bluuebunny/crossref_metadata_2025_split huggingface dataset:
MIP3α-RelMtbintranasal DNA vaccination induces reactive T-cell infiltration into the lungs in mice and macaques
Authors: Gordy James T. , Zheng Jean J. , Maxwell Amanda R. , Taylor Alannah D. , Karanika Styliani , Bates Rowan E. , Ton Heemee , Meza Jacob , Li Yangchen , Zhang Jiaqi , Karakousis Petros C. , Markham Richard B. 
Published: September 2024

ABSTRACTMycobacterium tuberculosis(Mtb), the causative agent of tuberculosis (TB), is the leading cause of mortality due to a single infectious organism. While generally curable, TB requires a lengthy and complex antibiotic regimen, due in large part to bacteria that can shift to a persistent state in the presence of antibiotic pressure. RelMtbis the primary enzyme regulating the stringent response, which contributes to the metabolic shift of Mtb to a persistent state. Targeting RelMtbwith a vaccine to eliminate persistent bacteria through the induction of RelMtb-specific T-cell immunity in combination with antibiotics to kill dividing bacteria has shown promise in model systems. In a mouse model of Mtb infection, a vaccine created by genetically fusingrelMtbto the chemokine macrophage inflammatory protein 3α (MIP3α), a ligand for the CC chemokine receptor type 6 (CCR6) present on immature dendritic cells, has been shown to enhance T-cell responses and accelerate eradication of infection in mouse models compared to a vaccine lacking the chemokine component. In this study, immunogenicity studies in the mouse and rhesus macaque models provide evidence that intranasal administrations of the DNA form of the MipRel vaccine led to enhanced lung infiltration of T cells after a series of immunizations. Furthermore, despite similar T-cell immunity seen in PBMCs between MipRel and Rel vaccinations, lung and bronchoalveolar lavage cell samples are more enriched for cytokine-secreting T cells in MipRel groups compared to Rel groups. We conclude that intranasal immunization with a MIP-3α fusion vaccine represents a novel strategy for use of a simple DNA vaccine formulation to elicit T-cell immune responses within the respiratory tract. That this formulation is immunogenic in a non-human primate model historically viewed as poorly responsive to DNA vaccines indicates the potential for clinical application in the treatment of Mtb infection, with possible application to other respiratory pathogens. Future studies will further characterize the protective effect of this vaccination platform.
Proximity labeling defines the phagosome lumen proteome of murine and primary human macrophages
Authors: Allsup Benjamin L. , Gharpure Supriya , Bryson Bryan D. 
Published: September 2024

AbstractProteomic analyses of the phagosome has significantly improved our understanding of the proteins which contribute to critical phagosome functions such as apoptotic cell clearance and microbial killing. However, previous methods of isolating phagosomes for proteomic analysis have relied on cell fractionation with some intrinsic limitations. Here, we present an alternative and modular proximity-labeling based strategy for mass spectrometry proteomic analysis of the phagosome lumen, termed PhagoID. We optimize proximity labeling in the phagosome and apply PhagoID to immortalized murine macrophages as well as primary human macrophages. Analysis of proteins detected by PhagoID in murine macrophages demonstrate that PhagoID corroborates previous proteomic studies, but also nominates novel proteins with unexpected residence at the phagosome for further study. A direct comparison between the proteins detected by PhagoID between mouse and human macrophages further reveals that human macrophage phagosomes have an increased abundance of proteins involved in the oxidative burst and antigen presentation. Our study develops and benchmarks a new approach to measure the protein composition of the phagosome and validates a subset of these findings, ultimately using PhagoID to grant further insight into the core constituent proteins and species differences at the phagosome lumen.
A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks
Authors: Allman Brent , Vieira Luiz , Diaz Daniel J. , Wilke Claus O. 
Published: September 2024

AbstractPredicting the evolutionary patterns of emerging and endemic viruses is key for mitigating their spread in host populations. In particular, it is critical to rapidly identify mutations with the potential for immune escape or increased disease burden (variants of concern). Knowing which circulating mutations are such variants of concern can inform treatment or mitigation strategies such as alternative vaccines or targeted social distancing. A recent study proposed that variants of concern can be identified using two quantities extracted from protein language models, grammaticality and semantic change. These quantities are defined in analogy to concepts from natural language processing. Grammaticality is intended to be a measure of whether a variant viral protein is viable, and semantic change is intended to be a measure of potential for immune escape. Here, we systematically test this hypothesis, taking advantage of several high-throughput datasets that have become available, and also testing additional machine learning models for calculating the grammaticality metric. We find that grammaticality can be a measure of protein viability, though the more traditional metric ΔΔGappears to be more effective. By contrast, we do not find compelling evidence that semantic change is a useful tool for identifying immune escape mutations.
Advancing Variant Phenotyping in Myelodysplastic Syndromes via Computational Genomics of Mitochondrial Enzyme Complexes
Authors: Dong Jing , Zimmermann Michael T. , Haque Neshatul , Arsang-Jang Shahram , Saber Wael , Urrutia Raul 
Published: September 2024

ABSTRACTMitochondria are essential cellular organelles that play critical roles in hematological disorders. Recurrent mutations in mitochondrial DNA (mtDNA) have been identified in patients with myelodysplastic syndromes (MDS) and serve as significant prognostic indicators for their outcomes following allogeneic hematopoietic stem-cell transplantation (allo-HCT). However, the biological mechanisms of mtDNA mutations remain unclear. The current study utilizes computational structural genomics to improve our understanding of pathogenic variants in mitochondria-encoded genes. This emerging genomics discipline employs structural models, molecular mechanic calculations, and accelerated molecular dynamic simulations to analyze gene products, focusing on their structures and motions that determine their function. We applied this methodology to perform deep variant phenotyping of entire mitochondria-encoded protein complexes associated with the pathobiology of MDS and their prognosis after HCT. Our results demonstrate that this approach significantly outperforms conventional analytical methods, providing enhanced and more accurate information to support the potential pathogenicity of these variants and better infer their dysfunctional mechanisms. We conclude that the adoption and further expansion of computational structural genomics approaches, as applied to the mitochondrial genome, have the potential to significantly increase our understanding of molecular mechanisms underlying the disease. Our study lays a foundation for translating mitochondrial biology into clinical applications, which is of significant mechanistic and biomedical relevance and should be considered in modern biomedical research.
Aberrant prefrontal activity and arousal level correlate with action initiation and response vigor
Authors: Klein Frederike J. , Vasilev Dmitrii , Iwai Ryo , Watanabe Masataka , Totah Nelson K. 
Published: September 2024

AbstractOrchestrating learned Stimulus-Response (S-R) mappings has been suggested as one of the central functions of the prefrontal cortex (PFC). While S-R selective activity has been demonstrated, it remains unclear whether the strength of such activity is related to the vigor of the subsequent response. Here, we trained male rats to perform a Go/NoGo response task while head-fixed on a treadmill. This allowed us to record PFC (cingulate, area 24) single unit spiking, as well as running speed as a proxy for response vigor. We show that aberrant activation of the “wrong” S-R mapping is correlated with initiation of the incorrect response. The vigor of the incorrect response was directly related to the strength of the aberrant stimulus-evoked activity. A similar relationship was observed for pre-trial arousal state and response vigor. Our findings confirm the long-standing concept, established in psychology and cognitive neuroscience, that S-R mappings are directly related to response vigor. Moreover, we provide evidence for the often suggested but rarely tested relationship between arousal and response vigor and a potential underlying neuronal mechanism involving neuromodulation of S-R mapping activity.Significance statementThe concept of stimulus-response (S-R) mappings is fundamental in psychology and has been widely documented as a key function of the prefrontal cortex. Here, the authors directly link prefrontal single neuron mapping-selective activity to the vigor of responses. Moreover, they link a physiological measure of arousal to response vigor and suggest that neuromodulatory systems invigorate responses by potentially modulating PFC S-R mapping-selective activity.
A Graph Curvature-Based Pipeline for Discovering Immune Checkpoint Response Biomarkers
Authors: Bannon James , Cantor Charles R. , Mishra Bud 
Published: September 2024

AbstractImmune checkpoint inhibitors (ICIs), also called immune checkpoint blockers, are a promising category of targeted therapy for solid tumors. Predicting which patients will respond to ICI therapy remains an open problem under active investigation. This paper adds to this effort by developing a modular pipeline for the discovery of biomarkers from tumor RNA-sequencing data. We contextualize gene expression measurements using a protein-protein interaction (PPI) network and use a notion of graph curvature to find (pairs of) genes in the PPI that could serve as potential biomarkers. Our candidate biomarkers are evaluated using an extensive literature search and transfer learning experiments. We also provide a harmonized collection of drug-specific candidate markers found through rank aggregation that we believe merit further study.
Combination of cycling hyperthermia and Echinacoside creates synergistic curing effect on pancreatic cancer PANC-1 cells
Authors: Chen Wei-Ting , Chen You-Ming , Lin Guan-Bo , Kuo Yu-Yi , Liu Hsu-Hsiang , Chao Chih-Yu 
Published: September 2024

AbstractTherapy targeting the suppression of human MutT homolog 1 (MTH1) has been gaining ground in recent years, thanks to its resulting significant increase of 8-hydroxy-2’-deoxyguanosine triphosphate (8-oxo-dGTP) accumulation in genomic DNA, causing DNA damage and apoptotic cell death. Echinacoside (Ech), a natural phenylethanoid glycoside first extracted from Echinacea angustifolia or desert plant Cistanches is one of a few natural products which are capable of inhibiting the MTH1 function. It, however, is difficult to apply it in clinical trials, due to high cost for effective dosage in need. In the study, we show that combination with thermal-cycling hyperthermia (TC-HT), a novel physical treatment, can amplify the curative effect of Ech, reducing its dosage in need significantly. The combination resulted in a multipronged mechanism targeting multiple key apoptotic regulating proteins such as Bcl-2 and MAPK family proteins. Its effect is expected to be comparable to the treatment strategy containing MTH1, Bcl-2, and ERK inhibitors, posing as new promising approach in cancer treatment.
Reclaiming Hand Functions after Complete Spinal Cord Injury with Epidural Brain-Computer Interface
Authors: Liu Dingkun , Shan Yongzhi , Wei Penghu , Li Wenzheng , Xu Honglai , Liang Fangshuo , Liu Tao , Zhao Guoguang , Hong Bo 
Published: September 2024

AbstractBackgroundSpinal cord injuries significantly impair patients’ ability to perform daily activities independently. While cortically implanted brain-computer interfaces (BCIs) offer high communication bandwidth to assist and rehabilitate these patients, their invasiveness and long-term stability limits broader adoption.MethodsWe developed a minimally invasive BCI with 8 chronic epidural electrodes above primary sensorimotor cortex to restore hand functions of tetraplegia patients. With wireless powering and neural data transmission, this system enables real-time BCI control of hand movements and hand function rehabilitation in home use. A complete spinal cord injury (SCI) patient with paralyzed hand functions was recruited in this study.ResultsOver a 9-month period of home use, the patient achieved an average grasping detection F1-score of 0.91, and a 100% success rate in object transfer tests, with this minimally invasive BCI and a wearable exoskeleton hand. This system allowed the patient to perform eating, drinking and other daily tasks involving hand functions. Additionally, the patient showed substantial neurological recovery through consecutive BCI training, regaining the ability to hold objects without BCI. The patient exhibited a 5-point improvement in upper limb motor scores and a 27-point increase in the action research arm test (ARAT). A maximal increase of 12.2 μV was observed in the peak of somatosensory evoked potential, which points to a considerable recovery in impaired spinal cord connections.ConclusionsIn a tetraplegia patient with complete spinal cord injury, an epidural minimally invasive BCI assisted the patient’s hand grasping to perform daily tasks, and 9-month consecutive BCI use significantly improved the hand functions.
A robust unsupervised clustering approach for high-dimensional biological imaging data reveals shared drug-induced morphological signatures
Authors: Bao Shaine Chenxin , Mizikovsky Dalia , Pishas Kathleen , Cowley Karla J , Zhao Qiongyi , Marinovic Evanny , Carey Mark , Campbell Ian , Simpson Kaylene J , Cheasley Dane , Palpant Nathan J. 
Published: September 2024

AbstractHigh-throughput analysis methods have emerged as central technologies to accelerate discovery by accelerating generation of large-scale data. Analysis and interpretation of these datasets remains challenging due to limitations in computational approaches for dimensionality reduction. Here, we present UnTANGLeD, a versatile computational pipeline that prioritises biologically robust and meaningful information to guide actionable strategies from input screening data which we demonstrate using results from image-based drug screening. By providing a robust framework for analysing high dimensional biological data, UnTANGLeD offers a powerful tool for analysis of theoretically any data type from any screening platform.
HHIP’s Dynamic Role in Epithelial Wound Healing Reveals a Potential Mechanism of COPD Susceptibility
Authors: Deritei Dávid , Anamika Wardatul Jannat , Zhou Xiaobo , Silverman Edwin K. , Regan Erzsébet Ravasz , Glass Kimberly 
Published: September 2024

AbstractA genetic variant nearHHIPhas been consistently identified as associated with increased risk for Chronic Obstructive Pulmonary Disease (COPD), the third leading cause of death worldwide. However HHIP’s role in COPD pathogenesis remains elusive. Canonically, HHIP is a negative regulator of the hedgehog pathway and downstream GLI1 and GLI2 activation. The hedgehog pathway plays an important role in wound healing, specifically in activating transcription factors that drive the epithelial mesenchymal transition (EMT), which in its intermediate state (partial EMT) is necessary for the collective movement of cells closing the wound. Herein, we propose a mechanism to explain HHIP’s role in faulty epithelial wound healing, which could contribute to the development of emphysema, a key feature of COPD. Using two different Boolean models compiled from the literature, we show dysfunctional HHIP results in a lack of negative feedback on GLI, triggering a full EMT, where cells become mesenchymal and do not properly close the wound. We validate these Boolean models with experimental evidence gathered from published scientific literature. We also experimentally test if low HHIP expression is associated with EMT at the edge of wounds by using a scratch assay in a human lung epithelial cell line. Finally, we show evidence supporting our hypothesis in bulk and single cell RNA-Seq data from different COPD cohorts. Overall, our analyses suggest that aberrant wound healing due to dysfunctional HHIP, combined with chronic epithelial damage through cigarette smoke exposure, may be a primary cause of COPD-associated emphysema.Graphical abstract
Dynamic epigenomic landscape of carbon-concentrating mechanisms in the model industrial oleaginous microalgaNannochloropsis oceanica
Authors: Gong Yanhai , Wang Qintao , Wei Li , Wang Lianhong , Lv Nana , Du Xuefeng , Shen Chen , Xin Yi , Sun Luyang , Xu Jian 
Published: September 2024

AbstractDespite their ecological and physiological significance, how carbon-concentrating mechanisms (CCM) are regulated in microalgae remains elusive. Here in the model industrial microalgaNannochloropsis oceanica, we uncovered an epigenetic regulatory mechanism for CCM via comprehensive, multi-dimensional epigenomic analyses. Our integrated study reveals the complex interplay among histone modifications, dynamic nucleosome positioning, and 3D chromatin structure in regulating gene expression during low CO2adaptation, despite minimal DNA methylation. Histone modifications, including lysine acetylation (H3K9ac and H3K27ac), crotonylation (Kcr), and methylation (H3K4me2), were associated with active chromatin states. Significantly altered ChIP-Seq peaks were linked to 43.1% of the differentially expressed genes (DEGs). Notably, H3K4me2 exhibited a distinct dual-peak profile around the transcription start site (TSS), which is unique among microalgae and plants. Chromatin compartment dynamics were correlated with gene expression and histone modifications, particularly H3K4me2, while differentially positioned nucleosomes were associated with key CCM-related genes and transcription factors. To further elucidate the role of H3K4me2, we knocked out its methyltransferase, resulting in genome-wide H3K4me2 peak shifts, slower growth, and reduced photosynthesis. These changes were accompanied by differential expression of key genes of NoHINT and NoPMA2, whose subsequent deletion and overexpression revealed their subtle yet significant impacts on growth and photosynthetic efficiency under low CO2conditions, with NoHINT regulating growth and NoPMA2 influencing photosynthesis. Finally, we proposed a comprehensive model for epigenetic regulation of CCM inN. oceanica, which established a foundation for enhancing microalgal productivity through targeted epigenetic modifications.HighlightsMulti-layered epigenetic modifications contribute to the regulation of CCM and its adaptation to low CO2inN. oceanica.The histone modification H3K4me2 regulates the growth and photosynthesis ofN. oceanicaunder low CO2conditions.H3K4me2 targets NoHINT and NoPMA2 inN. oceanica, with NoHINT influencing growth dynamics and NoPMA2 modulating photosynthetic efficiency under low CO2conditions.
Selection efficacy differs between lifestages in the haploid-diploidMarchantia polymorphasubsp.ruderalis
Authors: Shen Tianyu , Gadient Philippe , Goodrich Justin , Becher Hannes 
Published: September 2024

AbstractPloidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, the effects of non-dominant deleterious variants are ‘masked’ to some extent, leading to a reduction in the efficacy of selection. This, in turn, leads to increased levels of nucleotide diversity, and it may also affect nucleotide substitution rates.To test this predicted association between ploidy and the efficacy of selection, we studied genome scale per-gene patterns of genetic diversity and divergence in the genome of the haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as a continuous covariate and accounted for genomic autocorrelation patterns using smoothing splines in a general additive regression model (GAM) framework.Consistent with a lower efficacy of purifying selection, we found increased levels of sequence diversity, Watterson’sθ, and net divergence at non-degenerate sites in genes with diploid-biased gene expression. These genes also showed reduced levels of codon usage bias. In addition, we found chromosome 5 to be an outlier with overall decreased levels of diversity, the site-frequency spectrum skewed towards common alleles, and increased linkage disequilibrium.In this study, we show the utility of generalized additive models in population genomics, and we present evidence for a ploidy associated difference in the efficacy of selection. We discuss parallels to the evolution of (diploid) sex chromosomes and why the patterns observed are unlikely to be mediated by masking.
ATP Regeneration from Pyruvate in the PURE System
Authors: Yadav Surendra , Perkins Alexander J. P. , Liyanagedera Sahan B. W. , Bougas Anthony , Laohakunakorn Nadanai 
Published: September 2024

AbstractThe ‘Protein synthesis Using Recombinant Elements’ (‘PURE’) system is a minimal biochemical system capable of carrying out cell-free protein synthesis using defined enzymatic components. This study extends PURE by integrating an ATP regeneration system based on pyruvate oxidase, acetate kinase, and catalase. The new pathway generates acetyl phosphate from pyruvate, phosphate, and oxygen, which is used to rephosphorylate ATP in situ. Successful ATP regeneration requires a high initial concentration of∼10 mM phosphate buffer, which surprisingly does not affect the protein synthesis activity of PURE. The pathway can function independently or in combination with the existing creatine-based system in PURE; the combined system produces up to 233µg/ml of mCherry, an enhancement of 78% compared to using the creatine system alone. The results are reproducible across multiple batches of homemade PURE, and importantly also generalise to commercial systems such as PURExpress®from New England Biolabs. These results demonstrate a rational bottom-up approach to engineering PURE, paving the way for applications in cell-free synthetic biology and synthetic cell construction.