bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk factors for severe COVID-19 disease increase SARS-CoV-2 infectivity of endothelial cells and pericytes
Authors: Biasetti Luca , Zervogiannis Nikos , Shaw Kira , Trewhitt Harry , Serpell Louise , Bailey Dalan , Wright Edward , Hall Catherine N.
Published: June 2024

Coronavirus disease 2019 (COVID-19) was initially considered a primarily respiratory disease but is now known to affect other organs including the heart and brain. A major route by which COVID-19 impacts different organs is via the vascular system. We studied the impact of apolipoprotein E (APOE) genotype and inflammation on vascular infectivity by pseudo-typed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses in mouse and human cultured endothelial cells and pericytes. Possessing the APOE4 allele or having existing systemic inflammation is known to enhance the severity of COVID-19. Using targeted replacement human APOE3 and APOE4 mice and inflammation induced by bacterial lipopolysaccharide (LPS), we investigated infection by SARS-CoV-2. Here, we show that infectivity was higher in murine cerebrovascular pericytes compared to endothelial cells and higher in cultures expressing APOE4. Furthermore, increasing the inflammatory state of the cells by prior incubation with LPS increased infectivity into human and mouse pericytes and human endothelial cells. Our findings provide insights into the mechanisms underlying severe COVID-19 infection, highlighting how risk factors such as APOE4 genotype and prior inflammation may exacerbate disease severity by augmenting the virus’s ability to infect vascular cells.
Terminal regions of a protein are a hotspot for low complexity regions and selection
Authors: Teekas Lokdeep , Sharma Sandhya , Vijay Nagarjun
Published: June 2024

Volatile low complexity regions (LCRs) are a novel source of adaptive variation, functional diversification and evolutionary novelty. An interplay of selection and mutation governs the composition and length of low complexity regions. High %GC and mutations provide length variability because of mechanisms like replication slippage. Owing to the complex dynamics between selection and mutation, we need a better understanding of their coexistence. Our findings underscore that positively selected sites (PSS) and low complexity regions prefer the terminal regions of genes, co-occurring in most Tetrapoda clades. We observed that positively selected sites within a gene have position-specific roles. Central-positively selected site genes primarily participate in defence responses, whereas terminal-positively selected site genes exhibit non-specific functions. Low complexity region-containing genes in the Tetrapoda clade exhibit a significantly higher %GC and lower
ω
(d
N
/d
S
: non-synonymous substitution rate/synonymous substitution rate) compared with genes without low complexity regions. This lower
ω
implies that despite providing rapid functional diversity, low complexity region-containing genes are subjected to intense purifying selection. Furthermore, we observe that low complexity regions consistently display ubiquitous prevalence at lower purity levels, but exhibit a preference for specific positions within a gene as the purity of the low complexity region stretch increases, implying a composition-dependent evolutionary role. Our findings collectively contribute to the understanding of how genetic diversity and adaptation are shaped by the interplay of selection and low complexity regions in the Tetrapoda clade.
Plasmodium
LCCL domain-containing modular proteins have their origins in the ancestral alveolate
Authors: De Hoest-Thompson Callum , Marugan-Hernandez Virginia , Dessens Johannes T.
Published: June 2024

Plasmodium
species encode a unique set of six modular proteins named LCCL lectin domain adhesive-like proteins (LAPs) that operate as a complex and that are essential for malaria parasite transmission from mosquito to vertebrate. LAPs possess complex architectures obtained through unique assemblies of conserved domains associated with lipid, protein and carbohydrate interactions, including the name-defining LCCL domain. Here, we assessed the prevalence of
Plasmodium
LAP orthologues across eukaryotic life. Our findings show orthologous conservation in all apicomplexans, with lineage-specific repertoires acquired through differential
lap
gene loss and duplication. Besides Apicomplexa, LAPs are found in their closest relatives: the photosynthetic chromerids, which encode the broadest repertoire including a novel membrane-bound LCCL protein. LAPs are notably absent from other alveolate lineages (dinoflagellates, perkinsids and ciliates), but are encoded by predatory colponemids, a sister group to the alveolates. These results reveal that the LAPs are much older than previously thought and pre-date not only the Apicomplexa but the Alveolata altogether.
Unifying the Research Landscape of Desiccation Tolerance to Identify Trends, Gaps, and Opportunities
Authors: Lotreck Serena G. , Ghassemi Mohammad , VanBuren Robert T.
Published: June 2024

Desiccation tolerance, or the ability to survive extreme dehydration, has evolved recurrently across the tree of life. While our understanding of the mechanisms underlying desiccation tolerance continues to expand, the compartmentalization of findings by study system impedes progress. Here, we analyzed 5,963 papers related to desiccation and examined model systems, research topics, citation networks, and disciplinary siloing over time. Our results show significant siloing, with plant science dominating the field, and relatively isolated clustering of plants, animal, microbial, and fungal literature. Topic modeling identified 46 distinct research topics, highlighting both commonalities and divergences across the knowledge of desiccation tolerance in different systems. We observed a rich diversity of model desiccation tolerant species within the community, contrasting the single species model for most biology research areas. To address citation gaps, we developed a rule-based algorithm to recommend new invitees to a niche conference, DesWorks, enhancing the integration of diverse research areas. The algorithm, which considers co-citation, co-authorship, research topics, and geographic data, successfully identified candidates with novel expertise that was unrepresented in previous conferences. Our findings underscore the importance of interdisciplinary collaboration in advancing desiccation tolerance research and provide a framework for using bibliometric tools to foster scientific integration.
A library-on-library screen reveals the breadth expansion landscape of a broadly neutralizing betacoronavirus antibody
Authors: Ornelas Marya Y. , Ouyang Wenhao O. , Wu Nicholas C.
Published: June 2024

