bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Human iPSC-derived Organoid System to Model Myelin Destruction and Repair
Authors: Ramesan Shwathy , Mason Joel , Swanson Molly E.V. , Mills Samuel , Turner Bradley J. , Rutar Matthew , Gonsalvez David G. , Barton Samantha K. 
Published: May 2024

AbstractWe engineered a novel human iPSC-derived organoid system enriched with mature, myelinating oligodendrocytes and functionally reactive microglia. This model enables the study of human CNS remyelination following a demyelinating insult, encapsulating: myelin fragmentation, microglial clearance of myelin debris and oligodendrocyte genesis, differentiation, and axon ensheathment. This system provides a powerful and unparalleled capacity to interrogate complex human cell behaviour, relevant to those studying glial biology and neurological disease mechanisms.
The human and mouse dendritic cell receptor DCIR binds to LRP1 N-glycans containing terminal galactoses, including the α-Gal antigen
Authors: Raymond Benjamin B. A. , Sneperger Tamara , Rousset Stella , Gilles Nelly , Bally Aurélie , Stella Alexandre , Hipgrave Ederveen Agnes L. , Marcoux Julien , Trimaglio Giulia , Thépaut Michel , Lagarrigue Frederic , Burlet-Schiltz Odile , Wuhrer Manfred , Fieschi Franck , Demange Pascal , Neyrolles Olivier , Rombouts Yoann 
Published: May 2024

SUMMARYThe dendritic cell immunoreceptor (DCIR) is a C-type lectin receptor expressed by myeloid cells that plays a key immunoregulatory role in a wide range of diseases, from inflammation to cancer. However, the ligand(s) of DCIR remain(s) unknown, hampering our understanding of the exact function of this immune receptor. Here, we found that both human DCIR and mouse DCIR1 bind specifically to the low-density lipoprotein receptor-related protein 1 (LRP1), a heavily glycosylated receptor mediating the clearance of various molecules from the extracellular matrix and apoptotic cells. This interaction is mediated by galactose-terminated biantennary complex-type N-glycans, including those carrying the immunogenic α-Gal epitope. Our study provides a deeper understanding of the role of DCIR in immune regulation and its potential impact on a range of immune disorders, highlighting its specificity in ligand recognition which is crucial for developing therapeutic strategies.
Rtf1 HMD domain facilitates global histone H2B monoubiquitination and regulates morphogenesis and virulence in the meningitis-causing pathogenCryptococcus neoformans
Authors: Jiang Yixuan , Liang Ying , Zhao Fujie , Lu Zhenguo , Wang Siyu , Meng Yao , Liu Zhanxiang , Zhang Jing , Zhao Youbao 
Published: May 2024

AbstractRtf1 is generally considered to be a subunit of the Paf1 complex (Paf1C), which is a multifunctional protein complex involved in histone modification and RNA biosynthesis at multiple stages. Rtf1 is stably associated with the Paf1C inSaccharomyces cerevisiae, but not in other species including humans. Little is known about its function in human fungal pathogens. Here, we show that Rtf1 is required for facilitating H2B monoubiquitination (H2Bub1), and regulates fungal morphogenesis and pathogenicity in the meningitis-causing fungal pathogenCryptococcus neoformans. Rtf1 is not tightly associated with the Paf1C, and its histone modification domain (HMD) is sufficient to promote H2Bub1 and the expression of genes related to fungal mating and filamentation. Moreover, Rtf1 HMD fully restores fungal morphogenesis and pathogenicity; however, it fails to restore defects of thermal tolerance and melanin production in thertf1Δ strain background. The present study establishes a role for cryptococcal Rtf1 as a Paf1C-independent regulator in regulating fungal morphogenesis and pathogenicity, and highlights the function of HMD in facilitating global H2Bub1 inC. neoformans.
The Peptonizer2000: bringing confidence to metaproteomics
Authors: Holstein Tanja , Verschaffelt Pieter , Van Den Bossche Tim , Van de Vyver Simon , Martens Lennart , Mesuere Bart , Muth Thilo 
Published: May 2024

AbstractMetaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available datasets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities.
A PARP2-specific active site α-helix melts to permit DNA damage-induced enzymatic activation
Authors: Smith-Pillet Emily S. , Billur Ramya , Langelier Marie-France , Talele Tanaji T. , Pascal John M. , Black Ben E. 
Published: May 2024

