bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel 2D/3D Hybrid Organoid System for High-Throughput Drug Screening in iPSC Cardiomyocytes
Authors: Lewis Jordann , Yaseen Basil , Saraf Anita 
Published: May 2024

AbstractHuman induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) allow for high-throughput evaluation of cardiomyocyte (CM) physiology in health and disease. While multimodality testing provides a large breadth of information related to electrophysiology, contractility, and intracellular signaling in small populations of iPSC-CMs, current technologies for analyzing these parameters are expensive and resource-intensive. We sought to design a 2D/3D hybrid organoid system and harness optical imaging techniques to assess electromechanical properties, calcium dynamics, and signal propagation across CMs in a high-throughput manner. We validated our methods using a doxorubicin-based system, as the drug has well-characterized cardiotoxic, pro-arrhythmic effects. hiPSCs were differentiated into CMs, assembled into organoids, and thereafter treated with doxorubicin. The organoids were then replated to form a hybrid 2D/3D iPSC-CM construct where the 3D cardiac organoids acted as the source of electromechanical activity which propagated outwards into a 2D iPSC-CM sheet. The organoid recapitulated cardiac structure and connectivity, while 2D CMs facilitated analysis at an individual cellular level which recreated numerous doxorubicin-induced electrophysiologic and propagation abnormalities. Thus, we have developed a novel 2D/3D hybrid organoid model that employs an integrated optical analysis platform to provide a reliable high-throughput method for studying cardiotoxicity, providing valuable data on calcium, contractility, and signal propagation.
DeepKin: precise estimation of in-depth relatedness and its application in UK Biobank
Authors: Zhang Qi-Xin , Jayasinghe Dovini , Lee Sang Hong , Xu Hai-Ming , Chen Guo-Bo 
Published: May 2024

AbstractAccurately estimating relatedness between samples is crucial in genetics and epidemiological analysis. Using genome-wide single nucleotide polymorphisms (SNPs), it is now feasible to measure realized relatedness even in the absence of pedigree. However, the sampling variation in SNP-based measures and factors affecting method-of-moments relatedness estimators have not been fully explored, whilst static cut-off thresholds have traditionally been employed to classify relatedness levels for decades. Here, we introduce the deepKin framework as a moment-based relatedness estimation and inference method that incorporates data-specific cut-off threshold determination. It addresses the limitations of previous moment estimators by leveraging the sampling variance of the estimator to provide statistical inference and classification. Key principles in relatedness estimation and inference are provided, including inferring the critical value required to reject the hypothesis of unrelatedness, which we refer to as the deepest significant relatedness, determining the minimum effective number of markers, and understanding the impact on statistical power. Through simulations, we demonstrate that deepKin accurately infers both unrelated pairs and relatives with the support of sampling variance. We then apply deepKin to two subsets of the UK Biobank dataset. In the 3K Oxford subset, tested with four sets of SNPs, the SNP set with the largest effective number of markers and correspondingly the smallest expected sampling variance exhibits the most powerful inference for distant relatives. In the 430K British White subset, deepKin identifies 212,120 pairs of significant relatives and classifies them into six degrees. Additionally, cross-cohort significant relative ratios among 19 assessment centers located in different cities are geographically correlated, while within-cohort analyses indicate both an increase in close relatedness and a potential increase in diversity from north to south throughout the UK. Overall, deepKin presents a novel framework for accurate relatedness estimation and inference in biobank-scale datasets. For biobank-scale application we have implemented deepKin as an R package, available in the GitHub repository (https://github.com/qixininin/deepKin).
Taxonomic Treatment ofBlighiaK.D.Koenig occurring in Ghana
Authors: Larbi Samuel , Fatah Lateef Hanan Abdul , Anum Bismark , Williams Benjamin Darko 
Published: May 2024

