bluuebunny/crossref_metadata_2025 huggingface dataset:
Emergence of new enhancers at late DNA replicating regions
Authors: Cornejo-Páramo Paola , Petrova Veronika , Zhang Xuan , Young Robert S. , Wong Emily S.
Published: December 2022

Enhancers are fast-evolving genomic sequences that control spatiotemporal gene expression patterns. By examining enhancer turnover across mammalian species and in multiple tissue types, we uncovered a relationship between the emergence of novel enhancers and genome organization as a function of germline DNA replication time. While enhancers are most abundant in euchromatic regions, new enhancers emerged almost twice as often in late compared to early germline replicating regions, independent of transposable elements. Using a sequence model, we demonstrate that new enhancers are enriched for mutations that alter transcription factor (TF) binding. Recently evolved enhancers appeared to be mostly neutrally evolving and enriched in eQTLs. They also show more tissue specificity than conserved enhancers, and the TFs that bind to these elements, as inferred by binding sequences, also show increased tissue-specific gene expression. We find a similar relationship with DNA replication time in cancer, suggesting that these observations may be time-invariant principles of genome evolution. Our work underscores that genome organization has a profound impact in shaping mammalian gene regulation.
Fibroblasts-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis
Authors: Burgy Olivier , Mayr Christoph H. , Llobell Beatriz Ballester , Sengupta Arunima , Schenesse Déborah , Coughlan Christina , Parimon Tanyalak , Chen Peter , Lindner Michael , Hilgendorff Anne , Mann Matthias , Yildirim Ali Önder , Eickelberg Oliver , Schiller Herbert B. , Lehmann Mareike , Burgstaller Gerald , Königshoff Melanie
Published: December 2022

Idiopathic pulmonary fibrosis (IPF) is a lethal and chronic lung disease characterized by aberrant intercellular communication, increased extracellular matrix (ECM) deposition, and destruction of functional lung tissue. Extracellular vesicles (EVs) accumulate within the lung in IPF, but their cargo and biological effects remain unclear. Here, we provide the entire the proteome of EV and non-EV fraction during pulmonary fibrosis, and functionally characterize their contribution to fibrosis. EVs were isolated by differential ultracentrifugation of bronchoalveolar lavage fluid (BALF) collected from mice challenged with bleomycin (or PBS as control) or culture supernatants from primary mouse lung fibroblasts. EVs were characterized by nanoparticle tracking analysis, Western Blotting, and quantitative mass spectrometry to define their proteome. EVs accumulation peaked at 14 days post-bleomycin instillation and correlated with decreased lung function. Label-free proteomics identified 107 proteins specific to fibrotic BALF-EVs. This signature was associated with wound healing, extracellular matrix organization, and cell motility. BALF-EVs from fibrotic lungs promoted fibrogenesis, including induction of ECM proteins in precision cut lung slicesex vivoand impaired alveolar epithelial cell stem cell function. Deconvolution using single cell RNA sequencing datasets revealed that fibroblasts are the major cellular source of BALF-EVs. EVs from fibroblasts were significantly enriched in Secreted Frizzled Related Protein 1 (SFRP1). In the lungs of patients with IPF, SFRP1 was significantly increased in mesenchymal cells.Sfrp1deficiency reduced the ability of fibroblast-derived EVs to potentiate bleomycin-induced lung fibrosisin vivoand led to a reduction in fibrosis marker gene expression. In sum, EVs carry specific protein cargos, such as SFRP1, to contribute to organ remodeling during fibrosis. Our data identified EVs transporting SFRP1 as a potential therapeutic target for IPF.
Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens
Authors: Heo Seok-Jin , Enriquez Lauren D. , Federman Scot , Chang Amy Y. , Mace Rachel , Shevade Kaivalya , Nguyen Phuong , Litterman Adam J. , Shafer Shawn , Przybyla Laralynne , Chow Eric D.
Published: December 2022

The development of CRISPR genetic screening tools has improved functional genomics, as these tools enable precise genomic editing, provide broad access to genomic regions beyond protein-coding genes, and have fewer off-target effects than other functional genomics modalities, allowing for novel applications with smaller library sizes compared to prior technologies. Pooled functional genomics screens require high cellular coverage per perturbation to accurately quantify phenotypes and average out phenotype-independent variability across the population. While more compact libraries have decreased the number of cells needed for a given screen, the cell coverage required for large-scale CRISPR screens still poses technical hurdles to screen in more challenging systems, such as iPSC-derived and primary cells. A major factor that influences cell coverage is screening library uniformity, as larger variation in individual guide RNA abundance requires higher cell coverage to reliably measure low-abundance guides. In this work, we have systematically optimized guide RNA cloning procedures to decrease bias. We implement these protocols to demonstrate that CRISPRi screens using 10-fold fewer cells than the current standard provides equivalent statistically significant hit-calling results to screens run at higher coverage, opening the possibility of conducting genome-wide and other large-scale CRISPR screens in technically challenging models.
The Cost of Adaptability: Resource Availability Constrains Functional Stability Under Pulsed Disturbances
Authors: Rain-Franco Angel , Peter Hannes , de Moraes Guilherme P. , Beier Sara
Published: December 2022