Broadly neutralizing antibodies (bnAbs) typically evolve cross-reactivity breadth through acquiring somatic hypermutations. While evolution of breadth requires improvement of binding to multiple antigenic variants, most experimental evolution platforms select against only one antigenic variant at a time. In this study, a yeast display library-on-library approach was applied to delineate the affinity maturation of a betacoronavirus bnAb, S2P6, against 27 spike stem helix peptides in a single experiment. Our results revealed that the binding affinity landscape of S2P6 varies among different stem helix peptides. However, somatic hypermutations that confer general improvement in binding affinity across different stem helix peptides could also be identified. We further showed that a key somatic hypermutation for breadth expansion involves long-range interaction. Overall, our work not only provides a proof-of-concept for using a library-on-library approach to analyze the evolution of antibody breadth, but also has important implications for the development of broadly protective vaccines.
Leading causes of death among adult solid organ transplant recipients in the United States, 1999–2019
Authors: Volesky-Avellaneda Karena D , Wang Jeanny H , Pfeiffer Ruth M , Castenson David , Israni Ajay K , Miller Jonathan M , Musgrove Donnie , Shiels Meredith S , Snyder Jon J , Yu Kelly J , Engels Eric A
Published: June 2024

Underlying medical conditions, graft failure, and immunosuppression place solid organ transplant recipients (“recipients) at heighten risk of death. We report the underlying causes of death among adult US recipients and compare their mortality to the US general population. We obtained causes of death by linking a sample of deaths from the US organ transplant registry to the National Death Index and weighted the linked deaths to represent all deaths among recipients aged ≥18 years during 1999–2019. To compare mortality to the US general population, we calculated standardized mortality ratios (SMRs). Among 496,467 recipients, 153,491 deaths occurred, of which 99,373 were NDI-linked. Leading causes of death were heart disease (16.9% of deaths), graft failure (14.9%), and cancer (14.4%). Compared to the US general population, recipients had 4.02 times the risk of death, and mortality was elevated for all 16 causes analyzed (e.g., 3.32-fold for heart disease and 2.08-fold for cancer) except dementia/Alzheimer’s disease. During 2015–2019, overall mortality was elevated 3.08-fold, with lung recipients experiencing the highest elevation (SMR=7.91), followed by heart (3.20), liver (2.86), and kidney (2.81) recipients. Although mortality improved over time, US recipients continue to face substantially elevated mortality, both overall and for common causes of death.
Development and Evaluation of the DMIND Questionnaire: Preparing for AI Integration into an Effective Depression Screening Tool
Authors: Hemrungrojn Solaphat , Saengsai Kittipoch , Jakkrawankul Pasit , Kiattiporn-Opas Chanyanart , Chaichareenon Kantapat , Amrapala Arisara , Lapanan Kulvara , Hengprapom Sarunya , Hiransuthikul Narin , Achakulvisut Titipat , Nupairoj Natawut , Phutrakool Phanupong , Yodlorchai Rapinpat , Vateekul Peerapol
Published: June 2024

Objective

Thailand’s mental health crisis is exacerbated by high demand and a shortage of mental health professionals. The research objective was to develop and validate the Detection and Monitoring Intelligence Network for Depression (DMIND) questionnaire, designed to be culturally relevant and easily administered in clinical settings. Crafted with expert input, items specifically conducive to artificial intelligence (AI) analysis were selected to facilitate the future development of an AI-assisted depression scoring model. This approach underscores the tool’s dual utility in both human-led and technology-enhanced diagnostics.

Materials and Methods

We enrolled 81 participants from psychiatric and tertiary care hospitals in Bangkok. Participants were assessed using the DMIND questionnaire, followed by the Hamilton Depression Rating Scale (HDRS-17). Statistical analyses included the content validity index (CVI), Cronbach’s alpha, Pearson’s correlation coefficient, Cohen’s kappa, and receiver operating characteristic (ROC) analysis. The Liu method, Youden index, and nearest neighbor method were used to determine the optimal cut-off point

Results

The DMIND questionnaire showed strong validity, with an item-level CVI (I- CVI) and scale-level CVI (S-CVI) exceeding 1.0, indicating strong consensus on its relevance and utility. The tool also demonstrated high internal consistency (Cronbach’s alpha = 0.96). ROC analysis showed an AUC of 0.88, indicating high accuracy in depression screening. An optimal cut-off score of 11.5 was identified, balancing predictive value and sensitivity.

