bluuebunny/crossref_metadata_2025 huggingface dataset:
Within-subjects ultra-short sleep-wake protocol for characterising circadian variations in retinal function
Authors: Heinrichs Hannah Sophie , Spitschan Manuel
Published: March 2024

Prior studies suggest that visual functions undergo time-of-day variations. Under naturalistic entrainment, diurnal changes in physiology may be driven by circadian and/or homeostatic processes, and repeated measurements at different times of day are thus not suitable to draw unambiguous conclusions about circadian effects on visual function. In this study, we disentangle circadian and homeostatic effects on variations of retinal function. We examine the earliest stages of image-forming (temporal contrast sensitivity of the post-receptoral channels) and non-image forming visual functions (pupillary light response) by employing a short forced-desynchrony multiple-naps protocol lasting 40 hours. Participants (n=12, 50% female) will stay in a controlled time-isolating environment under dim light conditions and adhere to an ultra-short sleep-wake cycle, alternating between 2h30m of wake time in dim light and 1h15m hour of sleep in no light. During eleven intervals of wakefulness, participants will undergo psychophysical and pupillometric assessments with silent-substitution stimuli. We hypothesize that the sensitivity of retinal mechanisms undergoes circadian variations. This hypothesis will be investigated by separately determining psychophysical contrast thresholds to parafoveal silent-substitution stimuli targeting the postreceptoral pathways (isoluminant red-green, L − M; isoluminant blue-yellow, S; luminance, L+M+S). We will furthermore measure the pupillary light response to peripheral stimuli (annulus 10°–30°) in comparison to the response to stimuli isolating or including melanopsin stimulation. All stimuli will be delivered at constant retinal irradiance using a Maxwellian view system or artificially restricting pupil size. Additionally, we will quantify and report effects of our test stimuli on the circadian system by comparing the dim-light melatonin onset (DLMO) timing during two supplementary evening sessions, comparing dim-light conditions to such with experimental light exposure. Our work informs the fundamental biological mechanisms underlying the influence of light on the human circadian system. Based on our findings, current models about the sensitivity of the circadian system may need to be modified in order to account for the bidirectional influence of circadian function and photoreception.
Historical state compulsory schooling laws and pandemic-era mortality: A quasi-experimental study
Authors: Wells Whitney , Chen Yea-Hung , Charpignon Marie-Laure , Lee Ah-Reum , Chen Ruijia , Stokes Andrew C. , Torres Jacqueline M. , Glymour M. Maria
Published: March 2024

Introduction

Low educational attainment is associated with increased risk of COVID-19 mortality, but it remains unclear whether the link between education and COVID-19 mortality is causal or due to confounding factors, such as childhood socio-economic status or cognitive skills. To address this question, we evaluated whether older adults’ risk of COVID-19 mortality was associated with historical state-level compulsory schooling laws (CSLs) applicable when they were school-aged. We also evaluated whether that impact was unique to COVID-19 mortality or also applied to all-cause mortality, both before and during the pandemic.

Methods

We defined mortality outcomes using US death certificate data from Mar 2019-Dec 2021 for people born in the US before 1964 in three time periods: the year prior to the pandemic (Mar 2019-Feb 2020), pandemic year 1 (Mar 2020-Feb 2021), and pandemic year 2 (Mar-Dec 2021). We determined the population at risk using 2019 American Community Survey PUMS data with population weights, representing 78.7 million individuals born in the US before 1964. We linked individuals to the number of mandatory years of education defined by CSLs specific to their state of birth and years when school age. We estimated intention-to-treat effects of CSLs on mortality using logistic regressions controlling for state-of-birth fixed effects, birth year (linear and quadratic), sex, race, ethnicity, and state-level factors including percent urban, Black, and foreign-born (at age 6) and manufacturing jobs per capita and average manufacturing wages (at age 14).

Results

We identified a dose-response relationship between CSLs and mortality. In the first year of the pandemic, people mandated to receive 8 vs 9 (reference) years of education had higher odds of COVID-19 mortality (Odds Ratio [OR]: 1.15; 95% Confidence Interval [CI]: 1.10, 1.19), while those mandated to receive 10 vs 9 (reference) years of education had lower odds of COVID-19 mortality (OR: 0.96; 95% CI: 0.94, 0.98). The association of CSLs with COVID-19 mortality was similar in pandemic years 1 and 2; for all-cause mortality in pandemic years 1 and 2; and for all-cause mortality in the year prior to the pandemic. Results were robust to alternative model specifications.

Conclusions

These findings support a causal benefit of education for reduced mortality during the COVID-19 pandemic. State investments in children’s education may have reduced pandemic-era mortality decades later. Our research has implications beyond the pandemic context, as our results suggest the observed relationship mirrors a pre-existing relationship between CSLs and all-cause mortality.
GASTROINTESTINAL MUCOSAL DAMAGE AND SUBSEQUENT RISK OF PARKINSON’S DISEASE
Authors: Chang Jocelyn J. , Kulkarni Subhash , Pasricha Trisha S.
Published: March 2024

Introduction

The gut-first hypothesis of Parkinson’s Disease (PD) has gained traction, yet the inciting events triggering PD from gut-related factors remain unclear. While H. pylori infection is linked to peptic injury and is 1.47 times more prevalent in PD individuals, it is unknown how gastrointestinal mucosal damage (MD) may increase the risk of PD. We aimed to study the association between upper endoscopy findings of MD and subsequent PD development.