ABSTRACTBlighia, a genus consisting of trees in the Sapindaceae, is found in sub-Saharan Africa and other parts of the world. It is characterized by three species globally:B. unijugataBaker,B. sapidaK.D. Koenig, andB. welwitschii(Hiern) Radlk butB. unijugatais absent in Ghana. Research onBlighiain West Africa has been primarily conducted in Nigeria, Togo, and Benin. However, the taxonomy of the genus is lacking in West Africa, with the Flora of West Tropical Africa being the only authoritative literature. A revision of this genus in Ghana is needed due to the monotonous concentration of research onB. sapidaand the knowledge gap from Hutchinson & Dalziel. This paper seeks to update the taxonomy of members inBlighiaoccurring in Ghana.The study collected specimens ofBlighia sapidaandB. welwitschiifrom 15 localities across Ghana. Fossil records, voucher specimens, and digital collections obtained from the Ghana Herbarium and GBIF respectively, were also examined. Standard georeferencing software was used to generate distribution maps.B. sapidaproduces oblanceolate or obovate leaves with rounded or emarginate apices and acute bases. They are mostly distributed along the coastal belt of the country whileB. welwitschiiproduces lanceolate leaves with bluntly attenuate or acute apices and cuneate bases. They are however distributed mainly in the middle belt of the country.
CuBe: a geminivirus-based copper-regulated expression system suitable for post-harvest activation
Authors: Garcia-Perez Elena , Vazquez-Vilar Marta , Lozano-Duran Rosa , Orzaez Diego 
Published: May 2024

ABSTRACTThe growing demand for sustainable platforms for biomolecule manufacturing has fueled the development of plant-based production systems. Agroinfiltration, the current industry standard, offers several advantages but faces limitations for large-scale production due to high operational costs and batch-to-batch variability. Alternatively, here, we describe the CuBe system, a novel bean yellow dwarf virus (BeYDV)-derived conditional replicative expression platform stably transformed inNicotiana benthamianaand activated by copper sulfate (CuSO4), an inexpensive and widely used agricultural input. The CuBe system utilizes a synthetic circuit of four genetic modules integrated into the plant genome: (i) a replicative vector harboring the gene of interest (GOI) flanked by cis-acting elements for geminiviral replication and novelly arranged to enable transgene transcription exclusively upon formation of the circular replicon, (ii) copper-inducible Rep/RepA proteins essential for replicon formation, (iii) the yeast-derived CUP2-Gal4 copper-responsive transcriptional activator for Rep/RepA expression, and (iv) a copper-inducible Flp recombinase to minimize basal Rep/RepA expression. Copper sulfate application triggers the activation of the system, leading to the formation of extrachromosomal replicons, expression of the GOI, and accumulation of the desired recombinant protein. We demonstrate the functionality of the CuBe system inN. benthamianaplants expressing high levels of eGFP and an anti-SARS-CoV-2 antibody upon copper treatment. Notably, the system is also functional with post-harvest copper application, a strategy with potential advantages for large-scale biomanufacturing. This work presents the CuBe system as a promising alternative to agroinfiltration for cost-effective and scalable production of recombinant proteins in plants.
Darwinian Evolution of Self-Replicating DNA in a Synthetic Protocell
Authors: Abil Zhanar , Restrepo Sierra Ana María , Stan Andreea R. , Châne Amélie , del Prado Alicia , de Vega Miguel , Rondelez Yannick , Danelon Christophe 
Published: May 2024

ABSTRACTReplication, heredity, and evolution are characteristic of Life. We and others have postulated that the reconstruction of a synthetic living system in the laboratory will be contingent on the development of a genetic self-replicator capable of undergoing Darwinian evolution. Although DNA-based life dominates, the in vitro reconstitution of an evolving DNA self-replicator has remained challenging. We hereby emulate in liposome compartments the principles according to which life propagates information and evolves. Using two different experimental configurations supporting intermittent or semi-continuous evolution (i.e., with or without DNA extraction, PCR, and re-encapsulation), we demonstrate sustainable replication of a linear DNA template – encoding the DNA polymerase and terminal protein from the Phi29 bacteriophage – expressed in the ‘protein synthesis using recombinant elements’ (PURE) system. The self-replicator can survive across multiple rounds of replication-coupled transcription-translation reactions in liposomes and, within only ten evolution rounds, accumulates mutations conferring a selection advantage. Combined data from next-generation sequencing with reverse engineering of some of the enriched mutations reveal nontrivial and context-dependent effects of the introduced mutations. The present results are foundational to build up genetic complexity in an evolving synthetic cell, as well as to study evolutionary processes in a minimal cell-free system.
Highly Multiplexed Proteomic Analysis of HCMV-Infected Dendritic Cells Reveals Global Manipulation of Adaptive Immunity and Host Restriction of Viral Replication
Authors: Kerr-Jones Lauren E. , Soday Lior , Hughes Nia Cwyfan , Wang Xinyue , Hunter Leah H. , Antrobus Robin , Miners Kelly L. , Ladell Kristin , Price David A. , Fielding Ceri A. , Wang Eddie C. Y. , Weekes Michael P. , Stanton Richard J. 
Published: May 2024

