bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating cell-free chromatin using preclinical models for cancer-specific biomarker discovery
Authors: De Michino Steven D. , Main Sasha C. , Penny Lucas , Kridel Robert , Cescon David W. , Hoffman Michael M. , Lupien Mathieu , Bratman Scott V. 
Published: November 2023

ABSTRACTCell-free chromatin (cf-chromatin) is a rich source of biomarkers across various conditions, including cancer. Tumor-derived circulating cf-chromatin can be profiled for epigenetic features, including nucleosome positioning and histone modifications that govern cell type-specific chromatin conformations. However, the low fractional abundance of tumor-derived cf-chromatin in blood and constrained access to plasma samples pose challenges for epigenetic biomarker discovery. Conditioned media from preclinical tissue culture models could provide an unencumbered source of pure tumor-derived cf-chromatin, but large cf-chromatin complexes from such models do not resemble the nucleosomal structures found predominantly in plasma, thereby limiting the applicability of many analysis techniques. Here, we developed a robust and generalizable framework for simulating cf-chromatin with physiologic nucleosomal distributions using an optimized nuclease treatment. We profiled the resulting nucleosomes by whole genome sequencing and confirmed that inferred nucleosome positioning reflected gene expression and chromatin accessibility patterns specific to the cell type. Compared with plasma, simulated cf-chromatin displayed stronger nucleosome positioning patterns at genomic locations of accessible chromatin from patient tissue. We then utilized simulated cf-chromatin to develop methods for genome-wide profiling of histone post-translational modifications associated with heterochromatin states. Cell-free chromatin immunoprecipitation and sequencing (cf-ChIP-Seq) of H3K27me3 identified heterochromatin domains associated with repressed gene expression, and when combined with H3K4me3 cfChIP-Seq revealed bivalent domains consistent with an intermediate state of transcriptional activity. Combining cfChIP-Seq of both modifications provided more accurate predictions of transcriptional activity from the cell of origin. Altogether, our results demonstrate the broad applicability of preclinical simulated cf-chromatin for epigenetic liquid biopsy biomarker discovery.
PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation
Authors: Hu Mengwen , Yeh Yu-Han , Maezawa So , Nakagawa Toshinori , Yoshida Shosei , Namekawa Satoshi H. 
Published: November 2023

AbstractSpermatogonial stem cell functionality resides in the slow-cycling and heterogeneous undifferentiated spermatogonia cell population. This pool of cells supports lifelong fertility in adult males by balancing self-renewal and differentiation to produce haploid gametes. However, the molecular mechanisms underpinning long-term stemness of undifferentiated spermatogonia during adulthood remain unclear. Here, we discover that an epigenetic regulator, Polycomb repressive complex 1 (PRC1), shields adult undifferentiated spermatogonia from differentiation, maintains slow cycling, and directs commitment to differentiation during steady-state spermatogenesis in adults. We show that PRC2-mediated H3K27me3 is an epigenetic hallmark of adult undifferentiated spermatogonia. Indeed, spermatogonial differentiation is accompanied by a global loss of H3K27me3. Disruption of PRC1 impairs global H3K27me3 deposition, leading to precocious spermatogonial differentiation. Therefore, PRC1 directs PRC2-H3K27me3 deposition to maintain the self-renewing state of undifferentiated spermatogonia. Importantly, in contrast to its role in other tissue stem cells, PRC1 negatively regulates the cell cycle to maintain slow cycling of undifferentiated spermatogonia. Our findings have implications for how epigenetic regulators can be tuned to regulate the stem cell potential, cell cycle, and differentiation to ensure lifelong fertility in adult males.
Toxoplasma gondiiharbors a hypoxia-responsive coproporphyrinogen dehydrogenase-like protein
Authors: Key Melanie , Baptista Carlos Gustavo , Bergmann Amy , Floyd Katherine , Blader Ira J. , Dou Zhicheng 
Published: November 2023

