bluuebunny/crossref_metadata_2025 huggingface dataset:
Alterations in the Brain Lipidome of Alzheimer’s Disease Donors with Rare TREM2 Risk Variants
Authors: Proitsi Petroula , Ebshiana Amera , Wretlind Asger , Xu Jin , Hodges Angela , Legido-Quigley Cristina
Published: August 2024

TREM2 is a microglial receptor, sensitive to Phospholipids and Sphingomyelins, associated with neurodegeneration. Hypomorphic variants in theTREM2gene significantly increase the risk of developing AD.

The main aim of this study was to characterize networks of lipids in post-mortem brain from AD and control donors, and to identify key lipids that are associated with AD and impacted by dysfunctional TREM2.

We studied human post-mortem brain tissue from the hippocampus and the BA9 pre-association cortex from a total of 102 post-mortem brains. Specifically, brain tissue from the BA9 pre-association cortex was available for n=55 donors and brain tissue from the hippocampus was available for n=47 brain donors from three groups: AD donors with a non-synonymous risk DNA variant inTREM2(AD-TREM2var), AD donors with noTREM2-associated variant (AD-TREM2wt), and control donors. Mass Spectrometry was performed to obtain lipidomic signatures spanning 99 lipid species that included the following lipid classes: Ceramides, Sphingomyelins, Phosphatidic acids, Phopshatidyl-cholines, Phosphatidyl-ethalonamines, Phosphatidyl-glycerols, Phosphatidyl-inositols, Phosphatidyl-serines and Triglycerides. Weighted gene co-expression network analysis (WGCNA) was used to identify highly correlated lipid modules and ‘hub’ lipids. Linear mixed models and linear regression analyses, adjusted for age, biological sex, number of APOEε4 alleles and post-mortem delay were used to assess the association of modules and individual hub lipids with AD andTREM2status.

Four lipid modules were found to be relatively well-preserved between the two brain regions, and three of these modules were altered in AD donors and/or in AD donors withTREM2genetic variants. Levels of the BA9 “turquoise” module (“blue” hippocampus module), enriched in Sphingolipids and Phospholipids, were elevated in AD brain donors and in AD TREM2 carriers. The key lipid (hub) of the BA9 “turquoise”/ hippocampus “blue” module was a Phosphatidylserine (PS(32:1)), increased in both AD donors and TREM2 carriers (AD-TREM2wtversus controls: beta=0.468, 95% CI 0.05 – 0.89, p= 3.02E-02; and AD-TREM2varversus controls: beta=1.00, 95% CI 0.53 – 1.47, p= 5.57E-03), whereas the strongest association was observed with a Ceramide (Cer(d38:1)) (AD-TREM2wtversus controls: beta=0.663, 95% CI 0.17 – 1.16, p= 8.9E-03; and AD-TREM2varversus controls: beta=1.31, 95% CI 0.78 – 1.84, p= 4.35E-06).

The consistent increase in TREM2 ligands such as Ceramides and Phosphatidyl-serines in the brains of AD donors, particularly in carriers ofTREM2risk variants, could reflect the presence of AD-associated damage signals in the form of stressed/apoptotic cells and damaged myelin.
Effectiveness of bimodal neuromodulation for tinnitus treatment in a real-world clinical setting in United States: A retrospective chart review
Authors: McMahan Emily E. , Lim Hubert H.
Published: August 2024

Bimodal neuromodulation combining sound therapy with electrical tongue stimulation using the Lenire device is emerging as an effective treatment for tinnitus. A single-arm retrospective chart review analyzes real-world outcomes for 220 tinnitus patients from the Alaska Hearing and Tinnitus Center for the recently FDA-approved Lenire treatment for the first time in a United States clinic. The primary endpoint examines the responder rate and mean change in Tinnitus Handicap Inventory (THI) after approximately 12 weeks of treatment in eligible patients with moderate or worse tinnitus. A responder represents a THI improvement of greater than seven points (i.e., minimal clinically important difference, MCID). Of 212 patients with available data, there was a high responder rate of 91.5% (95% CI: 86.9%, 94.5%) with a mean improvement of 27.8 ± 1.3 (SEM) points, and no device-related serious adverse events. Furthermore, a THI MCID of seven points represents a consistent criterion for clinical benefit based on real-world evidence.
Shouldering our Way into a More Meaningful Research Agenda for Atraumatic Shoulder Pain: A Priority Setting Study
Authors: Lyng Kristian Damgaard , Boersting Torben Krejberg , Clausen Mikkel Bek , Larsen Annelene Houen , Liaghat Behnam , Ingwersen Kim Gordon , Bateman Marcus , Rangan Amar , Bjoernholdt Karen Toftdahl , Christiansen David Hoeyrup , Jensen Steen Lund , Thomsen Janus Laust , Thorborg Kristian , Ziegler Connie , Olesen Jens Lykkegaard , Rathleff Michael Skovdal
Published: August 2024

