bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive Models of Genome-wide Aryl Hydrocarbon Receptor DNA Binding Reveal Tissue Specific Binding Determinants
Authors: Filipovic David , Qi Wenjie , Kana Omar , Marri Daniel , LeCluyse Edward L. , Andersen Melvin E. , Cuddapah Suresh , Bhattacharya Sudin
Published: May 2022

Background

The Aryl Hydrocarbon Receptor (AhR) is an inducible transcription factor (TF) whose ligands include the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). TCDD-mediated toxicity occurs through activation of AhR and its subsequent binding to the Dioxin Response Element (DRE), comprising the DNA motif 5’-GCGTG-3’. However, AhR binding in human tissues is highly dynamic and tissue specific. Approximately 50% of all experimentally verified AhR binding sites do not contain a DRE. Additionally, most accessible DREs are not bound by AhR. Identification of tissue specific AhR binding determinants is crucial for understanding downstream gene regulation and potential adverse outcomes of AhR activation.

Results

We applied XGBoost, a supervised machine learning architecture, to predict the genome wide AhR binding status of DREs in open chromatin as a function of DNA sequence flanking the DRE, chromatin accessibility, histone modifications (HM), TF binding, and proximity of the DRE to gene promoters. We trained and validated our models using 5-fold cross validation to predict the binding status of DREs in AhR-activated MCF-7 breast cancer cells, primary human hepatocytes, and lymphoblastoid GM17212 cells, as well as AhR non-activated HepG2 hepatocellular carcinoma cells. Our results demonstrate highly accurate and robust models of AhR binding; and identify patterns of transcription factor binding and histone modifications predictive of AhR binding. These patterns are consistent within tissues but highly variable across tissues, which is suggestive of tissue-specific mechanisms of AhR binding.

Conclusions

AhR binding is driven by a complex interplay of tissue-agnostic DNA sequence flanking its binding motif and tissue-specific local chromatin context.
Blind spots on western blots: a meta-research study highlighting opportunities to improve figures and methods reporting
Authors: Kroon Cristina , Breuer Larissa , Jones Lydia , An Jeehye , Akan Ayça , Mohamed Ali Elkhansa Ahmed , Busch Felix , Fislage Marinus , Ghosh Biswajit , Hellrigel-Holderbaum Max , Kazezian Vartan , Koppold Alina , Moreira Restrepo Cesar Alberto , Riedel Nico , Scherschinski Lea , Urrutia Gonzalez Fernando Raúl , Weissgerber Tracey
Published: May 2022

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader’s ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n=151) and cell biology (n=400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps and antibody labeling protocol. Important antibody identifiers like source, catalog number or RRID were omitted frequently for primary antibodies, and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish and an antibody reporting template.
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

Intracellular 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

Action 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

Mitochondrial 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

Understanding 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

A 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 statement

The 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

Background

Male-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.

Results

We 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.

Conclusion

This 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

Crosstalk 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

Consecutive 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.

Significance

Angiogenesis, 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

Background

Rates 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.

Methods

Data 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).

Results

Approximately 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.

Conclusions

Individuals 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

Recent 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

Experimental 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

Sex 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

Glucose 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 Summary

Investigation of a 4D functional network of glucose metabolism uncovers a fundamental principal of subcellular metabolic regulation in human cells.
3D-surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semi-supervised deep learning
Authors: Dyhr Michael C. A. , Sadeghi Mohsen , Moynova Ralitsa , Knappe Carolin , Kepsutlu Burcu , Werner Stephan , Schneider Gerd , McNally James , Noe Frank , Ewers Helge
Published: May 2022