ABSTRACTToxoplasma gondiiis an apicomplexan parasite that is the cause of toxoplasmosis, a potentially lethal disease for immunocompromised individuals. Duringin vivoinfection, the parasites encounter various growth environments, such as hypoxia. Therefore, the metabolic enzymes in the parasites must adapt to such changes to fulfill their nutritional requirements.Toxoplasmacande novobiosynthesize some nutrients, such as heme. The parasites heavily rely on their own heme production for intracellular survival. Notably, the antepenultimate step within this pathway is facilitated by coproporphyrinogen III oxidase (CPOX), which employs oxygen to convert coproporphyrinogen III to protoporphyrinogen IX through oxidative decarboxylation. Conversely, some bacteria can accomplish this conversion independently of oxygen through coproporphyrinogen dehydrogenase (CPDH). Genome analysis found a CPDH ortholog inToxoplasma. The mutantToxoplasmalacking CPOX displays significantly reduced growth, implying that TgCPDH potentially functions as an alternative enzyme to perform the same reaction as CPOX under low oxygen conditions. In this study, we demonstrated that TgCPDH exhibits coproporphyrinogen dehydrogenase activity by complementing it in a heme synthesis-deficientSalmonellamutant. Additionally, we observed an increase in TgCPDH expression inToxoplasmawhen it grew under hypoxic conditions. However, deletingTgCPDHin both wildtype and heme-deficient parasites did not alter their intracellular growth under both ambient and low oxygen conditions. This research marks the first report of a coproporphyrinogen dehydrogenase-like protein in eukaryotic cells. Although TgCPDH responds to hypoxic conditions and possesses enzymatic activity, our findings suggest that it does not directly affect intracellular infection or the pathogenesis ofToxoplasmaparasites.IMPORTANCEToxoplasma gondiiis a ubiquitous parasite capable of infecting a wide range of warm-blooded hosts, including humans. During its lifecycle, these parasites must adapt to varying environmental conditions, including situations with low oxygen levels. Our research, in conjunction with studies conducted by other laboratories, has revealed thatToxoplasmaprimarily relies on its own heme production during acute infections. Intriguingly, in addition to this classical heme biosynthetic pathway, the parasites encode a putative oxygen-independent coproporphyrinogen dehydrogenase, suggesting its potential contribution to heme production under varying oxygen conditions, a feature typically observed in simpler organisms like bacteria. Notably, so far, coproporphyrinogen dehydrogenase has only been identified in some bacteria for heme biosynthesis. Our study discovered thatToxoplasmaharbors a functional enzyme displaying coproporphyrinogen dehydrogenase activity, which alters its expression in the parasites when they face fluctuating oxygen levels in their surroundings.
Following the p63/Keratin5 Basal Cells in the Sensory and Non-sensory Epithelia of The Vomeronasal Organ
Authors: LeFever Noah M. , Katreddi Raghu Ram , Dolphin Nikki M. , Mathias Nick A. , Forni Paolo E. 
Published: November 2023

AbstractThe Vomeronasal organ (VNO) is a part of the accessory olfactory system, which is responsible for detecting pheromones, chemical factors that trigger a spectrum of sexual and social behaviors. The vomeronasal epithelium (VNE) shares several features with the epithelium of the main olfactory epithelium (MOE). However, it is a distinct neuroepithelium populated by chemosensory neurons that differ from the olfactory sensory neurons (OSNs) in cellular structure, receptor expression, and connectivity.The vomeronasal organ of rodents comprises a sensory epithelium and a thin non-sensory epithelium that morphologically resembles the respiratory epithelium.Sox2-positive cells have been previously identified as the stem cell population that gives rise to neuronal progenitors in MOE and VNE. In addition to these, the MOE also comprises p63 positive horizontal basal cells (HBCs), a second pool of quiescent stem cells that become active in response to injury.Immunolabeling against the transcription factor p63, Keratin-5 (Krt5), Krt14 and Krt5Cre tracing experiments highlighted the existence of horizontal basal cells distributed along the basal lamina of the VNO forming from progenitors along the basal lamina of the marginal zones. Moreover, these experiments revealed that the NSE of rodents is, like the respiratory epithelium, a stratified epithelium where the p63/Krt5+ basal cells self-replicate and give rise to the apical columnar cells facing the lumen of the VNO.
A non-invasive method to sample immune cells in the lower female genital tract using menstrual discs
Authors: Quinn Peters M. , Domenjo-Vila Eva , Carlson Marc , Armistead Blair , Edlefsen Paul T. , Gasper Melanie , Dabee Smritee , Whidbey Christopher , Jaspan Heather B. , Prlic Martin , Harrington Whitney E. 
Published: November 2023