Methods

In our retrospective study of 18,305 adults without prior PD, undergoing upper endoscopy between 2000 and 2005, patients with MD were matched with non-MDs. PD risk in MDs versus non-MDs was assessed using incidence rate ratio (IRR) and multivariate Cox analysis, controlling for covariates.

Results

In the matched cohort, MD patients were significantly more likely to develop PD (IRR 3.00, p<0.0001), even after covariate adjustment (HR 2.42, p<0.001). Covariates including constipation, dysphagia, older age, and male sex were also associated with higher PD risk. Among MDs, H. pylori presence (AOR 5.38, p=0.04) and chronic NSAID use (AOR 3.28, p=0.04) increased PD odds, while chronic smoking decreased PD odds (AOR 0.19, p<0.05).

Conclusion

MD elevates PD risk, with H. pylori increasing risk only in the presence of MD, suggesting a closer link between PD and gastric mucosa disruption. Furthermore, chronic NSAID use significantly raises PD odds in MD, while chronic smoking reduces PD risk in this context. Increased vigilance among MD patients for future PD risk is warranted, with further studies needed to elucidate precise pathophysiology.
Identifying Appropriate Height Exponents and the Impact on Diagnosis and Prognosis of Left Ventricular Hypertrophy: the REMODEL Study
Authors: Lee Clement , Chan Ryan , Toh Desiree-Faye , Kui Michelle , Lee Vivian , Bryant Jennifer A , Bourbetakh Redha , Lee Chi-Hang , Ping Chai , Le Thu-Thao , Chin Calvin WL
Published: March 2024

BACKGROUND

Left ventricular hypertrophy (LVH) is a strong predictor of adverse outcomes. Although normalizing LV mass (LVM) to height exponents reduced variability from body size, specific recommendations for height exponents are lacking due to a scarcity of normal cohorts to define appropriate height exponents. We aimed to demonstrate the diagnostic and prognostic implications of establishing height exponents specific to sex, ethnicity and imaging modality.

METHODS

Non-overweight/non-obese Asian healthy volunteers (n=416) were used to establish appropriate height exponents. The impact of these height exponents was examined in a separate cohort of Asians with hypertension (n=878). All individuals underwent standardized cardiovascular magnetic resonance. Primary outcome was a composite of acute coronary syndrome, heart failure hospitalization, stroke, and cardiovascular mortality.

RESULTS

The height exponents for healthy females and males were 1.57 and 2.33, respectively. LVH was present in 27% of individuals with hypertension when indexed to body surface area (BSA) and 47% when indexed to sex-specific height exponents. Most individuals reclassified to LVH with height exponents were overweight or obese. There were 37 adverse events over 60 (37-73) months of follow-up. Regardless of indexing method, LVH was independently associated with increased adverse events (height exponent hazard ratio (HR): 2.8 [1.25-6.29], P=0.013;BSA HR: 5.43 [2.49-11.8], P<0.001).

CONCLUSIONS

Reference ranges specific to ethnicity, sex and imaging modality are necessary to establish appropriate height exponents. Although utilising height exponents resulted in more LVH reclassification, this did not translate to a notable improvement in event prediction.

Graphical Abstract

In this cardiovascular magnetic resonance study, the appropriate height exponents were 1.57 in Asian females and 2.33 in Asian males. Normalizing to height exponents increased the diagnosis of hypertensive left ventricular hypertrophy (LVH), predominantly in those who were overweight and obese. Regardless of the method of indexing, LVH was associated with adverse primary and secondary outcomes.
The fungal protein Jps1 facilitates unconventional protein secretion through a direct phosphoinositide interaction
Authors: Dali Sanchi , Schultz Michèle , Köster Marian , Kamel Michael , Busch Max , Steinchen Wieland , Hänsch Sebastian , Papadopoulos Athanasios , Reiners Jens , Smits Sander H. J. , Kedrov Alexej , Altegoer Florian , Schipper Kerstin
Published: March 2024

Protein secretion is indispensable for essential cellular processes in eukaryotic cells, contributing significantly to nutrient acquisition, defense or communication. Alternative pathways bypassing the endomembrane system collectively referred to as unconventional secretion are gaining increasing attention. A number of important molecules such as cytokines, fibroblast growth factor or viral proteins are being exported through these mechanistically diverse pathways. In the fungal modelUstilago maydis, cytokinesis-dependent unconventional secretion mediates export of the chitinase Cts1 via the fragmentation zone. This membrane-rich compartment is formed during cytokinesis between mother and daughter cells. Recently, we identified Jps1, a previously uncharacterized protein, as a crucial factor for Cts1 localization and export. Combining biochemical experiments andin vivostudies, we here uncover two pivotal features of Jps1: dimerization and phosphoinositide (PIP) binding. Our findings reveal that a conserved structural core domain mediates homodimerization, while surrounding flexible variable regions suggest potential diversification in different basidiomycete species. Jps1 does not harbor a canonical PIP-binding domain but instead specificity of the interaction with the preferred PIP PI(4,5)P2is determined by basic residues. Importantly, loss of PI(4,5)P2binding specificity results in mis-localisation, morphological defects and reduced extracellular Cts1 activity, particularly at low cell densities. This discovery sheds light on previously unknown key features of Jps1, elucidating its role in supporting Cts1 secretion, and representing a crucial step towards understanding the broader implications of unconventional secretion in eukaryotic cells.
Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions
Authors: Glukhov Ernest , Averkava Veranika , Kotelnikov Sergei , Stepanenko Darya , Nguyen Thu , Mitchell Julie C. , Simmerling Carlos , Vajda Sandor , Emili Andrew , Padhorny Dzmitry , Kozakov Dima
Published: March 2024

