bluuebunny/crossref_metadata_2025 huggingface dataset:
Longitudinal Investigation of Aortic Dissection in Mice with Computational Fluid Dynamics
Authors: Bäumler Kathrin , Phillips Evan H. , Gutiérrez Noelia Grande , Fleischmann Dominik , Marsden Alison L. , Goergen Craig J.
Published: April 2023

Patients with aortic dissection require lifelong surveillance to monitor disease progression and detect late adverse events such as aneurysmal dilation, malperfusion or refractory pain. The variety and complexity of aortic dissection have so far eluded definitive predictions of occurrence and timing of late adverse events. The search for early indicators of late adverse events has been based mostly on morphologic features, and one commonly observed risk factor is partial thrombosis of the false lumen. While the effect of partial thrombosis on disease progression is incompletely understood, hemodynamic factors, including low velocity or stagnant flow, are likely to play a role. In this study we investigated the progression of false lumen intramural thrombus formation in four mice with angiotensin IIinduced aortic dissection. Based on 3D B-mode ultrasound images, we created segmentations of the diseased aorta including the true lumen, false lumen, and thrombus. These geometries were then used to run computational fluid dynamic simulations with subject-specific boundary conditions. Each mouse was followed for seven days and 4-5 longitudinal image datasets were acquired for each animal. We found that false lumina with a single entry tear tend to have smaller mean relative velocities, and at the same time are subject to a larger false lumen thrombus ratio. Likewise, regions of low velocity correlated with regions of elevated endothelial cell activation potential and higher particle residence times. These findings support the hypothesis that flow stagnation is the predominant hemodynamic factor that results in a large thrombus ratio in false lumina, particularly those with a single entry tear. Additional work will be needed to further explore the intricacies of these complex experimental vascular lesions and how the hemodynamic conditions compare to human aortic dissections.
Rising minimum temperatures contribute to 50 years of shifting Arctic and boreal butterfly communities in North America
Authors: Shirey Vaughn , Neupane Naresh , Guralnick Robert , Ries Leslie
Published: April 2023

Abstract

Global climate change has been identified as a major driver of observed insect declines, yet in many regions there are critical knowledge gaps for how communities are responding to climate. Poleward regions are of particular interest because warming is most rapid while biodiversity data are most sparse. Building on recent advances in occupancy modeling of presence-only data, we reconstructed 50 years (1970-2019) of butterfly population trends in response to rising minimum temperatures in one of the most under sampled regions of the continent. Among 90 modeled species, we found that cold-adapted species are far more often in decline compared to their warm-adapted, more southerly distributed counterparts. Further, in a post-hoc analysis using species’ traits, we find that species’ range-wide average annual temperature and wingspan are a consistent predictor of occupancy changes. Species with warmer ranges and larger wingspans were most likely to be increasing in occupancy. Our results provide the first look at macroscale butterfly biodiversity shifts in a critically under sampled region of North America. Further, these results highlight the potential of leveraging the wealth of presence only data, the most abundant source of historical insect biodiversity. New approaches to the modeling of presence only data will match recent increases in community science participation with sparse historical records to reconstruct trends even in poorly sampled regions.
Amphiphilic particle-stabilized nanoliter droplet reactors with a multi-modal portable reader for distributive biomarker quantification
Authors: Shah Vishwesh , Yang Xilin , Arnheim Alyssa , Udani Shreya , Tseng Derek , Luo Yi , Ouyang Mengxing , Destgeer Ghulam , Garner Omai , Koydemir Hatice , Ozcan Aydogan , Carlo Dino Di
Published: April 2023

Compartmentalization, leveraging microfluidics, enables highly sensitive assays; but the requirement for significant infrastructure for their design, build, and operation limits access. Newer multi-material particle-based technologies thermodynamically stabilize monodisperse droplets as individual reaction compartments with simple liquid handling steps, precluding the need for expensive microfluidic equipment. Here, we further improve the accessibility of this lab on a particle technology to resource-limited settings by combining this assay system with a portable multi-modal reader, thus enabling nanoliter droplet assays in an accessible platform. We show the utility of this platform in measuring N-terminal propeptide B-type natriuretic peptide (NT-proBNP), a heart failure biomarker, in complex medium and patient samples. We report a limit of detection of ∼0.05 ng/ml and a linear response between 0.2 – 2 ng/ml in spiked plasma samples. We also show that, owing to the plurality of measurements per sample, “swarm” sensing acquires better statistical quantitation with a portable reader. Monte Carlo simulations show the increasing capability of this platform to differentiate between negative and positive samples, i.e. below or above the clinical cut-off for acute heart failure (∼0.1ng/ml), as a function of the number of particles measured. Our platform measurements correlate with gold standard ELISA measurement in cardiac patient samples, and achieve lower variation in measurement across samples compared to the standard well plate-based ELISA. Thus, we show the capabilities of a cost-effective droplet-reader system in accurately measuring biomarkers in nanoliter droplets for diseases that disproportionally affect underserved communities in resource-limited settings.
Study replication: Shape discrimination in a conditioning procedure on the jumping spiderPhidippus regius
Authors: Mannino Eleonora , Regolin Lucia , Moretto Enzo , De Agrò Massimo
Published: April 2023

