bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative risk assessment of human H5N1 infection from consumption of fluid cow’s milk
Authors: Koebel Katherine J. , Bulut Ece , Alcaine Samuel D. , Trmčić Aljoša , Nooruzzaman Mohammed , Covaleda Lina M. , Diel Diego G. , Ivanek Renata 
Published: December 2024

ABSTRACTThe spillover of highly pathogenic avian influenza H5N1 into dairy cattle has raised concerns over the safety of fluid milk. While no human foodborne infection has been reported, this strain has infected dozens of people and milk from infected cows is known to be infectious by ingestion in multiple other species. Investigation into the public health threat of this outbreak is critical. This study uses quantitative risk assessment (QRA) models to represent the United States raw and pasteurized fluid milk supply chains to estimate the risk of human infection from consumption of fluid cow’s milk. These models were parameterized with literature emerging from this outbreak, then employed to estimate the H5N1 infection risk and evaluate multiple potential interventions aimed at reducing this risk. The median (5th, 95thpercentiles) probabilities of infection per 240-mL serving of pasteurized, farmstore-purchased raw, or retail-purchased raw milk were 5.68E-15 (1.77E-16, 2.98E-13), 1.13E-03 (5.16E-06, 3.82E-02), and 1.02E-03 (5.20E-06, 3.64E-02), respectively. Our results demonstrate that pasteurization is highly effective at reducing H5N1 infection risk. Scenario analysis revealed quantitative real-time reverse transcriptase-polymerase chain reaction (qrRT-PCR) testing of bulk tank milk to be an effective method for reducing risk from raw milk. Additionally, we identify knowledge gaps related to human H5N1 dose-response by ingestion and raw milk consumption patterns. These findings emphasize the importance of pasteurization in protecting public health and will inform the implementation of control strategies to reduce the risk of human H5N1 infection from raw milk.
Strain-level antigen variation facilitates immune evasion inBacteroides thetaiotaomicron
Authors: Glowacki Robert W.P. , Till Jessica M. , Brock Orion D. , Engelhart Morgan J. , Ahern Philip P. 
Published: December 2024

AbstractThe T cell receptor (TCR) repertoire of intestinal CD4+ T cells is enriched for specificity towards microbiome-encoded epitopes shared among many microbiome members, providing broad microbial reactivity from a limited pool of cells. These cells actively coordinate mutualistic host-microbiome interactions, yet many epitopes are shared between gut symbionts and closely related pathobionts and pathogens. Given the disparate impacts of these agents on host health, intestinal CD4+ T cells must maintain strain-level discriminatory power to ensure protective immunity while preventing inappropriate responses against symbionts. However, to date, the mechanisms by which this occurs have remained enigmatic. To interrogate this, we leveraged BθOM mice that express a transgenic TCR specific for aBT4295-encoded epitope inB. thetaiotaomicron. While manyB. thetaiotaomicronstrains potently activated BθOM CD4+ T cellsin vitro, strain dnLKV9 escaped recognition. Bioinformatic analyses uncovered twoBT4295homologs inB. thetaiotaomicron-dnLKV9, with each homolog harboring sequence modifications relative to strain VPI-5482, specifically a premature stop codon and a T548S substitution within the epitope. Reconstruction of these variants inB. thetaiotaomicron-VPI-5482ΔBT4295conferred evasion from BθOM CD4+ T cellsin vitroto this otherwise permissive strain. Adoptive transfer of BθOM CD4+ T cells to gnotobiotic RAG1-/- colonized withB. thetaiotaomicronharboring these variantBT4295forms verified the sufficiency of these antigen modifications for evasion of BθOM CD4+ T cells. Collectively, these data uncover the existence of strain-level immune evasion inB. thetaiotaomicronand reveal a mechanism whereby strains evade recognition by CD4+ T cells, facilitating strain-level discrimination in responsiveness to the microbiome.Key Points-SelectB. thetastrains evade recognition by aB. theta-specific CD4+ T cell-Strain-specific antigen modifications rather than absence of antigen mediate evasion-Evasion strategies limitin vivoaccumulation ofB. theta-specific CD4+ T cells
A Co-essentiality Network of Cancer Driver Genes Better Prioritizes Anticancer Drugs
Authors: Lee Kwanghwan , Kim Donghyo , Kim Inhae , Lee Juhee , Ha Doyeon , Lim Seongsu , Kim Eunjee , Im Sin-Hyeog , Shin Kunyoo , Kim Sanguk 
Published: December 2024