In computational biology, accurate prediction of phosphopeptide-protein complex structures is essential for understanding cellular functions and advancing drug discovery and personalized medicine. While AlphaFold has significantly improved protein structure prediction, it faces accuracy challenges in predicting structures of complexes involving phosphopeptides possibly due to structural variations introduced by phosphorylation in the peptide component. Our study addresses this limitation by refining AlphaFold to improve its accuracy in modeling these complex structures. We employed weighted metrics for a comprehensive evaluation across various protein families. The enhanced model notably outperforms the original AlphaFold, showing a substantial increase in the weighted average local distance difference test (lDDT) scores for peptides: from 52.74 to 76.51 in the Top 1 model and from 56.32 to 77.91 in the Top 5 model. These advancements not only deepen our understanding of the role of phosphorylation in cellular signaling but also have extensive implications for biological research and the development of innovative therapies.
Nephronophthisis-associated FBW7 mediates cyst-dependent decline of renal function in ADPKD
Authors: Patel Maulin Mukeshchandra , Gerakopoulos Vasileios , Petsouki Eleni , Zimmerman Kurt A. , Tsiokas Leonidas
Published: March 2024

Nephronophthisis (NPHP) and autosomal dominant Polycystic Kidney Disease (ADPKD) are two genetically distinct forms of Polycystic Kidney Disease (PKD), yet both diseases present with kidney cysts and a gradual decline in renal function. Prevailing dogma in PKD is that changes in kidney architecture account for the decline in kidney function, but the molecular/cellular basis of such coupling is unknown. To address this question, we induced a form of proteome reprogramming by deletingFbxw7encoding FBW7, the recognition receptor of the SCFFBW7E3 ubiquitin ligase in different segments of the kidney tubular system. Deletion ofFbxw7in the medulla led to a juvenile-adult NPHP-like phenotype, where the decline in renal function was due to SOX9-mediated interstitial fibrosis rather than cystogenesis. In contrast, the decline of renal function in ADPKD is coupled to cystic expansion via the abnormal accumulation of FBW7 in the proximal tubules and other cell types in the renal cortex. We propose that FBW7 functions at the apex of a protein network that determines renal function in ADPKD by sensing architectural changes induced by cystic expansion.
Manifold learning uncovers nonlinear interactions between the adolescent brain and environment that predict emotional and behavioral problems
Authors: Busch Erica L. , Conley May I. , Baskin-Sommers Arielle
Published: March 2024

BackgroundTo progress adolescent mental health research beyond our present achievements - a complex account of brain and environmental risk factors without understanding neurobiological embedding in the environment - we need methods to unveil relationships between the developing brain and real-world environmental experiences.MethodsWe investigated associations among brain function, environments, and emotional and behavioral problems using participants from the Adolescent Brain and Cognitive Development Study (N=2,401 female). We applied manifold learning, a promising technique for uncovering latent structure from high-dimensional biomedical data like functional magnetic resonance imaging (fMRI). Specifically, we developedexogenousPHATE (E-PHATE) to model brain-environment interactions. We used E-PHATE embeddings of participants' brain activation during emotional and cognitive processing to predict individual differences in cognition and emotional and behavioral problems, both cross-sectionally and longitudinally.ResultsE-PHATE embeddings of participants' brain activation and environments at baseline show moderate-to-large associations with total, externalizing, and internalizing problems at baseline, across several subcortical regions and large-scale cortical networks, relative to the zero-to-small effects achieved by voxel or PHATE methods. E-PHATE embeddings of the brain and environment at baseline also relate to emotional and behavioral problems two years later. These longitudinal predictions show a consistent, moderate effect in the frontoparietal and attention networks.ConclusionsAdolescent brain's embedding in the environment yields enriched insight into emotional and behavioral problems. Using E-PHATE, we demonstrate how the harmonization of cutting-edge computational methods with longstanding developmental theories advances detection and prediction of adolescent emotional and behavioral problems.
Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
Authors: Lyu Ruitu , Gao Yun , Wu Tong , Ye Chang , Wang Pingluan , He Chuan
Published: March 2024

Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation network and dynamics during cellular processes. In this study, we developed Kethoxal-Assisted Single-stranded DNA Assay for Transposase-Accessible Chromatin with Sequencing (KAS-ATAC-seq) to provide quantitative insights into transcriptional activity of CREs. A main advantage of KAS-ATAC-seq lies in its precise measurement of ssDNA levels within both proximal and distal ATAC-seq peaks, enabling the identification of transcriptional regulatory sequences in genomes. This feature is particularly adept at defining Single-Stranded Transcribing Enhancers (SSTEs). SSTEs are highly enriched with nascent RNA transcription and specific transcription factors (TFs) binding sites that determine cellular identity. Moreover, KAS-ATAC-seq provides a detailed characterization and functional implications of various SSTE subtypes; KAS-ATAC-seq signals on SSTEs exhibit more robust correlation with enhancer activities when compared with ATAC-seq data and active histone mark profiles. Our analysis of promoters and SSTEs during mouse neural differentiation demonstrates that KAS-ATAC-seq can effectively identify immediate-early activated CREs in response to retinoic acid (RA) treatment. We further discovered that ETS TFs and YY1 are critical in initiating early neural differentiation from mESCs to NPCs. Our findings indicate that KAS-ATAC-seq provides more precise annotation of functional CREs in transcription. Future applications of KAS-ATAC-seq would help elucidate the intricate dynamics of gene regulation in diverse biological processes and biomedical applications.
Linked Exposures Across Databases (LEAD): An exposure data aggregation framework to facilitate clinical exposure review
Authors: Samuel Immanuel B.H. , Pollin Kamila , Tschida Sherri , Lu Calvin , Prisco Michelle , Forsten Robert , Ortiz Jose , Barrett John , Reinhard Matthew , Costanzo Michelle
Published: March 2024

Understanding the health outcomes of military exposures is a critical effort for Veterans, their health care team, and national leaders. Veterans Affairs providers receive reports of military exposure related concerns from 43% of Veterans. Understanding the causal influences of environmental exposures on health is a complex task advancement in exposure science and may require interpreting multiple data sources; particularly when exposure pathways and multi-exposure interactions are ill-defined, as is the case for complex and emerging military service-related exposures. Thus, there is a need to standardize clinically meaningful exposure metrics from different data sources to guide clinicians and researchers with a consistent model for investigating and communicating exposure risk profiles. The Linked Exposures Across Databases (LEAD) framework provides a unifying model for characterizing exposure from different exposure datatypes and databases with a focus on providing clinically relevant exposure metrics. Application of LEAD is demonstrated through comparison of different military exposure data sources: Veteran Military Occupational and Environmental Exposure Assessment Tool (VMOAT), Individual Longitudinal Exposure Record (ILER) database and a military incident report database, the Explosive Ordnance Disposal Information Management System (EODIMS). This cohesive method for evaluating military exposures leverages established information with new sources of data and has the potential to influence how military exposure data is integrated into exposure health care and investigational models.
Age-Specific All-Cause Mortality Disparities by Race and Ethnicity During the COVID-19 Pandemic
Authors: Faust Jeremy Samuel , Renton Benjamin , Bongiovanni Tasce , Chen Alexander Junxiang , Sheares Karen Dorsey , Du Chengan , Essien Utibe R. , Fuentes-Afflick Elena , Haywood Trent , Khera Rohan , King Terris , Li Shu-Xia , Lin Zhenqiu , Lu Yuan , Marshall Andrew D.A. , Ndumele Chima D. , Opara Ijeoma , Loarte-Rodriguez Tina , Sawano Mitsuaki , Taparra Kekoa , Taylor Herman A. , Watson Karol E. , Yancy Clyde W. , Krumholz Harlan M.
Published: March 2024

BACKGROUND

The end of the public health emergency provides an opportunity to fully describe disparities during the Covid-19 pandemic.

METHODS

In this retrospective cohort analysis of US deaths during the Covid-19 public health emergency (March 2020-April 2023), all-cause excess mortality and years of potential life lost (YPLL) were calculated by race or ethnicity overall and by age groups (ages <25 years, 25-64 years, ≥65 years). Temporal correlations with Covid-19-specific mortality were measured.

RESULTS

>1.38 million all-cause excess deaths and ~23 million corresponding YPLL occurred during the pandemic. Had the rate of excess mortality observed among the White population been observed among the total population, >252,300 (18%) fewer excess deaths, and >5,192,000 fewer (22%) YPLL would have occurred. The highest excess mortality rates were among the American Indian/Alaska Native (AI/AN, 822 per 100,000; ~405,700 YPLL) and the Black (549 per 100,000; ~4,289,200 YPLL) populations. The highest relative increase in mortality was observed in the AI/AN population (1.34; 95% CI 1.31-1.37), followed by Hispanic (1.31; 95% CI 1.27-1.34), Native Hawaiian or Other Pacific Islander (1.24; 95% CI 1.21-1.27), Asian (1.20; 95% CI 1.18-1.20), Black (1.20; 95% CI 1.18-1.22) and White (1.12; 95% CI 1.09-1.15) populations. Greater disparities occurred among children and adults <65 years.

CONCLUSIONS

Excess mortality occurred in all groups during the Covid-19 pandemic, with disparities by race and ethnicity, especially in younger and middle-aged populations. >252,000 and 5.2 million fewer YPLL would have been observed had increases in mortality among the total population been similar to the White population.
Copy number variants differ in frequency across genetic ancestry groups
Authors: Schultz Laura M. , Knighton Alexys , Huguet Guillaume , Saci Zohra , Jean-Louis Martineau , Mollon Josephine , Knowles Emma E.M. , Glahn David C. , Jacquemont Sébastien , Almasy Laura
Published: March 2024

Copy number variants (CNVs), which are duplicated or deleted genomic segments larger than 1000 base pairs1, have been implicated in a variety of neuropsychiatric and cognitive phenotypes2-4. In the first large-scale of examination of genome-wide CNV frequencies across ancestry groups, we found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.
Prevalence and Cumulative Incidence of Mortality Associated with Cardiovascular-Kidney-Metabolic Syndrome in the United States
Authors: Claudel Sophie E. , Schmidt Insa M. , Waikar Sushrut S. , Verma Ashish
Published: March 2024

Background

To inform public health policies regarding disease management, it is crucial to comprehend the prevalence and mortality rates linked to various stages of Cardiovascular-Kidney-Metabolic (CKM) syndrome.

