bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modular and flexible open source cell incubator system for mobile and stationary use
Authors: Duru Jens , Maurer Benedikt , Ruff Tobias , Hengsteler Julian , Girardin Sophie , Vörös János , Ihle Stephan J. 
Published: March 2024

AbstractCulturing living cellsin vitrorequires the maintenance of physiological conditions for extended periods of time. Here, we introduce a versatile and affordable incubation system, addressing the limitations of traditional incubation systems. Conventionally, stationary cell incubators maintain constant temperature and gas levels forin vitrocell culturing. Combining such incubators with additional lab equipment proves challenging. The presented platform offers modularity and adaptability, enabling customization to diverse experimental needs. The system includes a main unit with a user-friendly interface as well as an interchangeable incubation chamber. We present two incubation chambers targeting two completely different use cases. The first chamber, named “inkugo” facilitates the transportation of cells for up to two hours without external power and for more than a day without an external CO2source. The second chamber termed “inkubox” was designed to enable continuous electrophysiological recordings. Recordings from up to four neural cultures growing on high-density microelectrode arrays can be performed in parallel. The system’s unique feature lies in its separability of control and incubation components, allowing one control unit to manage various custom chambers. The design’s simplicity and the use of widely accessible components make the here proposed incubation system replicable for any laboratory. This platform fosters collaboration and experimentation in both decentralized and traditional laboratory settings, making it an invaluable addition to any cell culturing pipeline.Specifications table
Single nucleus RNA-sequencing reveals transcriptional synchrony across different relationships
Authors: Brusman Liza E. , Sadino Julie M. , Fultz Allison C. , Kelberman Michael A. , Dowell Robin D. , Allen Mary A. , Donaldson Zoe R. 
Published: March 2024

AbstractAs relationships mature, partners share common goals, improve their ability to work together, and experience coordinated emotions. However, the neural underpinnings responsible for this unique, pair-specific experience remain largely unexplored. Here, we used single nucleus RNA-sequencing to examine the transcriptional landscape of the nucleus accumbens (NAc) in socially monogamous prairie voles in peer or mating-based relationships. We show that, regardless of pairing type, prairie voles exhibit transcriptional synchrony with a partner. Further, we identify genes expressed in oligodendrocyte progenitor cells that are synchronized between partners, correlated with dyadic behavior, and sensitive to partner separation. Together, our data indicate that the pair-specific social environment profoundly shapes transcription in the NAc. This provides a potential biological mechanism by which shared social experience reinforces and strengthens relationships.
Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin
Authors: Wang Xutong , Duan Jingbo , Clark Chancelor B. , Feng Wanjie , Ma Jianxin 
Published: March 2024

AbstractAlternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes, but the extent to which it affects the products of gene expression, and how it evolves and is regulated remain unknown. We first identified transcription start sites (TSSs) in eight soybean tissues using recently developed STRIPE-seq and then analyzed ATI in the context of tissue identity and chromatin architecture. We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in putative regulatory regions upstream of start codons and 43.5% from start codons to 3’ untranslated regions, which, together, are responsible for changes in open reading frames of 24,131 genes. Overall, duplicated genes possess more TSRs, exhibited lower degrees of tissue-specificity, and have undergone stronger purifying selection than singletons. Strikingly, 6,845 genes possess ATI within coding sequences (CDSs). These CDS-TSRs are highly tissue-specific, shorter than those located in canonical regulatory regions, and do not have TATA-boxes typical for the core promoters. Furthermore, the CDS-TSRs are embedded in nucleosome-free regions and flanked by nucleosomes with enhanced levels of active histone marks associated with transcriptionally active chromatin, suggesting that non-canonical ATI is epigenetically regulated and largely responsible for tissue-specific functions and tissue identity. Our study highlights the genomic and epigenomic factors shaping the distribution patterns and tissue-specificity of ATI in regulatory and coding sequences, as well as the significance of ATI in the alternation of proteins encoded by tissue-specifically expressed genes in the context of genome duplication and fractionation.
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
Authors: Buddle Sarah , Forrest Leysa , Akinsuyi Naomi , Bernal Luz Marina Martin , Brooks Tony , Venturini Cristina , Miller Charles , Brown Julianne R , Storey Nathaniel , Atkinson Laura , Best Timothy , Roy Sunando , Goldsworthy Sian , Castellano Sergi , Simmonds Peter , Harvala Heli , Golubchik Tanya , Williams Rachel , Breuer Judith , Morfopoulou Sofia , Montaguth Oscar Enrique Torres 
Published: March 2024

AbstractBackgroundMetagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, barriers to broader take-up include the need for high sequencing depths, long turnaround times, and limited sensitivity. Newer metagenomics protocols based on Oxford Nanopore Technologies (ONT) sequencing allow acquisition and analysis of data in real time, potentially reducing the need for high-volume sequencing and enabling point-of-care testing. Furthermore, targeted approaches that selectively amplify known pathogens could improve sensitivity.MethodsWe evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Biosciences Comprehensive Viral Research Panel (VRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.ResultsCapture with the Twist VRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6,000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the VRP and ONT.ConclusionsMetagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist VRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.
Study protocol: A national cross-sectional study on psychology and behavior investigation of Chinese residents in 2023, PBICR
Authors: Liu Diyue , Fan Siyuan , Huang Xincheng , Gu Wenjing , Yin Yifan , Zhang Ziyi , Ma Baotong , Xia Ruitong , Lu Yuanwei , Liu Jingwen , Xin Hanjia , Cao Yumeng , Yang Saier , Li Runqing , Li Han , Zhao Ji , Zhang Jin , Gao Zheng , Zeng Yaxin , Ding Yixiao , Ren Zhuolun , Guan Yan , Zhang Na , Li Jia , Ma Yan , Wei Pei , Dong Jingjing , Zhou Yajing , Dong Yong , Qian Yan , chen Chen , Zhao Yujie , Li Yimiao , Zheng Yujia , Chen Rongyi , Li Xiaomeng , Han Yuke , Xia Yaoyao , Xu Huixin , Wu Zhaolin , Wu Mingyou , Wu Xinrui , Hou Junyi , Cai Yuelai , Dai Xiaofan , Li Wenbo , Nie Ting , Zhang Chongzhe , Wang Xiaoya , Li Dan , Yan Siyao , Liu Chenxi , Zhang Xinyue , Shi Lei , Li Haomiao , Jiang Feng , Zhou Xiaoming , Sun Xinying , Wu Yibo 
Published: March 2024

AbstractBackgroundThis study protocol specifies the primary research line and theoretical framework of the 2023 Survey of the Psychology and Behavior on Chinese Population. It aims to establish a database focused on psychology and behavior among Chinese residents through a multicenter, large-sample cross-sectional survey to provide strong data support for research and development in related fields. It will track the public’s physical and psychological health more comprehensively and systematically.MethodsThe study was conducted from 20 June 2023 to 31 August 2023, using stratified and quota sampling methods, and a total of 150 cities, 202 districts and counties, 390 townships/streets, and 800 communities/villages were surveyed (excluding Taiwan, which were selected from 23 provinces, five autonomous regions, and four municipalities directly under the central government in China). The questionnaires were distributed face-to-face by trained surveyors. The questionnaires included basic information about the individual, personal health status, basic information about the family, the social environment in which the individual lives, psychological condition scales, behavioral level scales, other scales, and attitudes towards topical social issues. Supervisors conducted quality control during the distribution process and returned questionnaires, logically checked and cleaned for data analysis.DiscussionData collection has been finished, and scientific outputs based on this data will support the development of health promotion strategies in China and globally. In the aftermath of the pandemic, it will guide policymakers and healthcare organizations to improve their existing policies and services to maximize the physical and mental health of the Chinese population.
Synthetic mycolates derivatives as molecular tools to decipher protein mycoloylation, a unique post-translational modification in bacteria
Authors: Lesur Emilie , Zhang Yijie , Dautin Nathalie , Dietrich Christiane , de la Sierra-Gallay Ines Li , Augusto Luis , Rollando Paulin , Lazar Noureddine , Urban Dominique , Doisneau Gilles , Constantinesco-Becker Florence , Van Tilbeurgh Herman , Guianvarc’h Dominique , Bourdreux Yann , Bayan Nicolas 
Published: March 2024