AbstractDiverse molecular networks have been extensively studied to discover therapeutic targets and repurpose approved drugs. However, it is necessary to select a suitable network since the performance of network medicine relies heavily on the completeness and characteristics of the selected network. Although a network using gene essentiality from cancer cells could be an effective platform for identifying anticancer targets, efforts to apply these networks in therapeutic applications have been limited. We constructed a phenotype-level network using the co-essentiality relationship between genes in CRISPR screens across 769 cancer cells to discover therapeutic targets for diverse cancer types. Leveraging cancer driver genes and network propagation on the networks, we found that the co-essentiality network better prioritized anticancer targets and biomarkers and predicted more precise drug responses in cancer cells than other molecular networks. The co-essentiality network outperformed conventional molecular networks in drug repurposing, which were validated in silico by clinical trial records. Notably, the co-essentiality network provided 37 repurposed drugs that the other networks have yet to cover, and we showcased three approved drugs repurposed for lung adenocarcinoma (Pioglitazone hydrochloride, Atovaquone, and Eflornithine). Our study provides a novel network for precision oncology to improve the identification of therapeutic targets in specific cancers.
Engineering Adaptive Alleles forEscherichia coliGrowth on Sucrose Using the EasyGuide CRISPR System
Authors: Barreto Joneclei Alves , e Silva Matheus Victor Maso Lacôrte , Marin Danieli Canaver , Brienzo Michel , Jacobus Ana Paula , Contiero Jonas , Gross Jeferson 
Published: December 2024

AbstractAdaptive Laboratory Evolution (ALE) is a powerful approach for mining genetic data to engineer industrial microorganisms. This evolution-informed design requires robust genetic tools to incorporate the discovered alleles into target strains. Here, we introduce the EasyGuide CRISPR, a five-plasmid platform that exploitsE. coli’s natural recombination system to assemble gRNA plasmids from overlapping PCR fragments. The production of gRNAs and donor DNA is further facilitated by using recombination cassettes generated through PCR with 40 to 60-mer oligos. With the new CRISPR toolkit, we constructed 22 gene edits inE. coliDH5α, most of which corresponded to alleles mapped inE. coliDH5α and E2348/69 ALE populations selected for sucrose propagation. For DH5α ALE, sucrose consumption was supported by thecscBKAoperon expression from a high-copy plasmid. During ALE, plasmid integration into the chromosome, or its copy number reduction due to thepcnBdeletion, conferred a 30–35% fitness gain, as demonstrated by CRISPR-engineered strains. A ∼5% advantage was also associated with a ∼40.4 kb deletion involvingflioperons for flagella assembly. In E2348/69 ALE, inactivation of thehflsystem suggested selection pressures for maintaining λ-prophage dormancy (lysogeny). We further enhanced our CRISPR toolkit using yeast for in vivo assembly of donors and expression cassettes, enabling the establishment of polyhydroxybutyrate synthesis from sucrose. Overall, our study highlights the importance of combining ALE with streamlined CRISPR-mediated allele editing to advance microbial production using cost-effective carbon sources.
Haplotype editing with CRISPR/Cas9 as a therapeutic approach for dominant-negative missense mutations inNEFL
Authors: Dua Poorvi H. , Simon Bazilco M. J. , Marley Chiara B.E. , Feliciano Carissa M. , Watry Hannah L. , Steury Dylan , Abraham Abin , Gilbertson Erin N. , Ramey Grace D. , Capra John A. , Conklin Bruce R. , Judge Luke M. 
Published: December 2024

ABSTRACTInactivation of disease alleles by allele-specific editing is a promising approach to treat dominant-negative genetic disorders, provided the causative gene is haplo-sufficient. We previously edited a dominantNEFLmissense mutation with inactivating frameshifts and rescued disease-relevant phenotypes in induced pluripotent stem cell (iPSC)-derived motor neurons. However, a multitude of differentNEFLmissense mutations cause disease. Here, we addressed this challenge by targeting common single-nucleotide polymorphisms in cis withNEFLdisease mutations for gene excision. We validated this haplotype editing approach for two different missense mutations and demonstrated its therapeutic potential in iPSC-motor neurons. Surprisingly, our analysis revealed that gene inversion, a frequent byproduct of excision editing, failed to reliably disrupt mutant allele expression. We deployed alternative strategies and novel molecular assays to increase therapeutic editing outcomes while maintaining specificity for the mutant allele. Finally, population genetics analysis demonstrated the power of haplotype editing to enable therapeutic development for the greatest number of patients. Our data serve as an important case study for many dominant genetic disorders amenable to this approach.
Genome-mining algorithm to identify identical repetitive sequences for sensitive and specific diagnostic assays for infectious diseases
Authors: Rajeswari Kalepu , Poojary Raksha , Padiwal Shruptha , Krishna Rajesh Muliyar , Satyamoorthy Kapaettu , Paul Bobby 
Published: December 2024