IMPORTANCE: Atraumatic shoulder pain significantly burdens society and the individual. There is a growing need for involving patients and other stakeholders in setting the research agenda. OBJECTIVE: To use the voices of people with atraumatic shoulder pain, healthcare practitioners, and their relatives to establish research questions. DESIGN, SETTING, AND PARTICIPANTS: This priority-setting study followed a modified approach originally formulated by the James Lind Alliance (JLA). The process consisted of six phases (initiation, consultation, collation, prioritization, validation, and reporting) and included two e-surveys and two separate virtual workshops. Data collection started on June 2021 until June 2023. We included people with atraumatic shoulder pain, relatives, healthcare practitioners managing shoulder pain, and researchers conducting research within the field. EXPOSURES: The first e-survey included basic demographic questions and the possibility to submit at least one and a maximum of five potential research questions. Based on a thematic analysis, questions were arranged into themes and related questions. In the second e-survey, participants were asked to prioritize the questions. Finally, two priority-setting partnership workshops were used to formulate a top-10 list. MAIN OUTCOMES AND MEASURES: A top-25 and top-10 list of research questions related to atraumatic shoulder pain. RESULTS: Initially, 297 participants submitted 1080 potential research questions. In the second e-survey, 290 participants prioritized these questions resulting in a compilation of the top 25. Based on discussions from the workshops with 21 participants, a top 10 list was created. CONCLUSIONS AND RELEVANCE: In the final top 10 list, the three research questions with the highest ranking concerned 1) translating the best available knowledge into clinical practice, 2) preventing shoulder pain, and 3) identifying who benefits from surgery. These questions inform future research funding and projects relating to atraumatic shoulder pain.
Evidence of Differences in Diurnal Electrodermal, Temperature, and Heart Rate Patterns by Mental Health Status in Free-Living Data
Authors: McDuff Daniel , Galatzer-Levy Isaac , Thomson Seamus , Barakat Andrew , Heneghan Conor , Abdel-Ghaffar Samy , Sunshine Jake , Zher-Poh Ming , Sunden Lindsey , Hernandez John , Jiang Allen , Liu Xin , Winbush Ari , Nelson Benjamin W. , Allen Nicholas B.
Published: August 2024

Electrodermal activity (EDA) is a measure of sympathetic arousal that has been linked to depression in laboratory experiments. However, the inability to measure EDA passively over time and in the real-world has limited conclusions that can be drawn about EDA as an indicator of mental health status outside of controlled settings. Recent smartwatches have begun to incorporate wrist-worn continuous EDA sensors that enable longitudinal measurement of sympathetic arousal in every-day life. This work (N=237, 4-week observation period) examines the association between passively collected, diurnal variations in EDA and symptoms of depression, anxiety and perceived stress in a large community sample. Subjects who exhibited elevated depressive and anxiety symptoms had higher tonic EDA, skin temperature, and heart rate, despite not engaging in greater physical activity, compared to those that were not depressed or anxious. In contrast, subjects who exhibited elevated stress only exhibited higher skin temperature. Most strikingly, differences in EDA between those with high versus low symptoms were most prominent during the early morning. We did not observe amplitude or phase differences in the diurnal patterns. Our work suggests that electrodermal sensors may be practical and useful in measuring the physiological correlates of mental health symptoms in free-living contexts and that recent consumer smartwatches might be a tool for doing so.
Lineage B Genotype III of Dengue Virus Serotype 3 (DENV-3III_B) is responsible for Dengue Outbreak in Dire Dawa City, Ethiopia, 2023
Authors: Aseffa Abebe , Alemayehu Dawit Hailu , Abrahim Saro Abdella , Wolde Tsigereda Kifle , Bulti Gutema , Bedasso Alemnesh Hailemariam , Tsega Danile Hailemariam , Abosex Ebise , Awule Eyilachew Zenebe , Rojas-Gallardo Diana M , Korkiso Asefa Konde , Melaku Kalkidan , Joseph Raffael , Ayele Abaysew , Tsegaye Mesfin Mengesha , Piantadosi Anne Mengesha , Tollera Getachew Mengesha , Abdissa Alemseged , Hailu Mesay , Mihret Adane , Mulu Andargachew , Gelanew Tesfaye
Published: August 2024

Background: The eastern parts of Ethiopia, including Dire Dawa City, have faced annual dengue fever (DF) outbreaks since 2013, resulting in substantial healthcare and economic consequences. However, there remains a lack of comprehensive evidence regarding the specific dengue virus (DENV) serotypes and genotypes associated with those outbreaks. Methodology: On December 14, 2023, the National Arbovirus Laboratory at the Ethiopian Public Health Institute received seventy serum samples from 70 patients suspected of DF during the outbreak in Dire Dawa City. Samples positive for DENV with adequate volume and CT values underwent sequencing of the CprM region of the DENV genome. The obtained sequences were typed using the Dengue Virus Typing Tool and underwent phylogenetic analysis to evaluate sequence diversity and relationships to DENV strains from other global DENV-endemic regions. Results: Overall, 32 (45.7%) of the patients displayed one or more early warning signs indicative of severe dengue. Among the 13 patients who were hospitalized for 2 to 10 days, all except two had at least one symptom indicative of severe dengue. Out of 67 samples with adequate volume, 44 (65.6%) were positive for DENV RNA using RT-PCR, and 21 successfully underwent CprM sequencing. All of them belonged to DENV-3, genotype III, major lineage B (DENV-3III_B), but represented two different minor lineages (DENV-3III_B.2 and DENV-3III_B.3). Phylogenetic analysis demonstrated that both lineages were closely related to sequences from the Afar region of Ethiopia collected in 2023, indicating that the outbreaks were related and were due to multiple co-circulating lineages. Conclusions: DENV-3III_B was identified as the cause of the 2023 DF outbreak in Dire Dawa City. The identification of two co-circulating lineages in this outbreak underscores the complex nature of DENV transmission in the African continent and highlights the need for increased viral genomic surveillance.
Investigating experiences of stigma and its impact on substance use recovery among residents of recovery residences in the United States: A scoping review protocol. BSGH020
Authors: Abu-Ba'are Gamji Rabiu , Hogarty Sahil , Shamrock Osman Wumpini , Russell Holly , Manchisi Kate , Smtih Van , Mericle Amy
Published: August 2024