Conclusion

The DMIND questionnaire represents a significant advancement in innovative mental health diagnostics, addressing unmet clinical needs by providing accurate and efficient assessments capable of AI integration for further enhancing mental health service delivery in Thailand.
Analysis of Unmapped RNA-seq Data from Cancer Spatial Transcriptome to Decipher Cancer Microbiome
Authors: Park Seo Hye , Park Jeongbin , Kim Jiwon , Choi Hongyoon , Kim In Gul , Chung Eun-Jae , Na Kwon Joong
Published: June 2024

Recent research increasingly emphasizes the importance of the microbiome in the development and progression of cancer. Thus, exploring the microbiome modulation in tumor microenvironment and understanding its composition and function are becoming important. The introduction of spatial transcriptomics has provided new insights into microbiome research, as it enables how microbiome affects tumor microenvironment. In this study, we analyzed the spatial distribution of microbial RNA observed through PathSeq and our extended method for unmapped RNA reads in oral squamous cell carcinoma, head and neck cancer, and colorectal cancer samples. Our novel method is designed to identify and classify microbial RNA, using a custom reference that includes species-specific microbial 16S rRNA sequences to enhance the accuracy of species-level microbiome analysis. The results of this study showed a potential for a deeper understanding of the microbial distribution and their functional roles within cancer tissues. These findings will reevaluate the role of the microbiome in cancer research, providing an insight for the development of microbiome-based therapies in the future.
Routine Blood Tests as Predictors of Periodontal Disease Risk Using a Machine Learning Approach
Authors: Ahmad Bushra , Saleh Khaled , Alharbi Saleh , Jeong Y. Natalie , Zavras Athanasios , Alqaderi Hend
Published: June 2024

Background

Periodontal disease is a prevalent chronic inflammatory condition associated with systemic health complications. Early identification of high-risk individuals is crucial for targeted preventive and therapeutic interventions. In this study, we aimed to develop and evaluate machine learning models using routine blood tests to predict periodontal disease risk. This will help to develop accessible and cost-effective screening tools for early detection in a non-dental setting.

Methods

This study utilized data from the 2013-2014 National Health and Nutrition Examination Survey (NHANES), including full-mouth periodontal examinations, demographic variables, and routine blood tests (complete blood count [CBC], lipid profile, liver and kidney function tests). Periodontitis was defined as a binary outcome based on attachment loss and probing depth at interproximal sites. Individuals meeting any of these criteria were classified as having periodontitis. Seven machine learning models were developed and evaluated using precision, recall, and accuracy metrics.

Results

The Random Forest Classifier achieved the highest performance, scoring 0.91 in precision, recall, and accuracy for predicting periodontitis. Key predictive features included smoking status, age, education level, gamma glutamyl transferase, albumin, blood urea nitrogen, glucose, phosphorus, creatinine, basophil count, and total calcium levels.

Conclusion

This study underscores the promise of machine learning, especially the Random Forest Classifier, in predicting periodontal disease risk using routine blood tests and demographics. The model accurately identified periodontitis cases, with key features revealing the complex relationship between systemic health and periodontal disease. This suggests the potential for developing machine learning-based screening tools for early periodontal disease detection in non-dental settings.
Public involvement to enhance care home research; collaboration on a minimum data set for care homes
Authors: Killett Anne , Micklewright Kerry , Carroll Rachael , Akdur Gizdem , Allinson Emily , Crellin Liz , de Corte Kaat , Fox Margaret , Hanratty Barbara , Irvine Lisa , Jones Liz , Auburn Mere Marlene Kelly , Lloyd Therese , Meyer Julienne , Spilsbury Karen , Towers Ann-Marie , Tracey Freya , Wilmott John , Goodman Claire
Published: June 2024

Introduction

Information on care home residents is captured in lots of datasets (care home records, GP records, community nursing etc) but little of this information is currently analysed in a way that is useful for care providers, current or future residents and families or that realises the potential of data to enhance care provision. The DACHA study aimed to develop and test a minimum data set (MDS) which would bring together data that is useful to support and improve care and facilitate research. It is that utility that underscores the importance of meaningful public involvement with the range of groups of people affected. This paper analyses the public involvement of family members of care home residents and care home staff through a Public Involvement (PI) Panel.

Objectives

The objective for the PI activities was to consistently bring the knowledge and perspectives of family members and care home staff to influence the ongoing design and conduct of the DACHA study.

Methods

The bespoke methods of PI included a dedicated PI team and a PI Panel of public involvement contributors. Meetings were recorded and minutes agreed, resulting actions were tracked, and reflections on the PI recorded. A democratic, social relations approach was used to frame the analysis.

Results

A PI panel met 17 times. All meetings included both family members and care home staff. The public involvement deepened the research team’s understanding of the data environment in care homes, influenced the inclusion of quality of life and community health data in the pilot MDS and shaped research practices with care homes. Some panel members expressed personal and professional development from their involvement. Expectations of what the project could achieve had to be negotiated.

Conclusions

PI shaped the design and conduct of the DACHA study, grounding it in the needs and perspectives of people using and providing social care. Data research has a huge responsibility to accurately incorporate relevant public perspectives. There is an implicit assumption that records and data are objective and “speak for themselves” however there can be unintended consequences from introduction of new data requirements in practice.