SummaryPARP1 and PARP2 recognize DNA breaks immediately upon their formation, generate a burst of local PARylation to signal their location, and are co-targeted by all current FDA-approved forms of PARP inhibitors (PARPi) used in the cancer clinic. Recent evidence indicates that the same PARPi molecules impact PARP2 differently from PARP1, raising the possibility that allosteric activation may also differ. We find that unlike for PARP1, destabilization of the autoinhibitory domain of PARP2 is insufficient for DNA damage-induced catalytic activation. Rather, PARP2 activation requires further unfolding of an active site α-helix absent in PARP1. Only one clinical PARPi, Olaparib, stabilizes the PARP2 active site α-helix, representing a structural feature with the potential to discriminate small molecule inhibitors. Collectively, our findings reveal unanticipated differences in local structure and changes in activation-coupled backbone dynamics between PARP1 and PARP2.
Identification of Small Molecule Inhibitors of PPM1D Using a Novel Drug Discovery Platform
Authors: Jiang Wei , Shaw Subrata , Rush Jason , Dumont Nancy , Kim John , Singh Ritu , Skepner Adam , Khodier Carol , Raffier Cerise , Yan Ni , Schluter Cameron , Yu Xiao , Szuchnicki Mateusz , Sathappa Murugappan , Kahn Josephine , Sperling Adam S. , McKinney David C. , Gould Alexandra E. , Garvie Colin W. , Miller Peter G. 
Published: May 2024

ABSTRACTProtein phosphatase, Mg2+/Mn2+dependent 1D (PPM1D), is a serine/threonine phosphatase that is recurrently activated in cancer, regulates the DNA damage response (DDR), and suppresses the activation of p53. Consistent with its oncogenic properties, genetic loss or pharmacologic inhibition of PPM1D impairs tumor growth and sensitizes cancer cells to cytotoxic therapies in a wide range of preclinical models. Given the therapeutic potential of targeting PPM1D specifically and the DDR and p53 pathway more generally, we sought to deepen our biological understanding of PPM1D as a drug target and determine how PPM1D inhibition differs from other therapeutic approaches to activate the DDR. We performed a high throughput screen to identify new allosteric inhibitors of PPM1D, then generated and optimized a suite of enzymatic, cell-based, andin vivopharmacokinetic and pharmacodynamic assays to drive medicinal chemistry efforts and to further interrogate the biology of PPM1D. Importantly, this drug discovery platform can be readily adapted to broadly study the DDR and p53. We identified compounds distinct from previously reported allosteric inhibitors and showedin vivoon-target activity. Our data suggest that the biological effects of inhibiting PPM1D are distinct from inhibitors of the MDM2-p53 interaction and standard cytotoxic chemotherapies. These differences also highlight the potential therapeutic contexts in which targeting PPM1D would be most valuable. Therefore, our studies have identified a series of new PPM1D inhibitors, generated a suite ofin vitroandin vivoassays that can be broadly used to interrogate the DDR, and provided important new insights into PPM1D as a drug target.
Synthetic Genitourinary Image Synthesis via Generative Adversarial Networks: Enhancing AI Diagnostic Precision
Authors: Van Booven Derek J , Chen Cheng-Bang , Malpani Sheetal , Mirzabeigi Yasamin , Mohammadi Maral , Wang Yujie , Arora Himanshu 
Published: May 2024