Methods

A longitudinal study was conducted using National Health and Nutrition Examination Survey (NHANES) data (1999-2018) from 50,624 U.S. adults, defining CKM syndrome stages based on the 2023 American Heart Association (AHA) Presidential Advisory Statement. The investigation aimed to assess changes in 10-and 15-year adjusted cumulative incidences of cardiovascular mortality with each CKD syndrome stage and describe the cross-sectional prevalence of CKM syndrome from 1999 to 2020.

Results

CKM syndrome prevalence by stage was as follows: Stage 0, 12.5% (95% CI, 12.0-12.9); Stage 1, 16.7% (95% CI, 16.2-17.2); Stage 2, 40.0% (95% CI, 38.4-39.6); Stage 3, 22.9% (95% CI, 22.5-23.4); Stage 4, 8.9% (95% CI, 8.6-9.2). Over a median 9.5-year follow-up, 2,557 participants experienced cardiovascular death. The proportion of participants in Stages 0 and 3 decreased, while Stage 1 increased. The 15-year adjusted cumulative incidences of cardiovascular mortality were: Stage 0, 4.8% (95% CI 3.1-6.6); Stage 1, 5.3% (95% CI 4.0-6.6); Stage 2, 7.9% (95% CI 8.1-10.3); Stage 3, 9.2% (95% CI 8.1-10.3); Stage 4, 15.6% (95% CI 14.7-16.6). The absolute risk difference between CKM Stage 4 and Stage 0 at 15 years was 10.8% (95% CI 8.8-12.8).

Conclusions

Our findings showed a graded increase in cardiovascular mortality associated with each CKM stage. The trends observed by stage prevalence emphasize critical opportunities for stabilizing risk factors, thereby preventing adverse cardiovascular outcomes.
PACT-3D, a Deep Learning Algorithm for Pneumoperitoneum Detection in Abdominal CT Scans
Authors: Chiu I-Min , Huang Teng-Yi , Kuo Kuei-Hong
Published: March 2024

Pneumoperitoneum, necessitates surgical intervention in 85-90% of cases, relies heavily on CT scans for diagnosis. Delay or misdiagnosis in detecting pneumoperitoneum can significantly increase mortality and morbidity. Our study introduced PACT-3D, a deep learning model developed to identify pneumoperitoneum in CT images. In this single hospital study, we retrospectively reviewed abdominal CT scans from January 2012 to December 2021, excluded CT of image acquisition error and without reports to form the development dataset for training the model. We evaluated the PACT- 3D model using a simulated test set of 14,039 scans and a prospective test set of 6,351 scans, collected from December 2022 to May 2023 at the same center. PACT-3D achieved a sensitivity of 0.81 and a specificity of 0.99 in retrospective testing, with prospective validation yielding a sensitivity of 0.83 and a specificity of 0.99. Sensitivity improved to 0.95 and 0.98 when excluding cases with a small amount of free air (total volume < 10ml) in simulated and prospective test sets, respectively. By delivering accurate and consistent patient-level predictions and providing segmented masks, PACT- 3D holds significant potential for assisting rapid decision-making in emergency care, thereby potentially improving patient outcomes.
RNA G-quadruplexes and calcium ions synergistically induce Tau phase transitionin vitro
Authors: Yabuki Yasushi , Matsuo Kazuya , Komiya Ginji , Kudo Kenta , Hori Karin , Ikenoshita Susumu , Kawata Yasushi , Mizobata Tomohiro , Shioda Norifumi
Published: March 2024

Tau aggregation is a defining feature of neurodegenerative tauopathies, including Alzheimer’s disease, corticobasal degeneration, and frontotemporal dementia. This aggregation involves the liquid–liquid phase separation (LLPS) of Tau, followed by its sol–gel phase transition, representing a crucial step in aggregate formation bothin vitroandin vivo. However, the precise cofactors influencing Tau phase transition and aggregation under physiological conditions (e.g., ion concentration and temperature) remain unclear. In this study, we unveil that nucleic acid secondary structures, specifically RNA G-quadruplexes (rG4s), and calcium ions (Ca2+) synergistically facilitated the sol–gel phase transition of human Tau under mimic intracellular ion conditions (140 mM KCl, 15 mM NaCl, and 10 mM MgCl2) at 37□in vitro. In the presence of molecular crowding reagents, Tau formed stable liquid droplets through LLPS, maintaining fluidity for 24 h under physiological conditions. Notably, cell-derived RNA promoted Tau sol–gel phase transition, with G4-forming RNA emerging as a crucial factor. Surprisingly, polyanion heparin did not elicit a similar response, indicating a distinct mechanism not rooted in electrostatic interactions. Further exploration underscored the significance of Ca2+, which accumulate intracellularly during neurodegeneration, as additional cofactors in promoting Tau phase transition after 24 h. Importantly, our findings demonstrate that rG4s and Ca2+synergistically enhance Tau phase transition within 1 h when introduced to Tau droplets. In conclusion, our study illuminates the pivotal roles of rG4s and Ca2+in promoting Tau aggregation under physiological conditionsin vitro, offering insights into potential triggers for tauopathy.
Light-microscopy based dense connectomic reconstruction of mammalian brain tissue
Authors: Tavakoli Mojtaba R. , Lyudchik Julia , Januszewski Michał , Vistunou Vitali , Agudelo Nathalie , Vorlaufer Jakob , Sommer Christoph , Kreuzinger Caroline , Oliveira Barbara , Cenameri Alban , Novarino Gaia , Jain Viren , Danzl Johann
Published: March 2024

The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.