Patient or Public Contribution

Public contributors to this manuscript include family members of older people living in care homes and staff of care homes. The wider study also involved as the public, older people living in care homes. Public contributors helped develop the project, contributed throughout the conduct of the study and some chose to be involved in preparing this manuscript.
Vitamin D levels and COVID-19 severe pneumonia: a prospective case-control study
Authors: Cardoso Fortunato José , Araújo Carla Adriane Leal de , Silva Junior José Roberto da , Guimarães Angélica , Taveiro Michelle Viana , Figueiroa José Natal , Bezerra Alves João Guilherme
Published: June 2024

Introduction

The hypothesis that a low vitamin D levels is associated with a higher risk for severe COVID-19 has not been completely proven, especially with severe pneumonia.

Objective

The goal of this study was to confirm the link between vitamin D levels and COVID-19 severe pneumonia.

Methods

This prospective case-control study involved 307 patients who developed severe SARS-CoV-2 pneumonia and were hospitalized in an intensive care unit. Age- and sex-matched controls (307) were selected from the same population; 307 patients with mild to moderate forms of COVID-19 who were not hospitalized. Vitamin D levels were assessed during the duration of the disease.

Results

The mean vitamin D level was lower in the severe COVID-19 pneumonia group as compared to the control group; 26.8 ± 7.6 ng/mLvs28.6 ± 7.4 ng/mL, p<0.002. There were more patients with a sufficient level of vitamin D in the control group as compared to the control group; 127 (20.6%) vs 89 (14.5%), p<0.001. Multivariable analysis showed that a deficient vitamin D level was associated with a higher risk for severe COVID-19 pneumonia (OR=3.0; 95% CI: 1.79, 5.10CI), p<0.001.

Conclusion

A sufficient vitamin D level is linked to a lower risk of COVID-19 severe pneumonia.
Neuroimaging Insights into Subjective Cognitive Decline: Differential Sensitivity of Cognitive Change Index and Everyday Cognition Scale
Authors: Morrison Cassandra , Anderson John A. E. , Dadar Mahsa ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2024

Introduction

Cognitively healthy older adults may experience self-perceived memory and cognitive deficits, known as subjective cognitive decline (SCD), increasing their risk for dementia- related brain and cognitive changes. This study investigated if questions from the Cognitive Change Index (CCI) and Everyday Cognition Scale (ECog) show similar associations with dementia-related changes.

Methods

Cognitively healthy older adults (n=332) from the Alzheimer’s Disease Neuroimaging Initiative were included. Partial-least-squares observed the latent variables (LVs) that maximize the relationship between the two questionnaires.

Results

Two LVs (p’s<0.001) explained 85.89% and 8.30% of the cross-block covariance. In the first LV, several CCI questions correlated with older age and frontal, parietal, and temporal WMHs, lower hippocampal and entorhinal cortex volume, and larger ventricles. The second LV showed younger individuals with higher SCD scores on three CCI questions correlated with temporal and parietal WMHs and entorhinal cortex volumes.

Conclusion

More questions from the CCI are associated with neuroimaging markers, unlike the ECog questions. These questionnaires may thus be measuring different neural decline patterns and may be sensitive to different etiologies.
Improved user-friendliness in the design and analysis of FAVITES-Lite simulations
Authors: Stadler Kate , Phillips Kayla , Moshiri Niema
Published: June 2024

After the rise of several different simulation tools that can simulate different aspects of an epidemic, FAVITES provides a framework to simulate an end-to-end epidemic (from contact network generation to infection transmission to viral phylogenies). To increase accessibility, FAVITES-Lite was developed with the key functionalities of FAVITES with the sacrifice of some flexibility. It remains that configuring and analyzing a complicated simulation like FAVITES or FAVITES-Lite can be extremely daunting, so we created example configuration files to help users learn the process behind parameter choice and a graph-visualization web application to help users visualize the results of their simulations.
Transcutaneous Electrical Spinal Cord Stimulation Promotes Focal Sensorimotor Activation that Accelerates Brain-Computer Interface Skill Learning
Authors: Alawieh Hussein , Liu Deland , Madera Jonathan , Kumar Satyam , Racz Frigyes Samuel , Fey Ann Majewicz , Millán José del R.
Published: June 2024

Injuries affecting the central nervous system may disrupt neural pathways to muscles causing motor deficits. Yet the brain exhibits sensorimotor rhythms (SMRs) during movement intents, and brain-computer interfaces (BCIs) can decode SMRs to control assistive devices and promote functional recovery. However, non-invasive BCIs suffer from the instability of SMRs, requiring longitudinal training for users to learn proper SMR modulation. Here, we accelerate this skill learning process by applying cervical transcutaneous electrical spinal stimulation (TESS) to inhibit the motor cortex prior to longitudinal upper-limb BCI training. Results support a mechanistic role for cortical inhibition in significantly increasing focality and strength of SMRs leading to accelerated BCI control in healthy subjects and an individual with spinal cord injury. Improvements were observed following only two TESS sessions and were maintained for at least one week in users who could not otherwise achieve control. Our findings provide promising possibilities for advancing BCI-based motor rehabilitation.
Wavelet transform of single-trial vestibular short-latency evoked potential reveals temporary reduction in signal detectability and temporal precision following noise exposure
Authors: Niwa Mamiko , Bauer David , Anderson Marie , Kanicki Ariane , Altschuler Richard A. , Stewart Courtney E. , King W. Michael
Published: June 2024