AbstractNucleic acid amplification-based approaches are extensively used as the first line of choice for infectious diseases. However, the success rates of DNA amplification or hybridization techniques are highly dependent on short primer or probe sequences. A pair of primers that can bind at multiple loci across the genome and randomly amplify multiple copies increases the analytical sensitivity of the currently used diagnostic assays. Herein, we developed a novel genome mining algorithm to identify short identical repeat sequences (IRSs) dispersed across the genome, which can amplify multiple nonhomologous regions of variable sizes via three potential priming combinations. Using this algorithm, we analysed the genomes of five pathogens, namely, gammaherpesvirus, vaccinia virus,Mycobacterium tuberculosis, Plasmodium falciparum, andPhytophthora palmivora, and identified short identical sequences that were repeated at multiple loci.In silicoPCR revealed that these identical repeat sequences can amplify multiple copies with different amplicon sizes in these five species. We further performed a polymerase chain reaction assay with short identical repeat pairs identified fromM. tuberculosis. Very interestingly, the amplification yielded multiple copies for individual IRSs and even more copies, as in a pair of IRSs. These results indicate that the IRS-based approach can detect pathogens during disease progression in the case of low-concentration DNA. The genome mining algorithm can be used as a translation technology platform for developing highly sensitive varieties of PCR, microarray, loop-mediated isothermal amplification, fluorescencein situhybridization, and DNA-DNA hybridization-based diagnostic assays.
Cancer Histone Mutations Impact Binding and DNA Repair Processes, Leading to Increased Mutagenesis
Authors: Espiritu Daniel , Sheng Yiru , Peng Yunhui , Ostroverkhova Daria , Li Shuxiang , Landsman David , Aristizabal Maria , Panchenko Anna R. 
Published: December 2024

AbstractHistones are key epigenetic factors for regulating the accessibility and compaction of eukaryotic genomes, affecting the replication, repair, and expression of DNA. Recent studies have demonstrated that histone missense mutations can perturb normal histone function, promoting the development of phenotypically distinguishable cancers. However, most histone mutations observed in cancer patients remain enigmatic in their potential to promote cancer development. To assess the oncogenic potential of histone missense mutations, we have gathered whole-exome sequencing data for the tumors of over 12,000 patients. Overall, histone mutations occurred in about 16% of cancer patients, although specific cancer types showed substantially higher rates. Using a combination of genomic, structural, and biophysical analyses, we found several predominant modes of action, where cancer missense mutations in histones affected acidic patches and protein binding interfaces in a cancer-specific manner and targeted interaction sites with specific DNA repair proteins. Consistent with this finding, we observed a high tumour mutational burden in patients with histone mutations affecting interactions of DNA repair proteins. We also identified potential cancer driver mutations in several histone genes, including histone H4-a highly conserved histone without previously documented driver mutations.
Antimitotic chemotherapy promotes tumor NF-kB secretory phenotype and immunosuppressive CXCR2+ neutrophils chemotaxis in triple-negative breast cancers
Authors: Chocteau Florian , Gautier Fabien , Josso Vanessa , Douillard Elise , Juin Philippe , Barillé-Nion Sophie 
Published: December 2024

ABSTRACTIntegrated approaches that help understand how tumors, as immune-surveilled ecosystems, respond to chemotherapy are crucial for developing effective antitumor treatments. We previously showed, in immunodeficient context, that antimitotic chemotherapy induced cGAS/STING pathway amplifying antitumor response through a paracrine IFN-1 secretome. We herein studied tumor progression and response to treatment using an immunocompetent murine model. scRNAseq analysis revealed that paclitaxel treatment altered tumor cell phenotypes, favoring tumor cells with a gene expression signature indicative of active NF-κB pathway with secretory phenotype. Treatment coincidently reduced IFN-I signature cells during tumor progression. The resulting secretory shift correlated with neutrophil recruitment to the tumor, particularly CXCR2+ neutrophils, thereby contributing to an immunosuppressive microenvironment. Pharmacological inhibition of CXCR2 receptor by navarixin reactivated antitumor immunity, enhancing NK cell infiltration and tumor cytotoxicity. Navarixin combination with paclitaxel significantly reduced tumor volume and metastasis. Targeting the NF-κB-driven secretory phenotype, in particular through neutrophil modulation, holds promise for improving TNBC treatment outcomes.
Sensory expectations shape neural population dynamics in motor circuits
Authors: Michaels Jonathan A. , Kashefi Mehrdad , Zheng Jack , Codol Olivier , Weiler Jeffrey , Kersten Rhonda , Gribble Paul L. , Diedrichsen Jörn , Pruszynski J. Andrew 
Published: December 2024