The objective of this scoping review is to systematically review the literature on stigma experienced by residents in recovery residences and its impact on substance use recovery outcomes. The review will use the PRISMA-ScR framework to identify studies focused on stigma and recovery in recovery residences published in English within the United States since 2000, including qualitative, quantitative, and mixed-methods studies. Data will be extracted and analyzed thematically to identify gaps in the literature and inform future research and policy development. Preliminary findings suggest that stigma, including labeling and discrimination, significantly hinders recovery by promoting secrecy and withdrawal among residents. Proximity to recovery residences has been shown to reduce community stigma, indicating the potential for better integration and acceptance. This study aims to provide a comprehensive understanding of stigma in recovery residences, its effects on substance use recovery, and recommendations for creating supportive recovery environments. The significance of this study lies in its potential to inform policy, practice, and research, highlighting the need for stigma reduction to improve recovery outcomes in recovery residences. By addressing gaps in the literature, the findings will contribute to developing more effective interventions and supportive environments for individuals recovering from substance use.
PROgressive struCturEd Simulation-based Surgical training program (PROCESS) - Open Vascular Surgery: Study protocol for triple-arm, randomized, single-blinded educational clinical trial
Authors: Velandia-Sánchez Alejandro , Polanía-Sandoval Camilo A. , Álvarez-Martínez José V. , Uribe-Ramírez Santiago , Tello-Pirateque Juliana , Pérez-Rivera Carlos J. , Ávila-Madrigal Juan P. , Cruz Reyes Danna L. , Cabrera-Rivera Paulo A. , Pérez-Cualtan Camilo E. , Barrera Edgar C. , Bustos-Martínez Yury F. , Galán Sebastián Gómez , Briceño Juan C. , Reijnen Michel M.P.J. , Camacho-Mackenzie Jaime , Mendivil Carlos O. , Barrera-Carvajal Juan G.
Published: August 2024

Introduction

Vascular surgery has been directed towards endovascular approaches; however, not all patients qualify for these procedures. Open vascular surgery remains crucial, demanding a steep learning curve. Exposure to these procedures has declined, resulting in a need for more standardization in acquiring open vascular surgery skills and potentially contributing to poorer outcomes. Simulation offers a solution, yet the evidence for structured programs in open vascular surgery is limited. This study aims to compare the efficacy of technical skill acquisition between a structured, progressive simulation-based training program and traditional experience-based training in open vascular surgery.

Methods

A randomized, single-blinded, triple-arm educational clinical trial will be conducted. A control and intervention phases of three groups with different exposure levels to the simulation program are proposed. Group 1: open abdominal aortic repair, Group 2: vascular anastomosis and open abdominal aortic repair, and Group 3: specific surgical skills, vascular anastomosis, and open abdominal aortic repair. The 3D-printed models from AngioCT will be used for the open abdominal aortic repair simulation. Surgical residents of general, vascular, or cardiothoracic surgery programs will be included. Sample size calculation resulted in 45 participants, 15 per group. Single blinding will involve external evaluators. Randomization will occur as a stratified randomization.

Discussion

We expect that the structured and progressive simulation-based training program would enhance technical surgical skills. Based on the progression through different modules within the program, we aim to evaluate differences in the acquisition of technical surgical skills. We hypothesize that 3D-printed patient-specific models can enhance participants’ vascular surgery training and provide optimal simulated scenarios while prioritizing patient safety. We hope this initiative will impact the formation of future vascular surgeons, shape future training programs, and ensure comprehensive preparation for open vascular surgery.

Trial registration

This study protocol was registered inclinicaltrials.govwith the NCT-ID:NCT06452901.
Multi-Year Comparison of VITEK® MS performance for identification of rarely encountered pathogenic gram-negative bacilli (GNBs) in a large integrated Canadian healthcare region.
Authors: Church Deirdre L. , Griener Thomas , Gregson Dan
Published: August 2024

Background: This multi-year study (2014-19) compared identification of rare and unusual GNB by MALDI-TOF MS (VITEK® MS, bioMérieux, Laval Que.) to 16S rRNA gene sequencing (16S) according to our laboratories routine workflow; 16S is done if initial MALDI-TOF MS results were discordant, wrong or absent. Materials and Methods: GNB isolates were first analyzed by standard phenotypic methods and MALDI-TOF MS using direct deposit with full formic acid extraction; proteomics was repeated if no result occurred. Medically approved 16S analyses were done using fast protocols. Isolate sequences were analyzed using IDNS3 bacterial database (SmartGene™, Lausanne, Switzerland). Results: 329 GNB isolates were recovered from 304 specimens; >1 isolate was recovered from 19(6%). 250(76%) NFGNBs, 62(19%) fGNBs, and 17(5%) CAMPB were mainly recovered from blood cultures (31.6%) and lower respiratory specimens (43%) (one-half were isolated from cystic fibrosis patients). Accurate genus vs. species identities were obtained for 67.2%/26% NFGNBs, 74.2%/53.2% fGNBs, and 22% CAMPB (with no discrepant species), respectively. Wrong or no results were obtained for 82(32.8%) NFGNB, 17(27.4%) fGNB, and 13(72.2%) CAMPB. Absent or misidentifications occurred for NFGNBs (33%), fGNBs (26%) and CAMPB (89%) due to absent species in the instrument’s database. VITEK MS performance remained stable for NFGNBs and fGNBs but improved for CAMPB but with the addition ofCampylobacter rectusandCampylobacter curvusto the database. Conclusions: VITEK® MS databases need to be continually updated to include an increasing number of rare and unusual GNBs causing invasive human infections. 16S remains important for GNB identification where proteomics fails.
Future Pandemics: AI-Designed Assays for Detecting Mpox, General and Clade 1b Specific
Authors: Mendoza-Maldonado Lucero , MacSharry John , Garssen Johan , Kraneveld Aletta D. , Tonda Alberto , Lopez-Rincon Alejandro
Published: August 2024

