bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galectin-9 interacts with Vamp-3 to regulate cytokine secretion in dendritic cells
Authors: Méndez Rui Santalla , Furones Andrea Rodgers , Classens René , Haverdil Manon , Capdevila Marta Canela , van Duffelen Anne , Spruijt Cornelia G. , Vermeulen Michiel , ter Beest Martin , van Spriel Annemiek B. , Cano Laia Querol 
Published: May 2022

AbstractIntracellular vesicle transport is essential for cellular homeostasis and is partially mediated by SNARE proteins. Endosomal trafficking to the plasma membrane ensures cytokine secretion in dendritic cells (DCs) and the initiation of immune responses. Despite its critical importance, the specific molecular agents that regulate DC cytokine secretion are poorly characterised. Galectin-9, a ß-galactoside-binding protein, has emerged as a novel cellular modulator although its exact intracellular roles in regulating (immune) cell homeostasis and vesicle transport are virtually unknown. We investigated galectin-9 function in primary human DCs and report that galectin-9 is essential for intracellular cytokine trafficking to the cell surface. Galectin-9-depleted DCs accumulate cytokine-containing vesicles in the Golgi complex that eventually undergo lysosomal degradation. We observed galectin-9 to molecularly interact with Vamp-3 using immunoprecipitation-mass-spectrometry and identified galectin-9 was required for rerouting Vamp-3-containing endosomes upon DC activation as the underlying mechanism. Overall, this study identifies galectin-9 as a necessary mechanistic component for intracellular trafficking. This may impact our general understanding of vesicle transport and shed new light into the multiple roles galectins play in governing cell function.
Interpretable machine learning of action potential duration restitution kinetics in single-cell models of atrial cardiomyocytes
Authors: Song Euijun , Lee Young-Seon 
Published: May 2022

AbstractAction potential duration (APD) restitution curve and its maximal slope (Smax) reflect single cell-level dynamic instability for inducing chaotic heart rhythms. However, conventional parameter sensitivity analysis often fails to describe nonlinear relationships between ion channel parameters and electrophysiological phenotypes, such as Smax. We explored the parameter–phenotype mapping in a population of 5,000 single-cell atrial cell models through interpretable machine learning (ML) approaches. Parameter sensitivity analyses could explain the linear relationships between parameters and electrophysiological phenotypes, including APD90, resting membrane potential, Vmax, refractory period, and APD/calcium alternans threshold, but not for Smax. However, neural network models had better prediction performance for Smax. To interpret the ML model, we evaluated the parameter importance at the global and local levels by computing the permutation feature importance and the local interpretable model-agnostic explanations (LIME) values, respectively. Increases in ICaL, INCX, and IKr, and decreases in IK1, Ib,Cl, IKur, ISERCA, and Ito are correlated with higher Smax values. The LIME algorithm determined that INaK plays a significant role in determining Smax as well as Ito and IKur. The atrial cardiomyocyte population was hierarchically clustered into three distinct groups based on the LIME values and the single-cell simulation confirmed that perturbations in INaK resulted in different behaviors of APD restitution curves in three clusters. Our combined top-down interpretable ML and bottom-up mechanistic simulation approaches uncovered the role of INaK in heterogeneous behaviors of Smax in the atrial cardiomyocyte population.
Conformational changes in mitochondrial complex I from the thermophilic eukaryote Chaetomium thermophilum
Authors: Laube Eike , Meier-Credo Jakob , Langer Julian D. , Kühlbrandt Werner 
Published: May 2022

AbstractMitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus Chaetomium thermophilum, determined by cryoEM up to 2.4 Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as form 1 and 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping.
Novel Mechanism for Tubular Injury in Nephropathic Cystinosis
Authors: Sur Swastika , Kerwin Maggie , Pineda Silvia , Sansanwal Poonam , Sigdel Tara K. , Sirota Marina , Sarwal Minnie M. 
Published: May 2022