Cryo-soft X-ray tomography (cryo-SXT) is a powerful method to investigate the ultrastructure of cells, offering resolution in the tens of nm range and strong contrast for membranous structures without requirement for labeling or chemical fixation. The short acquisition time and the relatively large volumes acquired allow for fast acquisition of large amounts of tomographic image data. Segmentation of these data into accessible features is a necessary step in gaining biologically relevant information from cryo-soft X-ray tomograms. However, manual image segmentation still requires several orders of magnitude more time than data acquisition. To address this challenge, we have here developed an end-to-end automated 3D-segmentation pipeline based on semi-supervised deep learning. Our approach is suitable for high-throughput analysis of large amounts of tomographic data, while being robust when faced with limited manual annotations and variations in the tomographic conditions. We validate our approach by extracting three-dimensional information on cellular ultrastructure and by quantifying nanoscopic morphological parameters of filopodia in mammalian cells.
CUGIC: The Consolidated Urban Green Infrastructure Classification for assessing ecosystem services and biodiversity
Authors: Morpurgo Joeri , Remme Roy P. , Van Bodegom Peter M.
Published: May 2022

Green infrastructure (GI) classifications are widely applied to predict and assess its suitability for urban biodiversity and ecosystem service (ES) provisioning. However, there is no consolidated classification, which hampers elucidating synthesis and consolidated relationships across ES and biodiversity.

In this research, we aim to bridge the gap between urban GI research on ES and biodiversity by providing a standardized common classification that enables consistent spatial analysis.

We analyzed GI classifications used across five ES and four taxa in scientific literature. GI classes were analyzed based on name, definition and characteristics. Results were used to create a novel classification scheme accounting for both ES and biodiversity.

We show that many GI classes are unique to a ES or taxon, indicating a lack of multifunctionality of the classification applied. Among the universally used classes, diversity in their definitions is large, reducing our mechanistic understanding of multifunctionality in GI. Finally, we show that most GI classes are solely based on land-use or land-cover, lacking in-depth detail on vegetation. Through standardization and incorporation of key characteristics, we created a consolidated classification. This classification is fully available through openly-accessible databases.

Our consolidated standardized classification accommodates interdisciplinary research on ES and biodiversity and allows elucidating urban biodiversity and ES relationships into greater detail, facilitating cross-comparisons and integrated assessments. This will provide a foundation for future research efforts into GI multi-functionality and urban greening policies.
Extensive lineage-specific rediploidisation masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Authors: Redmond Anthony K. , Gundappa Manu Kumar , Macqueen Daniel J. , McLysaght Aoife
Published: May 2022

Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to a preponderance of duplicate genes with independent histories. Here we show that although there is indeed a plurality of apparently ‘independent’ gene duplications, these derive from a shared genome duplication event occurring close to the Permian-Triassic mass extinction period, followed by a prolonged process of reversion to stable diploid inheritance (rediploidisation). We show that the sharing of this WGD is masked by the fact that paddlefish and sturgeon lineage divergence occurred before rediploidisation had proceeded even half-way. Thus, for most genes the resolution to diploidy was lineage-specific. Because genes are only truly duplicated once diploid inheritance is established, the paddlefish and sturgeon genomes are a mosaic of shared and non-shared gene duplications resulting from a shared genome duplication event. This is the first time that lineage-specific resolution of genes from a common WGD event has been shown to affect such a large proportion of the genome.
From cell size and first principles to structure and function of unicellular plankton communities
Authors: Andersen K.H. , Visser A.W.
Published: May 2022

Here we review, synthesize, and analyse the size-based approach to model unicellular plankton cells and communities. We first review how cell size influences processes of the individual the cell: uptake of dissolved nutrients and dissolved organic carbon, phototrophy, phagotrophy, and metabolism. We parameterise processes primarily from first principles, using a synthesis of existing data only when needed, and show how these processes determine minimum and maximum cell size and limiting resource concentrations. The cell level processes scale directly up to the structure and function of the entire unicellular plankton ecosystem, from heterotrophic bacteria to zooplankton. The structure is described by the Sheldon size spectrum and by the emergent trophic strategies. We develop an analytical approximate solution of the biomass size spectrum and show how the trophic strategies of osmotrophy, light- and nutrient-limited phototrophy, mixotrophy, phagotrophy depend on the resource environment. We further develop expressions to quantify the functions of the plankton community: production, respiration and losses, and carbon available to production of higher trophic levels, and show how the plankton community responds to changes in temperature and grazing from higher trophic levels. We finally discuss strengths and limitations of size-based representations and models of plankton communities and which additional trait axes will improve the representation of plankton functional diversity.
Pathogenic TDP-43 Disrupts Axon Initial Segment Structure and Neuronal Excitability in a Human iPSC Model of ALS
Authors: Harley Peter , Neves Guilherme , Riccio Federica , Machado Carolina Barcellos , Cheesbrough Aimee , R’Bibo Lea , Burrone Juan , Lieberam Ivo
Published: May 2022

Dysregulated neuronal excitability is a hallmark of amyotrophic lateral sclerosis (ALS). We sought to investigate how functional changes to the axon initial segment (AIS), the site of action potential generation, could impact neuronal excitability in a human iPSC model of ALS. We found that early (6-week) ALS-related TDP-43G298S motor neurons showed an increase in the length of the AIS, relative to CRISPR-corrected controls. This was linked to neuronal hyperexcitability and increased spontaneous contractions of hiPSC-myofibers in compartmentalised neuromuscular co-cultures. In contrast late (10-week) TDP-43G298S motor neurons showed reduced AIS length and hypoexcitability. At a molecular level aberrant expression of the AIS master scaffolding protein Ankyrin-G, and the AIS-specific voltage-gated ion channels SCN1A (Nav1.1) and SCN8A (Nav1.6) mirrored these dynamic changes in excitability. Finally, at all stages, TDP-43G298S motor neurons showed compromised activity-dependent plasticity of the AIS, further contributing to abnormal excitability. Our results point toward the AIS as an important subcellular target driving changes to neuronal excitability in ALS.
Transcription factors that specify cell fate activate cell cycle regulator genes to determine cell numbers in ascidian larval tissues
Authors: Kobayashi Kenji , Tokuoka Miki , Sato Hiroaki , Ariyoshi Manami , Kawahara Shiori , Fujiwara Shigeki , Kishimoto Takeo , Satou Yutaka
Published: May 2022

In animal development, most cell types stop dividing before terminal differentiation; thus, cell cycle control is tightly linked to cell differentiation programs. Although cell cycle control in animal development has been studied extensively, such links are not well understood. In ascidian embryos, cell lineages do not vary among individuals, and rounds of the cell cycle are determined according to cell lineages. In the present study, we first showed that maternal factors promote approximately 10 rounds of cell division without zygotic gene expression. Notochord and muscle cells stop dividing after fewer than 10 rounds of cell division, and we show that a Cdk inhibitor (Cdkn1.b) is responsible. Cdkn1.b is also necessary for epidermal cells to stop dividing. In contrast, mesenchymal and endodermal cells divided more than 10 times, and Myc, which encodes a proto-oncogenic transcription factor, is responsible for maintaining cell cycle progression in these tissues. Expression of Cdkn1.b in notochord and muscle is controlled by the same developmental programs that specify the developmental fate of notochord and muscle. Likewise, expression of Myc in mesenchyme and endoderm was under control of the same developmental programs that specify the developmental fate of mesenchyme and endoderm. Because these transcription factors that regulate Cdkn1.b and Myc are essential factors for fate specification of these tissues, cell fate specification and cell cycle control are linked by those transcription factors. In other words, ectodermal, mesodermal, and endodermal tissues in ascidian embryos control the cell cycle through Cdkn1.b and Myc, which are under the control of transcription factors that specify cell fate.
Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex
Authors: Gruszczyk Jakub , Grandvuillemin Loic , Lai-Kee-Him Josephine , Paloni Matteo , Savva Christos G. , Germain Pierre , Grimaldi Marina , Boulahtouf Abdelhay , Kwong Hok-Sau , Bous Julien , Ancelin Aurelie , Bechara Cherine , Barducci Alessandro , Balaguer Patrick , Bourguet William
Published: May 2022

Living organisms have developed protein sensors helping them to adapt to their environment1. The aryl hydrocarbon receptor (AHR) is an emblematic member of this class of proteins, and a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites2. However, in the absence of high-resolution structural data, a molecular understanding of how AHR is activated by such diverse compounds is lacking. Here we present a 2.85 Å cryo-electron microscopy structure of the cytosolic complex comprising AHR bound to the ligand indirubin, the chaperone Hsp90 and the co-chaperone XAP2. The structure reveals a closed Hsp90 dimer with AHR threaded through its lumen. XAP2 directly interacts with Hsp90 and the AHR ligand-binding domain, thereby acting as a brace stabilizing the entire complex. Importantly, we provide the first experimental visualization of the AHR PAS-B domain bound to a ligand, revealing a unique organization of the ligand-binding pocket and the structural determinants of ligand-binding specificity and promiscuity of the receptor. By providing unprecedented structural details of the molecular initiating event leading to AHR activation, our study rationalizes prior biochemical data and provides a framework for future mechanistic studies and structure-guided drug design.
SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to downregulate MHC-I surface expression
Authors: Arshad Najla , Laurent-Rolle Maudry , Ahmed Wesam S , Hsu Jack Chun-Chieh , Mitchell Susan M , Pawlak Joanna , Sengupta Debrup , Biswas Kabir H , Cresswell Peter
Published: May 2022

Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small protein β2-microglobulin (β2m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those containing viral peptides can be detected by CD8+ T lymphocytes that kill infected cells. Many viruses enhance their in vivo survival by encoding genes that downregulate MHC-I expression to avoid CD8+ T cell recognition. Here we report that two accessory proteins encoded by SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, downregulate MHC-I expression using distinct mechanisms. One, ORF3a, a viroporin, reduces global trafficking of proteins, including MHC-I, through the secretory pathway. The second, ORF7a, interacts specifically with the MHC-I heavy chain, acting as a molecular mimic of β2m to inhibit its association. This slows the exit of properly assembled MHC-I molecules from the endoplasmic reticulum. We demonstrate that ORF7a reduces antigen presentation by the human MHC-I allele HLA-A*02:01. Thus, both ORF3a and ORF7a act post-translationally in the secretory pathway to lower surface MHC-I expression, with ORF7a exhibiting a novel and specific mechanism that allows immune evasion by SARS-CoV-2.

Significance Statement

Viruses may down-regulate MHC class I expression on infected cells to avoid elimination by cytotoxic T cells. We report that the accessory proteins ORF7a and ORF3a of SARS-CoV-2 mediate this function and delineate the two distinct mechanisms involved. While ORF3a inhibits global protein trafficking to the cell surface, ORF7a acts specifically on MHC-I by competing with β2m for binding to the MHC-I heavy chain. This is the first account of molecular mimicry of β2m as a viral mechanism of MHC-I down-regulation to facilitate immune evasion.
OGG1 inhibitor TH5487 alleviates allergic airway inflammation in mice
Authors: Tanner Lloyd , Bergwik Jesper , Bhongir Ravi KV , Pan Lang , Dong Caijuan , Kalderén Christina , Helleday Thomas , Boldogh Istvan , Adner Mikael , Egesten Arne
Published: May 2022

Allergic asthma is a complex disease characterized by dyspnea, coughing, chest tightness and airway remodeling, for which there is no cure and is symptomatically treated with inhaled β2-agonist and/or corticosteroids. Molecular mechanisms underlying its complex pathogenesis are not fully understood. However, the 8-oxoguanine DNA glycosylase-1 (OGG1), a DNA repair protein may play a central role, as OGG1 deficiency decreases both innate and allergic inflammatory responses. In this study, administration of TH5487 to mice with OVA-induced allergic airway inflammation significantly decreased goblet cell hyperplasia and mucus production. TH5487 treatment also decreased levels of activated NF-κB and expression of proinflammatory cytokines resulting in significantly lower recruitment of eosinophils and other immune cells to the lungs. Gene expression profiling of asthma and allergy-related proteins after TH5487 treatment revealed down regulation of Arg1, Mcp1 and Ccl11, and upregulation of the negative regulator of TH2, Bcl6. In addition, the OVA-induced airway hyperresponsiveness was significantly reduced by TH5487 treatment. Taken together, the data presented in this study suggest a clinically relevant utilization of TH5487 for the treatment of allergic inflammation.

Graphical abstract
Disease-modifying effects of sodium selenate in a model of drug-resistant, temporal lobe epilepsy
Authors: Casillas-Espinosa Pablo M. , Anderson Alison , Harutyunyan Anna , Li Crystal , Lee Jiyoon , Braine Emma L. , Brady Rhys D. , Sun Mujun , Huang Cheng , Barlow Christopher K. , Shah Anup D. , Schittenhelm Ralf B. , Mychasiuk Richelle , Jones Nigel C. , Shultz Sandy R. , O’Brien Terence J.
Published: May 2022

There are no pharmacological disease-modifying treatments that can mitigate the seizures and comorbidities associated with established chronic temporal lobe epilepsy (TLE). This study evaluated the effect of sodium selenate in the post-status epilepticus (SE) rat model of chronic drug resistant TLE. Wistar rats underwent kainic acid-induced SE or sham. Ten-weeks post-SE, rats were randomly assigned to receive either sodium selenate, levetiracetam, or vehicle treatments continuously for 4 weeks. To evaluate the effects of the treatments, 1 week of continuous video-EEG was acquired before, during, and 4, 8 weeks post-treatment, followed by behavioral tests. Targeted and untargeted proteomics and metabolomics were performed on post-mortem brain tissue to identify potential pathways associated with modified disease outcomes. Telomere length was investigated as a novel surrogate marker of disease severity. Sodium selenate treatment was able to mitigate disease severity, reducing the number of spontaneous seizures (p< 0.05), cognitive dysfunction (p< 0.05 in both novel object placement and recognition tasks), and sensorimotor deficits (p< 0.01) 8 weeks post-treatment cessation. Moreover, increased protein phosphatase 2A (PP2A) expression, reduced hyperphosphorylated tau, and reversed telomere length shortening caused by SE (p< 0.05). Network medicine integration of multi-omics/ pre-clinical outcomes identified protein-metabolite modules positively correlated with the TLE phenotype. Our results provide evidence that treatment with sodium selenate results in a sustained disease modifying effect in chronically epileptic rats in the post-KA SE model of TLE, including improved comorbid learning and memory deficits.
Understanding digital entrepreneurial intentions: A capital theory perspective
Authors: Mir Ajaz Akbar , Hassan Sharfa , Khan Sher Jahan
Published: May 2022

Purpose

Digital entrepreneurship is a highly topical, sub-specialist and contemporary branch of entrepreneurship which is providing ever-increasing range of platforms for pursuing entrepreneurship-related career options. While the academic discourses in this area are increasingly growing, there is an equal level of scant attention paid to inquire how proclivity toward this career choice is developed and influenced. In the present study, this gap has been addressed by identifying major antecedents of digital entrepreneurship intentions under the aegis of capital theory.

Design/methodology/approach

Using the survey data from 287 respondents, structural equation modeling was utilized to explore the association of four antecedents: digital entrepreneurial competence, innovative cognition, social media adroitness and digital entrepreneurship role models on the goal intentions. Subsequently the association between goal intention and implementation intention to start a digital venture was also examined.

Findings

The analysis confirms the significant impact of the identified antecedents on the digital entrepreneurial volition of potential entrepreneurs. Our results demonstrate that innovativeness has the greatest impact on the goal intentions to create new digital ventures followed by the presence of role models. Digital competence is also a significant contributor in enhancing the propensity to start digital ventures while being digitally adroit has the least impact on such inclination. Lastly, our study provides empirical evidence to the linkage between goal and implementation intentions.

Originality/value

This paper informs practice on entrepreneurship education especially the role of skill-based education programs to enhance the information technology–related knowledge of students and incubation support for hands-on-training on the various dimensions of digital ventures. At policy-level institutions providing entrepreneurial education can design special tasks and learning activities that are focused on acquainting students with design thinking perspectives and lean start-up approaches.