The global outbreak of human monkeypox (mpox) in 2022, declared a Public Health Emergency of International Concern by the WHO, has underscored the urgent need for effective diagnostic tools. In August 2024 WHO again declared mpox as a Public Health Emergency of International Concern. This study presents an innovative approach using artificial intelligence (AI) to design primers for the rapid and accurate detection of mpox. Leveraging evolutionary algorithms, we developed primer sets with high specificity and sensitivity, validated insilicofor mpox main lineage and the Clade 1b. These primers are crucial for distinguishing mpox from other viruses, enabling precise diagnosis and timely public health responses. Our findings highlight the potential of AI-driven methodologies to enhance surveillance, vaccination strategies, and outbreak management, particularly for emerging zoonotic diseases. The emergence of new mpox clades, such as Clade1b, with higher mortality rates, further emphasizes the necessity for continuous monitoring and preparedness for future pandemics. This study advocates for the integration of AI in molecular diagnostics to improve public health outcomes.
Pemphigus vulgaris autoantibodies induce an ER stress response
Authors: Hoffman Coryn L , Bharathan Navaneetha Krishnan , Shibata Yoshitaka , Giang William , Gudjonsson Johann E , Seykora John T , Prouty Stephen M , Payne Aimee S , Kowalczyk Andrew P
Published: August 2024

Desmosomes are intercellular junctions that mediate cell-cell adhesion and are essential for maintaining tissue integrity. Pemphigus vulgaris (PV) is an autoimmune epidermal blistering disease caused by autoantibodies (IgG) targeting desmoglein 3 (Dsg3), a desmosomal cadherin. PV autoantibodies cause desmosome disassembly and loss of cell-cell adhesion, but the molecular signaling pathways that regulate these processes are not fully understood. Using high-resolution time-lapse imaging of live keratinocytes, we found that ER tubules make frequent and persistent contacts with internalizing Dsg3 puncta in keratinocytes treated with PV patient IgG. Biochemical experiments demonstrated that PV IgG activated ER stress signaling pathways, including both IRE1⍺ and PERK pathways, in cultured keratinocytes. Further, ER stress transcripts were upregulated in PV patient skin. Pharmacological inhibition of ER stress protected against PV IgG-induced desmosome disruption and loss of keratinocyte cell-cell adhesion, suggesting that ER stress may be an important pathomechanism and therapeutically targetable pathway for PV treatment. These data support a model in which desmosome adhesion is integrated with ER function to serve as a cell adhesion stress sensor that is activated in blistering skin disease.
Gut microbiota–mediated lipid accumulation as a driver of evolutionary adaptation to blue light toxicity inDrosophila
Authors: Takada Yuta , Ichinose Toshiharu , Fuse Naoyuki , Saito Kokoro , Ikeda-Ohtsubo Wakako , Tanimoto Hiromu , Hori Masatoshi
Published: August 2024

Since the origin of life, the sunlight-driven environment on Earth has shaped the evolution of organisms. Blue light (BL), a major component of sunlight, is crucial to the biological processes of many insect species, yet excessive exposure can be highly toxic. BL toxicity can affect fitness and act as a selective pressure in insects. However, tolerance and evolutionary adaptation to this stressor remain largely unexplored. Here, we usedDrosophila melanogasteras a model to select for BL tolerance over 60 generations. The selected line (SL) exhibited an obese phenotype accompanied by midgut elongation. Surprisingly, BL tolerance in the SL was dependent on gut microbiota–mediated lipid accumulation. In addition, we found that parental BL exposure plays a vital role in midgut elongation and increased abundance of beneficial bacteria. Whole-genome and transcriptome analyses consistently highlighted interactions between the microbiota and lipogenesis genes. Remarkably, manipulation of lipogenesis via these genes conferred BL tolerance even in the absence of selection. We hypothesise that the acquisition of BL tolerance occurs through ‘adaptive obesity’ by maximising the benefits of the gut microbiota. Our findings demonstrate that evolutionary adaptations to environmental stress can be driven by optimised interactions with the microbiota.
Carbonic anhydrase inhibitors prevent presymptomatic capillary flow disturbances in a model of cerebral amyloidosis
Authors: Gutiérrez-Jiménez Eugenio , Rasmussen Peter Mondrup , Mikkelsen Irene Klærke , Kura Sreekanth , Fruekilde Signe K. , Hansen Brian , Bordoni Luca , Carlsen Jasper , Palmfeldt Johan , Boas David A. , Sakadžić Sava , Vinogradov Sergei , Khatib Mirna El , Ramos-Cejudo Jaime , Wied Boris , Leduc-Galindo Desiree , Canepa Elisa , Mar Adam C. , Gamallo-Lana Begona , Fossati Silvia , Østergaard Leif
Published: August 2024

Structured abstract

INTRODUCTION

Disturbances in microvascular flow dynamics are hypothesized to precede the symptomatic phase of Alzheimer’s disease (AD). However, evidence in presymptomatic AD remains elusive, underscoring the need for therapies targeting these early vascular changes.