One-Sentence Summary

Hydrogel expansion enables molecularly informed reconstruction of brain tissue at synaptic resolution with light microscopy.
Phase Separation and Aggregation of α-Synuclein Diverge at Different Salt Conditions
Authors: Sternke-Hoffmann Rebecca , Sun Xun , Menzel Andreas , Pinto Miriam Dos Santos , Venclovaitė Urtė , Wördehoff Michael , Hoyer Wolfgang , Zheng Wenwei , Luo Jinghui
Published: March 2024

The coacervation and structural rearrangement of the protein alpha-synuclein (αSyn) into cytotoxic oligomers and amyloid fibrils are considered pathological hallmarks of Parkinson’s disease. While aggregation is recognized as the key element of amyloid diseases, liquid-liquid phase separation (LLPS) and its interplay with aggregation have gained increasing interest. Previous work showed that factors promoting or inhibiting amyloid formation have similar effects on phase separation. Here, we provide a detailed scanning of a wide range of parameters including protein, salt and crowding concentrations at multiple pH values, revealing different salt dependencies of aggregation and phase separation. The influence of salt on aggregation under crowded conditions follows a non-monotonic pattern, showing increased effects at medium salt concentrations. This behavior can be elucidated through a combination of electrostatic screening and salting-out effects on the intramolecular interactions between the N-terminal and C-terminal regions of αSyn. By contrast, we find a monotonic salt dependence of phase separation due to the intermolecular interaction. Furthermore, we observe the time evolution of the two distinct assembly states, with macroscopic fibrillar-like bundles initially forming at medium salt concentration but subsequently converting into droplets after prolonged incubation. The droplet state is therefore capable of inhibiting aggregation or even dissolving the aggregates through a variety of heterotypic interactions, thus preventing αSyn from its dynamically arrested state.
Coxiella burnetii-containing vacuoles interact with host recycling-endosomal proteins Rab11a and Rab35 for vacuolar expansion
Authors: Hall Brooke A. , Senior Kristen E. , Ocampo Nicolle T. , Samanta Dhritiman
Published: March 2024

Coxiella burnetiiis a gram-negative obligate intracellular bacterium and a zoonotic pathogen that causes human Q fever. Although acute Q fever manifests as atypical pneumonia, chronic infection may lead to life-threatening endocarditis. The lack of effective antibiotics and a licensed vaccine forCoxiellain the U.S. warrants further research intoCoxiellapathogenesis. Within the host cells,Coxiellareplicates in an acidic phagolysosome-like vacuole termedCoxiella-containing vacuole (CCV). Previously, we have shown that the CCV pH is critical forCoxiellasurvival and that theCoxiellaType 4B secretion system regulates CCV pH by inhibiting the host endosomal maturation pathway. However, the trafficking pattern of the ‘immature’ endosomes inCoxiella-infected cells remained unclear. Our recent CCV localization screen with host Rab proteins revealed that recycling endosome-associated proteins Rab11a and Rab35 localize to the CCV during infection, suggesting that CCV interacts with host recycling endosomes during maturation. Interestingly, only a subset of CCVs were Rab11a or Rab35-positive at any given time point. A quantitation of Rab11a/Rab35-positive CCVs at 3- and 6-days post-infection (dpi) revealed that at 3 dpi, ∼52% of CCVs were positive for Rab11a, whereas only ∼39% CCVs were positive for Rab35. This pattern reversed at 6-dpi, when only ∼22% of CCVs were positive for Rab11a and ∼64% of CCVs were positive for Rab35. These data suggest that the CCV preferentially interacts with Rab11a and Rab35-positive recycling endosomes depending on the stage of maturation. Furthermore, we observed a significant increase in Rab11a and Rab35 fluorescent intensity inCoxiella-infected cells compared to mock cells suggesting thatCoxiellaincreases the recycling endosome content in infected cells. Finally, a siRNA-mediated knockdown of both Rab11a and Rab35 resulted in significantly smaller CCVs, suggesting that recycling endosomal Rab proteins are essential for CCV expansion. Overall, our data, for the first time, show that the CCV dynamically interacts with host recycling endosomes for vacuolar expansion and potentially uncovers novel host cell factors essential forCoxiellapathogenesis.
Contribution of the Type 6 Secretion System to Apoptosis and Macrophage Polarization DuringBurkholderia pseudomalleiInfection
Authors: Stockton Jacob L. , Khakhum Nittaya , Torres Alfredo G.
Published: March 2024