AbstractIn the realm of computational pathology, the scarcity and restricted diversity of genitourinary (GU) tissue datasets pose significant challenges for training robust diagnostic models. This study explores the potential of Generative Adversarial Networks (GANs) to mitigate these limitations by generating high-quality synthetic images of rare or underrepresented GU tissues. We hypothesized that augmenting the training data of computational pathology models with these GAN-generated images, validated through pathologist evaluation and quantitative similarity measures, would significantly enhance model performance in tasks such as tissue classification, segmentation, and disease detection. To test this hypothesis, we employed a GAN model to produce synthetic images of eight different GU tissues. The quality of these images was rigorously assessed using a Relative Inception Score (RIS) of 17.2 ± 0.15 and a Fréchet Inception Distance (FID) that stabilized at 120, metrics that reflect the visual and statistical fidelity of the generated images to real histopathological images. Additionally, the synthetic images received an 80% approval rating from board-certified pathologists, further validating their realism and diagnostic utility. We used an alternative Spatial Heterogeneous Recurrence Quantification Analysis (SHRQA) to assess quality in prostate tissue. This allowed us to make a comparison between original and synthetic data in the context of features, which were further validated by the pathologist’s evaluation. Future work will focus on implementing a deep learning model to evaluate the performance of the augmented datasets in tasks such as tissue classification, segmentation, and disease detection. This will provide a more comprehensive understanding of the utility of GAN-generated synthetic images in enhancing computational pathology workflows. This study not only confirms the feasibility of using GANs for data augmentation in medical image analysis but also highlights the critical role of synthetic data in addressing the challenges of dataset scarcity and imbalance. Future work will focus on refining the generative models to produce even more diverse and complex tissue representations, potentially transforming the landscape of medical diagnostics with AI-driven solutions.CONSENT FOR PUBLICATIONAll authors have provided their consent for publication.
Loss of glia-neuronal interactions and age-dependent cell death in aDrosophilamodel of adult neurodegeneration
Authors: Jhuti Unmila P. , Blumenthal Edward M. 
Published: May 2024

AbstractWhile glial dysfunction has been implicated in the development of multiple neurodegenerative diseases, the role of glial cell morphology in neurodegeneration is underexplored. In the fruit flyDrosophila melanogaster, mutants of the genedrop-dead(drd) exhibit adult neurodegeneration and extremely short lifespans. The morphology of one class of glia, the cortex glia (CG), is abnormal indrdmutants. In controls, the CGs form a continuous network that wraps around all neuronal cell bodies, but indrdmutants, individual CGs are stunted and the CG network is disrupted. These phenotypes are present on the first day of adulthood. Apoptosis is the central mechanism of cell death indrdmutants; widespread cell death is observed on the first day of adulthood and increases with age and is primarily neuronal. Apoptotic cells are found both within and outside of the remaining CG network, with significant variation in the distribution among individual brains. The degree of cell death and CG network breakdown in young adults could explain whydrdmutant flies die within the first week of adulthood. TheDrosophila drdmutant is a unique model of adult neurodegeneration that provides new insight into the breakdown in interaction between glia and neuronal cell bodies.
L-Dopa incorporation into tubulin alters microtubule dynamics and reduces dendritic spine invasion and synapse maintenance
Authors: Zorgniotti Agustina , Sharma Aditi , Ramirez-Rios Sacnicte , Sanyal Chadni , Aleman Martina , Ditamo Yanina , Moutin Marie-Jo , Bisig C. Gastón , Peris Leticia 
Published: May 2024

ABSTRACTPrevious studies have shown that L-Dopa, a tyrosine analog used in Parkinson’s disease treatment, can be incorporated into α-tubulin C-terminal tail via the tubulin tyrosine ligase (TTL) and polymerize into microtubules. In this work, we demonstrated that mature wild type hippocampal neurons treated with L-Dopa exhibited reduced dendritic spine density, primarily affecting mature dendritic spines. In these neurons, L-Dopa treatment significantly reduced tyrosinated α-tubulin levels without altering detyrosinated or Δ2 α-tubulin levels, suggesting the formation of a new tubulin pool, likely composed of L-Dopa-α-tubulin.In vitro analysis of the activity of the purified VASH1-SVBP complex, the most abundant tubulin carboxypeptidase in brain, revealed that L-Dopa incorporation into α-tubulin modified the binding of the complex to microtubules and reduced its carboxypeptidase activity. These results suggest that L-Dopa incorporation into tubulin alters the properties of microtubules and affects their ability to interact with the enzyme.To confirm the implication of L-Dopa-microtubules in dendritic spine alterations observed in wild type neurons, we analyzed the effect of L-Dopa treatment in neurons lacking the enzymes of the α-tubulin detyrosination/tyrosination cycle. In these cells, L-Dopa cannot be incorporated into α-tubulin due to the absence of the ligase (in TTL KO neurons) or the reduction of detyrosinated α-tubulin levels (in SVBP KO neurons). L-Dopa treatment did not modify dendritic spine density in TLL KO or SVBP KO neurons, clearly demonstrating that the alterations in dendritic spines seen in WT neurons are due to the incorporation of L-Dopa into tubulin.Further analysis revealed that L-Dopa treatment decreased the percentage of spines containing excitatory synapses in wild type neurons, but not in TTL KO or SVBP KO neurons, suggesting a cumulative synaptic defect due to L-Dopa incorporation into microtubules. Additionally, L-Dopa altered microtubule dynamics by increasing catastrophe frequency and reducing comet lifetime, which led to fewer microtubules entering dendritic spines and decreased spine resistance to pruning.Taken together, our results demonstrate that L-Dopa incorporation into α-tubulin drastically affects synaptic homeostasis, reaffirming the importance of balanced detyrosination/tyrosination of tubulin within the synaptic compartment. The abnormal dynamics of L-Dopa-microtubules and the reduction of dendritic spines and excitatory synapses highlight a novel mechanism of L-Dopa-induced synaptotoxicity.
Acarbose Impairs GutBacteroidesGrowth by Targeting Intracellular GH97 Enzymes
Authors: Brown Haley A. , Morris Adeline L. , Pudlo Nicholas A. , Hopkins Ashley E. , Martens Eric C. , Golob Jonathan L. , Koropatkin Nicole M. 
Published: May 2024