AbstractHuman cytomegalovirus (HCMV) is a clinically significant herpesvirus and a paradigm for pathogen-mediated immune-evasion. Its broad tropism includes antigen-presenting cells such as dendritic cells (DCs), which may partly explain a unique, dramatic imprint on host immunity that occurs following lifelong carriage. Despite this breadth of infection, most studies use fibroblasts as a model. We therefore developed systems to isolate pure populations of DCs infected with wild-type HCMV, before applying quantitative temporal proteomic technologies to systematically characterise the virus:DC interaction within cells and at the cell surface. This comprehensive dataset quantifying almost 9,000 proteins throughout the infection timecourse revealed multiple DC-specific viral:host effects, including key impacts on innate, intrinsic, and adaptive immunity. These effects included observations that APOBEC3A is downregulated in infected cells and restricts HCMV infection inex vivoDCs, delaying the progression of lytic infection, and that cell surface ICOS-Ligand was downregulated by the viral genes US16 and US20, inhibiting the induction of adaptive immunity.
Late killing ofPlasmodium bergheisporozoites in the liver by an anti-circumsporozoite protein antibody
Authors: Aguirre-Botero Manuela C. , Pacios Olga , Celli Susanna , Aliprandini Eduardo , Gladston Anisha , Thiberge Jean-Michel , Formaglio Pauline , Amino Rogerio 
Published: May 2024

AbstractPlasmodiumsporozoites are inoculated into the skin during the bite of an infected mosquito. This motile stage invades cutaneous blood vessels to reach the liver and infect hepatocytes. The circumsporozoite protein (CSP) on the sporozoite surface is an important antigen targeted by protective antibodies in immunoprophylaxis or elicited by vaccination. Antibody-mediated protection mainly unfolds during parasite skin migration, but rare and potent protective antibodies additionally neutralize sporozoite in the liver. Here, using a rodent malaria model, microscopy and bioluminescence imaging, we show a late neutralizing effect of 3D11 anti-CSP monoclonal antibody (mAb) in the liver. The need for several hours to eliminate parasites in the liver was associated with an accumulation of 3D11 effects, starting with the inhibition of sporozoite motility, sinusoidal extravasation, cell invasion, and terminating with the parasite killing inside the invaded cell. This late neutralizing activity could be helpful to identify more potent therapeutic mAbs with stronger activity in the liver.
NSUN2 Facilitates DICER Cleavage of DNA Damage-Associated R-Loops to Promote Repair
Authors: Alagia Adele , Di Fazio Arianna , Ajit Kamal , Long Qilin , Gullerova Monika 
Published: May 2024

AbstractDNA integrity is constantly challenged by both endogenous and exogenous damaging agents, resulting in various forms of damage. Failure to repair DNA accurately leads to genomic instability, a hallmark of cancer. Distinct pathways exist to repair different types of DNA damage. Double-strand breaks (DSBs) represent particularly severe form of damage, due to the physical separation of DNA strands. The repair of DSBs requires the activity of RNA Polymerase II (RNAPII) and the generation of Damage-associated transcripts (DARTs).Here we show that the RNA m5C-methyltransferase NSUN2 localizes to DSBs in a transcription-dependent manner, where it binds to and methylates DARTs. The depletion of NSUN2 results in an accumulation of nascent primary DARTs around DSBs. Furthermore, we detected an RNA-dependent interaction between NSUN2 and DICER, which was stimulated by DNA damage. NSUN2 activity promoted DICER cleavage of DARTs-associated R-loops, which is required for efficient DNA repair.We report a previously unrecognized role of the RNA m5C-methyltransferase NSUN2 within the RNA-dependent DNA damage response, highlighting its function as a DICER chaperone for the clearance of non-canonical substrates such as DARTs, thereby contributing to genomic integrity.
Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations
Authors: Jäckering Anna , van der Kamp Marc , Strodel Birgit , Zinovjev Kirill 
Published: May 2024