Jumping spiders possess a unique visual system, split into 8 different eyes and divided into two fully independent visual pathways. This peculiar organization begs the question of how visual information is processed, and whether the classically recognized gestalt rules of perception hold true. In a previous experiment, we tested the ability of jumping spiders to associate a geometrical shape with a reward (sucrose solution), and then to generalize the learned association to a partially occluded version of it. The occluded shape was presented together with a broken version of the same shape. The former should be perceived as a whole shape only in the case the animals, like humans, are able of amodally complete an object partly hidden by an occluder; otherwise, the two shapes would be perceived as identical. There, the spiders learned the association but failed to generalize. Here, we present a replication of the experiment, with an increased number of subjects, a DeepLabCut-based scoring procedure, and an improved statistical analysis. The results of the experiment follow closely the direction of the effects observed in the previous work but fail to raise to significance. We discuss the importance of study replication, and we especially highlight the use of automated scoring procedures to maximize objectivity in behavioural studies.
A methodology combining reinforcement learning and simulation to optimize thein silicoculture of epithelial sheets
Authors: Castrignanò Alberto , Bardini Roberta , Savino Alessandro , Di Carlo Stefano
Published: April 2023

Tissue Engineering (TE) and Regenerative Medicine (RM) aim to replicate and replace tissues for curing disease. However, full tissue integration and homeostasis are still far from reach. Biofabrication is an emerging field that identifies the processes required for generating biologically functional products with the desired structural organization and functionality and can potentially revolutionize the regenerative medicine domain, which aims to use patients’ cells to restore the structure and function of damaged tissues and organs. However, biofabrication still has limitations in the quality of processes and products. Biofabrication processes are often improved empirically, but this is slow, costly, and provides partial results. Computational approaches can tap into biofabrication underused potential, supporting analysis, modeling, design, and optimization of biofabrication processes, speeding up their improvement towards a higher quality of products and subsequent higher clinical relevance. This work proposes a reinforcement learning-based computational design space exploration methodology to generate optimal in-silico protocols for the simulated fabrication of epithelial sheets. The optimization strategy relies on a Deep Reinforcement Learning (DRL) algorithm, the Advantage-Actor Critic, which relies on a neural network model for learning. In contrast, simulations rely on the PalaCell2D simulation framework. Validation demonstrates the proposed approach on two protocol generation targets: maximizing the final number of obtained cells and optimizing the spatial organization of the cell aggregate.
Time-course of antipredator behavioral changes induced by the helminthPomphorhynchus laevisin its intermediate hostGammarus pulex: the switch in manipulation according to parasite developmental stage differs between behaviors
Authors: Rigaud Thierry , Balourdet Aude , Bauer Alexandre
Published: April 2023

Many trophically transmitted parasites with complex life cycles manipulate their intermediate host’s antipredatory defenses in ways facilitating their transmission to final host by predation. Some parasites also protect the intermediate host from predation when noninfective during its ontogeny. The acanthocephalanPomphorynchus laevis, a fish intestinal helminth, infecting freshwater gammarid amphipods as intermediate hosts, is using such a strategy of protection-then-exposure to predation by the definitive host. However, the whole time-course of this sequence of behavioral switch is not yet known, and only one antipredator behavior has been studied to date. Here we show that the protective part of this manipulation begins quite late during the parasite ontogeny, suggesting that the advantages overpass the costs induced by this protective manipulation only at this stage. We confirmed that the refuge use behavior is showing a switch in the few days following the stage mature for the definitive host (switching from overuse to underuse). However, such a switch was not observed for the gammarids activity rate, a behavior also known to make the host less conspicuous to predators when weak. While we predicted a low activity during early development stages, then a switch to high activity, we observed general decrease in activity during the parasite ontogeny. The possible causes for this discrepancy between behaviors are discussed. All these behavioral changes were observed mostly when animals were tested in water scented by potential predators (here brown trout), suggesting condition-dependent manipulation.
Electrophysiological signatures of anxiety in Parkinson’s disease
Authors: Yassine Sahar , Almarouk Sourour , Gschwandtner Ute , Auffret Manon , Hassan Mahmoud , Verin Marc , Fuhr Peter
Published: April 2023