AbstractAcarbose is a type-2 diabetes medicine that inhibits dietary starch breakdown into glucose by inhibiting host amylase and glucosidase enzymes. Numerous gut species in theBacteroidesgenus enzymatically break down starch and change in relative abundance within the gut microbiome in acarbose-treated individuals. To mechanistically explain this observation, we used two model starch-degradingBacteroides,Bacteroides ovatus(Bo) andBacteroides thetaiotaomicron(Bt). Bt growth is severely impaired by acarbose whereas Bo growth is not. TheBacteroidesuse a starch utilization system (Sus) to grow on starch. We hypothesized that Bo and Bt Sus enzymes are differentially inhibited by acarbose. Instead, we discovered that although acarbose primarily targets the Sus periplasmic GH97 enzymes in both organisms, the drug affects starch processing at multiple other points. Acarbose competes for transport through the Sus beta-barrel proteins and binds to the Sus transcriptional regulators. Further, Bo expresses a non-Sus GH97 (BoGH97D) when grown in starch with acarbose. The Bt homolog, BtGH97H, is not expressed in the same conditions, nor can overexpression of BoGH97D complement the Bt growth inhibition in the presence of acarbose. This work informs us about unexpected complexities of Sus function and regulation inBacteroides, including variation between related species. Further, this indicates that the gut microbiome may be a source of variable response to acarbose treatment for diabetes.ImportanceAcarbose is a type 2 diabetes medication that works primarily by stopping starch breakdown into glucose in the small intestine. This is accomplished by inhibition of host enzymes, leading to better blood sugar control via reduced ability to derive glucose from dietary starches. The drug and undigested starch travel to the large intestine where acarbose interferes with the ability of some bacteria to grow on starch. However, little is known about how gut bacteria interact with acarbose, including microbes that can use starch as a carbon source. Here, we show that two gut species,Bacteroides ovatus(Bo) andBacteroides thetaiotaomicron(Bt), respond differently to acarbose: Bt growth is inhibited by acarbose while Bo growth is not. We reveal a complex set of mechanisms involving differences in starch import and sensing behind the different Bo and Bt responses. This indicates the gut microbiome may be a source of variable response to acarbose treatment for diabetes via complex mechanisms in common gut microbes.
Asymmetry of both repressor and operator is important for the transcriptional regulation of theP. putidaXre-RES system
Authors: Henriksen Frederik Oskar G. , Brodersen Ditlev E. , Skjerning Ragnhild B. 
Published: May 2024