AbstractPlastic-degrading enzymes, particularly poly(ethylene terephthalate) (PET) hydrolases, have garnered significant attention in recent years as potential eco-friendly solutions for recycling plastic waste. However, understanding of their PET-degrading activity and influencing factors remains incomplete, impeding the development of uniform approaches for enhancing PET hydrolases for industrial applications. A key aspect of PET hydrolase engineering is optimizing the PET-hydrolysis reaction by lowering the associated free energy barrier. However, inconsistent findings have complicated these efforts. Therefore, our goal is to elucidate various aspects of enzymatic PET degradation by means of quantum mechanics / molecular mechanics (QM/MM) reaction simulations and analysis, focusing on the initial reaction step, acylation, in two thermophilic PET hydrolases: LCC and PES-H1, along with their highly active variants, LCCICCGand PES-H1FY. Our findings highlight the impact of semi-empirical QM methods on proton transfer energies, affecting the distinction between a two-step reaction involving a metastable tetrahedral intermediate and a one-step reaction. Moreover, we uncovered a concerted conformational change involving the orientation of the PET benzene ring, altering its interaction with the side-chain of the ‘wobbling’ tryptophan from T-stacking to parallel π-π interactions, a phenomenon overlooked in prior research. Our study thus enhances the understanding of the acylation mechanism of PET hydrolases, in particular by characterizing it for the first time for the promising PES-H1FYusing QM/MM simulations. It also provides insights into selecting a suitable QM method and a reaction coordinate, valuable for future studies on PET degradation processes.TOC Graphic
Real-time label-free exploration of the dynamics and interactions of bacteriophages
Authors: Giorgi Francesco , Curran Judith M. , Duignan Liberty , Fothergill Joanne L. , Chenery Sam , Patterson Eann A. 
Published: May 2024

1.AbstractBacteriophages are the focus of extensive research and monitoring their dynamics and interactions with bacterial hosts is crucial to characterise the mechanisms of infection and support potential applications in biotechnology and medicine. Traditional monitoring techniques rely on the fluorescent labelling of bacteriophages due to their size being nanometric. In this paper, we propose a novel, label-free method to generate optical signatures of bacteriophages in a conventional microscopy setup by exploiting the optical phenomenon of caustics. We utilised previously isolatedPseudomonas aeruginosaphage (pelp20 and phiKZ) and a novelEscherichia coli phage(EcoLiv25) to demonstrate detection and tracking within liquid laboratory media. The results obtained confirm the feasibility of visualising and monitoring over time a diverse array of bacteriophages, offering a simpler and less invasive means of observation for research and application in microbiology and related fields.
Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library
Authors: Coffey Nicole R , Dewey Christian , Manning Kieran , Corilo Yuri , Kew William , Babcock-Adams Lydia , McKenna Amy M , Stuart Rhona K , Boiteau Rene M 
Published: May 2024

AbstractIncreased accessibility of liquid chromatography mass spectrometry (LC-MS) metabolomics instrumentation and software have expanded their use in studies of dissolved organic matter (DOM) and exometabolites released by microbes. Current strategies to annotate metabolomes generally rely on matching tandem MS/MS spectra to databases of authentic standards. However, spectral matching approaches typically have low annotation rates for DOM. An alternative approach is to annotate molecular formula based on accurate mass and isotopic fine structure measurements that can be obtained from state-of-the-art ultrahigh resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR-MS), but instrument accessibility for large metabolomic studies is generally limited. Here, we describe a strategy to annotate exometabolomes obtained from lower resolution LC-MS systems by matching metabolomic features to a molecular formula library generated for a representative sample analyzed by LC-21T FT-ICR MS. The molecular formula library approach successfully annotated 53% of exometabolome features of the marine diatomPhaeodactylum tricornutum– a nearly ten-fold increase over the 6% annotation rate achieved using a conventional MS/MS approach. There was 94% agreement between assigned formula that were annotated with both approaches, and mass error analysis of the discrepancies suggested that the FT-ICR MS formula assignments were more reliable. Differences in the exometabolome ofP. tricornutumgrown under iron replete and iron limited conditions revealed 668 significant metabolites, including a suite of peptide-like molecules released byP. tricornutumin response to iron deficiency. These findings demonstrate the utility of FT-ICR MS formula libraries for extending the accuracy and comprehensiveness of metabolome annotations.
ATP-Independent Water-Soluble Luciferins Enable Non-Invasive High-Speed Video-Rate Bioluminescence Imaging of Mice
Authors: Tian Xiaodong , Zhang Yiyu , Ai Hui-wang 
Published: May 2024