Anxiety is a common non-motor symptom in Parkinson’s disease (PD) occurring in up to 31% of the patients and affecting their quality of life. Despite the high prevalence, anxiety symptoms in PD are often underdiagnosed and, therefore, undertreated. To date, functional and structural neuroimaging studies have contributed to our understanding of the motor and cognitive symptomatology of PD. Yet, the underlying pathophysiology of anxiety symptoms in PD remains largely unknown and studies on their neural correlates are missing. Here, we used resting state electroencephalography (RS-EEG) of 68 non-demented PD patients with or without clinically-defined anxiety and 25 healthy controls (HC) to assess spectral and functional connectivity fingerprints characterizing the PD-related anxiety. When comparing the brain activity of the PD anxious group (PD-A, N=18) to both PD non-anxious (PD-NA, N=50) and HC groups (N=25) at baseline, our results showed increased fronto-parietal delta power and decreased frontal beta power depicting the PD-A group. Results also revealed hyper-connectivity networks predominating in delta, theta and gamma bands against prominent hypo-connectivity networks in alpha and beta bands as network signatures of anxiety in PD where the frontal, temporal, limbic and insular lobes exhibited the majority of significant connections. Moreover, the revealed EEG-based electrophysiological signatures were strongly associated with the clinical scores of anxiety over the course of the disease. We believe that the identification of the electrophysiological correlates of anxiety in PD using EEG is conducive toward more accurate prognosis and diagnosis and can ultimately support the development of new therapeutics strategies.
Group 2 innate lymphoid cells constrain type 3/17 lymphocytes in shared stromal niches to restrict liver fibrosis
Authors: Sbierski-Kind Julia , Cautivo Kelly M , Wagner Johanna C , Dahlgren Madelene W , Nilsson Julia , Krasilnikov Maria , Mroz Nicholas M. , Lizama Carlos O. , Gan Anna Lu , Matatia Peri R , Taruselli Marcela T , Chang Anthony A , Caryotakis Sofia , O’Leary Claire E , Kotas Maya , Mattis Aras N , Peng Tien , Locksley Richard M , Molofsky Ari B
Published: April 2023

Group 2 innate lymphoid cells (ILC2s) cooperate with adaptive Th2 cells as key organizers of tissue type 2 immune responses, while a spectrum of innate and adaptive lymphocytes coordinate early type 3/17 immunity. Both type 2 and type 3/17 lymphocyte associated cytokines are linked to tissue fibrosis, but how their dynamic and spatial topographies may direct beneficial or pathologic organ remodelling is unclear. Here we used volumetric imaging in models of liver fibrosis, finding accumulation of periportal and fibrotic tract IL-5+lymphocytes, predominantly ILC2s, in close proximity to expanded type 3/17 lymphocytes and IL-33highniche fibroblasts. Ablation of IL-5+lymphocytes worsened carbon tetrachloride-and bile duct ligation-induced liver fibrosis with increased niche IL-17A+type 3/17 lymphocytes, predominantly γδ T cells. In contrast, concurrent ablation of IL-5+and IL-17A+lymphocytes reduced this progressive liver fibrosis, suggesting a cross-regulation of type 2 and type 3 lymphocytes at specialized fibroblast niches that tunes hepatic fibrosis.
Active Transport by Cytoplasmic Dynein Maintains the Localization of MAP2 in Developing Neurons
Authors: Yonemura Yoji , Sakai Yuri , Nakata Rinaho , Hagita-Tatsumoto Ayaka , Miyasaka Tomohiro , Misonou Hiroaki
Published: April 2023

MAP2 has been widely used as a marker of neuronal dendrites because of its extensive restriction in the somatodendritic region of neurons. Despite that, how the precise localization of such a soluble protein is established and maintained against thermal forces and diffusion has been elusive and long remained a mystery in neuroscience. In this study, we aimed to uncover the mechanism behind how MAP2 is retained in the somatodendritic region. Using GFP-tagged MAP2 expressed in cultured hippocampal neurons, we discovered a crucial protein region responsible for the localization of MAP2, the serine/proline-rich (S/P) region. Our pulse-chase live-cell imaging revealed the slow but steady migration of MAP2 toward distal dendrites, which was not observed in a MAP2 mutant lacking the S/P region, indicating that S/P-dependent transport is vital for the proper localization of MAP2. Furthermore, our experiments using an inhibitor of cytoplasmic Dynein, ciliobrevin D, as well as Dynein knockdown, showed that cytoplasmic Dynein is involved in the transport of MAP2 in dendrites. We also found that Dynein complex binds to MAP2 through the S/P region in heterologous cells. Using mathematical modeling based on experimental data, we confirmed that an intermittent active transport mechanism is essential. Thus, we propose that the cytoplasmic Dynein recruits and transports free MAP2 toward distal dendrites, thereby maintaining the precise dendritic localization of MAP2 in neurons. Our findings shed light on the previously unknown mechanism behind MAP2 localization and provide a new direction for soluble protein trafficking research in the field of cell biology of neurons.
Spinal Cord Injury regulates circular RNA expression in axons
Authors: Siddiq Mustafa M. , Toro Carlos A. , Johnson Nicholas P. , Hansen Jens , Xiong Yuguang , Mellado Wilfredo , Tolentino Rosa E. , Johnson Kaitlin , Jayaraman Gomathi , Suhail Zaara , Harlow Lauren , Beaumont Kristin G. , Sebra Robert , Willis Dianna E. , Cardozo Christopher P. , Iyengar Ravi
Published: April 2023

Introduction

Neurons transport mRNA and translational machinery to axons for local translation. After spinal cord injury (SCI),de novotranslation is assumed to enable neurorepair. Knowledge of the identity of axonal mRNAs that participate in neurorepair after SCI is limited. We sought to identify and understand how axonal RNAs play a role in axonal regeneration.

Methods

We obtained preparations enriched in axonal mRNAs from control and SCI rats by digesting spinal cord tissue with cold-active protease (CAP). The digested samples were then centrifuged to obtain a supernatant that were then sequenced. We used bioinformatics analyses to identify DEGS and map them to various biological processes. We validated the DEGs by RT-qPCR and RNA-scope.