ABSTRACTTranscriptional regulation is a fundamental mechanism in bacteria and is often mediated by repressor proteins. In the type II toxin-antitoxin (TA) system.xre-res, the Xre antitoxin contains a putative helix-turn-helix (HTH) DNA-binding domain and could thus potentially bind to and repress transcription from thexre-respromoter. The structure of thePseudomonas putidaXre-RES TA complex revealed an unusual 4:2 stoichiometry with two potential DNA-binding sites, suggesting a non-canonical mechanism of transcriptional autoregulation. Here, we show that the activity of thexre-respromoter requires both an intact σ70element and the transcriptional start site, and that the Xre–RES complex represses transcription via binding to an imperfect inverted repeat region downstream of the σ70element. We furthermore confirm the presence of the unusual 4:2 TA complex in solution and show that it preferably binds the imperfect inverted repeat in a 1:1 ratio. In addition, we show that the isolated Xre antitoxin is an aggregation-prone monomerin vitroand a weak repressorin vivo.We find that the Xre dimer can dissociates within the 4:2 complex and result in a 2:2 TA complex that still neutralizes the RES toxin but cannot bind DNA. Together, our data suggests that the asymmetry of the promoter is important for both transcription and repression, and we propose a model in which the Xre-RES complex regulates transcription through a dynamic and concentration-dependent equilibrium between a non-binding (2:2) and a DNA-binding (4:2) form.IMPORTANCETranscriptional regulation is fundamental for bacteria to survive in a constantly changing environment and requires the RNA polymerase, which recognizes and binds to a DNA element (the promoter) located upstream of the gene and initiates transcription. Transcriptional repressors can bind DNA and inhibit transcription by the RNA polymerase, but the exact recognition of DNA binding sites remains unclear. The Xre antitoxin from thePseudomonas putidatoxin-antitoxin system Xre-RES contains a putative DNA-binding domain, and the unusual ratio of antitoxin to toxin within the protein complex suggests two potential DNA-binding sites. In this work, we show that Xre-RES auto-regulates its own transcription through an asymmetrical DNA binding-site, optimized to bind both the RNA polymerase and the Xre-RES complex, as well as a concentration-dependent ratio of toxin to antitoxin within the complex. Our work provides insight on how promoters can evolve to fine-tune the regulation of bacterial transcription.
A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection
Authors: Aquino Jelard , Witoslawski Daniel , Park Steve , Holder Jessica , Amei Amei , Han Mira V. 
Published: May 2024

AbstractThere are primarily two computational approaches to alternative splicing detection: splice junction-based and exon-based approaches. Despite their shared goal of addressing the same biological problem, these approaches have not been reconciled before. We devised a novel graph structure and algorithm aimed at mapping between the exonic parts and splicing events detected by the two different methods. Through simulations, we demonstrated disparities in sensitivity and specificity between splice junction-based and exon-based methods. When applied to empirical data, there were large discrepancies in the results, suggesting that the methods are complementary. With the discrepancies localized to individual events and exonic parts, we were able to gain insights into the strengths and weaknesses inherent in each approach. Finally, we integrated the results to generate a comprehensive list of both common and unique alternative splicing events detected by both methodologies.Availabilityhttps://github.com/HanLabUNLV/GrASEContactmira.han@unlv.eduSupplementary informationSupplementary data are available online.
The Prefrontal Cortex to the Hippocampus Glutamatergic Pathway Regulates Reward Effects of Methamphetamine
Authors: Zhao Dongdong , Shi Wenjing , Li Minyu , Xue Rui , Wang Hang , Zhang Le , Huang Mengbing , Bai Liping , Gu Rou , Li Ye , Zhang Xianwen , Kalivas Peter , Bai Jie 
Published: May 2024

AbstractMethamphetamine (METH) induces reward effects. The prefrontal cortex (PFC) plays a role in regulating top-down. The hippocampus is closely involved reward memory. However, the direct projects from the PFC to the hippocampus have not been studied well. Here, we use conditioned place preference (CPP), a recombinant adeno-associated virus 2/9 (rAAV2/9) and optogenetic approaches to explore a role in METH-CPP for a novel pathway projecting from the medial prefrontal prelimbic cortex (PrL) directly to the dorsal hippocampus CA1 (dCA1). Expressing CaMKIIα-ChR2 or CaMKIIα-eNpHR3.0 in the PrL and optically stimulating in the dCA1 blocks or enhances METH-CPP, respectively. Moreover, silencing the PrL to dCA1 glutamatergic pathway with tetanus neurotoxin (TeNT) enhances METH-CPP. These results identify a novel PrL-to-dCA1 glutamatergic pathway regulating METH-CPP.