The vestibular short-latency evoked potential (VsEP) reflects the activity of irregular vestibular afferents and their target neurons in the brain stem. Attenuation of trial-averaged VsEP waveforms is widely accepted as an indicator of vestibular dysfunction, however, more quantitative analyses of VsEP waveforms could reveal underlying neural properties of VsEP waveforms. Here, we present a time-frequency analysis of the VsEP with a wavelet transform on a single-trial basis, which allows us to examine trial-by-trial variability in the strength of VsEP waves as well as their temporal coherence across trials. Using this method, we examined changes in the VsEP following 110 dB SPL noise exposure in rats. We found detectability of head jerks based on the power of wavelet transform coefficients was significantly reduced 1 day after noise exposure but recovered nearly to pre-exposure level in 3 - 7 days and completely by 28 days after exposure. Temporal coherence of VsEP waves across trials was also significantly reduced on 1 day after exposure but recovered with a similar time course. Additionally, we found a significant reduction in the number of calretinin-positive calyces in the sacculi collected 28 days after noise exposure. Furthermore, the number of calretinin-positive calyces was significantly correlated with the degree of reduction in temporal coherence and/or signal detectability of the smallest-amplitude jerks. This new analysis of the VsEP provides more quantitative descriptions of noise-induced changes as well as new insights into potential mechanisms underlying noise-induced vestibular dysfunction.

Significance Statement

Our study presents a new method of VsEP quantification using wavelet transform on a single-trial basis. It also describes a novel approach to determine the stimulus threshold of the VsEP based on signal-detection theory and Rayleigh statistics. The present analysis could also be applied to analysis of auditory brain stem response (ABR). Thus, it has the potential to provide new insights into the physiological properties that underlie peripheral vestibular and auditory dysfunction.
B-BIND: BIOPHYSICAL BAYESIAN INFERENCE FOR NEURODEGENERATIVE DYNAMICS
Authors: Agrawal Anamika , Rachleff Victoria M. , Travaglini Kyle J. , Mukherjee Shubhabrata , Crane Paul K. , Hawrylycz Michael , Keene C. Dirk , Lein Ed , Mena Gonzalo E. , Gabitto Mariano I.
Published: June 2024

Throughout an organism’s life, a multitude of complex and interdependent biological systems transition through biophysical processes that serve as indicators of the underlying biological states. Inferring these latent, unobserved states is a goal of modern biology and neuroscience. However, in many experimental setups, we can at best obtain discrete snapshots of the system at different times and for different individuals. This challenge is particularly relevant in the study of Alzheimer’s Disease (AD) progression, where we observe the aggregation of pathology in brain donors, but the underlying disease state is unknown. This paper proposes a biophysically motivated Bayesian framework (B-BIND: Biophysical Bayesian Inference for Neurode-generative Dynamics), where the disease state is modeled and continuously inferred from observed quantifications of multiple AD pathological proteins. Inspired by biophysical models, we describe pathological burden as an exponential process. The progression of AD is modeled by assigning a latent score, termed pseudotime, to each pathological state, creating a pseudotemporal order of donors based on their pathological burden. We study the theoretical properties of the model using linearization to reveal convergence and identifiability properties. We provide Markov chain Monte Carlo estimation algorithms, illustrating the effectiveness of our approach with multiple simulation studies across various data conditions. Applying this methodology to data from the Seattle Alzheimer’s Disease Brain Cell Atlas, we infer the pseudotime ordering of donors. Finally, we analyze the information within each pathological feature to refine the model, focusing on the most informative pathologies. This framework lays the groundwork for continuous pseudotime modeling in the analysis of neurodegenerative diseases.
Mg2+-dependent mechanism of environmental versatility in a multidrug efflux pump
Authors: Russell Lewis Benjamin , Uddin Muhammad R. , Kuo Katie M. , Shah Laila M. N. , Harris Nicola J. , Booth Paula J. , Hammerschmid Dietmar , Gumbart James C. , Zgurskaya Helen I. , Reading Eamonn
Published: June 2024

Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+and pH in modulating the dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug efflux pump fromEscherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+is bound this is ameliorated, resulting in domain specific organisation in neutral to weakly acidic regimes. We establish a unique histidine residue directs these structural dynamics and is essential for sustaining pump efflux activity across acidic, neutral, and alkaline conditions. Overall, we propose Mg2+conserves the structural mobility of AcrA to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced by the periplasm during bacterial infection and colonization. This work highlights that Mg2+is an important mechanistic component in this pump class and possibly across other periplasmic lipoproteins.
Rapid emergence of latent knowledge in the sensory cortex drives learning
Authors: Drieu Celine , Zhu Ziyi , Wang Ziyun , Fuller Kylie , Wang Aaron , Elnozahy Sarah , Kuchibhotla Kishore
Published: June 2024

