bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Th17 cell-intrinsic glutathione/mitochondrial-IL-22 axis protects against intestinal inflammation
Authors: Bonetti Lynn , Horkova Veronika , Longworth Joseph , Guerra Luana , Kurniawan Henry , Franchina Davide G. , Soriano-Baguet Leticia , Grusdat Melanie , Spath Sabine , Koncina Eric , Ewen Anouk , Binsfeld Carole , Verschueren Charlène , Gérardy Jean-Jacques , Kobayashi Takumi , Dostert Catherine , Farinelle Sophie , Härm Janika , Chen Ying , Harris Isaac S. , Lang Philipp A. , Vasiliou Vasilis , Waisman Ari , Letellier Elisabeth , Becher Burkhard , Mittelbronn Michel , Brenner Dirk 
Published: July 2023

SummaryAlthough the intestinal tract is a major site of reactive oxygen species (ROS) generation, the mechanisms by which antioxidant defense in gut T cells contribute to intestinal homeostasis are currently unknown. Here we show, using T cell-specific ablation of the catalytic subunit of glutamate cysteine ligase (Gclc), that the ensuing loss of glutathione (GSH) impairs the production of gut-protective IL-22 by Th17 cells within the lamina propria. AlthoughGclcablation does not affect T cell cytokine secretion in the gut of mice at steady-state, infection withC. rodentiumincreases ROS, inhibits mitochondrial gene expression and mitochondrial function inGclc-deficient Th17 cells. These mitochondrial deficits affect the PI3K/AKT/mTOR pathway, leading to reduced phosphorylation of the translation repressor 4E-BP1. As a consequence, the initiation of translation is restricted, resulting in decreased protein synthesis of IL-22. Loss of IL-22 results in poor bacterial clearance, enhanced intestinal damage, and high mortality. ROS-scavenging, reconstitution of IL-22 expression or IL-22 supplementationin vivoprevent the appearance of these pathologies. Our results demonstrate the existence of a previously unappreciated role for Th17 cell-intrinsic GSH coupling to promote mitochondrial function, IL-22 translation and signaling. These data reveal an axis that is essential for maintaining the integrity of the intestinal barrier and protecting it from damage caused by gastrointestinal infection.Executive summary-GSH-regulated Th17 cell-derived IL-22, but not IL-17 is required to maintain intestinal barrier integrity and to revent lethality followingC. rodentiuminfection.-GCLCexpression in IBD patients correlates positively with expression of genes related to gut integrity.-Gclc-deficient Th17 cells accumulate mitochondrial ROS, which is linked to impaired mitochondrial function, ysregulated PI3K/AKT/mTOR signaling and impaired translation of IL-22.-ROS-scavenging, IL-22 reconstitution or T cell-specific expression of IL-22 inGclc-deficient T cells rescues utant mice from the lethal infection outcomein vivo.
Reusability Report: Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients
Authors: So Emily , Yu Fengqing , Wang Bo , Haibe-Kains Benjamin 
Published: July 2023

AbstractMachine learning (ML) and artificial intelligence (AI) methods are increasingly used in personalized medicine, including precision oncology. Ma et al. (Nature Cancer 2021) developed a new method c alled “Transfer of Cell Line Response Prediction” (TCRP) to train predictors of drug response in cancer cell lines and optimize their performance in higher complex cancer model systems via few-shot learning. TCRP was presented as a successful modeling approach in multiple case studies. Given the importance of this approach to assist clinicians in their treatment decision process, we sought to reproduce independently the authors’ findings and improve the reusability of TCRP in new case studies, including validation in clinical trial datasets, a high bar for drug response prediction. Our results support the superiority of TCRP over established statistical and machine learning approaches in preclinical and clinical settings. We developed new resources to increase the reusability of the TCRP model for future improvements and validation studies.
Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues
Authors: Caron Daniel P. , Specht William L. , Chen David , Wells Steven B. , Szabo Peter A. , Jensen Isaac J. , Farber Donna L. , Sims Peter A. 
Published: July 2023