Results

The supernatant fraction was highly enriched for axonal mRNA. Using Gene Ontology, the second most significant pathway for all differentially expressed genes (DEGs) was axonogenesis. Among the DEGs was Rims2, which is predominately a circular RNA (circRNA) in the CNS. We show that Rims2 RNA within spinal cord axons is circular. We found an additional 200 putative circRNAs in the axonal-enriched fraction. Knockdown in primary rat cortical neurons of the RNA editing enzyme ADAR1, which inhibits formation of circRNAs, significantly increased axonal outgrowth. Focusing on Rims2 we used Circular RNA Interactome to predict that several of the miRNAs that bind to circRims2 also bind to the 3’UTR of GAP-43, PTEN or CREB1, all known regulators of axonal outgrowth. Axonally-translated GAP-43 supports axonal elongation and we detect GAP-43 mRNA in the rat axons by RNAscope.

Discussion

By using our method for enrichment of axonal RNA, we detect SCI induced DEGs, including circRNA such as Rims2. Ablation of ADAR1, the enzyme that regulates circRNA formation, promotes axonal outgrowth of cortical neurons. We developed a pathway model using Circular RNA Interactome that indicates that Rims2 through miRNAs can regulate the axonal translation GAP-43 a known regulator of axonal regeneration indicating that axonal mRNA contribute to regeneration.
Evaluation and optimization of sequence-based gene regulatory deep learning models
Authors: Rafi Abdul Muntakim , Nogina Daria , Penzar Dmitry , Lee Dohoon , Lee Danyeong , Kim Nayeon , Kim Sangyeup , Kim Dohyeon , Shin Yeojin , Kwak Il-Youp , Meshcheryakov Georgy , Lando Andrey , Zinkevich Arsenii , Kim Byeong-Chan , Lee Juhyun , Kang Taein , Vaishnav Eeshit Dhaval , Yadollahpour Payman , DREAM Challenge Consortium Random Promoter , Kim Sun , Albrecht Jake , Regev Aviv , Gong Wuming , Kulakovskiy Ivan V. , Meyer Pablo , de Boer Carl
Published: April 2023

Neural networks have emerged as immensely powerful tools in predicting functional genomic regions, notably evidenced by recent successes in deciphering gene regulatory logic. However, a systematic evaluation of how model architectures and training strategies impact genomics model performance is lacking. To address this gap, we held a DREAM Challenge where competitors trained models on a dataset of millions of random promoter DNA sequences and corresponding expression levels, experimentally determined in yeast, to best capture the relationship between regulatory DNA and gene expression. For a robust evaluation of the models, we designed a comprehensive suite of benchmarks encompassing various sequence types. While some benchmarks produced similar results across the top-performing models, others differed substantially. All top-performing models used neural networks, but diverged in architectures and novel training strategies, tailored to genomics sequence data. To dissect how architectural and training choices impact performance, we developed the Prix Fixe framework to divide any given model into logically equivalent building blocks. We tested all possible combinations for the top three models and observed performance improvements for each. The DREAM Challenge models not only achieved state-of-the-art results on our comprehensive yeast dataset but also consistently surpassed existing benchmarks on Drosophila and human genomic datasets. Overall, we demonstrate that high-quality gold-standard genomics datasets can drive significant progress in model development.
Protective effects of polyphenol-rich extracts against neurotoxicity elicited by paraquat or rotenone in cellular models of Parkinson’s disease
Authors: Tambe Mitali A. , de Rus Jacquet Aurelie , Strathearn Katherine E. , Yousef Gad G. , Grace Mary H. , Ferruzzi Mario G. , Wu Qingli , Simon James E. , Lila Mary Ann , Rochet Jean-Christophe
Published: April 2023

Parkinson’s disease (PD) is a neurodegenerative disorder involving motor symptoms caused by a loss of dopaminergic neurons in the substantia nigra region of the brain. Epidemiological evidence suggests that anthocyanin (ANC) intake is associated with a low risk of PD. Previously, we reported that extracts enriched with ANC and proanthocyanidins (PAC) suppressed dopaminergic neuron death elicited by the PD-related toxin rotenone in a primary midbrain culture model. Here, we characterized botanical extracts enriched with a mixed profile of polyphenols, as well as a set of purified polyphenolic standards, in terms of their ability to mitigate dopaminergic cell death in midbrain cultures exposed to another PD-related toxicant, paraquat (PQ), and we examined underlying neuroprotective mechanisms. Extracts prepared from blueberries, black currants, grape seeds, grape skin, mulberries, and plums, as well as several ANC, were found to rescue dopaminergic neuron loss in PQ-treated cultures. Comparison of a subset of ANC-rich extracts for the ability to mitigate neurotoxicity elicited by PQ versus rotenone revealed that a hibiscus or plum extract was only neuroprotective in cultures exposed to rotenone or PQ, respectively. Several extracts or compounds with the ability to protect against PQ neurotoxicity increased the activity of the antioxidant transcription factor Nrf2 in cultured astrocytes, and PQ-induced dopaminergic cell death was attenuated in Nrf2-expressing midbrain cultures. In other studies, we found that extracts prepared from hibiscus, grape skin, or purple basil (but not plums) rescued defects in O2consumption in neuronal cells treated with rotenone. Collectively, these findings suggest that extracts enriched with certain combinations of ANC, PAC, stilbenes, and other polyphenols could potentially slow neurodegeneration in the brains of individuals exposed to PQ or rotenone by activating cellular antioxidant mechanisms and/or alleviating mitochondrial dysfunction.
Learning the Language of Antibody Hypervariability
Authors: Singh Rohit , Im Chiho , Qiu Yu , Mackness Brian , Gupta Abhinav , Sorenson Taylor , Sledzieski Samuel , Erlach Lena , Wendt Maria , Nanfack Yves Fomekong , Bryson Bryan , Berger Bonnie
Published: April 2023