Rapid learning confers significant advantages to animals in ecological environments. Despite the need for speed, animals appear to only slowly learn to associate rewarded actions with predictive cues. This slow learning is thought to be supported by a gradual expansion of predictive cue representation in the sensory cortex. However, evidence is growing that animals learn more rapidly than classical performance measures suggest, challenging the prevailing model of sensory cortical plasticity. Here, we investigated the relationship between learning and sensory cortical representations. We trained mice on an auditory go/no-go task that dissociated the rapid acquisition of task contingencies (learning) from its slower expression (performance). Optogenetic silencing demonstrated that the auditory cortex (AC) drives both rapid learning and slower performance gains but becomes dispensable at expert. Rather than enhancement or expansion of cue representations, two-photon calcium imaging of AC excitatory neurons throughout learning revealed two higher-order signals that were causal to learning and performance. First, a reward prediction (RP) signal emerged rapidly within tens of trials, was present after action-related errors only early in training, and faded at expert levels. Strikingly, silencing at the time of the RP signal impaired rapid learning, suggesting it serves an associative and teaching role. Second, a distinct cell ensemble encoded and controlled licking suppression that drove the slower performance improvements. These two ensembles were spatially clustered but uncoupled from underlying sensory representations, indicating a higher-order functional segregation within AC. Our results reveal that the sensory cortex manifests higher-order computations that separably drive rapid learning and slower performance improvements, reshaping our understanding of the fundamental role of the sensory cortex.
Pharmacologic Activation of Integrated Stress Response Kinases Inhibits Pathologic Mitochondrial Fragmentation
Authors: Baron Kelsey R. , Oviedo Samantha , Krasny Sophia , Zaman Mashiat , Aldakhlallah Rama , Bora Prerona , Mathur Prakhyat , Pfeffer Gerald , Bollong Michael J. , Shutt Timothy E. , Grotjahn Danielle A. , Wiseman R. Luke
Published: June 2024

Excessive mitochondrial fragmentation is associated with the pathologic mitochondrial dysfunction implicated in the pathogenesis of etiologically-diverse diseases, including many neurodegenerative disorders. The integrated stress response (ISR) – comprising the four eIF2α kinases PERK, GCN2, PKR, and HRI – is a prominent stress-responsive signaling pathway that regulates mitochondrial morphology and function in response to diverse types of pathologic insult. This suggests that pharmacologic activation of the ISR represents a potential strategy to mitigate pathologic mitochondrial fragmentation associated with human disease. Here, we show that pharmacologic activation of the ISR kinases HRI or GCN2 promotes adaptive mitochondrial elongation and prevents mitochondrial fragmentation induced by the calcium ionophore ionomycin. Further, we show that pharmacologic activation of the ISR reduces mitochondrial fragmentation and restores basal mitochondrial morphology in patient fibroblasts expressing the pathogenic D414V variant of the pro-fusion mitochondrial GTPase MFN2 associated with neurological dysfunctions including ataxia, optic atrophy, and sensorineural hearing loss. These results identify pharmacologic activation of ISR kinases as a potential strategy to prevent pathologic mitochondrial fragmentation induced by disease-relevant chemical and genetic insults, further motivating the pursuit of highly selective ISR kinase-activating compounds as a therapeutic strategy to mitigate mitochondrial dysfunction implicated in diverse human diseases.
E3 ligase Praja1 mediates ubiquitination and degradation of microtubule-associated protein Tau
Authors: Aoki Shiho , Kawasaki Kotaro , Imadegawa Kazuki , Oishi Mizuho , Asahi Toru , Onodera Wataru
Published: June 2024

RING-H2 type E3 ligase Praja family is composed of Praja1 and Praja2, which promote the degradation of substrates through the ubiquitin-proteasome system. Both paralogs contribute to neuronal maturation and differentiation, indicating a significant role in the nervous system. Aggregation-prone proteins associated with neurodegenerative diseases, including TDP-43 and α-synuclein, are degraded and/or suppressed by Praja1. Furthermore, the expression level of theMAPTgene, which is frequently mutated in Alzheimer’s, is regulated by Praja2. While the Praja family has been shown to recognize various aggregation-prone proteins as substrates, it has not been determined whether Tau, a key protein that aggregates in tauopathies, is also recognized by Praja proteins. In this study, we show that Praja1, but not Praja2, recognizes Tau as a candidate substrate. We observed that Tau expression in human neuroblastoma SH-SY5Y cells decreased depending on the E3 ligase activity of Praja1. Furthermore, Praja1 polyubiquitinated and interacted with Tau, indicating that it is a target substrate. Next, by combining ancestral sequence reconstruction and mutational analysis, we revealed that the Praja1-Tau interaction began via deletion of the N- and C-terminal regions of Praja1, occurring just after the duplication of the Praja family in the common ancestor of placentals. Lastly, to test whether this interaction is disrupted under pathological conditions, P301L Tau was introduced, resulting in a degradation similar to that of wild-type Tau. These results reveal an unidentified mechanism of Tau proteostasis by Praja1 and may provide insight into the pathogenesis of neurodegenerative diseases, including tauopathy.
Novel Exploration Growth Quantifies Anxiety-like Behaviour in the Elevated Plus Maze
Authors: Zelko Matthew D. , Robinson Stephen R. , Hill-Yardin Elisa , Nasser Helen
Published: June 2024