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and dissecting transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins, as in cells of the immune system. Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell type annotation requires a classifier that integrates multimodal data. Here, we describeMultiModalClassifierHierarchy (MMoCHi), a marker-based approach for classification, reconciling gene and protein expression without reliance on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal novel subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.
Increasing Signal Intensity of Fluorescent Oligo-Labeled Antibodies to Enable Combination Multiplexing
Authors: McCarthy Madeline E. , Lu Xiaoming , Ogunleye Oluwaferanmi , Latham Danielle R. , Abravanel Megan , Pritko Daniel , Huggins Jonah R. , Haskell Charlotte V. , Patel Nishi D. , Pittman Zachariah A. , Sanabria Hugo , Birtwistle Marc R. 
Published: July 2023

AbstractFull-spectrum flow cytometry has increased antibody-based multiplexing, yet further increases remain potentially impactful. We recently proposed how fluorescence Multiplexing using Spectral Imaging and Combinatorics (MuSIC) could do so using tandem dyes and an oligo-based antibody labeling method. In this work, we found that such labeled antibodies had significantly lower signal intensity than conventionally-labeled antibodies in human cell experiments. To improve signal intensity, we tested moving the fluorophores from the original external (ext.) 5’ or 3’ end-labeled orientation to internal (int.) fluorophore modifications. Cell-free spectrophotometer measurements showed a ∼6-fold signal intensity increase of the new int. configuration compared to the previous ext. configuration. Time-resolved fluorescence and fluorescence correlation spectroscopy showed that ∼3-fold brightness difference is due to static quenching most likely by the oligo or solution in the ext. configuration. Spectral flow cytometry experiments using peripheral blood mononuclear cells show int. MuSIC probe-labeled antibodies (i) retained increased signal intensity while having no significant difference in the estimated % of CD8+ lymphocytes and (ii) labeled with Atto488, Atto647, and Atto488/647 combinations can be demultiplexed in triple-stained samples. The antibody labeling approach is general and can be broadly applied to many biological and diagnostic applications where spectral detection is available.
Heat Stress-induced Activation of MAPK Pathway Attenuates Atf1-dependent Epigenetic Inheritance of Heterochromatin in Fission Yeast
Authors: Sun Li , Wang Yamei , Jin Quan-wen 
Published: July 2023

ABSTRACTEukaryotic cells are constantly exposed to various environmental stimuli. It remains largely unexplored how environmental cues bring about epigenetic fluctuations and affect heterochromatin stability. In the fission yeastSchizosaccharomyces pombe, heterochromatic silencing is quite stable at pericentromeres but unstable at the mating-type (mat) locus under chronic heat stress, although both loci are within the major constitutive heterochromatin regions. Here, we found that the compromised gene silencing at thematlocus at elevated temperature is linked to the phosphorylation status of Atf1, a member of the ATF/CREB superfamily. Constitutive activation of MAPK signaling disrupts epigenetic maintenance of heterochromatin at thematlocus even under normal temperature. Mechanistically, phosphorylation of Atf1 impairs its interaction with heterochromatin protein Swi6HP1, resulting in lower site-specific Swi6HP1enrichment. Expression of non-phosphorylatable Atf1, tethering Swi6HP1to themat3M-flanking site or absence of the anti-silencing factor Epe1 can largely or partially rescue heat stress-induced defective heterochromatic maintenance at thematlocus.
Abscisic acid inhibits germination of Striga seeds and is released by them as a rhizospheric signal providing competitive advantage and supporting host infestation
Authors: Jamil Muhammad , Alagoz Yagiz , Wang Jian You , Chen Guan-Ting Erica , Berqdar Lamis , Kharbatia Najeh M. , Moreno Juan C. , Kuijer Hendrik N. J. , Al-Babili Salim 
Published: July 2023

