bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dehydroascorbic acid sensitizes cancer cells to system xc- inhibition-induced ferroptosis by promoting lipid droplet peroxidation
Authors: Ferrada Luciano , Barahona María José , Vera Matías , Stockwell Brent R. , Nualart Francisco 
Published: September 2023

AbstractSince the discovery of ferroptosis, it has been postulated that this type of cell death could be utilized in treatments for cancer. Unfortunately, several highly aggressive tumor models are resistant to the pharmacological induction of ferroptosis. However, with the use of combined therapies, it is possible to recover sensitivity to ferroptosis in certain cellular models. Here, we discovered that co-treatment with the metabolically stable ferroptosis inducer imidazole ketone erastin (IKE) and the oxidized form of vitamin C, dehydroascorbic acid (DHAA), is a powerful therapy that induces ferroptosis in tumor cells previously resistant to IKE-induced ferroptosis. We determined that DHAA and IKE + DHAA delocalize and deplete GPX4 in tumor cells, specifically inducing lipid droplet peroxidation, which leads to ferroptosis. Moreover, in vivo, IKE + DHAA has high efficacy with regard to the eradication of highly aggressive tumors such as glioblastomas. Thus, the use of IKE + DHAA could be an effective and safe therapy for the eradication of difficult-to-treat cancers.
Targeted inhibition of the methyltransferase SETD8 synergizes with the Wee1 inhibitor adavosertib in restraining glioblastoma growth
Authors: Della Monica Rosa , Buonaiuto Michela , Cuomo Mariella , Pagano Cristina , Trio Federica , Costabile Davide , de Riso Giulia , Cicala Francesca Sveva , Raia Maddalena , Franca Raduan Ahmed , Del Basso De Caro Marialaura , Sorrentino Domenico , Navarra Giovanna , Coppola Laura , Tripodi Lorella , Pastore Lucio , Hench Juergen , Frank Stephan , Schonauer Claudio , Catapano Giuseppe , Bifulco Maurizio , Chiariotti Lorenzo , Visconti Roberta 
Published: September 2023

AbstractDespite intense research efforts, glioblastoma remains an incurable brain tumor with a dismal median survival time of 15 months. Thus, identifying new therapeutic targets is an urgent need. Here, we show that the lysine methyltransferase SETD8 is overexpressed in 50% of high-grade gliomas. The small molecule SETD8 inhibitor UNC0379, as well as siRNA-mediated inhibition of SETD8, blocked glioblastoma cell proliferation, by inducing DNA damage and activating cell cycle checkpoints. Specifically, in p53-proficient glioblastoma cells, SETD8 inhibition and DNA damage induced p21 accumulation and G1/S arrest whereas, in p53-deficient glioblastoma cells, DNA damage induced by SETD8 inhibition resulted in G2/M arrest mediated by Chk1 activation. Checkpoint abrogation, by the Wee1 kinase inhibitor adavosertib, induced glioblastoma cell lines and primary cells, DNA-damaged by UNC0379, to progress to mitosis where they died by mitotic catastrophe. Finally, UNC0379 and adavosertib synergized in restraining glioblastoma growth in a murine xenograft model, providing a strong rationale to further explore this novel pharmacological approach for adjuvant glioblastoma treatment.
The reaction-diffusion basis of animated patterns in eukaryotic flagella
Authors: Cass James F. , Bloomfield-Gadêlha Hermes 
Published: September 2023

AbstractThe flagellar beat of bull spermatozoa and C. Reinhardtii are modelled by a minimal, geometrically exact, reaction-diffusion system. Spatio-temporal animated patterns describe flagellar waves, analogous to chemical-patterns from classical reaction-diffusion systems, with sliding-controlled molecular motor reaction-kinetics. The reaction-diffusion system is derived from first principles as a consequence of the high-internal dissipation by the flagellum relative to the external hydrodynamic dissipation. Quantitative comparison with nonlinear, large-amplitude simulations shows that animated reaction-diffusion patterns account for the experimental beating of both bull sperm and C. Reinhardtii. Our results suggest that a unified mechanism may exist for motors controlled by sliding, without requiring curvature-sensing, and uninfluenced by hydrodynamics. High-internal dissipation instigates autonomous travelling waves independently of the external fluid, enabling progressive swimming, otherwise not possible, in low viscosity environments, potentially critical for external fertilizers and aquatic microorganisms. The reaction-diffusion system may prove a powerful tool for studying pattern formation of movement on animated structures.
Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly
Authors: Sherman Shachar , Arnold-Ammer Irene , Schneider Martin W. , Kawakami Koichi , Baier Herwig 
Published: September 2023