ABSTRACTT cells in the human female genital tract (FGT)2are key mediators of susceptibility to and protection from infection, including HIV and other sexually transmitted infections. There is a critical need for increased understanding of the distribution and activation of T cell populations in the FGT, but current sampling methods require a healthcare provider and are expensive, limiting the ability to study these populations longitudinally. To address these challenges, we have developed a method to sample immune cells from the FGT utilizing disposable menstrual discs which are non-invasive, self-applied, and low-cost. To demonstrate reproducibility, we sampled the cervicovaginal fluid (CVF)3of healthy, reproductive-aged individuals using menstrual discs over three sequential days. CVF was processed for cervicovaginal cells, and high parameter flow cytometry was used to characterize immune populations. We identified large numbers of live, CD45+ leukocytes, as well as distinct populations of T cells and B cells. Within the T cell compartment, activation and suppression status of T cell subsets were consistent with previous studies of the FGT utilizing current approaches, including identification of both tissue resident and migratory populations. In addition, the T cell population structure was highly conserved across days within individuals but divergent across individuals. Our approach to sample immune cells in the FGT with menstrual discs will decrease barriers to participation and empower longitudinal sampling in future research studies.
DNA from non-viable bacteria biases diversity estimates in the coralsAcropora loripesandPocillopora acuta
Authors: Dungan Ashley M. , Geissler Laura , Williams Amanda , Gotze Cecilie Ravn , Flynn Emily C. , Blackall Linda L. , van Oppen Madeleine J. H. 
Published: November 2023

AbstractBackgroundNucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.ResultsBy combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes,A. millepora,A. kenti,Platygyra daedalea,Pocillopora acuta, andPorites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue forA. loripesonly. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, >30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples forA. loripesandP. acutaindicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.ConclusionsOur study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
CRF release from a unique subpopulation of accumbal neurons constrains action-outcome acquisition in reward learning
Authors: Eckenwiler Elizabeth A. , Ingebretson Anna E. , Stolley Jeffrey J. , Fusaro Maxine A. , Romportl Alyssa M. , Ross Jack M. , Petersen Christopher L. , Kale Eera M. , Clark Michael S. , Schattauer Selena S. , Zweifel Larry S. , Lemos Julia C. 
Published: November 2023