SUMMARYSeeds of the root parasitic plantStriga hermonthicaundergo a conditioning process under humid and warm environments before germinating in response to host-released stimulants, particularly strigolactones (SLs). The plant hormone abscisic acid (ABA) regulates different growth and developmental processes, and stress response; however, its role during Striga seed germination and early interactions with host plants is under-investigated.Here, we show that ABA inhibited Striga seed germination and that hindering its biosynthesis induced conditioning and germination in unconditioned seeds, which was significantly enhanced by treatment with the SL analograc-GR24. However, the inhibitory effect of ABA remarkably decreased during conditioning, confirming the loss of sensitivity towards ABA in later developmental stages. ABA measurement showed a significant reduction of its content during the early conditioning stage and a significant increase uponrac-GR24-triggered germination. We observed this increase also in released seed exudates, which was further confirmed by using the Arabidopsis ABA-reporter GUS marker line.Seed exudates of germinated seeds, containing elevated levels of ABA, impaired the germination of surrounding Striga seedsin vitroand promoted root growth of a rice host towards germinated Striga seeds. Application of ABA as a positive control caused similar effects, indicating its function in Striga/Striga and Striga/host communications.In summary, we show that ABA is an essential player during seed dormancy and germination processes in Striga and acts as a rhizospheric signal released by germinated parasitic seeds to provide a competitive advantage and support host infestation.Societal Impact StatementThe root parasitic plantStriga hermonthicais a severe threat to cereal’s yield, endangering global food security. Herein, we uncover a new role of the known plant hormone abscisic acid (ABA) as a rhizospheric signal released by germinated Striga seeds, allowing them to better compete with surrounding un-conditioned seeds and facilitating host infestation. Our findings can help in developing strategies to control this parasite and mitigate its negative impact on the food supply and income of smallholder farmers.
Helicity of a tardigrade disordered protein promotes desiccation tolerance
Authors: Biswas Sourav , Gollub Edith , Yu Feng , Ginell Garrett , Holehouse Alex , Sukenik Shahar , Boothby Thomas C. 
Published: July 2023

AbstractIn order to survive extreme drying (anhydrobiosis), many organisms, spanning every kingdom of life, accumulate intrinsically disordered proteins (IDPs). For decades, the ability of anhydrobiosis-related IDPs to form transient amphipathic helices has been suggested to be important for promoting desiccation tolerance. However, evidence empirically supporting the necessity and/or sufficiency of helicity in mediating anhydrobiosis is lacking. Here we demonstrate that the linker region of CAHS D, a desiccation-related IDP from tardigrades that contains significant helical structure, is the protective portion of this protein. Perturbing the sequence composition and grammar of the linker region of CAHS D, through the insertion of helix-breaking prolines, modulating the identity of charged residues, sequence scrambling, or replacement of hydrophobic amino acids with serine or glycine residues results in variants with different degrees of helical structure. Importantly, the resulting helicity of these variants generated through similar helix breaking modalities correlates strongly with their ability to promote desiccation tolerance, providing direct evidence that helical structure is necessary for robust protection conferred by this desiccation-related IDP. However, correlation of protective capacity and helical content in variants generated through different helix perturbing modalities do not show as strong a trend, suggesting that while helicity is important it is not the only property that makes a protein protective during desiccation. These results provide direct evidence for the decades old theory that helicity of desiccation-related IDPs is linked to their anhydrobiotic capacity.
Allelic variation in the wheat homolog of topoisomeraseIIis associated with crossover rate
Authors: Jordan Katherine W. , Fernandez-de Soto Monica , Korol Abraham , Akhunova Alina , Akhunov Eduard 
Published: July 2023