AbstractNanoLuc luciferase and its derivatives are attractive bioluminescent reporters recognized for their efficient photon production and ATP independence. However, utilizing them forin vivoimaging poses notable challenges. Low substrate solubility has been a prominent problem, limitingin vivobrightness, while substrate instability hampers consistent results and handling. To address these issues, we developed a range of caged PEGylated luciferins with improved stability and water solubility of up to 25 mM, resulting in substantial bioluminescence increases in mouse models. This advancement has created the brightest and most sensitive luciferase-luciferin combination, enabling high-speed video-rate imaging of freely moving mice with brain-expressed luciferase. Furthermore, we developed a bioluminescent Ca2+indicator with exceptional sensitivity to physiological Ca2+changes and paired it with a new substrate to showcase non-invasive, video-rate imaging of Ca2+activity in a defined brain region in awake mice. These innovative substrates and the Ca2+indicator are poised to become invaluable resources for biological and biomedical fields.
A system for functional studies of the major virulence factor of malaria parasites
Authors: Cronshagen Jakob , Allweier Johannes , Mesén-Ramírez Paolo , Stäcker Jan , Vaaben Anna Viktoria , Ramón-Zamorano Gala , Naranjo-Prado Isabel , Ofori Susann , Jansen Pascal WTC , Hornebeck Joëlle , Kieferle Florian , Murk Agnes , Martin Elicia , Castro-Peña Carolina , Bártfai Richárd , Lavstsen Thomas , Bruchhaus Iris , Spielmann Tobias 
Published: May 2024

SummaryPfEMP1 is a variable antigen displayed on erythrocytes infected with the malaria parasitePlasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a cause of severe malaria. Each parasite encodes ∼60 different PfEMP1 variants but only one is expressed at a time. Switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 is difficult to study due to expression heterogeneity between parasites which also renders genetic modification approaches ineffective. Here, we used selection linked integration (SLI) to generate parasites all expressing the same PfEMP1 variant and genome edit the expressed locus. Moving this system from the reference strain 3D7 to IT4 resulted in PfEMP1 expressor parasites with effective receptor binding capacities. We also introduce a second version of SLI (SLI2) to introduce additional genome edits. Using these systems, we study PfEMP1 trafficking, generate cell lines binding to all major endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell and identify new proteins needed for PfEMP1 mediated sequestration. These findings show the usefulness of the system to study the key virulence factor of malaria parasites.
Doubly heavy dibaryons as seen by string theory
Authors: Andreev Oleg 
Published: May 2024

We propose the stringy description of the system consisting of two heavy and four light quarks in the case of two light flavors of equal mass. As an application, we consider the three low-lying Born-Oppenheimer potentials as a function of the heavy quark separation. Our analysis shows that the ground state potential is described in terms of both hadroquarkonia and hadronic molecules. A connected string configuration makes the dominant contribution to the potential of an excited state at small separations, and for separations larger than 0.1 fm, it exhibits the diquark-diquark-diquark structure [Qq][Qq][qq]. For better understanding the quark organization inside the system, we introduce several critical separations related to the processes of string reconnection, breaking and junction annihilation. We also discuss the simplest string configurations including the five-string junctions and their implications for the system, in particular the emergence of composite quark objects different from diquarks and the process of junction fusion.

Published by the American Physical Society
2024