Global change exposes ecosystems to changes in the frequency, magnitude and concomitancy of disturbances, which impact the composition and functioning. Here we experimentally evaluate effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The resistance, resilience and functional stability of these communities is critically important for water quality, productivity and consequently ecosystem services, such as fishery yields. Yet, little is known about the underlying traits. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. To study the impact of pulsed disturbances on community assembly and functioning in dependence of metabolic costs, we performed a 41-days pulse disturbance experiment crossed with two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability dependent patterns of superordinate community structural patterns and functioning, such as genomic trait distributions, species diversity, and functional resistance in response to disturbances. Genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings thereby mark an important step towards unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience. This has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.

Significance

Understanding the responses of communities to disturbances is a prerequisite to predict ecosystem dynamics and thus highly relevant in light of global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth and phenotypic plasticity of microorganisms are thought to allow for high resistance and resilience. While potential metabolic costs associated with adaptions to fluctuating environments have been debated, little evidence supports trade-offs between resource availability and resistance and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is encoded in genomic traits and constrained by resource availability.
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Authors: Penzar Dmitry , Nogina Daria , Noskova Elizaveta , Zinkevich Arsenii , Meshcheryakov Georgy , Lando Andrey , Rafi Abdul Muntakim , de Boer Carl , Kulakovskiy Ivan V.
Published: December 2022

Motivation

The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex deep learning approaches for DNA regulatory grammar.

Results

Here we introduce LegNet, an EfficientNetV2-inspired convolutional network for modeling short gene regulatory regions. By approaching the sequence-to-expression regression problem as a soft classification task, LegNet secured first place for theautosome.orgteam in the DREAM 2022 challenge of predicting gene expression from gigantic parallel reporter assays. Using published data, here we demonstrate that LegNet outperforms existing models and accurately predicts gene expressionper seas well as the effects of single-nucleotide variants. Furthermore, we show how LegNet can be used in a diffusion network manner for the rational design of promoter sequences yielding the desired expression level.

Availability and Implementation

https://github.com/autosome-ru/LegNet. The GitHub repository includes the Python code under the MIT license to reproduce the results presented in the study and a Jupyter Notebook tutorial.

Supplementary Information

Online-only supplementary data are available at Bioinformatics online.

Contact

dmitrypenzar1996@gmail.com,ivan.kulakovskiy@gmail.com
WUREN: Whole-modal fUsion Representation for protein interaction interfacE predictioN
Authors: Wang Xiaodong , Gao Xiangrui , Fan Xuezhe , Huai Zhe , Yao Mengcheng , Wang Tianyuan , Huang Xiaolu , Lai Lipeng
Published: December 2022

Proteins are one of the most important components in life, and the research on protein complex and the development of protein or antibody drugs relies on effective representation of proteins. Both experimental methods like cryo-electron microscopy and computational methods like molecular dynamic simulation suffer from high cost, long time investment and low throughput, and cannot be used in large-scale studies. Some examples of artificial intelligence for protein complex prediction tasks show that different representations of proteins have their own limitations. This paper constructs a multimodal model named WUREN (Whole-modal fUsion Representation for protein interaction interfacE predictioN), which effectively fuses sequence, graph, and structural features. WUREN has achieved state-of-the-art performance on both the antigen epitope prediction task and the protein-protein interaction interface prediction task, with AUC-PR reaching 0.462 and 0.516, respectively. Our results show that WUREN is a general and effective feature extraction model for protein complex, which can be used in the development of protein-based drugs. Furthermore, the general framework in WUREN can be potentially applied to model similar biologics to proteins, such as DNA and RNA.
Biodiversity and Conservation Priority Setting for the Vascular Flora of New Guinea
Authors: Smith Michael Gerard , Forest Felix , Rosindell James
Published: December 2022

Aims

New Guinea is one of the world’s most floristically diverse islands, but its plant collection records are very uneven. We aim to identify which areas have the highest diversity of vascular plant genera, and which areas have the highest deforestation risk. Combining these findings we highlight priority regions for research and conservation.

Location

New Guinea

Time period

1900–2021

Taxa studied

Tracheophyta (Vascular plants)

Methods

We obtained collection records and environmental variables and prepared a cost-distance map of New Guinea to indicate accessibility. We modelled the joint distribution of 1,156 genera with the ‘Hmsc’ package in R to predict biodiversity across space, accounting for collection bias. We combined these results with a genus-level phylogenetic tree to predict phylogenetic endemism. We then modelled deforestation risk with the ‘R-INLA’ package, using forest clearance data and variables including cost-distance. We compared actual and predicted deforestation, and made predictions for 2021–25. Finally, we developed a combined measure of predicted biodiversity plus deforestation risk.

Results

A mean Spearman’s rank correlation of 0.462 was obtained on five-fold cross-validation of the genus biodiversity model; bias-correction shifted the predicted distribution of biodiversity towards western New Guinea, but had less effect on estimates of phylogenetic endemism.

Predictions of relative deforestation probability were accurate over 5 and 10 years (Spearman values 0.66 and 0.71). We postulate a ‘deforestation debt’ to explain the persistence in accuracy. Over time, the areas which survive early deforestation gradually become more rewarding targets and the proportion of at-risk forest lost to clearance accumulates.

Main conclusions

We present a method for rapid assessment of biodiversity and deforestation risk in data-deficient tropical forest regions. Areas of high predicted biodiversity such as the Merauke and Jayapura lowlands are at high near-term risk from commercial deforestation, requiring urgent interventions to record and preserve threatened species.
Contact-number-driven virus evolution: a multi-level modeling framework for the evolution of acute or persistent RNA virus infection
Authors: Sunagawa Junya , Komorizono Ryo , Hart William S. , Thompson Robin N. , Makino Akiko , Tomonaga Keizo , Iwami Shingo , Yamaguchi Ryo
Published: December 2022

Viruses evolve in infected host populations, and host population dynamics affect viral evolution. RNA viruses with a short duration of infection and a high peak viral load, such as and SARS-CoV-2, are maintained in human populations. By contrast, RNA viruses characterized by a long infection duration and a low peak viral load (e.g., borna disease virus) can be maintained in nonhuman populations, and why the persistent viruses evolved has been rarely explored. Here, using a multi-level modeling approach including both individual-level virus infection dynamics and population-scale transmission, we consider virus evolution based on the host environment, specifically, the effect of the contact history of infected hosts. We found that, with a highly dense contact history, viruses with a high virus production rate but low accuracy are likely to be optimal, resulting in a short infectious period with a high peak viral load. In contrast, with a low-density contact history, viral evolution is toward low virus production but high accuracy, resulting in long infection durations with low peak viral load. Our study sheds light on the origin of persistent viruses and why acute viral infections but not persistent virus infection tends to prevail in human society.
Pheromone-based animal communication influences the production of somatic extracellular vesicles
Authors: Szczepańska Agata , Olek Katarzyna , Kołodziejska Klaudia , Yu Jingfang , Ibrahim Abdulrahman Tudu , Adamkiewicz Laura , Schroeder Frank C. , Pokrzywa Wojciech , Turek Michał
Published: December 2022

Extracellular vesicles (EVs) are involved in multiple biological processes; however, there is limited knowledge of the influence of environmental factors or other individuals in a population on EV-regulated systems. The largest evolutionarily conserved EVs, exophers, are a component of theC. elegansmaternal somatic tissue resource management system induced by embryos developingin utero, and thus progeny of individuals with active exopher biogenesis (exophergenesis) appear to be privileged. Using this model, we investigated the inter-tissue and social regulatory mechanisms of exophergenesis. We found that the predominant male pheromone, ascr#10, increases exopher production in hermaphrodites via the G-protein-coupled receptor STR-173 in the ASK sensory neurons. In contrast, pheromones from other hermaphrodites in the population temper exophergenesis. Within the hermaphrodite, an increase in embryo accumulation drives pro-exopher signals, and the internal sensory neurons AQR, PQR, and URX play a central role in modulating exopher levels. This intricate process is regulated partly via the neuropeptides FLP-8 and FLP-21, which originate from the URX and AQR/PQR/URX neurons, respectively. Our results reveal a regulatory network integrating internal and external cues, including control of somatic EVs production by the nervous system in response to social signals.
Understanding the effects of moisture content and temperature on dormancy release in sunflower (Helianthus annuusL) achenes
Authors: Arata Gonzalo Joaquín , Batlla Diego , Demkura Patricia Verónica , Rodríguez María Verónica
Published: December 2022

The effects of moisture content (MC) and storage temperature (ST) on seed longevity have been modeled for many species. In contrast, our understanding on the combined effects of MC and ST on dormancy release (DR) in “dry” orthodox seeds is still insufficient to build robust predictive models. We used freshly harvested, dormant sunflower achenes to explore the effects of MC (4-10%) in combination with a wide range of ST (−18°C to +30°C) on DR dynamics, embryo responsiveness to abscisic acid (ABA) and deterioration indicators. Storage temperatures allowing full DR were inversely related to achene MC, ranging from >25°C for MC4% to sub-zero temperatures for MC10%, resembling a phase diagram. Rates of DR were plotted along a RH gradient. Combinations of MCxST optimal for DR were betweenca. 40-60%RH. Increasing RH from 60 to 80% inhibited DR. Higher RH>80-85% promoted partial DR together with rapid ageing. We suggest that reactions promoting full DR are favored alongside a physical (glassy) transition and are not oxidative. We propose biophysical coordinates to guide future studies on the mechanisms involved in DR, but also to develop predictive models useful to define post-harvest conditions that maximize sunflower seed quality.

Highlights

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The effects of moisture content (MC) and storage temperature (ST) on dormancy release and deterioration were investigated in sunflower achenes using a factorial design.

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Dormancy release was promoted by MCxST combinations in equilibrium with a RH between 40 and 60% and was delayed outside this range.

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Storage temperatures optimal for dormancy release were inversely related to achene MC, ranging from >25°C for MC4% to sub-zero temperatures for MC10%, resembling a phase diagram.

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Dormancy release and ageing are promoted within distinct, non-overlapping regions along the RH gradient supporting different types of reactions for each process.
Disrupting central carbon metabolism increases antibiotic susceptibility inVibrio cholerae
Authors: Keller Megan , Han Xiang , Dörr Tobias
Published: December 2022

Antibiotic tolerance, the ability of bacteria to sustain viability in the presence of typically bactericidal antibiotics for extended time periods, is an understudied contributor to treatment failure. The Gram-negative pathogenVibrio cholerae, the causative agent of cholera disease, becomes highly tolerant to β-lactam antibiotics (penicillin and related compounds) in a process requiring the two-component system VxrAB. VxrAB is induced by exposure to cell wall damage conditions, which results in the differential regulation of >100 genes. While the effectors of VxrAB are relatively well-known, VxrAB environment-sensing and activation mechanisms remain a mystery. Here, we used transposon mutagenesis to screen for mutants that spontaneously upregulate VxrAB signaling. This screen was answered by genes known to be required for proper cell envelope homeostasis, validating the approach. Unexpectedly, we also uncovered a new connection between central carbon metabolism and antibiotic tolerance. Inactivation ofpgi(vc0374, coding for Glucose-6-phosphate isomerase) resulted in an intracellular accumulation of glucose-6-phosphate and fructose-6-phosphate, concomitant with a marked cell envelope defect, resulting in VxrAB induction. Deletion ofpgialso increased sensitivity to β-lactams and conferred a growth defect on salt-free LB; phenotypes that could be suppressed by deleting sugar uptake systems and by supplementing cell wall precursors in the growth medium. Our data suggest an important connection between central metabolism and cell envelope integrity and highlight a potential new target for developing novel antimicrobial agents.

Importance

Antibiotic tolerance (the ability to survive exposure to antibiotics) is a stepping-stone towards antibiotic resistance (the ability to grow in the presence of antibiotics), an increasingly common cause of antibiotic treatment failure. The mechanisms promoting tolerance are poorly understood. Herein, we discovered central carbon metabolism as a key contributor to antibiotic tolerance and resistance. A mutant in a sugar utilization pathway accumulates metabolites that likely shut down the synthesis of cell wall precursors, which weakens the cell wall and thus increases susceptibility to cell wall-active drugs. Our results illuminate the connection between central carbon metabolism and cell wall homeostasis inV. choleraeand suggest that interfering with metabolism may be a fruitful future strategy for development of antibiotic adjuvants.
Tumor Microenvironment Cellular Crosstalk Predicts Response to Adoptive TIL Therapy in Melanoma
Authors: Barras David , Ghisoni Eleonora , Chiffelle Johanna , Orcurto Angela , Dagher Julien , Fahr Noémie , Benedetti Fabrizio , Crespo Isaac , Zimmermann Stefan , Duran Rafael , Imbimbo Martina , de Olza Maria Ochoa , Navarro Blanca , Homiscko Krisztian , Bobisse Sara , Labes Danny , Tsourti Zoe , Andriakopoulou Charitini , Herrera Fernanda , Grimm Alizée , Morotti Matteo , Pétremand Rémy , Dummer Reinhard , Berthod Gregoire , Bassani-Sternberg Michal , Schaefer Niklaus , Prior John O , Matter Maurice , Demartines Nicolas , Aedo Veronica , Dromain Clarisse , Corria-Osorio Jesus , Tissot Stephanie , Kandalaft Lana E. , Gottardo Raphael , Pittet Mikael , Sempoux Christine , Michielin Olivier , Dafni Urania , Trueb Lionel , Harari Alexandre , Laniti Denarda Dangaj , Coukos George
Published: December 2022

Adoptive cell therapy (ACT) usingex vivoexpanded tumor-infiltrating T lymphocytes (TILs) can mediate responses in metastatic melanoma, but long-term efficacy remains limited to a fraction of patients. Here we interrogated tumor-microenvironment (TME) cellular states and interactions of longitudinal samples from 13 metastatic melanoma patients treated with TIL-ACT in our clinical study (NCT03475134). We performed single-cell RNA-seq and spatial proteomic analyses in pre- and post-ACT tumor tissues and showed that responders exhibited higher tumor cell-intrinsic immunogenicity. Also, endogenous CD8+TILs and myeloid cells of responders were characterized by increased cytotoxicity, exhaustion and costimulation and type-I IFN signaling, respectively. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders have rich baseline intratumoral and stromal tumor-reactive T-cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study reveals CD8+T-cell network-based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

One-Sentence Summary

Response to adoptive TIL therapy in melanoma is determined by CD8+TIL-myeloid cell networks
Combination of Expert Guidelines-based and Machine Learning-based Approaches Leads to Superior Accuracy of Automated Prediction of Clinical Effect of Copy Number Variations
Authors: Sládeček Tomáš , Gažiová Michaela , Kucharík Marcel , Zaťková Andrea , Pös Zuzana , Pös Ondrej , Krampl Werner , Tomková Erika , Hýblová Michaela , Minárik Gabriel , Radvanszky Ján , Budiš Jaroslav , Szemes Tomáš
Published: December 2022

Clinical interpretation of copy number variants (CNVs) is a complex process that requires skilled clinical professionals. General recommendations have been recently released to guide the CNV interpretation based on predefined criteria to uniform the decision process. Several semiautomatic computational methods have been proposed to recommend appropriate choices, relieving the clinicians from the tedious search in vast genomic databases. We have developed and evaluated such a tool called MarCNV and tested it on CNV records collected from the ClinVar database. Alternatively, the emerging machine learning-based tools, such as the recently published ISV (Interpretation of Structural Variants), showed promising ways of even fully automated predictions using wider characterization of affected genomic elements. Such tools utilize features that are additional to ACMG criteria, thus, they have the potential to significantly improve and/or provide supportive evidence for accurate CNV classification. Since both approaches contribute to evaluation of CNVs clinical impact, we propose a combined solution in the form of adecision support toolbased on automated ACMG guidelines (MarCNV) supplemented by a machine learning-based pathogenicity prediction (ISV) for classification of CNVs. We provide evidence that such a combined approach is able to reduce the number of uncertain classifications and reveal potentially incorrect classifications using automated guidelines. CNV interpretation using MarCNV, ISV, and combined approach is available for non-commercial use athttps://predict.genovisio.com/.
Structural perspective on the design of selective DYRK1B inhibitors
Authors: Grygier Przemyslaw , Pustelny Katarzyna , Menezes Filipe , Jemiola-Rzeminska Malgorzata , Suder Piotr , Dubin Grzegorz , Czarna Anna
Published: December 2022

DYRK1B, has been recently recognized as a critical therapeutic target in oncology, metabolic syndrome, and non-alcoholic fatty liver disease. However, the development of selective inhibitors for DYRK1B, has been constrained by the lack of structural information. In this study, we employed recombinant protein production, activity assays, and crystallization to elucidate the structure of DYRK1B. We present a crystal structure of DYRK1B in complex with a known inhibitor, AZ191. For comparative analysis, we provide the crystal structure of the closely related DYRK1A kinase in complex with AZ191. Our analysis identifies a distinct binding site in the hinge region of DYRK1B, which is pivotal for the design of selective inhibitors. Quantum mechanical calculations reveal a notable difference in the accessibility of the catalytic lysine between DYRK1B and DYRK1A, suggesting a potential avenue for selective inhibitor design. These findings mark a significant advancement in the quest for specific DYRK1B inhibitors, potentially offering focused efficacy compared to the current dual-specificity inhibitors targeting both DYRK1B and DYRK1A.
Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging
Authors: Renton Angela I. , Dao Thanh Thuy , Abbott David F. , Amos Toluwani J , Bollmann Saskia , Botting Andy , Campbell Megan E. J. , Chang Jeryn , Civier Oren , Close Thomas G. , Eckstein Korbinian , Egan Gary F. , Evas Stefanie , Flandin Guillaume , Garner Kelly G. , Garrido Marta I. , Ghosh Satrajit S , Grignard Martin , Hannan Anthony J. , Huber Renzo , Hughes Matthew E , Johnstone Tom , Kaczmarzyk Jakub R. , Kasper Lars , Kuhlmann Levin , Lou Kexin , Lyons Paris , Mantilla-Ramos Yorguin-Jose , Mattingley Jason B. , Morris Jo , Narayanan Akshaiy , Pestilli Franco , Puce Aina , Ribeiro Fernanda L. , Rogasch Nigel C. , Rorden Chris , Schira Mark , Shaw Thomas B. , Slade Benjamin M , Spitz Gershon , Stewart Ashley , Sullivan Ryan P. , White David J. , Ye Xincheng , Zhu Judy D. , Narayanan Aswin , Bollmann Steffen
Published: December 2022

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.
GSK3 and Lamellipodin balance lamellipodial protrusions and focal adhesion maturation in mouse neural crest migration
Authors: Dobson Lisa , Barrell William B , Seraj Zahra , Lynham Steven , Wu Sheng-yuan , Krause Matthias , Liu Karen J
Published: December 2022

Neural crest cells are multipotent cells that delaminate from the neuroepithelium, migrating to distant destinations throughout the embryo. Aberrant migration has severe consequences, such as congenital disorders. While animal models have improved our understanding of neural crest anomalies, the in vivo contributions of actin-based protrusions are still poorly understood. Here, we demonstrate that murine neural crest cells use lamellipodia and filopodia in vivo. Using neural crest-specific knockouts or inhibitors, we show that the serine-threonine kinase, Glycogen Synthase Kinase-3 (GSK3), and the cytoskeletal regulator, Lamellipodin (Lpd), are required for lamellipodia formation whilst preventing focal adhesion maturation. We consequently identified Lpd as a novel substrate of GSK3 and found that phosphorylation of Lpd favours Lpd interactions with the Scar/WAVE complex (lamellipodia formation) at the expense of Ena/VASP protein interactions (adhesion maturation and filopodia formation). All together, we provide an improved understanding of cytoskeletal regulation in mammalian neural crest migration, which has general implications for neural crest anomalies and cancer.
Neuronal-immune Axis Alters Pain and Sensory Afferent Damage During Dental Pulp Injury
Authors: Erdogan Ozge , Michot Benoit , Xia Jinya , Alabdulaaly Lama , Rubi Pilar Yesares , Chiu Isaac , Gibbs Jennifer L.
Published: December 2022

Dental pulp tissue is densely innervated by afferent fibers of the trigeminal ganglion. When bacteria cause dental decay near the pulpal tissue, a strong neuronal and immune response occur, creating pulpitis, which is associated with severe pain and pulp tissue damage. Neuro-immune interactions have the potential to modulate both the pain and pathological outcome of pulpitis. We first investigated the role of the neuropeptide calcitonin-gene related peptide (CGRP), released from peptidergic sensory afferents, in dental pain and immune responses by using calca knock out (calca−/−) and wild type (calca+/+) mice, in a model of pulpitis by creating a mechanical exposure of the dental pulp horn. While CGRP did not contribute to facial mechanical hypersensitivity, at an early time point, it did contribute to spontaneous pain-like behavior. We also found that CGRP contributed to recruitment of neutrophils and monocytes, while not clearly affecting the progression of pulpal pathology histologically. When we depleted neutrophils and monocytes, we found that there was more sensory afferent loss, tissue damage and deeper spread of bacteria into the pulp tissue, while there was a reduction in facial mechanical hypersensitivity compared to control animals at a later time point. Overall, we showed that there is a crosstalk between peptidergic neurons and neutrophils in the pulp, modulating the pain and inflammatory outcomes of the disease.
Detection of A-to-I microRNA editing with miRmedon reveals widespread co-editing of mature microRNA in the human brain
Authors: Mordechai Amitai , Eran Alal
Published: December 2022

microRNA (miRNA), key regulators of gene expression, are prime targets for adenosine deaminase acting on RNA (ADAR) enzymes. Although ADAR-mediated adenosine-to-inosine (A-to-I) miRNA editing has been shown to be essential for orchestrating complex processes, including neurodevelopment and cancer progression, only few human miRNA editing sites have been reported. Several computational approaches have been developed for the detection of miRNA editing in small RNAseq data, all based on the identification of systematic mismatches of ‘G’ at primary adenosine sites in known miRNA sequences. However, these methods have several limitations, including their ability to detect only one editing site per sequence (although editing of multiple sites per miRNA has been reproducibly validated), their focus on uniquely mapping reads (even though 20% of human miRNA are transcribed from multiple loci), and their inability to detect editing in miRNA harboring genomic variants (though 73% of human miRNA loci include a reported SNP or indel). To overcome these limitations, we developed miRmedon, that leverages large-scale human variation data, a combination of local and global alignments, and a comparison of the inferred editing and error distributions, for confident detection of miRNA editing in small RNAseq data. We demonstrate the improved performance of miRmedon as compared to currently available methods and describe its advantages. We further use miRmedon to discover editing haplotypes of mature human brain miRNA for the first time. We find that doubly edited mature miRNA are common in the adult human prefrontal cortex, most include a frequently edited site within the miRNA seed region, and are predicted to maintain a stable pre-miRNA structure. These results suggest that co-editing of mature miRNA could enable efficient shifting of gene expression programs.
Generation and characterization of two immortalized dermal fibroblast cell lines from the spiny mouse (Acomys)
Authors: Dill Michele N. , Tabatabaei Mohammad , Kamat Manasi , Basso Kari B. , Simmons Chelsey S.
Published: December 2022

The spiny mouse (Acomys) is gaining popularity as a research organism due to its phenomenal regenerative capabilities.Acomysrecovers from injuries to several organs without fibrosis. For example,Acomysheals full thickness skin injuries with rapid re-epithelialization of the wound and regeneration of hair follicles, sebaceous glands, erector pili muscles, adipocytes, and dermis without scarring. Understanding mechanisms ofAcomysregeneration may uncover potential therapeutics for wound healing in humans. However, access toAcomyscolonies is limited and primary fibroblasts can only be maintained in culture for a limited time. To address these obstacles, we generated immortalizedAcomysdermal fibroblast cell lines using two methods: transfection with the SV40 large T antigen and spontaneous immortalization. The two cell lines (AcoSV40 and AcoSI-1) maintained the morphological and functional characteristics of primaryAcomysfibroblasts, including maintenance of key fibroblast markers and ECM deposition. The availability of these cells will lower the barrier to working withAcomysas a model research organism, increasing the pace at which new discoveries to promote regeneration in humans can be made.
Discovery of prevalent naturalWolbachiainAedes aegyptiin Metropolitan Manila, Philippines using locally designed primers: bacterial density is influenced by strain and host sex
Authors: Reyes Jerica Isabel L. , Suzuki Takahiro , Suzuki Yasutsugu , Watanabe Kozo
Published: December 2022

Wolbachiaare maternally transmitted bacteria that are utilized for arboviral disease prevention. Cytoplasmic incompatibility (CI) and viral blocking, two characteristics that makeWolbachiasuitable for vector control, both depend on bacterial infection prevalence and density. Although numerous mosquito species naturally harborWolbachia, the prevalence ofWolbachiainAedes aegyptivaries from minimal to absent. The absence of naturalWolbachiainAe. aegyptiis considered advantageous for novelWolbachiatransinfection because interference caused by incompatibleWolbachiastrains will not occur. In this study, we screened forWolbachiadensity in 429 individualAe. aegypticollected from Metropolitan Manila, Philippines using locally designed primers to determine whether primer compatibility improvesWolbachiadetection in naturally infectedAe. aegypti. We also investigated the effects of host sex andWolbachiastrain onWolbachiadensity. We found a highWolbachiaprevalence for16S rRNA(40%) andwsp(62%) markers. RelativeWolbachiadensities ranged from −3.840 to 2.710 for16S rRNAand from −4.020 to 1.810for wsp, and these relative densities were higher among male mosquitoes than female mosquitoes. Phylogenetic analysis revealed that most of theAe. aegyptiwere clustered into supergroup B, with 63% (142/226) of these sequences representing a unique strain referred to here as “wAegML,” which exhibited a significantly lower density inAe. aegyptithan the other twoWolbachiastrains detected (wAegB/wAlbB andwAlbA) as well as a higher density in maleAe. aegyptithan in females. Overall, locally designed primers improvedWolbachiadetection in naturally infectedAe. aegypti. The unique strainwAegML occurs at a low density and is related to the use ofwAlbB in mass-release programs; therefore, it is unlikely to interfere with such programs. Further studies on naturalWolbachiainfection inAe. aegypticombining methodological and biological factors are warranted to help resolve current conflicts in the field.
Single-cell analysis maps distinct cellular responses to rhizobia and identifies the novel infection regulator SYMRKL1 inLotus japonicus
Authors: Frank Manuel , Fechete Lavinia Ioana , Tedeschi Francesca , Nadzieja Marcin , Malekzadeh Nørgaard Malita Malou , Montiel Jesus , Andersen Kasper Røjkjær , Schierup Mikkel H. , Reid Dugald , Andersen Stig Uggerhøj
Published: December 2022

Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we nameSYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.
Combination of transcriptomic, proteomic and degradomic profiling reveals common and distinct patterns of pathogen-induced cell death in maize
Authors: Barghahn Sina , Saridis Georgios , Mantz Melissa , Meyer Ute , Mellüh Jaqueline C , Misas Villamil Johana C , Huesgen Pitter F , Doehlemann Gunther
Published: December 2022

Regulated cell death (RCD) is crucial for plant development, as well as in decision-making in plant-microbe interactions. Previous studies revealed components of the molecular network controlling RCD, including different proteases. However, the identity, the proteolytic network as well as molecular components involved in the initiation and execution of distinct plant RCD processes, still remain largely elusive. In this study, we analyzed the transcriptome, proteome and N-terminome ofZ. maysleaves treated with the Xanthomonas effector avrRxo1, the mycotoxin Fumonisin B1 (FB1), or the phytohormone salicylic acid (SA) to dissect plant cellular processes related to cell death and plant immunity. We found highly distinct and time-dependent biological processes being activated on transcriptional and proteome levels in response to avrRxo1, FB1 and SA. A correlation analysis of the transcriptome and proteome identified general, as well as trigger-specific markers for cell death inZ. mays. We found that proteases, particularly papain-like cysteine proteases, are specifically regulated during RCD. Collectivley, this study characterizes distinct RCD responses inZ. maysand provides a framework for the mechanistic exploration of components involved in the initiation and execution of cell death.
Unbalancing cAMP and Ras/MAPK pathways as a therapeutic strategy for cutaneous neurofibromas
Authors: Mazuelas Helena , Magallón-Lorenz Míriam , Uriarte-Arrázola Itziar , Negro Alejandro , Rosas Inma , Blanco Ignacio , Castellanos Elisabeth , Lázaro Conxi , Gel Bernat , Carrió Meritxell , Serra Eduard
Published: December 2022

Cutaneous neurofibromas (cNFs) are benign Schwann cell (SC) tumors arising from subepidermal glia. Neurofibromatosis Type 1 (NF1) individuals may develop thousands of cNFs, greatly affecting their quality of life. cNF growth is governed by the proliferation ofNF1(-/-) SCs, highly influenced by the interaction with aNF1(+/-) microenvironment, consisting of fibroblasts (FBs), immune cells, etc. To decompose crosstalk between SCs and the microenvironment we used single cultures and co-cultures of cNF-derived SCs and FBs and identified an expression signature specific to SC-FB interaction. This signature was enriched in genes involved in immune cell migration, that were functionally validated by secretion analysis of SC-FB co-cultures, suggesting a role of SC-FB crosstalk in immune cell recruitment. The signature also captured components of different developmental signaling pathways, among them, the cAMP elevator G protein-coupled receptor 68 (GPR68). Activation of Gpr68 by Ogerin reduced the viability and proliferation of cNF-derived SCs and SC-FB co-cultures. Moreover, Ogerin in combination with the MEKi Selumetinib induced loss of viability, SC differentiation, and death. These results were corroborated using an iPSC-derived 3D neurofibromasphere model. The unbalancing of the Ras and cAMP pathways by combining a MEKi and a cAMP elevator arises as a potential treatment for cNFs.
PhyloAcc-GT: A Bayesian method for inferring patterns of substitution rate shifts and associations with binary traits under gene tree discordance
Authors: Yan Han , Hu Zhirui , Thomas Gregg , Edwards Scott V. , Sackton Timothy B. , Liu Jun S.
Published: December 2022

An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype to phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity to detect rate shifts across genomic regions. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target-lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. In summary, PhyloAcc-GT is a useful tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
Reliability of resting-state functional connectivity in the human spinal cord: assessing the impact of distinct noise sources
Authors: Kaptan Merve , Horn Ulrike , Vannesjo S. Johanna , Mildner Toralf , Weiskopf Nikolaus , Finsterbusch Jürgen , Brooks Jonathan C.W. , Eippert Falk
Published: December 2022

The investigation of spontaneous fluctuations of the blood-oxygen-level-dependent (BOLD) signal has recently been extended from the brain to the spinal cord, where it has stimulated interest from a clinical perspective. A number of resting-state functional magnetic resonance imaging (fMRI) studies have demonstrated robust functional connectivity between the time series of BOLD fluctuations in bilateral dorsal horns and between those in bilateral ventral horns, in line with the functional neuroanatomy of the spinal cord. A necessary step prior to extension to clinical studies is assessing the reliability of such resting-state signals, which we aimed to do here in a group of 45 healthy young adults at the clinically prevalent field strength of 3T. When investigating connectivity in the entire cervical spinal cord, we observed fair to good reliability for dorsal-dorsal and ventral-ventral connectivity, whereas reliability was poor for within- and between-hemicord dorsal-ventral connectivity. Considering how prone spinal cord fMRI is to noise, we extensively investigated the impact of distinct noise sources and made two crucial observations: removal of physiological noise led to a reduction in functional connectivity strength and reliability – due to the removal of stable and participant-specific noise patterns – whereas removal of thermal noise considerably increased the detectability of functional connectivity without a clear influence on reliability. Finally, we also assessed connectivity within spinal cord segments and observed that while the pattern of connectivity was similar to that of whole cervical cord, reliability at the level of single segments was consistently poor. Taken together, our results demonstrate the presence of reliable resting-state functional connectivity in the human spinal cord even after thoroughly accounting for physiological and thermal noise, but at the same time urge caution if focal changes in connectivity (e.g. due to segmental lesions) are to be studied, especially in a longitudinal manner.