The elevated plus maze is intended to provoke anxiety-like behaviour, which is primarily measured by the degree to which the rodent explores or avoids the risker, unenclosed arms. Measures such as arm entries and total time spent within the arm are conventionally used, but their analysis often produces inconsistent inferences about the level of anxiety-like behaviour being observed. This inconsistency occurs because the measures do not correlate with one another, raising the question of how validly they capture both the exploratory and avoidance motivations that typify anxiety-like behaviour. Given this inconsistency, we propose a new measure, novel exploration growth, that captures avoidance and exploratory behaviours within the maze. The growth of novel exploration tracks the first visit to discrete areas of the maze over time. The absolute amount of novel exploration, combined with the phasic nature of the exploration, reveals behavioural phenotypes with both avoidance and exploration quantified in a single time series. By addressing both motivations evoked by the maze through a single coherent measure, we provide a superior estimation of anxiety-like behaviour and resolve inconsistencies that arise when applying conventional measures alone.
Spatio-temporal analysis of the innate immune response to cytoplasmic dsDNA using a novel cGAMP biosensor
Authors: Smarduch S , Moreno-Velasquez SD , Dadsena S , Ilic D , Morant R , Pereira G , Binder M , García-Sáez AJ , Acebrón SP
Published: June 2024

The cGAS-STING signalling pathway acts as gatekeeper in the innate immune response towards extrinsic and intrinsic sources of cytoplasmic double stranded DNA (dsDNA). At the core of this pathway is the cGAS-dependent production of the intra- and extra-cellular messenger 2’3’-cyclic GMP-AMP (cGAMP), which activates STING and leads to IRF3-dependent expression of cytokines and interferon. Despite its relevance to monitor viral and bacterial infections, cell death, and genome instability, the lack of specific live reporters has precluded spatio-temporal analyses of cGAS-STING signalling. Here, we generate a fluorescent cGAMP biosensor by engineering the functional interaction of activated STING and IRF3 at the Golgi. We show that cells encoding for the cGAMP biosensor react within 45 minutes, and in a time- and concentration-dependent manner to STING agonists and cGAMP. We demonstrate that the cGAMP biosensor is suitable for single cell characterisation of the dynamics of Herpes Simplex Virus 1 infection, mtDNA release upon apoptosis, and other sources of cytoplasmic dsDNA. Intriguingly, we show that STING signalling is not activated by ruptured micronuclei, suggesting that other cytosolic pattern recognition receptors underlie the interferon response upon chromosomal instability. Furthermore, we demonstrate that the biosensor sensitivity is sufficient to report microenvironmental cGAMP, allowing to analyse how STING signalling spreads through neighbouring cells, including upon viral infection. Taken together, we provide a tool to easily monitor the activation cGAS-STING signalling pathway by live cell imaging, plate reader or immunofluorescence analyses; and to capture the spatio-temporal and heterogenous dynamics of the response to cGAMP.
Amyloid β oligomers dysregulate oligodendrocyte differentiation and myelination via PKC in the zebrafish spinal cord
Authors: Balantzategi U. , Gaminde-Blasco A. , Bayón-Cordero L. , Sánchez-Gómez M. V. , Zugaza J. L. , Appel B. , Alberdi E
Published: June 2024

Amyloid β oligomers (Aβo) have been proposed as candidates to induce oligodendrocyte (OL) and myelin dysfunctions in early stages of Alzheimer’s disease (AD) pathology. Nevertheless, little is known about how Aβo affect OL differentiation and myelinationin vivo, and the underlying molecular mechanisms. In this study, we explored the effects of a brain intraventricular injection of Aβo on OLs and myelin in the developing spinal cord of zebrafish larvae. Using quantitative fluorescentin situRNA hybridization assays, we demonstrated that Aβo alteredmyrfandmbpmRNA levels and the regional distribution ofmbpduring larval development, suggesting an early differentiation of OLs. Through live imaging of Tg(myrf:mScarlet) and Tg(mbp:tagRFP) zebrafish lines, both crossed with Tg(olig2:EGFP), we found that Aβo increased the number ofmyrf+andmbp+OLs in the dorsal spinal cord at 72 hpf and 5 dpf, respectively, without affecting total cell numbers. Furthermore, Aβo also increased the number of myelin sheaths per OL and the number of myelinated axons in the dorsal spinal cord compared to vehicle-injected control animals. Interestingly, the treatment of Aβo-injected zebrafish with the pan-PKC inhibitor Gö6983 restored the aforementioned alterations in OLs and myelin to control levels. Altogether, not only do we demonstrate that Aβo induce a precocious oligodendroglial differentiation leading to dysregulated myelination, but we also identified PKC as a key player in Aβo-induced pathology.
Structural Insight into the Function of Human Peptidyl Arginine Deiminase 6
Authors: Williams Jack P. C. , Mouilleron Stephane , Hernandez Trapero Rolando , Bertran M. Teresa , Marsh Joseph A. , Walport Louise J.
Published: June 2024

