory cell precursors express Hey1, encoding a transcriptional repressor. We also found that Notch signaling acts on intermediate cells to repress Mycl and induce Hey1. We further show MYCL expression is sufficient to drive multiciliated cell fate, whereas HEY1 expression is sufficient to repress multiciliated cell fate. Using CUT&RUN, we made the surprising observation that MYCL and HEY1 bind to many of the same regulatory elements near genes encoding early regulators of multiciliated cell differentiation. We conclude that intermediate cells receiving Notch signals induce HEY1 to repress the multiciliated cell fate and become secretory cells, while intermediate cells not receiving Notch signals induce MYCL to promote the multiciliated cell fate. These experiments reveal that during airway stem cell differentiation Notch signaling balances the production of two different cell types by regulating the functions of two opposing transcription factors, MYCL and HEY1.
Characterizing Aerosol Generating Procedures with Background Oriented Schlieren
Authors: Howard N. Scott , Alrefaie Abdulaziz , Mejia Nicholas A. , Ugbeye Tosan , Schmidt Bryan E. 
Published: October 2022

ABSTRACTThe potential for characterizing aerosol generating procedures (AGPs) using background oriented schlieren (BOS) flow visualization was investigated in two clinical situations. A human-scale BOS system was used on a manikin simulating jet ventilation and extubation. A novel approach to representation of the BOS images using line integral convolution allows direct evaluation of both magnitude and direction of the refractive index gradient field. Plumes issuing from the manikin’s mouth were clearly visualized and characterized in both experiments, and it is recommended that BOS be adapted into a clinical tool for risk evaluation in clinical environments.