AbstractBackgroundThe nucleus accumbens (NAc) mediates reward learning and motivation. Despite an abundance of neuropeptides, peptidergic neurotransmission from the NAc has not been integrated into current models of reward learning. The existence of a sparse population of neurons containing corticotropin releasing factor (CRF) has been previously documented. Here we provide a comprehensive analysis of their identity and functional role in shaping reward learning.MethodsTo do this, we took a multidisciplinary approach that included florescent in situ hybridization (Nmice≥ 3), tract tracing (Nmice= 5), ex vivo electrophysiology (Ncells≥ 30), in vivo calcium imaging with fiber photometry (Nmice≥ 4) and use of viral strategies in transgenic lines to selectively delete CRF peptide from NAc neurons (Nmice≥ 4). Behaviors used were instrumental learning, sucrose preference and spontaneous exploration in an open field.ResultsHere we show that the vast majority of NAc CRF-containing (NAcCRF) neurons are spiny projection neurons (SPNs) comprised of dopamine D1-, D2- or D1/D2-containing SPNs that primarily project and connect to the ventral pallidum and to a lesser extent the ventral midbrain. As a population, they display mature and immature SPN firing properties. We demonstrate that NAcCRFneurons track reward outcomes during operant reward learning and that CRF release from these neurons acts to constrain initial acquisition of action-outcome learning, and at the same time facilitates flexibility in the face of changing contingencies.ConclusionWe conclude that CRF release from this sparse population of SPNs is critical for reward learning under normal conditions.
Intervention Characteristics and Mechanisms and their Relationship with the Influence of Social Prescribing: a Systematic Review
Authors: Dubbeldeman Eveline M. , Kiefte-de Jong Jessica C. , Ardesch Frank H. , Boelens Mirte , van der Velde Laura A. , van der Steen Sophie G.L. , Heijnders Miriam L. , Crone Mathilde R. 
Published: November 2023

AbstractIntroductionSocial Prescribing (SP) is an integrated care program aimed to improve individuals’ health and wellbeing. Understanding the influence of SP and determining best practices and processes is challenging due to variability in its delivery, implementation, and intervention characteristics between different studies and countries. This study aimed to identify the intervention characteristics, mechanisms, and outcomes associated with SP research, and explore how these factors relate to the influence of SP on health and wellbeing, healthcare utilization, and care experiences.MethodA comprehensive search was conducted in 12 databases, Google Scholar, and reference lists of relevant studies published from January 2010 up to April 2023. Searches were limited to literature written in English or Dutch. The methodological quality of the included studies was assessed using the Mixed Methods Appraisal Tool and the risk of bias was evaluated using the Cochrane RoB2 and the ROBINS-I. We coded all intervention characteristics, mechanisms, and relevant outcomes. Qualitative data were visually presented using Harvest Plots and qualitative data were narratively summarized.Results and discussionIn total, 49 papers were included, of which seven qualitative, seventeen quantitative, and 25 mixed method studies. Moreover, the findings highlights the importance of social-related mechanisms, including loneliness and social connectedness, in contributing to the observed positive influence of SP on mental health and wellbeing. The observed outcomes seem to be influenced by various characteristics, including gender, age, the presence of a link worker, and the use of behavior change techniques. However, we should be cautious when interpreting these results due to limitations in study designs, such as the lack of controlled trials and statistical considerations. Further rigorous research is needed to comprehensively understand the impact and potential benefits of SP.
Brain signaling becomes less integrated and more segregated with age
Authors: Razban Rostam M , Antal Botond B , Dill Ken A , Mujica-Parodi Lilianne R 
Published: November 2023

ABSTRACTThe integration-segregation framework is a popular first step to understand brain dynamics because it simplifies brain dynamics into two states based on global vs. local signaling patterns. However, there is no consensus for how to best define what the two states look like. Here, we map integration and segregation to order and disorder states from the Ising model in physics to calculate state probabilities,PintandPseg, from functional MRI data. We find that integration/segregation decreases/increases with age across three databases, and changes are consistent with weakened connection strength among regions rather than topological connectivity based on structural and diffusion MRI data.AUTHOR SUMMARYThe integration-segregation framework succinctly captures the tradeoff brains face between seamless function (more integration) in light of energetic constrains (more segregation). Despite its ubiquitous use in the field, there is no consensus on its definition with various graph theoretical properties being proposed. Here, we define the two states based on the underlying mechanism of neuronal coupling strength to provide a physical foundation for the framework. We find that younger adults’ brains are close to perfectly balancing between integration and segregation, while older adults’ brains veer off towards random signaling.
An NMR-guided approach for identifying co-factors in boosting the Pfu DNA polymerase
Authors: Chen Yihao , Zhu Mingjun , Zhao Xiaoling , Tao Zhiqing , Xiang Dan , Zhang Xu , Liu Maili , He Lichun 
Published: November 2023