AbstractBrain development is orchestrated by both innate and experience-dependent mechanisms, but their relative contributions are difficult to disentangle. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum, thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated, the complete set of 77 neuronal types develops in apparently normal proportions, at normal locations, and along normal differentiation trajectories. Strikingly, the cell-cycle exits of proliferating progenitors in these areas are delayed, and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a pre-glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion, we show that signals emitted by retinal axons influence the pace of neurogenesis in visual brain areas, but do not detectably affect the specification or wiring of downstream neurons.
Twisted moiré photonic crystal enabled optical vortex generation through bound states in the continuum
Authors: Zhang Tiancheng , Dong Kaichen , Li Jiachen , Meng Fanhao , Li Jingang , Munagavalasa Sai , Grigoropoulos Costas P. , Wu Junqiao , Yao Jie 
Published: September 2023

AbstractThe twisted stacking of two layered crystals has led to the emerging moiré physics as well as intriguing chiral phenomena such as chiral phonon and photon generation. In this work, we identified and theoretically formulated a non-trivial twist-enabled coupling mechanism in twisted bilayer photonic crystal (TBPC), which connects the bound state in the continuum (BIC) mode to the free space through the twist-enabled channel. Moreover, the radiation from TBPC hosts an optical vortex in the far field with both odd and even topological orders. We quantitatively analyzed the twist-enabled coupling between the BIC mode and other non-local modes in the photonic crystals, giving rise to radiation carrying orbital angular momentum. The optical vortex generation is robust against geometric disturbance, making TBPC a promising platform for well-defined vortex generation. As a result, TBPCs not only provide a new approach to manipulating the angular momentum of photons, but may also enable novel applications in integrated optical information processing and optical tweezers. Our work broadens the field of moiré photonics and paves the way toward the novel application of moiré physics.
Efficient optimization with higher-order Ising machines
Authors: Bybee Connor , Kleyko Denis , Nikonov Dmitri E. , Khosrowshahi Amir , Olshausen Bruno A. , Sommer Friedrich T. 
Published: September 2023

AbstractA prominent approach to solving combinatorial optimization problems on parallel hardware is Ising machines, i.e., hardware implementations of networks of interacting binary spin variables. Most Ising machines leverage second-order interactions although important classes of optimization problems, such as satisfiability problems, map more seamlessly to Ising networks with higher-order interactions. Here, we demonstrate that higher-order Ising machines can solve satisfiability problems more resource-efficiently in terms of the number of spin variables and their connections when compared to traditional second-order Ising machines. Further, our results show on a benchmark dataset of Boolean k-satisfiability problems that higher-order Ising machines implemented with coupled oscillators rapidly find solutions that are better than second-order Ising machines, thus, improving the current state-of-the-art for Ising machines.
All-optical spatiotemporal mapping of ROS dynamics across mitochondrial microdomains in situ
Authors: Koren Shon A. , Ahmed Selim Nada , De la Rosa Lizbeth , Horn Jacob , Farooqi M. Arsalan , Wei Alicia Y. , Müller-Eigner Annika , Emerson Jacen , Johnson Gail V. W. , Wojtovich Andrew P. 
Published: September 2023

AbstractHydrogen peroxide (H2O2) functions as a second messenger to signal metabolic distress through highly compartmentalized production in mitochondria. The dynamics of reactive oxygen species (ROS) generation and diffusion between mitochondrial compartments and into the cytosol govern oxidative stress responses and pathology, though these processes remain poorly understood. Here, we couple the H2O2 biosensor, HyPer7, with optogenetic stimulation of the ROS-generating protein KillerRed targeted into multiple mitochondrial microdomains. Single mitochondrial photogeneration of H2O2 demonstrates the spatiotemporal dynamics of ROS diffusion and transient hyperfusion of mitochondria due to ROS. This transient hyperfusion phenotype required mitochondrial fusion but not fission machinery. Measurement of microdomain-specific H2O2 diffusion kinetics reveals directionally selective diffusion through mitochondrial microdomains. All-optical generation and detection of physiologically-relevant concentrations of H2O2 between mitochondrial compartments provide a map of mitochondrial H2O2 diffusion dynamics in situ as a framework to understand the role of ROS in health and disease.
A systematic analysis of marine lysogens and proviruses
Authors: Yi Yi , Liu Shunzhang , Hao Yali , Sun Qingyang , Lei Xinjuan , Wang Yecheng , Wang Jiahua , Zhang Mujie , Tang Shan , Tang Qingxue , Zhang Yue , Liu Xipeng , Wang Yinzhao , Xiao Xiang , Jian Huahua 
Published: September 2023

AbstractViruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
Authors: Homma Felix , Huang Jie , van der Hoorn Renier A. L. 
Published: September 2023

AbstractAdapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato. This screen of 11,274 protein pairs identified 15 non-annotated SSPs that are predicted to obstruct the active site of chitinases and proteases with an intrinsic fold. Four SSPs were experimentally verified to be inhibitors of pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) and secreted-into-xylem-15 (Six15) of the fungal pathogens Cladosporium fulvum and Fusarium oxysporum, respectively. Together with a P69B inhibitor from the bacterial pathogen Xanthomonas perforans and Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans, P69B emerges as an effector hub targeted by different microbial kingdoms, consistent with a diversification of P69B orthologs and paralogs. This study demonstrates the power of artificial intelligence to predict cross-kingdom interactions at the plant-pathogen interface.
A digital twin for DNA data storage based on comprehensive quantification of errors and biases
Authors: Gimpel Andreas L. , Stark Wendelin J. , Heckel Reinhard , Grass Robert N. 
Published: September 2023

AbstractArchiving data in synthetic DNA offers unprecedented storage density and longevity. Handling and storage introduce errors and biases into DNA-based storage systems, necessitating the use of Error Correction Coding (ECC) which comes at the cost of added redundancy. However, insufficient data on these errors and biases, as well as a lack of modeling tools, limit data-driven ECC development and experimental design. In this study, we present a comprehensive characterisation of the error sources and biases present in the most common DNA data storage workflows, including commercial DNA synthesis, PCR, decay by accelerated aging, and sequencing-by-synthesis. Using the data from 40 sequencing experiments, we build a digital twin of the DNA data storage process, capable of simulating state-of-the-art workflows and reproducing their experimental results. We showcase the digital twin’s ability to replace experiments and rationalize the design of redundancy in two case studies, highlighting opportunities for tangible cost savings and data-driven ECC development.
Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex
Authors: Salamon Iva , Park Yongkyu , Miškić Terezija , Kopić Janja , Matteson Paul , Page Nicholas F. , Roque Alfonso , McAuliffe Geoffrey W. , Favate John , Garcia-Forn Marta , Shah Premal , Judaš Miloš , Millonig James H. , Kostović Ivica , De Rubeis Silvia , Hart Ronald P. , Krsnik Željka , Rasin Mladen-Roko 
Published: September 2023

AbstractAbnormalities in neocortical and synaptic development are linked to neurodevelopmental disorders. However, the molecular and cellular mechanisms governing initial synapse formation in the prenatal neocortex remain poorly understood. Using polysome profiling coupled with snRNAseq on human cortical samples at various fetal phases, we identify human mRNAs, including those encoding synaptic proteins, with finely controlled translation in distinct cell populations of developing frontal neocortices. Examination of murine and human neocortex reveals that the RNA binding protein and translational regulator, CELF4, is expressed in compartments enriched in initial synaptogenesis: the marginal zone and the subplate. We also find that Celf4/CELF4-target mRNAs are encoded by risk genes for adverse neurodevelopmental outcomes translating into synaptic proteins. Surprisingly, deleting Celf4 in the forebrain disrupts the balance of subplate synapses in a sex-specific fashion. This highlights the significance of RNA binding proteins and mRNA translation in evolutionarily advanced synaptic development, potentially contributing to sex differences.
Mechanically enhanced biogenesis of gut spheroids with instability-driven morphomechanics
Authors: Lin Feng , Li Xia , Sun Shiyu , Li Zhongyi , Lv Chenglin , Bai Jianbo , Song Lin , Han Yizhao , Li Bo , Fu Jianping , Shao Yue 
Published: September 2023

AbstractRegion-specific gut spheroids are precursors for gastrointestinal and pulmonary organoids that hold great promise for fundamental studies and translations. However, efficient production of gut spheroids remains challenging due to a lack of control and mechanistic understanding of gut spheroid morphogenesis. Here, we report an efficient biomaterial system, termed micropatterned gut spheroid generator (μGSG), to generate gut spheroids from human pluripotent stem cells through mechanically enhanced tissue morphogenesis. We show that μGSG enhances the biogenesis of gut spheroids independent of micropattern shape and size; instead, mechanically enforced cell multilayering and crowding is demonstrated as a general, geometry-insensitive mechanism that is necessary and sufficient for promoting spheroid formation. Combining experimental findings and an active-phase-field morphomechanics theory, our study further reveals an instability-driven mechanism and a mechanosensitive phase diagram governing spheroid pearling and fission in μGSG. This work unveils mechanobiological paradigms based on tissue architecture and surface tension for controlling tissue morphogenesis and advancing organoid technology.
Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization
Authors: Bie Fenglong , Wang Zhijie , Li Yulong , Guo Wei , Hong Yuanyuan , Han Tiancheng , Lv Fang , Yang Shunli , Li Suxing , Li Xi , Nie Peiyao , Xu Shun , Zang Ruochuan , Zhang Moyan , Song Peng , Feng Feiyue , Duan Jianchun , Bai Guangyu , Li Yuan , Huai Qilin , Zhou Bolun , Huang Yu S. , Chen Weizhi , Tan Fengwei , Gao Shugeng 
Published: September 2023

AbstractMultimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the performance of blood-based early cancer detection. However, integrative profiling of cfDNA methylome and fragmentome has been technologically challenging. Here, we adapt an enzyme-mediated methylation sequencing method for comprehensive analysis of genome-wide cfDNA methylation, fragmentation, and copy number alteration (CNA) characteristics for enhanced cancer detection. We apply this method to plasma samples of 497 healthy controls and 780 patients of seven cancer types and develop an ensemble classifier by incorporating methylation, fragmentation, and CNA features. In the test cohort, our approach achieves an area under the curve value of 0.966 for overall cancer detection. Detection sensitivity for early-stage patients achieves 73% at 99% specificity. Finally, we demonstrate the feasibility to accurately localize the origin of cancer signals with combined methylation and fragmentation profiling of tissue-specific accessible chromatin regions. Overall, this proof-of-concept study provides a technical platform to utilize multimodal cfDNA features for improved cancer detection.
Vaccination of cattle with the Babesia bovis sexual-stage protein HAP2 abrogates parasite transmission by Rhipicephalus microplus ticks
Authors: Silva Marta G. , Bastos Reginaldo G. , Laughery Jacob M. , Alzan Heba F. , Rathinasamy Vignesh A. , Cooke Brian M. , Suarez Carlos E. 
Published: September 2023

AbstractThe apicomplexan parasite Babesia bovis is responsible for bovine babesiosis, a poorly controlled tick-borne disease of global impact. The widely conserved gametocyte protein HAPLESS2/GCS1 (HAP2) is uniquely expressed on the surface of B. bovis sexual stage parasites and is a candidate for transmission-blocking vaccines (TBV). Here, we tested whether vaccination of calves with recombinant HAP2 (rHAP2) interferes with the transmission of B. bovis by competent ticks. Calves vaccinated with rHAP2 (n = 3), but not control animals (n = 3) developed antibodies specific to the vaccine antigen. Vaccinated and control animals were infested with Rhipicephalus microplus larvae and subsequently infected with virulent blood stage B. bovis parasites by needle inoculation, with all animals developing clinical signs of acute babesiosis. Engorged female ticks fed on the infected calves were collected for oviposition, hatching, and obtention of larvae. Transmission feeding was then conducted using pools of larvae derived from ticks fed on rHAP2-vaccinated or control calves. Recipient calves (n = 3) exposed to larvae derived from control animals, but none of the recipient calves (n = 3) challenged with larvae from ticks fed on rHAP2-vaccinated animals, developed signs of acute babesiosis within 11 days after tick infestation. Antibodies against B. bovis antigens and parasite DNA were found in all control recipient animals, but not in any of the calves exposed to larvae derived from HAP2-vaccinated animals, consistent with the absence of B. bovis infection via tick transmission. Overall, our results are consistent with the abrogation of parasite tick transmission in rHAP2-vaccinated calves, confirming this antigen as a prime TBV candidate against B. bovis.
Using spectral characterization to identify healthcare-associated infection (HAI) patients for clinical contact precaution
Authors: Cui Jiaming , Cho Sungjun , Kamruzzaman Methun , Bielskas Matthew , Vullikanti Anil , Prakash B. Aditya 
Published: September 2023

AbstractHealthcare-associated infections (HAIs) are a major problem in hospital infection control. Although HAIs can be suppressed using contact precautions, such precautions are expensive, and we can only apply them to a small fraction of patients (i.e., a limited budget). In this work, we focus on two clinical problems arising from the limited budget: (a) choosing the best patients to be placed under precaution given a limited budget to minimize the spread (the isolation problem), and (b) choosing the best patients to release when limited budget requires some of the patients to be cleared from precaution (the clearance problem). A critical challenge in addressing them is that HAIs have multiple transmission pathways such that locations can also accumulate ‘load’ and spread the disease. One of the most common practices when placing patients under contact precautions is the regular clearance of pathogen loads. However, standard propagation models like independent cascade (IC)/susceptible-infectious-susceptible (SIS) cannot capture such mechanisms directly. Hence to account for this challenge, using non-linear system theory, we develop a novel spectral characterization of a recently proposed pathogen load based model, 2-Mode-SIS model, on people/location networks to capture spread dynamics of HAIs. We formulate the two clinical problems using this spectral characterization and develop effective and efficient algorithms for them. Our experiments show that our methods outperform several natural structural and clinical approaches on real-world hospital testbeds and pick meaningful solutions.