METHODS

We employed a multimodal approach, combining in vivo optical imaging, molecular techniques, and ex vivo MRI, to investigate early capillary dysfunction in Tg-SwDI mice without memory impairment. We also assessed the efficacy of carbonic anhydrase inhibitors (CAIs) in preventing capillary flow disturbances.

RESULTS

Our study revealed capillary flow disturbances associated with alterations in capillary morphology, adhesion molecule expression, and Amyloid-β (Aβ) load in 9–10-month-old Tg-SwDI mice without memory impairment. CAI treatment ameliorated these capillary flow disturbances, enhanced oxygen availability, and reduced Aβ load.

DISCUSSION

These findings underscore the importance of capillary flow disturbances as early biomarkers in presymptomatic AD and highlight the potential of CAIs for preserving vascular integrity in the early stages of AD.
Acclimation to high daily thermal amplitude converts a defense response regulator into susceptibility factor
Authors: Didelon Marie , Sucher Justine , Carvalho-Silva Pedro , Zaffuto Matilda , Barbacci Adelin , Raffaele Sylvain
Published: August 2024

Acclimation enables plants to adapt to immediate environmental fluctuations, supporting biodiversity and ecosystem services. However, global changes are altering conditions for plant disease outbreaks, increasing the risk of infections by pathogenic fungi and oomycetes, and often undermining plant immune responses. Understanding the molecular basis of plant acclimation is crucial for predicting climate change impacts on ecosystems and improving crop resilience. Here, we investigated howArabidopsis thalianaquantitative immune responses acclimates to daily temperature fluctuations. We analyzed responses to the fungal pathogenSclerotinia sclerotiorumfollowing three acclimation regimes that reflect the distribution areas of both species. Mediterranean acclimation, characterized by broad diurnal temperature amplitudes, resulted in a loss of disease resistance in three naturalA. thalianaaccessions. Global gene expression analyses revealed that acclimation altered nearly half of the pathogen-responsive genes, many of which were down-regulated by inoculation and associated with disease susceptibility. Phenotypic analysis ofA. thalianamutants identified novel components of quantitative disease resistance following temperate acclimation. Several of these mutants were however more resistant than wild type following Mediterranean acclimation. Notably, mutant lines in the NAC42-like transcription factor did not show a loss of resistance under Mediterranean acclimation. This resistance was linked to an acclimation-mediated switch in the repertoire of NAC42-like targets differentially regulated by inoculation. These findings reveal the rewiring of immune gene regulatory networks by acclimation and suggest new strategies to maintain plant immune function in a warming climate.
Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis
Authors: Tsitsikli Magdalini , Simonsen Bine W. , Larsen Maria M. , Andersen Camilla G. , Gysel Kira , Lironi Damiano , Krönauer Christina , Rübsam Henriette , Luu Thi-Bich , Hansen Simon B. , Kaya Gülendam , Stougaard Jens , Andersen Kasper R. , Radutoiu Simona
Published: August 2024

Receptor signaling shapes cellular functions and specificity in the signaling output is central for delineating biological processes. In legume root cells, very similar and structurally conserved chitin and Nod factor receptor kinases activate immunity, or symbiosis, respectively after perception of chitinous ligands. Here we show that individual residues in the intracellular part of the Nod factor receptor NFR1 determine signal specificity and efficiency distinguishing immunity and symbiotic signaling. Functional investigation of CERK6, NFR1 and receptor variants hereof revealed a conserved motif that we term Symbiosis Determinant 1 in the juxtamembrane region of the kinase domain that is key for symbiotic signaling. We demonstrate that two residues in Symbiosis Determinant 1 are indispensable hallmarks for NFR1 receptors and are sufficient to convertLotusCERK6 and barley RLK4 functioning in immunity, to initiate symbiotic signaling.
Open-hardware solutions for light sheet microscopy specimen chambers
Authors: Golden Artemiy , Colombelli Julien , Stelzer Ernst H.K. , Pampaloni Francesco
Published: August 2024

Light sheet fluorescence microscopy (LSFM) is a powerful tool for imaging large three-dimensional biological samples. However, the design and fabrication of specimen chambers for these systems present significant challenges, particularly in maintaining water-tight seals, preventing contamination, and ensuring the flexibility needed for precise positioning of the objective and sample. This study introduces open-hardware solutions to address these challenges, utilising a combination of 3D printing, silicone injection moulding, and FEP-foil thermoforming. We describe the development of custom, highly flexible silicone seals and connectors through a laboratory-scale injection moulding process. These components enable precise, low-resistance movement of imaging objectives and specimen holders, which is crucial for maintaining imaging accuracy. Additionally, we introduce a novel “optical window” design that isolates the objective lens from the immersion medium, significantly reducing the risk of contamination and facilitating easy exchange of chambers and lenses without compromising sterility. The practicality of these designs is demonstrated through their application in long-term live imaging ofTribolium castaneumembryos, honey bee embryos, and human mesenchymal stem cell spheroids. By providing open-source CAD and 3D printing files, this work promotes accessibility and customization in microscopy, enabling researchers to easily replicate and adapt these solutions to their specific needs.
Biophysical limits of ultrafast cellular motility
Authors: Chang Ray , Prakash Manu
Published: August 2024