AbstractProtein mycoloylation is a newly characterized post-translational modification (PTM) specifically found inCorynebacteriales, an order of bacteria that includes numerous human pathogens. Their envelope is composed of a unique outer membrane, the so-called mycomembrane made of very-long chain fatty acids, named mycolic acids. Recently, some mycomembrane proteins including PorA have been unambiguously shown to be covalently modified with mycolic acids in the model organismCorynebacterium glutamicumby a mechanism that relies on the mycoloyltransferase MytC. This PTM represents the first example of proteinO-acylation in prokaryotes and the first example of protein modification by mycolic acid. Through the design and synthesis of trehalose monomycolate (TMM) analogs, we prove thati) MytC is the mycoloyltransferase directly involved in this PTM,ii) TMM, but not TDM, is a suitable mycolate donor for PorA mycoloylation,iii) MytC is able to discriminate between an acyl and a mycoloyl chainin vitrounlike other trehalose mycoloyltransferases. We also solved the structure of MytC acyl-enzyme obtained with a soluble short TMM analogs which constitutes the first mycoloyltransferase structure with a covalently linked to an authentic mycolic acid moiety. These data highlight the great conformational flexibility of the active site of MytC during the reaction cycle and pave the way for a better understanding of the catalytic mechanism of all members of the mycoloyltransferase family including the essential Antigen85 enzymes inMycobacteria.
A new cellular platform for studying autophagy
Authors: Goldin-Azulay Korina , Fraiberg Milana , Trofimyuk Olena , Levin Yishai , Reuven Nina , Kopitman Ekaterina , Elazar Zvulun 
Published: March 2024

AbstractAtg8 proteins play a crucial role in autophagy. There is a single Atg8 isoform in yeast, while mammals have up to seven homologs categorized into LC3s and GABARAPs. The GABARAP subfamily consists of GABARAP, GABARAPL1, and GABARAPL2/GATE16, implicated in various stages along the pathway. However, the intricacies among GABARAP proteins are complex and require a more precise delineation.Here, we introduce a new cellular platform to study autophagy using CRISPR/Cas9-mediated tagging of endogenous genes of the GABARAP subfamily with different fluorescent proteins. This platform allows robust examination of autophagy by flow cytometry of cell populations and monitoring of GABARAP homologs at single-cell resolution using fluorescence microscopy. Strikingly, the simultaneous labeling of the different endogenous GABARAPs allows the identification and isolation of autophagosomes differentially marked by these proteins. Using this system, we found that the different GABARAPs are associated with different autophagosomes. We argue that this new cellular platform will be crucial in studying the unique roles of individual GABARAP proteins in autophagy and other putative cellular processes.
Plant Cleavage Factor I complex is essential for precise cleavage and polyadenylation site determination
Authors: Szewc Lukasz , Zhang Xiaojuan , Bajczyk Mateusz , Bielewicz Dawid , Zimna Marta , Yura Kei , Kato Mariko , Nomoto Mika , Garcia-León Marta , Rubio Vicente , Tada Yasuomi , Furumoto Tsuyoshi , Aoyama Takashi , Szweykowska-Kulinska Zofia , Staiger Dorothee , Jarmolowski Artur , Tsuge Tomohiko 
Published: March 2024

ABSTRACTCleavage factor I (CFI) is a four-subunit protein complex of the pre-mRNA 3’ end processing machinery in eukaryotes. In Arabidopsis, AtCFI25a, AtCFI25b, AtCFI59, and AtCFI68 have been identified as potential components of AtCFI,in silico. Here, we show that the AtCFI25a, AtCFI59, and AtCFI68 proteins each pulled down all components of the CFI, confirming that these subunits form the plant CFI complex. Furthermore, either AtCFI59 or AtCFI68 was essential for nuclear localization of the smallest subunit, AtCFI25a. Mutants with single loss-of-function forAtCFI59orAtCFI68showed no obvious morphological defects compared to wild-type plants, while the double mutant displayed pleiotropic morphological defects, identical to those previously reported forAtCFI25aloss-of-function plants. Moreover, these morphological defects correlated with alterations in the usage of 3’ UTR cleavage and polyadenylation sites.atcfi25a,atcfi25a atcfi25bandatcfi59 atcfi68double mutants showed widespread changes in the choice of cleavage and polyadenylation sites. In most cases, more proximal cleavage and polyadenylation sites were used, leading to shorter 3’ UTRs. In particular, genes involved in light intensity, light harvesting, photosynthesis and cold responses showed significant dependence on AtCFI function. Furthermore, transcripts coding for AtCFI subunits showed altered 3’ end processing in these mutants, suggesting self-regulation function of AtCFI in plants.
Beyond Accuracy: Refining Brain-Age Models for Enhanced Disease Detection
Authors: Schulz Marc-Andre , Siegel Nys Tjade , Ritter Kerstin 
Published: March 2024