Protein language models (PLMs) based on machine learning have demon-strated impressive success in predicting protein structure and function. However, general-purpose (“foundational”) PLMs have limited performance in predicting antibodies due to the latter’s hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a new transfer learning framework called AbMAP, which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples. Our feature representations accurately predict an antibody’s 3D structure, mutational effects on antigen binding, and paratope identification. AbMAP’s scalability paves the way for large-scale analyses of human antibody repertoires. AbMAP representations of immune repertoires reveal a remarkable overlap across individuals, overcoming the limitations of sequence analyses. Our findings provide compelling evidence for the hypothesis that antibody repertoires of individuals tend to converge towards comparable structural and functional coverage. We validate AbMAP for antibody optimization, applying it to optimize a set of antibodies that bind to a SARS-CoV-2 peptide and obtaining 82% hit-rate and upto 22-fold increase in binding affinity. We anticipate AbMAP will accelerate the efficient design and modeling of antibodies and expedite the discovery of antibody-based therapeutics.

Availability:https://github.com/rs239/ablm
Excitatory drive to spinal motoneurones is necessary for serotonin to modulate motoneurone excitability via 5-HT2receptors in humans
Authors: Henderson Tyler T. , Taylor Janet L. , Thorstensen Jacob R. , Kavanagh Justin J.
Published: April 2023

Serotonin modulates corticospinal excitability, motoneurone firing rates and contractile strength via 5-HT2receptors. However, the effects of these receptors on cortical and motoneurone excitability during voluntary contractions have not been explored in humans. Therefore, the purpose of this study was to investigate how 5-HT2antagonism affects corticospinal and motoneuronal excitability with and without descending drive to motoneurones. Twelve individuals (aged 24 ± 4 years old) participated in a double-blind, placebo-controlled, crossover study, whereby the 5-HT2antagonist cyproheptadine was administered. Transcranial magnetic stimulation (TMS) was delivered to the motor cortex to produce motor evoked potentials (MEPs) and electrical stimulation at the cervicomedullary junction was used to generate cervicomedullary motor evoked potentials (CMEPs) in the biceps brachii at rest and during a range of submaximal elbow flexions. Evoked potentials were also obtained after a conditioning TMS pulse to produce conditioned MEPs and CMEPs (100 ms inter-stimulus interval). Compared to placebo, 5-HT2antagonism reduced maximal elbow flexion torque (p = 0.004), unconditioned MEP amplitude at rest (p = 0.003), conditioned MEP amplitude at rest (p = 0.033), and conditioned MEP amplitude during contractions (p = 0.020). 5-HT2antagonism also increased unconditioned CMEP amplitude during voluntary contractions (p = 0.041) but not at rest. Although 5-HT2antagonism increased long-interval intracortical inhibition, net corticospinal excitability was unaffected during voluntary contractions. Given that spinal motoneurone excitability was only affected when descending drive to motoneurones was present, the current study indicates that excitatory drive is necessary for 5-HT2receptors to regulate motoneurone excitability but not intracortical circuits.

Significance statement

Cellular and animal preparations have revealed that somatodendritic 5-HT2receptors on motoneurones can modulate motoneurone excitability. However, it is mostly unknown how 5-HT2receptors modulate motor cortical and motoneurone activity to generate muscle contractions in humans. Here we show that antagonism of 5-HT2receptors reduced muscle responses to motor cortical stimulation only when the muscle was at rest, or when voluntary motor activity was interrupted by a conditioning TMS stimulus. In contrast, antagonism of 5-HT2receptors increased the muscle response to cervicomedullary electrical stimulation, but only when descending drive to motoneurones was present. These findings not only suggest that 5-HT2receptors modulate intracortical and motoneurone activity, but sustained synaptic excitation of motoneurones is required for serotonergic mechanisms to modulate motoneurones.
HlyF, an underestimated virulence factor of uropathogenicEscherichia coli
Authors: Chagneau Camille V. , Payros Delphine , Goman Audrey , Goursat Cécile , David Laure , Okuno Miki , Bordignon Pierre-Jean , Séguy Carine , Massip Clémence , Branchu Priscilla , Ogura Yoshitoshi , Nougayrède Jean-Philippe , Marenda Marc , Oswald Eric
Published: April 2023