Many single-celled organisms and specialized cell types can surprisingly achieve speed and acceleration significantly faster than multicellular counterparts. These remarkable cellular machines must integrate energy storage and amplification in actuation, latches for triggered release, and energy dissipation without failure — all implemented in macro-molecular assemblies inside a single cell. However, a universal biophysical framework that can comparatively evaluate extreme cellular motility remains lacking. Scaling laws have long been recognized as powerful tools for revealing universal principles in physical systems. We map the atlas of ultrafast motility for single cells across the tree of life. We then introduce a new quantitative framework that can be used to evaluate and compare extreme acceleration, speed, area strain rate, volume expansion strain rate, and density changes in single cells. Recognizing that many single cells operate in low-Reynolds number environments, we introduce a new dimensionless number, the “cellular acceleration number,” based on energy dissipation at this scale. Using this new framework, we discover a scaling law between the cellular acceleration number and the transient Reynolds number, valid across six orders of magnitude in a range of single-cell organisms. We further generalize these ideas by placing various trigger, actuation, and dissipation mechanisms within the same framework and estimating the fundamental limits of speed and acceleration at the cellular scale. We conclude with a detailed summary of the range of functions implemented via ultrafast cellular phenomena, laying down a quantitative foundation for extreme biophysics at the cellular scale.
Capturing changes to animal complexity from quantifiable patterns in genomic data
Authors: Peterson Kevin J , Clarke Alexander , Zolotarov Grygoriy , Deline Brad , McPeek Mark , Martinez Pedro , Fromm Bastian
Published: August 2024

A prevailing problem in evolutionary biology is elucidating the genotype-phenotype map that characterizes how genomic activities regulate different aspects of organismal morphology and their variability in both space and time. Here, we explore potential causality between genome content and both morphological complexity and disparity by compiling the regulatory components (i.e., transcription factors, RNA binding proteins, and microRNA families) as well as a representative set of non-regulatory housekeeping genes in 32 species belonging to a wide variety of animal phyla, altogether encapsulating a number of varying genomic characteristics and morphological diversities. A principal component analysis of these four non-overlapping genomic components from each of these 32 species in relation to their last common ancestor revealed that no relationship exists between genome space and disparity, as changes to animal body plans appear to be largely the result of changes to the gene regulatory networks that govern animal development rather than gaining or losing specific sets of regulatory genes. However, using both phylogenetically correlated as well as phylogenetically uncorrelated statistical tests, we find a strong relationship between the loss of all considered gene types and the advent of some parasitic taxa, as well as between microRNA innovations and organismal complexity. While this analysis of genomic features suggests how complexity and disparity are each encoded in the genome, further analysis of the regulatory networks in which they participate should provide a more comprehensive description of how organisms diversify their morphologies over time through alterations in their genomic components.
Leveraging Chlorination-Based Mechanism for Resolving Subcellular Hypochlorous Acid
Authors: Tang Fung Kit , Tucker Lawrence , Nadiveedhi Maheshwara Reddy , Hladun Colby , Morse Jared , Ali Mahnoor , Payne Noah , Schmidt Matthias , Leung Kaho
Published: August 2024

Hypochlorous acid (HOCl) is crucial for pathogen defense, but an imbalance in HOCl levels can lead to tissue damage and inflammation. Existing HOCl indicators employ an oxidation approach, which may not truly reveal the chlorinative stress environment. We designed a suite of indicators with a new chlorination-based mechanism, termed HOClSense dyes, to resolve HOCl in sub-cellular compartments. HOClSense dyes allow the visualization of HOCl with both switch-on and switch-off detection modes with diverse emission colors, as well as a unique redshift in emission. HOClSense features a minimalistic design with impressive sensing performance in terms of HOCl selectivity, and our design also facilitates functionalization through click chemistry for resolving subcellular HOCl. As a proof of concept, we targeted plasma membrane and lysosomes with HOClSense for subcellular HOCl mapping. With utilizing HOClSense, we discovered the STING pathway-induced HOCl production and the abnormal HOCl production in Niemann-Pick diseases. To the best of our knowledge, this is the first chlorination-based HOCl indicator series for resolving subcellular HOCl.
Detecting genetically variant peptides in non-human samples
Authors: Chu Fanny , Lin Andy
Published: August 2024

During proteomics data analysis, experimental spectra are searched against a user-defined protein database consisting of proteins that are reasonably expected to be present in the sample. Typically, this database contains the proteome of the organism under study concatenated with expected contaminants such as trypsin and human keratins. However, there are additional contaminants that are not commonly added to the database. In this study, we describe a new set of protein contaminants and provide evidence that they are detectable in mass spectrometry-based proteomics data. Specifically, we provide evidence that human genetically variant peptides (GVPs) can be detected in non-human samples. GVPs are peptides that contain single amino acid polymorphisms that result from non-synonymous single nucleotide polymorphisms in protein coding regions of DNA. We reanalyzed previously collected non-human data-dependent acquisition (DDA) and data-independent acquisition (DIA) datasets and detected between 0 and 135 GVPs per dataset. In addition, we show that GVPs are unlikely to originate from non-human sources and that a subset of eight GVPs are commonly detected across datasets.
Damsels in a hidden colour: development of ultraviolet sensitivity and colour patterns in damselfishes (Pomacentridae)
Authors: Tettamanti Valerio , Marshall Justin , Cheney Karen , Cortesi Fabio
Published: August 2024