AbstractThe neural basis of movement preparation has been extensively studied during self-initiated actions where motor cortical activity during preparation shows a lawful relationship to the parameters of the subsequent action1,2. However, movements are regularly triggered and constantly corrected based on sensory inputs caused by disturbances to the body or environment. Since such disturbances are often predictable and since preparing for disturbances would make movements better, we hypothesized that expectations about sensory inputs also influence preparatory activity in motor circuits. Here we show that when humans and monkeys are probabilistically cued about the direction of a future mechanical perturbation, they incorporate sensory expectations into their movement preparation and improve their corrective responses. Using high-density neural recordings, we establish that sensory expectations are widespread across the brain, including the motor cortical areas involved in preparing self-initiated actions. The geometry of these preparatory signals in the neural population state is simple, scaling directly with the probability of each perturbation direction. After perturbation onset, a condition-independent perturbation signal shifts the neural state leading to rapid responses that initially reflect sensory expectations. Based on neural networks coupled to a biomechanical model of the arm3, we show that this neural geometry emerges through training, but only when the incoming sensory information indicating perturbation direction coincides with – or is preceded by – a condition-independent signal indicating that a perturbation has occurred. Thus, motor circuit dynamics are shaped by future sensory inputs, providing clear empirical support for the idea that movement is governed by the sophisticated manipulation of sensory feedback4.
Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids
Authors: Kim Eunjee , Kim Yunhee , Hong Soojung , Kim Inha , Lee Juhee , Lee Kwanghwan , An Myungmo , Kim Sung-Yon , Kim Sanguk , Shin Kunyoo 
Published: December 2024

AbstractAlthough abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.
The Role of Cytonemes and Diffusive Transport in the Establishment of Morphogen Gradients
Authors: Stotsky Jay , Othmer Hans G. 
Published: December 2024

AbstractSpatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but recent experimental work has shown that cells can also communicate by filopodia-like structures called cytonemes that make direct cell-to-cell contacts. Here we investigate the roles each may play individually in a complex tissue and how they can jointly establish a reliable spatial distribution of a morphogen. To this end, we formulate models that capture fundamental aspects of various cytoneme-based transport mechanisms. In simple cases, exact solutions are attainable, and in more complex cases, we discuss results of numerical simulations.
Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling
Authors: Santos Cristiana C , Schweizer Nadine , Cairrão Fátima , Ramirez Juanma , Osinalde Nerea , Yang Ming , Gaspar Catarina J , Rasheva Vanya I , Hensel Zach , Adrain Colin , Cordeiro Tiago N , Voigt Franka , Gameiro Paulo A , Mayor Ugo , Domingos Pedro M 
Published: December 2024

SUMMARYThe Unfolded Protein Response (UPR) is composed by homeostatic signaling pathways that are activated by the accumulation of misfolded proteins in the Endoplasmic Reticulum (ER), a condition known as ER stress. Prolonged ER stress and activation of the UPR causes cell death, by mechanisms that remain poorly understood. Here, we report that regulation of Ataxin-2 by Fbxo42 is a crucial step during UPR-induced cell death. From a genetic screen inDrosophila, we identified loss of function mutations inFbxo42that suppress cell death and retinal degeneration induced by the overexpression of Xbp1spliced, an important mediator of the UPR. We identified the RNA binding protein Ataxin-2 as a substrate of Fbxo42, which, as part of a Skp-A/Cullin-1 complex, promotes the ubiquitylation and degradation of Ataxin-2. Upon ER-stress, the mRNA of Xbp1 is not immediately translated but instead it is sequestered and stabilized in Ataxin-2 granules, until the Fbxo42 recruitment to these granules promotes the degradation of Ataxin-2, allowing the translation of Xbp1 mRNA at later stages of UPR activation. Our results identify Fbxo42-mediated degradation of Ataxin-2 as a key mechanism regulating the levels of Xbp1 mRNA and protein, to trigger cell death during the terminal stages of UPR activation.