AbstractUnderstanding the unique susceptibility of the human kidney to pH dysfunction and injury in cystinosis is paramount to developing new therapies to preserve renal function. Renal proximal tubular epithelial cells (RPTECs) and fibroblasts isolated from patients with cystinosis were transcriptionally profiled. Lysosomal fractionation, immunoblotting, confocal microscopy, intracellular pH, TEM, mitochondrial stress test, and membrane integrity assays were performed for validation. CRISPR,CTNS-/-RPTECs were generated. Alterations in cell stress, pH, autophagic turnover, and mitochondrial energetics highlighted key changes in the vacuolar (V)-ATPases in patient-derived andCTNS-/-RPTECs. ATP6V0A1 was significantly downregulated in cystinosis and highly co-regulated with loss ofCTNS. Correction of ATP6V0A1 rescued cell stress and mitochondrial function. Treatment ofCTNS-/-RPTECs with antioxidants astaxanthin (ATX) induced ATP6V0A1 expression and improved autophagosome turnover and mitochondrial integrity.In conclusion, our exploratory transcriptional and in vitro cellular and functional studies confirm that loss of cystinosin in RPTECs, results in a reduction in ATP6V0A1 expression, with changes in intracellular pH, mitochondrial integrity, mitochondrial function, and autophagosome-lysosome clearance. The novel findings are ATP6V0A1’s role in cystinosis-associated renal pathology and among other antioxidants, ATX specifically upregulated ATP6V0A1, improved autophagosome turnover or reduced autophagy and mitochondrial integrity. This is a pilot study highlighting a novel mechanism of tubular injury in cystinosis and requires further study in animal models to clarify its utility in clinical settings.
Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila
Authors: Frampton Sophie L , Sutcliffe Catherine , Baldock Clair , Ashe Hilary L 
Published: May 2022

AbstractA BMP gradient is essential for patterning the dorsal-ventral axis of invertebrate and vertebrate embryos. The extracellular BMP binding protein Short Gastrulation (Sog) in Drosophila plays a key role in BMP gradient formation. In this study, we combine genome editing, structural and developmental approaches to study Sog function in Drosophila. We generate a sog knockout fly stock, which allows simple reintegration of altered versions of the sog coding sequence. As proof-of-principle, we test the requirement for two cysteine residues that were previously identified as targets for palmitoylation, which has been proposed to enhance Sog secretion. However, we show that the SogC27,28S mutant is viable with only very mild phenotypes, indicating that these residues and their potential modification are not critical for Sog secretion in vivo. Additionally, we use experimental negative stain EM imaging and hydrodynamic data to validate the AlphaFold structure prediction for Sog. The model suggests a more compact shape than the vertebrate ortholog Chordin and conformational flexibility between the C-terminal von Willebrand C domains. We discuss how this altered compactness may contribute to mechanistic differences in Sog and Chordin function during BMP gradient formation.Summary statementThe authors model the structure of Sog and establish a new sog knockout fly stock that they validate for the testing of specific sog mutations.
Female factors are important for the seminal Sex Peptide’s association with sperm in mated D. melanogaster
Authors: Misra Snigdha , Singh Akanksha , Wolfner Mariana F. 
Published: May 2022

AbstractBackgroundMale-derived seminal fluid proteins (SFPs) enter and induce a myriad of physiological and behavioral changes in mated female flies optimizing fertility. Many post-mating changes in female Drosophila melanogaster persist for ∼10-14 days, because the seminal protein that induces them, Sex Peptide (SP), is retained long-term in females by binding to sperm, with gradual release of its active domain from sperm. Several other “long-term response SFPs” (LTR-SFPs) “prime” sperm to bind SP. Whether female factors play a role in this process is unknown, though it is important to study both sexes for a comprehensive physiological understanding of this reproductive process and for consideration in models of sexual conflict.ResultsWe report here that sperm in male ejaculates bind SP more weakly than sperm that have entered females, and that the amount of SP and other SFPs bound to sperm increases with time and transit of individual seminal proteins within the female reproductive tract. Thus, female contributions are needed for maximal and appropriate binding of SP, and other SFPs, to sperm. Towards understanding the molecular roles of the female, we found no dramatic change in pH of the female reproductive tract after mating and that initial binding of SP to sperm is normal in females with ablated or defective spermathecal secretory cells and/or parovaria, but that higher levels of SP (and sperm) are retained in the latter females.ConclusionThis study reveals that the SP pathway is not entirely male-biased and that females also contribute to regulating it.
Arf GTPase activates the WAVE Regulatory Complex through a novel binding site
Authors: Yang Sheng , Liu Yijun , Brown Abbigale , Schaks Matthias , Ding Bojian , Kramer Daniel A. , Ding Li , Alekhina Olga , Billadeau Daniel D. , Chowdhury Saikat , Wang Junmei , Rottner Klemens , Chen Baoyu 
Published: May 2022

SummaryCrosstalk between Rho- and Arf-family GTPases plays an important role in linking actin cytoskeletal remodeling to membrane protrusion, organelle structure, and vesicle trafficking. The central actin regulator, WAVE Regulatory Complex (WRC), is a converging point of Rac1 (a Rho-family GTPase) and Arf signaling in many processes, but how Arf promotes WRC activation is unknown. Here we reconstituted a direct interaction between Arf and WRC. This interaction can be greatly enhanced by Rac1 binding to the D site of the WRC. Arf1 binds to a newly identified conserved surface on Sra1 located between the D site and the WH2 helix of WAVE1, which can drive WRC activation using a mechanism distinct from that of Rac1. Mutating Arf binding site abolishes Arf1-WRC interaction, disrupts Arf1-mediated WRC activation, and impairs lamellipodia morphology. This work uncovers a new mechanism underlying WRC activation and provides a mechanistic foundation for studying how WRC-mediated actin polymerization links Arf and Rac signaling in the cell.
The 5-LOX/COX-2 cross-over metabolite, hemiketal E2, enhances VEGFR2 activation and promotes angiogenesis
Authors: Nakashima Fumie , Giménez-Bastida Juan A. , Luis Paula B. , Presley Sai H. , Boer Robert E. , Chiusa Manuel , Shibata Takahiro , Sulikowski Gary A. , Pozzi Ambra , Schneider Claus 
Published: May 2022

AbstractConsecutive oxygenation of arachidonic acid by 5-lipoxygenase (5-LOX) and cyclooxygenase-2 (COX-2) yields the hemiketal (HK) eicosanoids, HKE2 and HKD2. HKs stimulate angiogenesis by inducing endothelial cell tubulogenesis in culture; however, how this process is regulated has not been determined. Here, we identify vascular endothelial growth factor receptor 2 (VEGFR2) as a mediator of HKE2-induced angiogenesis in vitro and in vivo. HKE2 treatment of human umbilical vein endothelial cells dose-dependently increased phosphorylation of VEGFR2 and the downstream kinases ERK and Akt that mediated endothelial cell tubulogenesis. In vivo, HKE2 induced the growth of blood vessels into polyacetal sponges implanted in mice. HKE2-mediated effects in vitro and in vivo were blocked by the VEGFR2 inhibitor vatalanib, indicating that the pro-angiogenic effect of HKE2 was mediated by VEGFR2. We found that HKE2 covalently bound and inhibited PTP1B, a protein tyrosine phosphatase that dephosphorylates VEGFR2, thereby providing a possible molecular mechanism for how HKE2 induced pro-angiogenic signaling. Our studies indicate that biosynthetic cross-over of the 5-LOX and COX-2 pathways gives rise to a potent lipid autacoid that regulates endothelial cell function in vitro and in vivo.SignificanceAngiogenesis, the growth of new blood vessels from existing vessels, contributes to both physiological and pathological conditions, including tissue repair after injury and tumorigenesis. Novel approaches to control pathologic angiogenesis are urgently needed since current therapy targeting the pro-angiogenic receptor VEGFR2 has significant side effects. We show that a metabolite of arachidonic acid, formed in a biosynthetic cross-over of the enzymes that generate the pro-inflammatory leukotriene and prostaglandin mediators, respectively, promotes VEGFR2 activation to induce angiogenesis. This finding suggests that common drugs targeting the arachidonic acid pathway may be viewed as valid anti-angiogenic candidates.
Effects of social support on depression risk during the COVID-19 pandemic: What support types and for whom?
Authors: Choi Karmel W. , Lee Younga H. , Liu Zhaowen , Fatori Daniel , Bauermeister Joshua R. , Luh Rebecca A. , Clark Cheryl R. , Brunoni André R. , Bauermeister Sarah , Smoller Jordan W. 
Published: May 2022

AbstractBackgroundRates of depression have increased worldwide during the COVID-19 pandemic. One known protective factor for depression is social support, but more work is needed to quantify the extent to which social support could reduce depression risk during a global crisis, and specifically to identify which types of support are most helpful, and who might benefit most.MethodsData were obtained from participants in the All of Us Research Program who responded to the COVID-19 Participant Experience (COPE) survey administered monthly from May 2020 to July 2020 (N=69,066, 66% female). Social support was assessed using 10 items measuring emotional/informational support (e.g., someone to confide in or talk to about yourself or your problems), positive social interaction support (e.g., someone to do things with to help you get your mind off things), and tangible support (e.g., someone to help with daily chores if sick). Elevated depression symptoms were defined based on having a moderate-to-severe (≥10) score on the Patient Health Questionnaire (PHQ-9). Mixed-effects logistic regression models were used to test associations across time between overall social support and its subtypes with depression, adjusting for age, sex, race, ethnicity, and socioeconomic factors. We then assessed interactions between social support and potential effect modifiers: age, sex, pre-pandemic mood disorder, and pandemic-related stressors (e.g., financial insecurity).ResultsApproximately 16% of the sample experienced elevated depressive symptoms. Overall social support was associated with significantly reduced odds of depression (adjusted odds ratio, aOR [95% CI]=0.44 [0.42-0.45]). Among subtypes, emotional/informational support (aOR=0.42 [0.41-0.43]) and positive social interactions (aOR=0.43 [0.41-0.44]) showed the largest protective associations with depression, followed by tangible support (aOR=0.63 [0.61-0.65]). Sex, age, and pandemic-related financial stressors were statistically significant modifiers of the association between social support and depression.ConclusionsIndividuals reporting higher levels of social support were at reduced risk of depression during the early COVID-19 pandemic. The perceived availability of emotional support and positive social interactions, more so than tangible support, was key. Individuals more vulnerable to depression (e.g., women, younger individuals, and those experiencing financial stressors) may particularly benefit from enhanced social support, supporting a precision prevention approach.
Built to last? Reproducibility and Reusability of Deep Learning Algorithms in Computational Pathology
Authors: Wagner Sophia J. , Matek Christian , Boushehri Sayedali Shetab , Boxberg Melanie , Lamm Lorenz , Sadafi Ario , Waibel Dominik J. E. , Marr Carsten , Peng Tingying 
Published: May 2022

AbstractRecent progress in computational pathology has been driven by deep learning. While code and data availability are essential to reproduce findings from preceding publications, ensuring a deep learning model’s reusability is more challenging. For that, the codebase should be well-documented and easy to integrate in existing workflows, and models should be robust towards noise and generalizable towards data from different sources. Strikingly, only a few computational pathology algorithms have been reused by other researchers so far, let alone employed in a clinical setting.To assess the current state of reproducibility and reusability of computational pathology algorithms, we evaluated peer-reviewed articles available in Pubmed, published between January 2019 and March 2021, in five use cases: stain normalization, tissue type segmentation, evaluation of cell-level features, genetic alteration prediction, and direct extraction of grading, staging, and prognostic information. We compiled criteria for data and code availability, and for statistical result analysis and assessed them in 161 publications. We found that only one quarter (42 out of 161 publications) made code publicly available and thus fulfilled our minimum requirement for reproducibility and reusability. Among these 42 papers, three quarters (30 out of 42) analyzed their results statistically, less than half (20 out of 42) have released their trained model weights, and only about a third (16 out of 42) used an independent cohort for evaluation.This review highlights candidates for reproducible and reusable algorithms in computational pathology. It is intended for both pathologists interested in deep learning, and researchers applying deep learning algorithms to computational pathology challenges. We provide a list of reusable data handling tools and a detailed overview of the publications together with our criteria for reproducibility and reusability.
De NovoRNA Tertiary Structure Prediction at Atomic Resolution Using Geometric Potentials from Deep Learning
Authors: Pearce Robin , Omenn Gilbert S. , Zhang Yang 
Published: May 2022

ABSTRACTExperimental characterization of RNA structure remains difficult, especially for non-coding RNAs that are critical to many cellular activities. We developed DeepFoldRNA to predict RNA structures from sequence alone by coupling deep self-attention neural networks with gradient-based folding simulations. The method was tested on two independent benchmark datasets from Rfam families and RNA-Puzzle experiments, where DeepFoldRNA constructed models with an average RMSD=2.69 Å and TM-score=0.743, which outperformed state-of-the-art methods and the best models submitted from the RNA-Puzzles community by a large margin. On average, DeepFoldRNA required ~1 minute to fold medium-sized RNAs, which was ~350-4000 times faster than the leading Monte Carlo simulation approaches. These results demonstrate the major advantage of advanced deep learning techniques to learn more accurate information from evolutionary profiles than knowledge-based potentials derived from simple statistics of the PDB library. The high speed and accuracy of the developed method should enable large-scale atomic-level RNA structure modeling applications.
Generation of a human ovarian granulosa cell model from induced pluripotent stem cells
Authors: Hart Dirk , Gutiérrez Daniel Rodríguez , Biason-Lauber Anna 
Published: May 2022

SUMMARYSex development is an intricate and crucial process in all vertebrates that ensures the continued propagation of genetic diversity within a species, and ultimately their survival. Perturbations in this process can manifest as variations/differences of sex development (VSD/DSD). Primary gonadal somatic cells – the ovarian granulosa cells (GCs) in the case of women – represent the absolute model to investigate mechanism of disease in VSDs. Collection of these cells in humans is laborious and invasive, while classical animal models fail to recapitulate the human phenotype and function. Furthermore, in patients with the most severe forms of VSD gonadal cells are totally absent. It is therefore vital to develop an alternative cell-model. In view of this, we established an efficient method to reprogram donor-derived urinary progenitor cells (UPs) and differentiate iPSCs into granulosa-like cells (GLCs). The UPs presented a less invasive and high-quality cell source, improving the clinical applicability of the model along with utilising a non-integrative reprogramming method that eliminates alteration of the original genome. This novel GLC model closely resembles human GCs in morphology and marker gene expression of GC cell-fate and essential function. These results provide the prospect to generate patient-specific personalised GC models to investigate mechanism of disease in VSDs and could improve understanding of the intricacies in female gonadal development.
Functional regulation of 4D metabolic network between multienzyme glucosome condensates and mitochondria
Authors: Kennedy Erin L. , Jeon Miji , Augustine Farhan , Chauhan Krishna M. , An Songon , Kyoung Minjoung 
Published: May 2022

AbstractGlucose metabolism is biochemically intertwined between energy metabolism and building block biosynthesis in living cells. However, it has not been investigated yet how its metabolic network is orchestrated to govern glucose flux in space and time. Since we reported that human enzymes in glucose metabolism are spatially organized into metabolically active membraneless compartments (i.e., glucosomes), we have employed lattice light sheet microscopic imaging and other biophysical and biochemical techniques to understand their functional significance in cellular metabolism. Now, we demonstrated that glucosome assemblies behave like liquid droplets in human cells and thus reversibly respond to environmental changes. In addition, we characterized a molecular architecture of the glucosome, which appears to be constructed from higher-ordered oligomeric structures of its scaffolder enzyme along with transient enzyme-enzyme interactions. Importantly, we found that enzymatic compositions of glucosomes are altered when they are spatially in proximity to mitochondria to functionally couple glycolysis with mitochondrial metabolism in human cells. Collectively, we envision that the subcellular localization-function relationship between glucosomes and mitochondria may represent one of fundamental principles by which 4-dimensional metabolic networks are not only dynamically but also efficiently regulated in living human cells.One Sentence SummaryInvestigation of a 4D functional network of glucose metabolism uncovers a fundamental principal of subcellular metabolic regulation in human cells.