Damselfishes (Pomacentridae) are widespread and highly abundant on tropical coral reefs. They exhibit diverse body colouration within and between the ~250 species and across ontogenetic stages. In addition to human visible colours (i.e., 400-700 nm), most adult damselfishes reflect ultraviolet (UV, 300-400 nm) colour patches. UV sensitivity and UV colour signals are essential for feeding and form the basis for a secret communication channel invisible to the many UV-blind predatory fish on the reef; however, how these traits develop across ontogenetic stages, and their distribution across the damselfish family is poorly characterised. Here, we used UV photography, phylogenetic reconstructions of opsin genes, differential gene expression analysis (DGE) of retinal samples, to investigate the development of UV vision and colour patterns in three ontogenetic stages (pre-settlement larval, juvenile, and adult) of eleven damselfish species. Using DGE, we found similar gene expression between juveniles and adults, which strongly differed from larvae. All species and all stages expressed at least one UV-sensitivesws1opsin gene. However, UV body colour patterns only started to appear at the juvenile stage. Moreover,Pomacentrusspecies displayed highly complex UV body patterns that were correlated with the expression of twosws1copies. This could mean that some damselfishes can discriminate colours that change only in their UV component. We demonstrate dramatic shifts in both UV sensitivity and UV colouration across the development stages of damselfish, while highlighting the importance of considering ontogeny when studying the coevolution of visual systems and colour signals.
The applicability of Regional Red List assessments for soil invertebrates: First assessment of five native earthworm species in Canada
Authors: Phillips Helen R. P. , Brown George G. , James Sam W. , Mathieu Jérôme , Reynolds John Warren , Dharmasiri Maheshi E. , Singer Claire L. , Briones Maria J. I. , Proctor Heather C. , Cameron Erin K.
Published: August 2024

Earthworms (Annelida: Clitellata: Crassiclitellata) are prominent members of the soil community, important to many ecosystem functions. Despite this, and like many other soil invertebrates, they are rarely considered in conservation assessments, including the IUCN Red List assessments used to assess species’ extinction risk. To investigate the applicability of the IUCN Regional Red Listing protocol to soil invertebrates, we assessed the conservation status of five earthworm species known to be native to Canada using this protocol and all available occurrence records. In Canada, no earthworm species have yet been assessed by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). Due to the lack of data on population sizes and their trends, all five species were assessed using their Extent of Occurrence (EOO) (Criterion B). One species was assessed as Vulnerable, two were assessed in non-threatened categories, and two were assessed as Data Deficient. For the majority, the main threats identified were the continuing loss of potential habitat due to land conversion and resource exploitation, as well as the effects of climate change. Increasing the amount of data, including but not limited to distribution and habitat preferences, would make the assessment process easier and status decisions better supported. By undertaking regional assessments for five native earthworm species in Canada, we show that Regional Red List assessments are feasible for soil invertebrates.
DNA methylation protects cancer cells against senescence
Authors: Chen Xiaoying , Yamaguchi Kosuke , Rodgers Brianna , Goehrig Delphine , Vindrieux David , Lahaye Xavier , Nolot Matthieu , Ferry Laure , Martin Nadine , Dubus Pierre , Miura Fumihito , Ito Takashi , Manel Nicolas , Kanemaki Masato , Bernard David , Defossez Pierre-Antoine
Published: August 2024

Inhibitors of DNA methylation such as 5-aza-deoxycytidine are widely used in experimental and clinical settings. However, their mechanism of action is such that DNA damage inevitably co-occurs with loss of DNA methylation, making it challenging to discern their respective effects. Here we deconvolute the effects of decreased DNA methylation and DNA damage on cancer cells, by using degron alleles of key DNA methylation regulators. We report that cancer cells with decreased DNA methylation —but no DNA damage— enter cellular senescence, with G1 arrest, SASP expression, and SA-β-gal positivity. This senescence is independent of p53 and Rb, but involves p21, which is cytoplasmic and inhibits apoptosis, and cGAS, playing a STING-independent role in the nucleus. Xenograft experiments show that tumor cells can be made senescentin vivoby decreasing DNA methylation. These findings reveal the intrinsic effects of loss of DNA methylation in cancer cells and have practical implications for future therapeutic approaches.
FGF9 treatment reduces off-target chondrocytes from iPSC-derived kidney organoids
Authors: Joris Virginie , Schumacher Anika , Marks Paula , Eischen-Loges Maria , van Griensven Martijn , LaPointe Vanessa L.S.
Published: August 2024

Renal failure due to drug nephrotoxicity or disease is frequently observed in patients. The development ofin vitromodels able to recapitulate kidney biology offers new possibilities to study drug toxicity or model diseases. Induced pluripotent stem cell–derived kidney organoids already show promise, but several drawbacks must be overcome to maintain them in culture, among which is the presence of non-renal cell populations such as cartilage. We modified the culture protocol and maintained kidney organoids in medium containing FGF9 for one additional week compared to the control protocol (Takasato). In comparison to the control, the FGF9-treated kidney organoids had reduced cartilage at day 7+25 and diminished chondrocyte marker expression. Importantly, the renal structures assessed by immunofluorescence were unaffected by the FGF9 treatment. This reduction of cartilage produces a higher quality kidney organoid that can be maintained longer in culture to improve their maturation for furtherin vivowork.