Burkholderia pseudomallei(Bpm) is the causative agent of the disease melioidosis. As a facultative intracellular pathogen,Bpmhas a complex lifestyle that culminates in cell-to-cell fusion and multinucleated giant cells (MNGCs) formation. The virulence factor responsible for MNGC formation is the type 6 secretion system (T6SS), a contractile nanomachine. MNGC formation is a cell-to-cell spread strategy that allows the bacteria to avoid the extracellular immune system and our previous data highlighted cell death, apoptosis, and inflammation as pathways significantly impacted by T6SS activity. Thusly, we investigated how the T6SS influences these phenotypes within the macrophage and pulmonary models of infection. Here we report that the T6SS is responsible for exacerbating apoptotic cell death during infection in both macrophages and the lungs of infected mice. We also demonstrate that although the T6SS does not influence differential macrophage polarization, the M2 polarization observed is potentially beneficial forBpmpathogenesis and replication. Finally, we show that the T6SS contributes to the severity of inflammatory nodule formation in the lungs, which might be potentially connected to the amount of apoptosis that is triggered by the bacteria.
Freeing P300-Based Brain-Computer Interfaces from Daily Calibration by Extracting Daily Common ERPs
Authors: Heo Dojin , Kim Sung-Phil
Published: March 2024

When people use brain-computer interfaces (BCIs) based on event-related potentials (ERPs) over different days, they often need to repeatedly calibrate BCIs every day using ERPs acquired on the same day. This cumbersome recalibration procedure would make it difficult to use BCIs on a daily basis. We aim to address the daily calibration issue by examining across-day variation of the BCI performance and proposing a method to avoid daily calibration. To this end, we implemented a P300-based BCI system designed to control a home appliance over five days in nineteen healthy subjects. We first examined how the BCI performance varied across days with or without daily calibration. On each day, P300-based BCIs were tested using calibration-based and calibration-free decoders (CB and CF), with a CB or a CF decoder being built on the training data on each day or those on the first day, respectively. Using the CF decoder resulted in lower BCI performance on subsequent days compared to the CB decoder. Then, we developed a method to extract daily common ERP patterns from observed ERP signals using the sparse dictionary learning algorithm. We applied this method to the CF decoder and retested the BCI performance over days. Using the proposed method improved the CF decoder performance on subsequent days; the performance was closer to the level of the CB decoder, with improvement of accuracy by 2.28%, 1.93%, 1.75%, and 3.86 % on the subsequent four days, respectively, compared to the original CF decoder. The method proposed by our study may provide a novel approach to addressing the daily-calibration issue for P300-based BCIs, which is essential to implementing BCIs into daily life.
Focal cortical dysplasia type II-dependent maladaptive myelination in the human frontal lobe
Authors: Donkels Catharina , Huber Susanne , Demerath Theo , Scheiwe Christian , Shah Mukesch J. , Heers Marcel , Urbach Horst , Schulze-Bonhage Andreas , Prinz Marco , Häussler Ute , Vlachos Andreas , Beck Jürgen , Nakagawa Julia M. , Haas Carola A.
Published: March 2024

Focal cortical dysplasias (FCDs) are local malformations of the human neocortex and a leading cause of intractable epilepsy. FCDs are classified into different subtypes including FCD IIa and IIb, characterized by a blurred gray-white matter boundary or a transmantle sign indicating abnormal white matter myelination. Recently, we have shown that myelination is also compromised in the gray matter of FCD IIa of the temporal lobe. Since myelination is key for brain function which is imbalanced in epilepsy, in the current study we investigated myelination in the gray matter of FCD IIa and IIb from the frontal lobe. We found that in particular FCD IIb showed myelination disturbances such as increased numbers of myelinating oligodendrocytes (OLs) and an irregular and disorganized myelination pattern covering an enlarged area in comparison to FCD IIa and controls. Interestingly, both FCD types presented with larger axon diameters when compared to controls. A significant correlation of axon diameter and myelin sheath thickness was found for FCD IIb and controls, whereas in FCD IIa large caliber axons were less myelinated. On the level of gene expression, FCD IIb presented with a significant up-regulation of myelin-associated mRNA synthesis in comparison to FCD IIa and by enhanced binding-capacities of the transcription factor MYRF to promoters of myelin-associated genes reflecting the need for more myelin due to increased axon diameters. These data show that FCD IIa and IIb are characterized by divergent signs of maladaptive myelination which may contribute to the epileptic phenotype.

Main points

In the gray matter of the frontal lobe, FCD IIa and FCD IIb are characterized by divergent signs of maladaptive myelination.

FCD IIa presents with an ordinary radial fiber pattern, but with a reduced thickness of the myelin sheath around large diameter axons and with an attenuation of the myelin synthesis machinery.

FCD IIb is characterized by an irregular and disorganized myelin fiber pattern, a higher density of myelinating oligodendrocytes and an elevated transcriptional turnover of myelin-associated genes.
Metabolic rate and foraging behaviour: A mechanistic link across body size and temperature gradients
Authors: Shokri Milad , Cozzoli Francesco , Basset Alberto
Published: March 2024

The mechanistic link between metabolic rate and foraging behaviour is a crucial aspect of several energy-based ecological theories. Despite its importance to ecology however, it remains unclear whether and how energy requirements and behavioural patterns are mechanistically connected. Here we aimed to assess how modes of behaviour, in terms of cumulative space use, patch selection and time spent in an experimental resource patchy environment, are influenced by the foragers’ metabolic rate (SMR) and its main determinants i.e. body mass and temperature. We tested the individual behavioural patterns and metabolic rates of a model organism, the amphipodGammarus insensibilis, across a range of body masses and temperatures. We demonstrated that body mass and temperature exert a major influence on foraging decisions and space use behaviour via their effects on metabolic rates. Individual cumulative space use was found to scale allometrically with body mass and exponentially with temperature, with patch giving-up time falling as body mass and temperature increased. Moreover, SMR had greater predictive power for behavioural patterns, explaining variation beyond that accounted for by body mass and temperature combined. Our results showed that cumulative space use scaled positively with Mass- and-Temperature-independent SMR (residual). Furthermore, the foraging decisions regarding patch choice and partitioning were strongly related to M-T independent SMR; individuals with higher M-T independent SMR initially preferred the most profitable patch and, as time progressed, abandoned the patch earlier compared to others. Our findings regarding the mechanistic relationship between behavioural patterns and metabolic rate across body mass and temperature shed light on higher-order energy-based ecological processes, with implications in the face of climate change.
MdfA is a novel ClpC adaptor protein that functions in the developingBacillus subtilisspore
Authors: Massoni Shawn C. , Evans Nicola J. , Hantke Ingo , Fenton Colleen , Torpey James H. , Collins Katherine M. , Krysztofinska Ewelina M. , Muench Janina H. , Thapaliya Arjun , Martínez-Lumbreras Santiago , Martin Sé Hart , Slater Celia , Wang Xinyue , Fekade Ruth , Obwar Sandra , Yin Siyu , Vazquez Alishba , Prior Christopher B. , Turgay Kürşad , Isaacson Rivka L. , Camp Amy H.
Published: March 2024

Bacterial protein degradation machinery consists of chaperone-protease complexes that play vital roles in bacterial growth and development and have sparked interest as novel antimicrobial targets. ClpC-ClpP (ClpCP) is one such chaperone-protease, recruited by adaptors to specific functions in the model bacteriumBacillus subtilisand other Gram-positive bacteria including the pathogensStaphylococcus aureusandMycobacterium tuberculosis. Here we have identified a new ClpCP adaptor protein, MdfA (“Metabolic differentiation factor A”, formerly YjbA), in a genetic screen for factors that help driveB. subtilistoward metabolic dormancy during spore formation. A knockout ofmdfAstimulates gene expression in the developing spore, while aberrant expression ofmdfAduring vegetative growth is toxic. MdfA binds directly to ClpC to induce its oligomerization and ATPase activity, and this interaction is required for the in vivo effects ofmdfA. Finally, a co-crystal structure reveals that MdfA binds to the ClpC N-terminal domain at a location analogous to that on theM. tuberculosisClpC1 protein where bactericidal cyclic peptides bind. Altogether our data and that of an accompanying study by Riley, Lyda and colleagues support a model in which MdfA induces ClpCP-mediated degradation of metabolic enzymes in the developing spore, helping drive it toward metabolic dormancy.
Emotion induction modulates neural dynamics during ideational originality
Authors: Khalil Radwa , Frühholz Sascha , Godde Ben
Published: March 2024

Emotions remarkably impact our creative minds; nevertheless, a comprehensive mapping of their underlying neural mechanisms remains elusive. Therefore, we explored the influence of induced emotional states on ideational originality and its associated neural dynamics. Participants were randomly presented with three short videos with sad, neutral, and happy content. After each video, ideational originality was evaluated using the alternate uses task (AUT). Ideational originality was significantly higher after induction of the happy state than the neutral state; in contrast, there was a nonsignificant difference between the sad and neutral states. Associated neural dynamics were assessed through EEG time-frequency (TF) power and phase-amplitude coupling (PAC) analysis. Our findings suggest that emotional states elicit distinct TF and PAC profiles associated with ideational originality. Relative to baseline, gamma activity was enhanced after the neutral induction and more enhanced after the induction of a happy state but reduced after the induction of a sad state in 2-4 seconds after starting the task. Our PAC findings suggest that the attention system may be silent after the induction of a happy emotional state to load rich materials into working memory (WM) and active in the sad state to maintain these materials in WM.

Highlight

Ideational originality was significantly higher after the induction of a happy state than in a neutral state.

Emotional states elicited distinct EEG time-frequency and phase-amplitude coupling profiles associated with ideational originality.

Relative to baseline, gamma activity was enhanced in the neutral state and more robust in a happy state but reduced in a sad state 2-4 seconds after starting AUT.

Enhancing ideational originality requires the induction of emotional states to suppress overlearned associations and strengthen weaker coupling associations, which is the case after the induction of a happy emotional state.
A universal niche geometry governs the response of ecosystems to environmental perturbations
Authors: Goyal Akshit , Rocks Jason W. , Mehta Pankaj
Published: March 2024

How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due to the strong coupling between species and their environment. Here, we introduce a theoretical framework for calculating the linear response of ecosystems to environmental perturbations in generalized consumer-resource models. Our construction is applicable to a wide class of systems, including models with non-reciprocal interactions, cross-feeding, and non-linear growth/consumption rates. Within our framework, all ecological variables are embedded into four distinct vector spaces and ecological interactions are represented by geometric transformations between these spaces. We show that near a steady state, such geometric transformations directly map environmental perturbations – in resource availability and mortality rates – to shifts in niche structure. We illustrate these ideas in a variety of settings including a minimal model for pH-induced toxicity in bacterial denitrification.