Urinary tract infections (UTIs) are predominantly caused by uropathogenicEscherichia coli(UPEC). By analysing a representative collection of UPEC strains from community-acquired infections, we showed that 20 % of these strains had the ability to produce the protein HlyF. ThesehlyF+ UPEC strains were the most virulent, mostly responsible for pyelonephritis, often with bloodstream infections. Using a mouse model of UTI, we showed that HlyF was associated with the ability of UPEC to develop a urosepsis, with the presence of bacteria in the spleen and an exacerbated inflammatory response. In contrast to archetypical UPEC strains,hlyF+ UPEC strains are not restricted to phylogroup B2 and harbor a specific repertoire of virulence factors reflecting the fact that HlyF is encoded by conjugative ColV-like plasmids. These plasmids also carry antimicrobial resistance genes, which may facilitate their selection and spreading amongst people receiving antimicrobial therapy. Overall, our data suggest that HlyF is a virulence factor in UPEC and spreading of ColV-like plasmids encodinghlyFwarrants further investigation.
Exploring Correlation-Based Brain Networks with Adaptive Signed Random Walks
Authors: Sotero Roberto C. , Sanchez-Bornot Jose M.
Published: April 2023

The human brain is a highly connected network with complex patterns of correlated and anticorrelated activity. Analyzing functional connectivity matrices derived from neuroimaging data can provide insights into the organization of brain networks and their association with cognitive processes or disorders. Common approaches, such as thresholding or binarization, often disregard negative connections, which may result in the loss of critical information. This study introduces an adaptive signed random walk (ASRW) model for analyzing correlation- based brain networks that incorporates both positive and negative connections. The model calculates transition probabilities between brain regions as a function of their activities and connection strengths, dynamically updating probabilities based on the differences in node activity and connection strengths at each time step. Results show that the classical random walk approach, which only considers the absolute value of connections, underestimates the mean first passage time (MFPT) compared to the proposed ASRW model. Our model captures a wide range of interactions and dynamics within the network, providing a more comprehensive understanding of its structure and function. This study suggests that considering both positive and negative connections, has the potential to offer valuable insights into the interregional coordination underlying various cognitive processes and behaviors.
p53 promotes revival stem cells in the regenerating intestine after severe radiation injury
Authors: Morral Clara , Ayyaz Arshad , Kuo Hsuan-Cheng , Fink Mardi , Verginadis Ioannis , Daniel Andrea R. , Burner Danielle N. , Driver Lucy M. , Satow Sloane , Hasapis Stephanie , Ghinnagow Reem , Luo Lixia , Ma Yan , Attardi Laura D. , Koumenis Costas , Minn Andy J , Wrana Jeffrey L. , Lee Chang-Lung , Kirsch David G.
Published: April 2023

Ionizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced GI injury. Through single-cell RNA-sequencing of the irradiated mouse intestine, we find that p53 target genes are specifically enriched in stem cells of the regenerating epithelium, including revival stem cells that promote animal survival after GI damage. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce revival stem cells. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells that is controlled by an Mdm2-mediated negative feedback loop. These results suggest that p53 suppresses severe radiation-indued GI injury by promoting intestinal epithelial cell reprogramming.

One-Sentence Summary

After severe radiation injury to the intestine, transient p53 activity induces revival stem cells to promote regeneration.
Macrophage migration is differentially regulated by distinct ECM components
Authors: Stinson Matthew W. , Laurenson Alexander J. , Rotty Jeremy D.
Published: April 2023

Macrophages are indispensable for proper immune surveillance and inflammatory regulation. They also exhibit dramatic phenotypic plasticity and are highly responsive to their local microenvironment, which includes the extracellular matrix (ECM). The present work demonstrates that two fibrous ECM glycoproteins, fibronectin (FN) and laminin (LAM), elicit distinct morphological and migratory responses to macrophages in 2D environments. Laminin 111 inhibits macrophage cell spreading, but drives them to migrate rapidly and less persistently compared to cells on fibronectin. Differential integrin engagement and ROCK/myosin II organization helps explain why macrophages alter their morphology and migration character on these two ECM components. The present study also demonstrates that laminin 111 exerts a suppressive effect toward fibronectin, as macrophages plated on a LAM/FN mixture adopt a morphology and migratory character almost identical to LAM alone. This suggests that distinct responses can be initiated downstream of receptor-ECM engagement, and that one component of the microenvironment may affect the cell’s ability to sense another. Overall, macrophages appear intrinsically poised to rapidly switch between distinct migratory modes based on their ECM environments. The role of ECM composition in dictating motile and inflammatory responses in 3D andin vivocontexts warrants further study.
Development of heat shock resistance inL. pneumophilamodeled by experimental evolution
Authors: Liang Jeffrey , Faucher Sebastien P.
Published: April 2023

Because it can grow in buildings with complex hot water distribution systems (HWDS), healthcare facilities recognize the waterborne bacteriumLegionella pneumophilaas a major nosocomial infection threat and often try to clear the systems with a pasteurization process known as superheat-and-flush. After this treatment, many facilities find that the contaminating populations slowly recover, suggesting the possibility ofin situevolution favouring increased survival in high temperature conditions. To mimic this process in a controlled environment, an adaptive laboratory evolution (ALE) model was used to select a wild-type strain ofL. pneumophilafor survival to transient exposures to temperatures characteristic of routine hot water use or failed pasteurization processes in HWDS. Over their evolution, these populations became insensitive to exposure to 55 °C and innovated the ability to survive short exposures to 59 °C heat shock. Heat-adapted lineages maintained a higher expression of heat shock genes during low-temperature incubation in freshwater, suggesting a pre-adaptation to heat stress. Although there were distinct mutation profiles in each of the heat-adapted lineages, each acquired multiple mutations in the DnaJ/DnaK/ClpB disaggregase complex, as well as mutations in chaperonehtpGand proteaseclpX.These mutations were specific to heat shock survival and were not seen in control lineages included in the ALE without exposure to heat shock. This study supportsin situobservations of adaptation to heat stress and demonstrate the potential ofL. pneumophilato develop resistance to control measures.