Highlights

Kidney organoids develop cartilage between days 7+18 and 7+25

Extending the FGF9 supplementation reduces cartilage and chondrocyte markers

FGF9-treated organoids present less EMT marker expression than control organoids

Renal structures are not affected by the extended FGF9 treatment

eTOC blurb

LaPointe and colleagues showed that a one-week extension of FGF9 supplementation in iPSC-derived kidney organoids leads to a reduction of off-target cartilage. The renal structures are not impacted by FGF9 treatment and EMT markers are reduced. This modified organoid protocol will enable longer culture periods, a benefit for the use of organoids for screening or therapies.
Relaxation dynamics in the self-propelled Voronoi model for epithelial monolayers
Authors: Li Meng-Yuan , Li Yan-Wei
Published: August 2024

Cell monolayers and epithelial tissues display slow relaxation dynamics during the reversible transition between mesenchymal and epithelial cells, a phenomenon directly relevant to embryogenesis, tumor metastases, and wound healing. In active cells, persistent motion induces collective dynamics that significantly influence relaxation behavior. To better understand the role of persistence in cell relaxations, we perform extensive simulations and employ cage-relative measures to address the previously overlooked system size effects in model active cells. We identify the glass transition at various persistence values, demonstrating conventional near-equilibrium supercooled dynamics at low persistence. However, highly persistent cells exhibit distinctive intermittent dynamics associated with intermittent local T1 transitions, where cell velocity correlates over space with a characteristic length ξ. More significantly, we formulate a universal relationship predicting the global relaxation time based on the T1 transition and the spatial velocity correlation across a wide range of persistence values. Specifically, the relaxation time demonstrates a power-law dependence on the irreversible T1 transition rate, multiplied by exp(ξ). Here, ξ vanishes at small persistence in nearly equilibrated cells, and the irreversible T1 transition rate diminishes towards the mode-coupling glass transition point.

Published by the American Physical Society
2024
Structure–property relationship of a complex photoluminescent arylacetylide-gold(I) compound. I: a pressure-induced phase transformation caught in the act
Authors: Jastrzębska Róża , Poręba Tomasz , Cova Federico , Tchoń Daniel M. , Makal Anna
Published: August 2024

A pressure-induced triclinic-to-monoclinic phase transition has been caught `in the act' over a wider series of high-pressure synchrotron diffraction experiments conducted on a large, photoluminescent organo-gold(I) compound. Here, we describe the mechanism of this single-crystal-to-single-crystal phase transition, the onset of which occurs at ∼0.6 GPa, and we report a high-quality structure of the new monoclinic phase, refined using aspherical atomic scattering factors. Our case illustrates how conducting a fast series of diffraction experiments, enabled by modern equipment at synchrotron facilities, can lead to overestimation of the actual pressure of a phase transition due to slow transformation kinetics.
Crystal structures of two unexpected products of vicinal diamines left to crystallize in acetone
Authors: Dival Bruno , Pitinato Leonardo , Develly Letícia , Oliveira Willian X. C.
Published: August 2024

Herein we report the crystal structures of two benzodiazepines obtained by reacting N,N′-(4,5-diamino-1,2-phenylene)bis(4-methylbenzenesulfonamide) (1) or 4,5-(4-methylbenzenesulfonamido)benzene-1,2-diaminium dichloride (1·2HCl) with acetone, giving 2,2,4-trimethyl-8,9-bis(4-methylbenzenesulfonamido)-2,3-dihydro-5H-1,5-benzodiazepine, C26H30N4O4S2 (2), and 2,2,4-trimethyl-8,9-bis(4-methylbenzenesulfonamido)-2,3-dihydro-5H-1,5-benzodiazepin-1-ium chloride 0.3-hydrate, C26H31N4O4S2
+·Cl−·0.3H2O (3). Compounds 2 and 3 were first obtained in attempts to recrystallize 1 and 1·2HCl using acetone as solvent. This solvent reacted with the vicinal diamines present in the molecular structures, forming a 5H-1,5-benzodiazepine ring. In the crystal structure of 2, the seven-membered ring of benzodiazepine adopts a boat-like conformation, while upon protonation, observed in the crystal structure of 3, it adopts an envelope-like conformation. In both crystalline compounds, the tosylamide N atoms are not in resonance with the arene ring, mainly due to hydrogen bonds and steric hindrance caused by the large vicinal groups in the aromatic ring. At a supramolecular level, the crystal structure is maintained by a combination of hydrogen bonds and hydrophobic interactions. In 2, amine-to-tosyl N—H...O and amide-to-imine N—H...N hydrogen bonds can be observed. In contrast, in 3, the chloride counter-ion and water molecule result in most of the hydrogen bonds being of the amide-to-chloride and ammonium-to-chloride N—H...Cl types, while the amine interacts with the tosyl group, as seen in 2. In conclusion, we report the synthesis of 1, 1·2HCl and 2, as well as their chemical characterization. For 2, two synthetic methods are described, i.e. solvent-mediated crystallization and synthesis via a more efficient and cleaner route as a polycrystalline material. Salt 3 was only obtained as presented, with only a few crystals being formed.