ABSTRACTWith rapid developments of emerging technologies like synthetic biology, the demand for DNA polymerases with superior activities including higher thermostability and processivity has increased significantly. Thus, rational optimization of the performance of DNA polymerase is of great interest. Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique used for studying protein structure and dynamics. It provides the atomic resolution information of enzymes under its functional solution environment to reveal the active sites (hot spots) of the enzyme, which could be further used for optimizing the performance of enzymes. Here we applied NMR spectroscopy to determine hot spots of the Pfu polymerase. Employing these hot spots as probes, two new co-factors, the heat shock protein TkHSP20 fromThermococcus Kodakaraensisand the chemical chaperone L-arginine, are identified to interact with Pfu polymerase to boost its performance in amplifying long DNA fragments by enhancing the thermal stability and the processivity of the Pfu polymerase. This NMR-guided approach requires no prior assignment information of target enzymes, simplifying the exploration of novel co-factors for Pfu polymerase. Moreover, our approach is not dependent on structural data or bioinformatics. Therefore, it has significant potential for application in various enzymes to expedite the progress in enzyme engineering.GRAPHICAL ABSTRACT
Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion
Authors: Plunder Steffen , Danesin Cathy , Glise Bruno , Ferreira Marina A. , Aceituno Sara Merino , Theveneau Eric 
Published: November 2023

AbstractEpithelial-Mesenchymal Transition (EMT) is a key process in physiological and pathological settings (i.e. development, fibrosis, cancer). EMT is often presented as a linear sequence of events including (i) disassembly of cell-cell junctions, (ii) loss of epithelial polarity and (iii) reorganization of the cytoskeleton leading to basal extrusion from the epithelium. Once out, cells can adopt a migratory phenotype with a front-rear polarity and may additionally become invasive. While this stereotyped sequence can occur, many in vivo observations have challenged this notion. It is now accepted that there are multiple EMT scenarios and that cell populations implementing EMT are often heterogeneous. However, the relative importance of each EMT step towards extrusion is unclear. Similarly, the overall impact of variability and heterogeneity on the efficiency and directionality of cell extrusion has not been assessed. Here we used computational modelling of a pseudostratified epithelium to model multiple EMT-like scenarios. We confronted these in silico data to the EMT occurring during neural crest delamination. Overall, our simulated and biological data point to a key role of nuclear positioning and protrusive activity to generate timely basal extrusion of cells and suggest a non-linear model of EMT allowing multiple scenarios to co-exist.
Whole organism and tissue specific analysis of pexophagy inDrosophila
Authors: Barone Francesco G. , Marcello Marco , Urbé Sylvie , Sanchez-Soriano Natalia , Clague Michael J. 
Published: November 2023

AbstractPeroxisomes are essential organelles involved in critical metabolic processes in animals such as fatty acid oxidation, ether phospholipid production and reactive oxygen species detoxification. We have generated transgenicDrosophila melanogastermodels expressing fluorescent reporters for the selective autophagy of peroxisomes, a process known as pexophagy. Using light sheet microscopy, we have been able to obtain a global overview of pexophagy levels, across the entire organism at different stages of development. Tissue specific control of pexophagy is exemplified by areas of peroxisome abundance but minimal pexophagy observed in clusters of oenocytes, which are the major site of long chain fatty acid synthesis. They are surrounded by epithelial cells where pexophagy is much more evident. Enhancement of pexophagy was achieved by feeding flies with the iron chelator deferiprone, in line with past results using mammalian cells. Specific drivers were used to visualise pexophagy in neurons, in which we tested the role of two proteins proposed to regulate pexophagy. Firstly, depletion of CG8814, theDrosophilahomologue of the yeast protein Atg37, had no noticeable impact on pexophagy. In contrast, specific depletion in the larval central nervous system of Hsc70-5, theDrosophilahomologue of the chaperone HSPA9/Mortalin, led to a substantial elevation in pexophagy.