AbstractMeiotic recombination is a fundamental biological process that impacts genetic diversity and response of variants to selection. The increase in crossover (CO) frequency by modulating the activity of meiotic genes has been suggested as potential means to improve the efficiency of selection and mitigate the negative impact of linkage drag in crop improvement programs. In this study, we used the wheat nested association mapping (NAM) population to map QTL associated with CO rate and harboringTaTOPII-A1, a gene encoding topoisomerase II that is involved in the regulation of meiosis. An amino acid changing SNP (T/C) located in exon 19 ofTaTOPII-A1with a predicted functional effect showed an association with CO rate. The T-allele ofTaTOPII-A1was associated with a statistically significant 5.9 % increase in COs across several NAM families. The involvement ofTaTOPII-A1in processes affecting CO rate in wheat was confirmed using aTaTOPII-A1mutant. A strong-effect missense mutation in theTaTOPII-A1coding region resulted in 1.4-fold increase in the genetic map length and 53% increase in CO rate compared to the wild-type allele. These results demonstrate that functional mutations inTaTOPII-A1can lead to increased CO frequency. The mutant and natural alleles ofTaTOPII-A1identified in our study could serve as new sources of recombination-promoting genes to manipulate CO rate in wheat and possibly other crops.
Functional Protein Dynamics in a Crystal
Authors: Klyshko Eugene , Kim Justin Sung-Ho , McGough Lauren , Valeeva Victoria , Lee Ethan , Ranganathan Rama , Rauscher Sarah 
Published: July 2023

AbstractProteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.
Massive RNA editing in ascetosporean mitochondria
Authors: Yabuki Akinori , Fujii Chihaya , Yazaki Euki , Tame Akihiro , Mizuno Keiko , Obayashi Yumiko , Takao Yoshitake 
Published: July 2023

AbstractAscetosporeans are parasitic protists of invertebrates. As only two species of Mikrocytida, an ascetosporean subgroup, have ever been sequenced deeply and analyzed using cells isolated from infected organisms, it was shown that their mitochondria are functionally reduced and the organellar genome is lacking. However, molecular studies on other ascetosporeans have not been conducted, and whether reduced mitochondria is common in ascetosporeans remains unclear. In the present study, we established two cultures of Paradinida, another ascetosporean subgroup, and reconstructed their mitochondrial genomes. As they were compared with their RNA-seq data, massive A-to-I and C-to-U types of RNA editing were detected. Many editing sites are shared between two paradinids, but strain-unique sites also exist. As the mitochondrial genes are involved in the electron transfer system, their mitochondria are not functionally reduced, unlike that in Mikrocytida. Furthermore, we detected adenosine deaminase acting on RNA (ADAR), which is a key enzyme of A-to-I substitution, in paradinids as well as several other protists. Immunostaining showed that this ADAR is specifically localized in the mitochondria of paradinids, suggesting that A-to-I substitution in paradinid mitochondria is mediated by ADAR. These findings elucidated the functional diversity and evolutionary process of ascetosporean mitochondria as well as ADAR.
Neuropathic pain has sex-specific effects on oxycodone seeking and drug-seeking ensembles in the dorsomedial prefrontal cortex
Authors: Sarka Bailey C. , Liu Shuai , Banerjee Anjishnu , Stucky Cheryl L. , Liu Qing-song , Olsen Christopher M. 
Published: July 2023

AbstractApproximately 50 million Americans suffer from chronic pain, and opioids are commonly prescribed for such individuals. Unfortunately, nearly a quarter of chronic pain patients have reported misusing their prescription. We are investigating the effect of chronic pain on drug-seeking behavior at the neuronal level. Repeated drug-seeking is associated with reactivation of an ensemble of neurons sparsely scattered throughout the dorsomedial prefrontal cortex (dmPFC). Prior research has demonstrated that chronic pain increases intrinsic excitability of dmPFC neurons, which may increase the likelihood of reactivation during drug seeking. We tested the hypothesis that chronic pain would increase oxycodone seeking behavior, and that the pain state would differentially increase intrinsic excitability in dmPFC drug seeking ensemble neurons. TetTag mice self-administered intravenous oxycodone. After 7 days of forced abstinence, a drug seeking session (extinction conditions) was performed and the ensemble was tagged. Mice received spared nerve injury (SNI) to induce chronic pain during the period between a first and second seeking session, and we measured persistence of seeking between the two sessions to determine if the SNI exacerbated seeking. Following the second seeking session we performed electrophysiology on individual neurons within the dmPFC to assess intrinsic excitability of the drug-seeking ensemble and non-ensemble neurons. We found significant sex differences in the effect of SNI on oxycodone seeking and electrophysiology, such that the induction of chronic pain could modulate seeking behavior in mice that have previously self-administered oxycodone prior to injury.HighlightsOxycodone seeking was higher in females following SNI that cameafterthe 10-day SA timeline.An increase in intrinsic excitability was detected among non-ensemble neurons from female mice that received SNI, and this correlated with an increase in seeking behavior.
Calcimycin mediates apoptosis in Breast and Cervical cancer cells by inducing intracellular calcium levels in a P2RX4-dependent manner
Authors: Neha  , Ranjan Prashant , Das Parimal 
Published: July 2023

AbstractCalcimycin (A23187) is a polyether antibiotic and divalent cation ionophore, extracted fromStreptomyces chartrecensis. With wide variety of antimicrobial activities, it also exhibits cytotoxicity of tumor cells. Calcimycin exhibit therapeutic potential against tumor cell growth; however, the molecular mechanism remains to be fully elucidated. Present study explores the mechanism of calcimycin-induced apoptosis cancer cell lines. Calcimycin induces apoptosis accompanied by increased intracellular calcium-level and increased expression of purinergic receptor-P2RX4, a ligand-gated ion channel. The percentage of apoptotic cancer cells in a dose-dependent manner quickly rose as recorded with MTT assays, Phase contrast imaging, wound healing assay, fluorescence imaging by DAPI and AO/EB staining and FACS. Mitochondrial potential was analyzed by TMRM assay as Ca2+signaling is well known to be influenced and synchronized by mitochondria also. Calcimycin treatment tends to increase the intracellular calcium level, mRNA expression of ATP receptor P2RX4, and phosphorylation of p38. Blocking of either intracellular calcium by BAPTA-AM, P2RX4 expression by antagonist 5-BDBD, and phospho-p38 by SB203580, abrogated the apoptotic activity of calcimycin. Taken together, these results show that calcimycin induces apoptosis in P2RX4 dependent ATP mediated intracellular Ca2+and p38 MAPK mediated pathway in both the cancer cell lines.
The magnitude and time course of pre-saccadic foveal prediction depend on the conspicuity of the saccade target
Authors: Kroell Lisa M. , Rolfs Martin 
Published: July 2023

AbstractWe previously demonstrated that during the preparation of a large-scale saccadic eye movement, defining features of the eye movement target (i.e., its orientation) are anticipated in pre-saccadic foveal vision (Kroell & Rolfs, 2022). In this Research Advance, we show that the conspicuity of orientation information at the saccade target location influences the magnitude and time course of foveal enhancement. As in our previous study, observers prepared a saccade to a peripheral orientation signal (the target) while monitoring the appearance of a second orientation signal (the probe) in their pre-saccadic center of gaze. The probe appeared in 50% of trials and either had the same orientation as the target (congruent) or a different orientation (incongruent). In the current study, we manipulated the opacity of the target against the 1/f background noise in four logarithmic steps from 25% to 90%. An increase in opacity translated to an increase in luminance contrast and the signal-to-noise ratio of orientation information within the target region. We made three main observations: First, foveal Hit Rates for target-congruentandincongruent probes decreased as target opacity increased, presumably since attention was increasingly drawn to the target the more salient it became. Crucially, foveal enhancement defined as the difference between congruent and incongruent Hit Rates increased with opacity. Second, the time course of foveal enhancement showed an oscillatory pattern that was particularly pronounced at higher target opacities. Third, unlike the difference in Hit Rates, the difference in False Alarm Rates did not vary with opacity. Instead, reverse correlations suggest that at higher target opacities, False Alarms were increasingly triggered by signal, that is, by incidental orientation information in the foveal noise. Beyond providing new mechanistic insights into active foveal processing, these findings are relevant for researchers planning to adapt our paradigm to study related questions. Presenting the saccade target at a high signal-to-noise ratio appears beneficial as congruency effects, especially when time-resolved, are most robustly detectable.