Importance

As a bacterium that thrives in warm water ecosystems,Legionella pneumophilais a key factor motivating regulations on hot water systems. Two major measures intended to controlLegionellaare the maintenance of high circulating temperatures to curtail growth and the use of superheat-and-flush pasteurization processes to eliminate established populations. Although hospitals are particularly vulnerable to nosocomial pneumoniae caused byLegionella, they recurrently experience recolonization of their hot water systems after treatment. To understand these long-term survivors, we have used an experimental evolution model to replicate this process. We find major differences between the mutational profiles of heat-adapted and heat-naïveL. pneumophilapopulations, including mutations in major heat shock genes like chaperones and proteases. This model demonstrates the value of appropriate heat treatment ofL. pneumophilacontaminated systems and – in an analogue to antibiotic resistance – the importance of complete eradication of the resident population to prevent selection for more persistent bacteria.
GluN2C/D-containing NMDA receptors enhance temporal summation and increase sound-evoked and spontaneous firing in the inferior colliculus
Authors: Drotos Audrey C. , Zarb Rachel L. , Booth Victoria , Roberts Michael T.
Published: April 2023

Along the ascending auditory pathway, there is a broad shift from temporal coding, which is common in the lower auditory brainstem, to rate coding, which predominates in auditory cortex. This temporal-to-rate transition is particularly prominent in the inferior colliculus (IC), the midbrain hub of the auditory system, but the mechanisms that govern how individual IC neurons integrate information across time remain largely unknown. Here, we report the widespread expression ofGlun2candGlun2dmRNA in IC neurons. GluN2C/D-containing NMDA receptors are relatively insensitive to voltage-dependent Mg2+block, and thus can conduct current at resting membrane potential. Using in situ hybridization and pharmacology, we show that VIP neurons in the IC express GluN2D-containing NMDA receptors that are activatable by commissural inputs from the contralateral IC. In addition, GluN2C/D-containing receptors have much slower kinetics than other NMDA receptors, and we found that GluN2D-containing receptors facilitate temporal summation of synaptic inputs in VIP neurons. In a model neuron, we show that a GluN2C/D-like conductance interacts with the passive membrane properties of the neuron to alter temporal and rate coding of stimulus trains. Consistent with this, we show in vivo that blocking GluN2C/D-containing receptors decreases both the spontaneous firing rate and the overall firing rate elicited by amplitude-modulated (AM) sounds in many IC neurons. These results suggest that GluN2C/D-containing NMDA receptors influence rate coding for auditory stimuli in the IC by facilitating the temporal integration of synaptic inputs.

Significance statement

NMDA receptors are critical components of most glutamatergic circuits in the brain, and the diversity of NMDA receptor subtypes yields receptors with a variety of functions. We found that many neurons in the auditory midbrain express GluN2C and/or GluN2D NMDA receptor subunits, which are less sensitive to Mg2+block than the more commonly expressed GluN2A/B subunits. We showed that GluN2C/D-containing receptors conducted current at resting membrane potential and enhanced temporal summation of synaptic inputs. In a model, we show that GluN2C/D-containing receptors provide additive gain for input-output functions driven by trains of synaptic inputs. In line with this, we found that blocking GluN2C/D-containing NMDA receptors in vivo decreased both spontaneous firing rates and firing evoked by amplitude-modulated sounds.
Molecular mechanism of complement inhibition by the trypanosome receptor ISG65
Authors: Cook Alexander D. , Carrington Mark , Higgins Matthew K.
Published: April 2023

African trypanosomes replicate within infected mammals where they are exposed to the complement system. This system centres around complement C3, which is present in a soluble form in serum but becomes covalently deposited onto the surfaces of pathogens after proteolytic cleavage to C3b. Membrane-associated C3b triggers different complement-mediated effectors which promote pathogen clearance. To counter complement-mediated clearance, African trypanosomes have a cell surface receptor, ISG65, which binds to C3b and which decreases the rate of trypanosome clearance in an infection model. However, the mechanism by which ISG65 reduces C3b function has not been determined. We reveal through cryogenic electron microscopy that ISG65 has two distinct binding sites for C3b, only one of which is available in C3 and C3d. We show that ISG65 does not block the formation of C3b or the function of the C3 convertase which catalyses the surface deposition of C3b. However, we show that ISG65 forms a specific conjugate with C3b, perhaps acting as a decoy. ISG65 also occludes the binding sites for complement receptors 2 and 3, which may disrupt recruitment of immune cells, including B cells, phagocytes and granulocytes. This suggests that ISG65 protects trypanosomes by combining multiple approaches to dampen the complement cascade.

Impact Statement

A structure derived from cryogenic electron microscopy shows how ISG65, an African trypanosome receptor that aids virulence, binds C3b and suggests mechanisms through which ISG65 might aid complement resistance.
Flexing fish: cell surface plasticity in response to shape change in the whole organism
Authors: Hall TE , Ariotti N , Lo HP , Ferguson C , Martel N , Lim Y-W , Giacomotto J , Parton RG
Published: April 2023

Plasma membrane rupture can result in catastrophic cell death. The skeletal muscle fibre plasma membrane, the sarcolemma, provides an extreme example of a membrane subject to mechanical stress since these cells specifically evolved to generate contraction and movement. A quantitative model correlating ultrastructural remodelling of surface architecture with tissue changesin vivois required to understand how membrane domains contribute to the shape changes associated with tissue deformation in whole animals. We and others have shown that loss of caveolae, small invaginations of the plasma membrane particularly prevalent in the muscle sarcolemma, renders the plasma membrane more susceptible to rupture during stretch1–3. While it is thought that caveolae are able to flatten and be absorbed into the bulk membrane to buffer local membrane expansion, a direct demonstration of this modelin vivohas been unachievable since it would require measurement of caveolae at the nanoscale combined with detailed whole animal morphometrics under conditions of perturbation. Here, we describe the development and application of the “active trapping model” where embryonic zebrafish are immobilised in a curved state that mimics natural body axis curvature during an escape response. The model is amenable to multiscale, multimodal imaging including high-resolution whole animal three-dimensional quantitative electron microscopy. Using the active trapping model, we demonstrate the essential role of caveolae in maintaining sarcolemmal integrity and quantify the specific contribution of caveolar-derived membrane to surface expansion. We show that caveolae directly contribute to an increase in plasma membrane surface area under physiologically relevant membrane deformation conditions.
Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
Authors: Fukushima Hiroto S. , Takeda Hiroyuki , Nakamura Ryohei
Published: April 2023

Epigenetic modifications undergo drastic erasure and reestablishment after fertilization. This reprogramming is required for proper embryonic development and cell differentiation. In mammals, some histone modifications are not completely reprogrammed and play critical roles in later development. In contrast, in nonmammalian vertebrates, most histone modifications are thought to be more intensively erased and reestablished by the stage of zygotic genome activation (ZGA). However, histone modifications that escape reprogramming in nonmammalian vertebrates and their potential functional roles remain unknown. Here, we quantitatively and comprehensively analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we experimentally showed the functional roles of such retained modifications at early stages: (i) H3K27ac premarks promoters during the cleavage stage, and inhibition of histone acetyltransferases disrupts proper patterning of H3K4 and H3K27 methylation at CpG-dense promoters, but does not affect chromatin accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously uncharacterized functions of histone modifications retained during epigenetic reprogramming.
Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii
Authors: Zhou Yong , Wannapaiboon Suttipong , Prongjit Methinee , Pornsuwan Soraya , Sucharitakul Jeerus , Kamonsutthipaijit Nuntaporn , Robinson Robert C. , Suginta Wipa
Published: April 2023

Vibrio spp. play a crucial role in the global recycling of the highly abundant recalcitrant biopolymer chitin in marine ecosystems through their ability to secrete chitin-degrading enzymes to efficiently hydrolyse chitinous materials and use them as their major carbon source. In this study, the first crystal structures of a complete four-domain chitin-active AA10 lytic polysaccharide monooxygenase from the chitinolytic bacterium Vibrio campbellii type strain ATCC BAA-1116 are reported. The crystal structures of apo and copper-bound VhLPMO10A were resolved as homodimers with four distinct domains: an N-terminal AA10 catalytic (CatD) domain connected to a GlcNAc-binding (GbpA_2) domain, followed by a module X domain and a C-terminal carbohydrate-binding module (CBM73). Size-exclusion chromatography and small-angle X-ray scattering analysis confirmed that VhLPMO10A exists as a monomer in solution. The active site of VhLPMO10A is located on the surface of the CatD domain, with three conserved residues (His1, His98 and Phe170) forming the copper(II)-binding site. Metal-binding studies using synchrotron X-ray absorption spectroscopy and X-ray fluorescence, together with electron paramagnetic resonance spectroscopy, gave consistently strong copper(II) signals in the protein samples, confirming that VhLPMO10A is a copper-dependent enzyme. ITC binding data showed that VhLPMO10A could bind various divalent cations but bound most strongly to copper(II) ions, with a K
d of 0.1 ± 0.01 µM. In contrast, a K
d of 1.9 nM was estimated for copper(I) ions from redox-potential measurements. The presence of ascorbic acid is essential for H2O2 production in the reaction catalysed by VhLPMO10A. MALDI-TOF MS identified VhLPMO10A as a C1-specific LPMO, generating oxidized chitooligosaccharide products with different degrees of polymerization (DP2ox–DP8ox). This new member of the chitin-active AA10 LPMOs could serve as a powerful biocatalyst in biofuel production from chitin biomass.