AbstractThis study critically reevaluates the utility of brain-age models within the context of detecting neurological and psychiatric disorders, challenging the conventional emphasis on maximizing chronological age prediction accuracy. Our analysis of T1 MRI data from 46,381 UK Biobank participants reveals a paradox: simpler machine learning models, and notably those with excessive regularization, demonstrate superior sensitivity to disease-relevant changes compared to their more complex counterparts. This counterintuitive discovery suggests that models traditionally deemed less accurate in predicting chronological age might, in fact, offer a more meaningful biomarker for brain health by capturing variations pertinent to disease states. Our findings challenge the traditional understanding of brain-age prediction as normative modeling, emphasizing the inadvertent identification of non-normative pathological markers over precise age prediction.
Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers
Authors: Tang Jun , Weiser Natasha E. , Wang Guiping , Chowdhry Sudhir , Curtis Ellis J. , Zhao Yanding , Wong Ivy Tsz-Lo , Marinov Georgi K. , Li Rui , Hanoian Philip , Tse Edison , Hansen Ryan , Plum Joshua , Steffy Auzon , Milutinovic Snezana , Meyer S. Todd , Curtis Christina , Greenleaf William J. , Bafna Vineet , Benkovic Stephen J. , Pinkerton Anthony B. , Kasibhatla Shailaja , Hassig Christian A. , Mischel Paul S. , Chang Howard Y. 
Published: March 2024

AbstractExtrachromosomal DNA (ecDNA) presents a major challenge for precision medicine, contributing to poor survival for patients with oncogene-amplified tumours. EcDNA renders tumours resistant to targeted treatments by facilitating massive transcription of oncogenes and rapid genome evolution. At present, there are no ecDNA- specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers, exposing an actionable vulnerability. Stepwise analyses of ecDNA transcription reveal landscapes of pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription replication conflicts and replication stress (RS) compared to chromosomal loci. Nucleotide incorporation onto growing DNA strands is markedly slower on ecDNA, and RS is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. Replication Protein A2 phosphorylated on serine 33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition abrogates the DNA replication check point, causing extensive and preferential tumour cell death in ecDNA-containing tumours as they enter S-phase. To exploit this vulnerability, we develop a highly selective, potent, and bioavailable oral CHK1 inhibitor, BBI-2779, and demonstrate that it preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containingFGFR2on ecDNA, BBI-2779, suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. These results reveal transcription-replication conflict as an ecDNA-generated vulnerability that can be targeted as an ecDNA-directed therapy and suggest that synthetic lethality of excess can be exploited as a strategy for treating cancer.
Loss ofLkb1cooperates withBrafV600Eand UV radiation increasing melanoma multiplicity and neural-like dedifferentiation
Authors: McGrail Kimberley , González-Sánchez Elena , Granado-Martínez Paula , Orsenigo Roberto , Ding Yuxin , Ferrer Berta , Hernández-Losa Javier , Ortega Iván , Caballero Juan M. , Muñoz-Couselo Eva , García-Patos Vicenç , Recio Juan A. 
Published: March 2024

ABSTRACTThe mechanisms cooperating withBRAFV600Eoncogene in addition to ultraviolet (UV) radiation in melanoma development are of great interest. Analysis of human melanoma tumors (TCGA) indicates that 50% or more of the samples express no or low amounts of LKB1 protein. Here, we report that the concomitant neonatalBrafV600Eactivation andLkb1tumor suppressor ablation in melanocytes led to full melanoma development. A postnatal single-dose of UVB radiation had no effect on melanoma onset inLkb1-depleted mice in respect toBrafV600E-irradiated mice, but increased tumor multiplicity. In agreement to this and previous reports,Lkb1null irradiated mice showed a deficient DNA damage repair (DDR). Histologically, tumors lackingLkb1were enriched in neural-like tumor morphology. Genetic profiling and gene set enrichment analyses of tumor samples-mutated genes indicated that loss ofLkb1promoted the selection of altered genes associated to neural differentiation processes. Thus, these results suggest that loss ofLkb1cooperates withBrafV600Eand UVR impairing DDR and increasing melanoma multiplicity and neural-like dedifferentiation.
Twisting Urea- to Imide-Based Mass Spectrometry-Cleavable Cross-Linkers Enables Affinity Tagging
Authors: Di Ianni Alessio , Ihling Christian H. , Vranka Tomáš , Matoušek Václav , Sinz Andrea , Iacobucci Claudio 
Published: March 2024

ABSTRACTDisuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas-phase. In this study, we further advance the structural capabilities of DSBU by twisting the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS-cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl disuccinic imide (DSSI) as prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography (IMAC) enrichment. We detail DSSI synthesis and describe its behavior in solution and in the gas-phase while cross-linking isolated proteins and human cell lysates. DSSI and DSBU cross-links are compared at the same enrichment depths to bridge these two cross-linker classes. We validate DSSI cross-links by mapping them in high-resolution structures of large protein assemblies. The cross-links observed yield insights into the morphology of intrinsically disordered proteins (IDPs) and their complexes. The DSSI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers.