bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-Depth Mapping of DNA-PKcs Signaling Uncovers Conserved Features of Its Kinase Specificity
Authors: Marshall Shannon , Navarro Marcos V.A.S. , Ascenҫão Carolline F.R. , Smolka Marcus B. 
Published: January 2024

ABSTRACTDNA-PKcs is a DNA damage sensor kinase with established roles in DNA double-strand break repair via non-homologous end joining. Recent studies have revealed additional roles of DNA-PKcs in the regulation of transcription, translation and DNA replication. However, the substrates through which DNA-PKcs regulates these processes remain largely undefined. Here we utilized quantitative phosphoproteomics to generate a high coverage map of DNA-PKcs signaling in response to ionizing radiation and mapped its interplay with the ATM kinase. Beyond the detection of the canonical S/T-Q phosphorylation motif, we uncovered a non-canonical mode of DNA-PKcs signaling targeting S/T-ψ-D/E motifs. Cross-species analysis in mouse pre-B and human HCT116 cell lines revealed splicing factors and transcriptional regulators phosphorylated at this novel motif, several of which contain SAP domains. These findings expand the list of DNA-PKcs and ATM substrates and establish a novel preferential phosphorylation motif for DNA-PKcs that connects it to proteins involved in nucleotide processes and interactions.
In vivorescue of arboviruses directly from subgenomic DNA fragments
Authors: Cochin Maxime , Driouich Jean-Sélim , Moureau Grégory , Piorkowski Géraldine , de Lamballerie Xavier , Nougairède Antoine 
Published: January 2024

AbstractReverse genetic systems are mainly used to study RNA viruses and rescue recombinant strains in cell culture. Here, we provide proof-of-concept for directin vivoviral generation using the ‘Infectious Subgenomic Amplicons’ method. So far, this procedure allowed to rescuein vitroRNA viruses, by the transfection of several overlapping subgenomic DNA fragments encoding the entire virus genome.We adapted and optimized this technique to generate a pathogenic tick-borne encephalitis virus strain in mice. To define optimal protocol parameters, we injected intramuscularly different amounts of DNA fragments associated, or not, to electroporation. The injection of only 1µg of DNA fragments combined with electroporation resulted in an infection rate of 100%. Then, these parameters were applied to rescue another flavivirus and an alphavirus.This method provides a novel and efficient strategy forin vivoviral generation, which is typically achieved by injecting infectious clones. Furthermore, as part of the development of DNA- launched live attenuated vaccines, this approach, which also has the advantage of not injecting vector DNA, may simplify the generation of attenuated strainsin vivo.
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events
Authors: Bennett Jamie J. R. , Stern Alan D. , Zhang Xiang , Birtwistle Marc R. , Pandey Gaurav 
Published: January 2024

AbstractUnderstanding the dynamics of intracellular signaling pathways, such as ERK1/2 (ERK) and Akt1/2 (Akt), in the context of cell fate decisions is important for advancing our knowledge of cellular processes and diseases, particularly cancer. While previous studies have established associations between ERK and Akt activities and proliferative cell fate, the heterogeneity of single-cell responses adds complexity to this understanding. This study employed a data-driven approach to address this challenge, developing machine learning models trained on a dataset of growth factor-induced ERK and Akt activity time courses in single cells, to predict cell division events. The most effective predictive models were developed by applying discrete wavelet transforms (DWTs) to extract low-frequency features from the time courses, followed by using Ensemble Integration, an effective data integration and predictive modeling framework. The results demonstrated that these models effectively predicted cell division events in MCF10A cells (F-measure=0.524, AUC=0.726). ERK dynamics were found to be more predictive than Akt, but the combination of both measurements further enhanced predictive performance. The ERK model’s performance also generalized to predicting division events in RPE cells, indicating the potential applicability of these models and our data-driven methodology for predicting cell division across different biological contexts. Interpretation of these models suggested that ERK dynamics throughout the cell cycle, rather than immediately after growth factor stimulation, were associated with the likelihood of cell division. Overall, this work contributes insights into the predictive power of intra-cellular signaling dynamics for cell fate decisions, and highlights the potential of machine learning approaches in unraveling complex cellular behaviors.
Pharmacological manipulations of the dorsomedial and dorsolateral striatum during fear extinction have opposing effects on fear renewal
Authors: Tanner Margaret K , Hohorst Alyssa A , Westerman Jessica , Mendoza Carolina Sanchez , Han Rebecca , Moya Nicolette A , Jaime Jennifer , Alvarez Lareina M , Dryden Miles , Balolia Aleezah , Abdul Remla , Loetz Esteban C , Greenwood Benjamin N 
Published: January 2024

AbstractSystemic manipulations that enhance dopamine (DA) transmission around the time of fear extinction can strengthen fear extinction and reduce conditioned fear relapse. Prior studies investigating the brain regions where DA augments fear extinction focus on targets of mesolimbic and mesocortical DA systems originating in the ventral tegmental area, given the role of these DA neurons in prediction error. The dorsal striatum (DS), a primary target of the nigrostriatal DA system originating in the substantia nigra (SN), is implicated in behaviors beyond its canonical role in movement, such as reward and punishment, goal-directed action, and stimulus-response associations, but whether DS DA contributes to fear extinction is unknown. We have observed that chemogenetic stimulation of SN DA neurons during fear extinction prevents the return of fear in contexts different from the extinction context, a form of relapse called renewal. This effect of SN DA stimulation is mimicked by a DA D1 receptor (D1R) agonist injected into the DS, thus implicating DS DA in fear extinction. Different DS subregions subserve unique functions of the DS, but it is unclear where in the DS D1R agonist acts during fear extinction to reduce renewal. Furthermore, although fear extinction increases neural activity in DS subregions, whether neural activity in DS subregions is causally involved in fear extinction is unknown. To explore the role of DS subregions in fear extinction, adult, male Long-Evans rats received microinjections of either the D1R agonist SKF38393 or a cocktail consisting of GABAA/GABABreceptor agonists muscimol/baclofen selectively into either dorsomedial (DMS) or dorsolateral (DLS) DS subregions immediately prior to fear extinction, and extinction retention and renewal were subsequently assessed drug-free. While increasing D1R signaling in the DMS during fear extinction did not impact fear extinction retention or renewal, DMS inactivation reduced later renewal. In contrast, DLS inactivation had no effect on fear extinction retention or renewal but increasing D1R signaling in the DLS during extinction reduced fear renewal. These data suggest that DMS and DLS activity during fear extinction can have opposing effects on later fear renewal, with the DMS promoting renewal and the DLS opposing renewal. Mechanisms through which the DS could influence the contextual gating of fear extinction are discussed.HighlightsDorsolateral striatum D1 receptor signaling during fear extinction reduces renewalNeural activity in the dorsomedial striatum during fear extinction permits renewalDorsal striatum subregions have opposing roles in contextual gating of fear extinctionGraphical Abstract
Group A Streptococcal Collagen-like Protein 1 Restricts Tumor Growth in Murine Pancreatic Adenocarcinoma and Inhibits Cancer-Promoting Neutrophil Extracellular Traps
Authors: Henderson Emily A. , Ivey Abby , Choi Soo , Santiago Stell , McNitt Dudley , Liu Tracy W. , Lukomski Slawomir , Boone Brian A. 
Published: January 2024

AbstractPancreatic ductal adenocarcinoma (PDAC) is a lethal cancer associated with an immunosuppressive environment. Neutrophil extracellular traps (NETs) were initially described in the context of infection but have more recently been implicated in contributing to the tolerogenic immune response in PDAC. Thus, NETs are an attractive target for new therapeutic strategies. Group A Streptococcus (GAS) has developed defensive strategies to inhibit NETs. In the present work, we propose utilizing intra-tumoral GAS injection to stimulate anti-tumor activity by inhibiting cancer-promoting NETs. Injection of three different M-type GAS strains reduced subcutaneous pancreatic tumor volume compared to control in two different murine PDAC models. Limitation of tumor growth was dependent on streptococcal collagen-like protein 1 (Scl1), as isogenic mutant strain devoid of Scl1 did not reduce tumor size. We further show that Scl1 plays a role in localizing GAS to the tumor site, thereby limiting the systemic spread of bacteria and off-target effects. While mice did elicit a humoral immune response to GAS antigens, tested sera were negative toward Scl1 antigen following intra-tumoral treatment with Scl1-expressing GAS. M1 GAS inhibited NET formation when co-cultured with neutrophils while Scl1-devoid mutant strain did not. Recombinant Scl1 protein inhibited NETsex vivoin a dose-dependent manner by suppressing myeloperoxidase activity. Altogether, we demonstrate that intra-tumoral GAS injections reduce PDAC growth, which is facilitated by Scl1, in part through inhibition of cancer promoting NETs. This work offers a novel strategy by which NETs can be targeted through Scl1 protein and potentiates its use as a cancer therapeutic.
Shared Transcriptomic Signatures of Inflammaging Among Diverse Strains ofDrosophila melanogaster
Authors: Perna Sabrina Isabel , Tang Weihao , Blimbaum Sydney Danielle , Li Andrew , Zhou Lei 
Published: January 2024

AbstractBackgroundA prominent hallmark of aging is inflammaging—the increased expression of innate immune genes without identifiable infection. Model organisms with shorter lifespans, such as the fruit fly, provide an essential platform for probing the mechanisms of inflammaging. Multiple groups have reported that, like mammalian models, old flies have significantly higher levels of expression of anti-microbial peptide genes. However, whether some of these genes—or any others—can serve as reliable markers for assessing and comparing inflammaging in different strains remains unclear.Methods and ResultsWe compared RNA-Seq datasets generated by different groups. Although the fly strains used in these studies differ significantly, we found that they share a core group of genes with strong aging-associated expression. In addition to anti-microbial peptide genes, we identified other genes that have prominently increased expression in old flies, especiallySPH93. We further showed that machine learning models can be used to predict the “inflammatory age” of the fruit fly.ConclusionA core group of genes may serve as markers for studying inflammaging inDrosophila. RNA-Seq profiles, in combination with machine-learning models, can be applied to measure the acceleration or deceleration of inflammaging.
Intestinal barrier function in the naked mole-rat: an emergent model for gastrointestinal insights
Authors: Aguilera-Lizarraga Javier , Ritoux Anne , Bulmer David C. , Smith Ewan St. John 
Published: January 2024

AbstractThe intestinal barrier plays a crucial role in homeostasis, both by facilitating absorption of nutrients and fluids, and providing a tight shield to prevent the invasion by either pathogen or commensal microorganisms. Intestinal barrier malfunction is associated with systemic inflammation, oxidative stress, and decreased insulin sensitivity, which may lead to the dysregulation of other tissues. Therefore, a deeper understanding of physiological aspects related to an enhanced barrier function is of significant scientific and clinical relevance. The naked mole-rat has many unusual biological features, including attenuated colonic neuron sensitivity to acid and bradykinin, and resistance to chemical-induced intestinal damage. However, insight into their intestinal barrier physiology is scarce. Here, we observed notable macroscopic and microscopic differences in intestinal tissue structure between naked mole-rats and mice. Moreover, naked mole-rats showed increased number of larger goblet cells and elevated mucus content. In measuring gut permeability, naked mole-rats showed reduced permeability compared to mice, measured as transepithelial electrical resistance, especially in ileum. Furthermore, intestinal ion secretion induced by serotonin, bradykinin, histamine, and capsaicin was significantly reduced in naked mole-rats compared to mice, despite the expression of receptors for all these agonists. In addition, naked mole-rats exhibited reduced pro-secretory responses to the non-selective adenylate cyclase activator forskolin. Collectively, these findings indicate that naked mole-rats possess a robust and hard-to-penetrate gastrointestinal barrier, that is resistant to environmental and endogenous irritants. Naked mole-rats may therefore provide valuable insights into the physiology of the intestinal barrier and set the stage for the development of innovative and effective therapies.Graphical abstract
A new class of human CpG island promoters with primate-specific repeats
Authors: Mohan K Naga , Anne Anuhya , Kumar Lov , Chaillet J Richard 
Published: January 2024

AbstractA subset of imprinting control regions (ICRs) in the human and mouse possess CpG islands associated with imperfect tandem repeats (TRs) that were shown to be essential for genomic imprinting through genetic studies. To identify whether this feature is also present in non-imprinted CpG island promoters, we performed extensive dot plot analyses and identified 365 CpG island gene promoters associated with imperfect TRs of ≥ 400nt. These TRs are absent in the orthologous mouse CGI promoters, and most occur as clusters at the human chromosome ends, distinct from the clusters of imprinted genes. These genes showed an enrichment in neurodevelopmental/behavioral disorders and show interindividual variation in methylation levels. A subset of TR-CGIs is highly methylated and remains so during reprogramming to primed iPSCs, but become unmethylated in naïve iPSCs, as has been shown for the ICRs. Transcript levels correlate with methylation levels for some TR-CGI genes suggesting their gene regulatory potential. Orthologs of the subset of methylated TR-CGIs are unmethylated in mouse, suggesting the role of TRs in imparting methylation in humans. The human TR-CGIs accompanied primate evolution after divergence from the rodent lineage with evidence of recent additions in human evolution. In summary, the incorporation of TRs in certain CGI promoters in primate evolution results in the unique ability to acquire methylation during embryonic development and resist reprogramming to a pluripotent stem cell state with a possible effect on gene expression.
Cholinergic neuromodulation of prefrontal attractor dynamics controls performance in spatial working memory
Authors: Mahrach Alexandre , Bestue David , Qi Xue-Lian , Constantinidis Christos , Compte Albert 
Published: January 2024

AbstractThe behavioral and neural effects of the endogenous release of acetylcholine following stimulation of the Nucleus Basalis of Meynert (NB) have been recently examined (Qi et al. 2021). Counterintuitively, NB stimulation enhanced behavioral performance while broadening neural tuning in the prefrontal cortex (PFC). The mechanism by which a weaker mnemonic neural code could lead to better performance remains unclear. Here, we show that increased neural excitability in a simple continuous bump attractor model can induce broader neural tuning and decrease bump diffusion, provided neural rates are saturated. Increased memory precision in the model overrides memory accuracy, improving overall task performance. Moreover, we show that bump attractor dynamics can account for the nonuniform impact of neuromodulation on distractibility, depending on distractor distance from the target. Finally, we delve into the conditions under which bump attractor tuning and diffusion balance in biologically plausible heterogeneous network models. In these discrete bump attractor networks, we show that reducing spatial correlations or enhancing excitatory transmission can improve memory precision. Altogether, we provide a mechanistic understanding of how cholinergic neuromodulation controls spatial working memory through perturbed attractor dynamics in PFC.Significance statementAcetylcholine has been thought to improve cognitive performance by sharpening neuronal tuning in prefrontal cortex. Recent work has shown that electrical stimulation of the cholinergic forebrain in awake-behaving monkeys induces a reduction in prefrontal neural tuning under stimulation conditions that improve performance. To reconcile these divergent observations, we provide network simulations showing that these derive consistently from specific conditions in prefrontal attractor dynamics: firing rate saturation leads to increased storage precision and reduced neural tuning upon cholinergic activation via an increase in neural excitability, a reduction in neural correlations, and an increase in excitatory transmission. Our study integrates previously reported data into a consistent mechanistic view of how acetylcholine controls spatial working memory via attractor network dynamics in prefrontal cortex.
Niche partitioning in a cyanobacterium through divergence of its novel chlorophylld-based light-harvesting system
Authors: Ulrich Nikea J. , Shen Gaozhong , Bryant Donald A. , Miller Scott R. 
Published: January 2024

AbstractThe evolution of novel traits can have important consequences for biological diversification. New ecological opportunities provided by a novel trait can trigger subsequent trait modification or niche partitioning; however, the underlying mechanisms of novel trait diversification are still poorly understood. Here, we report that the innovation of a new chlorophyll (Chl) pigment, Chld,by the cyanobacteriumAcaryochloris marinawas followed by the functional divergence of its light-harvesting complex. We identified three major photosynthetic spectral types based on Chl fluorescence properties forA. marinalaboratory strains, with shorter and longer wavelength types more recently derived from an ancestral intermediate phenotype. Members of the different spectral types exhibited extensive variation in the Chl-binding proteins as well as the Chl energy levels of their photosynthetic complexes. This spectral type divergence is associated with differences in the wavelength dependence of both growth rate and photosynthetic oxygen evolution. We conclude that the divergence of the light-harvesting apparatus has consequently impactedA. marinaecological diversification through specialization on different far-red photons for photosynthesis.
Spectrally Resolved Localization Microscopy with Ultrahigh-Throughput
Authors: Batey James Ethan , Kim Geun Wan , Yang Meek , Heffer Darby Claire , Pott Elric Dion , Giang Hannah , Dong Bin 
Published: January 2024

AbstractSingle-molecule localization microscopy (SMLM) has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features quickly and accurately in complex environments at the nanoscopic level. Multicolor super-resolution imaging has seen the greatest advancement among SMLM techniques, drastically improving the differentiation ability of nanostructures beyond the diffraction limit and increasing the resolution with which previously unresolvable structures are studied. However, current multicolor SMLM methodologies present low spatial resolution and throughput and require complex optical systems. Here, we overcome these drawbacks by developing an ultrahigh-throughput SMLM methodology that allows for ultrahigh throughput multicolor imaging at the nanoscopic level using a color glass filter. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5nm spectral precisions.
Modular Phoneme Processing in Human Superior Temporal Gyrus
Authors: Cleary Daniel R. , Tchoe Youngbin , Bourhis Andrew , Dickey Charles W. , Stedelin Brittany , Ganji Mehran , Lee Sang Hoen , Lee Jihwan , Siler Dominic A. , Brown Erik C. , Rosen Burke Q. , Kaestner Erik , Yang Jimmy C. , Soper Daniel J. , Han Seunggu Jude , Paulk Angelique C. , Cash Sydney S. , Raslan Ahmed M. T. , Dayeh Shadi A. , Halgren Eric 
Published: January 2024

AbstractModular organization is fundamental to cortical processing, but its presence is human association cortex is unknown. We characterized phoneme processing with 128-1024 channel micro-arrays at 50-200μm pitch on superior temporal gyrus of 7 patients. High gamma responses were highly correlated within ∼1.7mm diameter modules, sharply delineated from adjacent modules with distinct time-courses and phoneme-selectivity. We suggest that receptive language cortex may be organized in discrete processing modules.
miRNA family miR-29 inhibits PINK1-PRKN dependent mitophagy via ATG9A
Authors: Markham Briana N , Ramnarine Chloe , Kim Songeun , Grever William E , Soto-Beasley Alexandra I , Heckman Michael , Ren Yingxue , Osborne Andrew C , Bhagwate Aditya V , Liu Yuanhang , Wang Chen , Kim Jungsu , Wszolek Zbigniew K , Ross Owen A , Springer Wolfdieter , Fiesel Fabienne C 
Published: January 2024

ABSTRACTLoss-of-function mutations in the genes encoding PINK1 and PRKN result in early-onset Parkinson disease (EOPD). Together the encoded enzymes direct a neuroprotective pathway that ensures the elimination of damaged mitochondria via autophagy.We performed a genome-wide high content imaging miRNA screen for inhibitors of the PINK1-PRKN pathway and identified all three members of the miRNA family 29 (miR-29). Using RNAseq we identified target genes and found that siRNA against ATG9A phenocopied the effects of miR-29 and inhibited the initiation of PINK1-PRKN mitophagy. Furthermore, we discovered two rare, potentially deleterious, missense variants (p.R631W and p.S828L) in our EOPD cohort and tested them experimentally in cells. While expression of wild-type ATG9A was able to rescue the effects of miR-29a, the EOPD-associated variants behaved like loss-of-function mutations.Together, our study validates miR-29 and its target gene ATG9A as novel regulators of mitophagy initiation. It further serves as proof-of-concept of finding novel, potentially disease-causing EOPD-linked variants specifically in mitophagy regulating genes. The nomination of genetic variants and biological pathways is important for the stratification and treatment of patients that suffer from devastating diseases, such as EOPD.