Peptidyl arginine deiminase 6 (PADI6) is vital for early embryonic development in mice and humans, yet its function remains elusive. PADI6 is less conserved than other PADIs and it is currently unknown whether it has a catalytic function. Here we have shown that human PADI6 dimerises like hPADIs 2-4, however, does not bind Ca2+and is inactive inin vitroassays against standard PADI substrates. By determining the crystal structure of hPADI6, we show that hPADI6 is structured in the absence of Ca2+where hPADI2 and hPADI4 are not, and the Ca-binding sites are not conserved. Moreover, we show that whilst the key catalytic aspartic acid and histidine residues are structurally conserved, the cysteine is displaced far from the active site centre and the hPADI6 active site pocket appears closed through a unique evolved mechanism in hPADI6, not present in the other PADIs. Taken together, these findings provide insight into how the function of hPADI6 may differ from the other PADIs based on its structure and provides a resource for characterising the damaging effect of clinically significantPADI6variants.
Anoctamins mediate polymodal sensory perception and larval metamorphosis in a non-vertebrate chordate
Authors: Liang Zonglai , Hoyer Jorgen , Chatzigeorgiou Marios
Published: June 2024

An exceptional feature of most animals is their ability to perceive diverse sensory cues from the environment and integrate this information in their brain to yield ethologically relevant behavioral output. For the myriad of marine species, the ocean represents a complex sensory environment, which acts as a crucible of evolution for polymodal sensory perception. The cellular and molecular bases of polymodal sensory perception in a marine environment remain enigmatic.

Here we use Ca2+imaging and quantitative behavioral analysis to show that in the tunicateCiona intestinalistwo members of the evolutionarily conserved Anoctamin family1–4(Tmem16E/Ano5 and Tmem16F/Ano6), are required for sensing chemosensory and mechanosensory metamorphic cues. We find that they act by modulating neuronal excitability and Ca2+response kinetics in the primary sensory neurons and axial columnar cells of the papillae, a widely conserved sensory-adhesive organ across ascidians5–9. Finally, we use electrophysiological recordings and a scramblase assay in tissue culture to demonstrate that Tmem16E/Ano5 acts as a channel, while Tmem16F/Ano6 is a bifunctional ion channel and phospholipid scramblase. Our results establish Ano5 and Ano6 as novel players in the zooplanktonic, pre-vertebrate molecular toolkit that controls polymodal sensory perception in aquatic environments.
Quorum Sensing Regulates Virulence Factors in the Coral PathogenVibrio coralliilyticus
Authors: Lydick Victoria N. , Mass Shir , Pepin Robert , Podicheti Ram , Klempic Emra , Rusch Douglas B. , Ushijima Blake , Brown Laura C. , Salomon Dor , van Kessel Julia C.
Published: June 2024

The bacterial pathogenVibrio coralliilyticus(Vcor) causes disease in coral species worldwide. The mechanisms ofVcorcoral colonization, coral microbiome interactions, and virulence factor production are understudied. In other modelVibriospecies, virulence factors like biofilm formation, toxin secretion, and protease production are controlled through a density-dependent communication system called quorum sensing (QS). Comparative genomics indicated thatV. coralliilyticusgenomes share high sequence identity for most of the QS signaling and regulatory components identified in otherVibriospecies. Here, we identify an active QS signaling pathway in twoV. coralliilyticusstrains with distinct infection etiologies: type strain BAA-450 and coral isolate OCN008. The inter-species AI-2 autoinducer signaling pathway in both strains controls expression of the master QS transcription factor VcpR to regulate >300 genes, including protease production, biofilm formation, and two conserved type VI secretion systems (T6SSs). Activation of T6SS1 by QS results in secretion of effectors and enables interbacterial competition and killing of prey bacteria. We conclude that the QS system inV. coralliilyticusis functional and controls expression of genes involved in relevant bacterial behaviors that may influence coral infection.

IMPORTANCE

Vibrio coralliilyticusinfects many marine organisms, including multiple species of corals, and is a primary causative agent of tissue loss diseases and bacterial-induced bleaching. Here we investigate a common cell-cell communication mechanism called quorum sensing, which is known to be intimately connected to virulence in otherVibriospecies. Our genetic and chemical studies ofV. coralliilyticusquorum sensing uncovered an active pathway that directly regulates key virulence factors: proteases, biofilms, and secretion systems. These findings connect bacterial signaling in communities to infection of corals, which may lead to novel treatments and earlier diagnoses of coral diseases in reefs.
Kinome-wide RNAi screen inCaenorhabditis elegansreveals new modulators of insulin signaling and longevity
Authors: Chamoli Manish , Foulger Anna , Singh Prachi , Lithgow Gordon , Mukhopadhyay Arnab
Published: June 2024

The insulin/IGF-I-like signaling (IIS) pathway is a highly conserved signaling cascade that plays a crucial role in regulating longevity across species. Given its significance in aging, identifying novel kinases interacting with the IIS pathway can provide deeper insights into the mechanisms governing longevity. In this study, we performed a targeted RNAi screen of theCaenorhabditis eleganskinome, utilizing dauer formation as a phenotypic readout. We identified several known and novel kinase modulators of the IIS pathway. These hits were enriched with both previously documented as well as undocumented lifespan regulators. Thermotolerance assays revealed mixed trends, with some kinase inhibitions increasing while others decreasing protection. We observed a positive correlation between thermotolerance and lifespan extension, as well as between dauer formation and lifespan extension, with thermotolerance proving to be a better predictor of longevity. Our findings offer a valuable resource for researchers exploring the IIS pathway and highlight novel, unannotated kinases as potential new therapeutic targets for aging interventions.