bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving the Dynamic Interplay of the Conformational States in the TPR
Domain of Human AMPylase FicD
Authors: Runge Svenja , Bilgen Ecenaz , Itzen Aymelt , Lamb Don C. 
Published: January 2025

Abstract
The human Fic-enzyme FicD plays an important role in regulating the Hsp70
homolog BiP in the endoplasmic reticulum (ER): FicD reversibly modulates BiP’s
activity through attaching an adenosine monophosphate (AMP) to the substrate
binding domain. This reduces BIP’s chaperone activity by shifting it into a
conformation with reduced substrate affinity. Crystal structures of FicD in the
apo, ATP-bound, and BiP-bound states revealed significant conformational
variability in the tetratricopeptide repeat (TPR) motifs. In this study, we
investigate the conformational dynamics of FicD’s TPR motifs using two-color
single-molecule Förster resonance energy transfer (smFRET). We demonstrate that
the TPR motifs exhibit conformational dynamics between the TPR-out and TPR-in
conformations on timescales ranging from milliseconds to microseconds. In
addition, we extend our investigation on multiple labeling positions within
FicD, revealing how conformational dynamics vary depending on the location
within the TPR motif. We quantify the motions with dynamic photon distribution
analysis (PDA) for the FRET constructs and propose a conformational landscape
model for FicD where the TPR-in/out states exist in an equilibrium that is
altered due to the presence of ATP and BiP.
Sustained efficacy of CRISPR-Cas13b gene therapy for FSHD is challenged by immune response to Cas13b
Authors: Rashnonejad Afrooz , Farea Manal , Amini-Chermahini Gholamhossein , Coulis Gerald , Taylor Noah , Fowler Allison , Villalta Armando , King Oliver D. , Harper Scott Q. 
Published: January 2025

AbstractFacioscapulohumeral muscular dystrophy (FSHD) is a potentially devastating muscle disease caused by de-repression of the toxicDUX4gene in skeletal muscle. FSHD patients may benefit fromDUX4inhibition therapies, and although several experimental strategies to reduceDUX4levels in skeletal muscle are being developed, no approved disease modifying therapies currently exist. We developed a CRISPR-Cas13b system that cleavesDUX4mRNA and reduces DUX4 protein level, protects cells from DUX4-mediated death, and reduces FSHD-associated biomarkersin vitro.In vivodelivery of the CRISPR-Cas13b system with adeno-associated viral vectors reduced acute damage caused by highDUX4levels in a mouse model of severe FSHD. However, protection was not sustained over time, with decreases in Cas13b and guide RNA levels between 8 weeks and 6 months after injection. In addition, wild-type mice injected with AAV6.Cas13b showed muscle inflammation with infiltrates containing Cas13b-responsive CD8+ cytotoxic T cells. Our RNA-seq data confirmed that several immune response pathways were significantly increased in human FSHD myoblasts transfected with Cas13b. Overall, our findings suggest that CRISPR-Cas13b is highly effective forDUX4silencing but successful implementation of CRISPR/Cas13-based gene therapies may require strategies to mitigate immune responses.
A simple silicone elastomer colonisation model highlights complexities ofCandida albicansandStaphylococcus aureusinteractions in biofilm formation
Authors: McConnell Gail , Rooney Liam M. , Sandison Mairi E. , Hoskisson Paul A. , Baxter Katherine J. 
Published: January 2025

AbstractHealthcare-associated infections (HAIs) significantly contribute to the burden of antimicrobial resistance (AMR). A major factor in HAIs is the colonisation of indwelling medical devices by biofilm-forming opportunistic pathogens such asCandida albicansandStaphylococcus aureus. These organisms frequently co-infect, resulting in synergistic interactions with enhanced virulence and resistance to treatment.C. albicansandS. aureusreadily form dual-species biofilms on silicone elastomers, a commonly used medical device material, yet the colonisation phenotypes of these organisms on such surfaces remains poorly understood.We developed a simple, optically tractable model to mimic the colonisation of indwelling medical devices to investigateC. albicansandS. aureusbiofilm formation. The system utilises discs of a silicone elastomer embedded in agar, reflecting device-associated conditions and enabling high-resolution imaging of biofilms formed byC. albicansandS. aureusco-culture. Initial results using the silicone elastomer colonisation model reveal robust biofilm formation. These biofilms exhibited morphological differences between dual species biofilms formed byS. aureusco-cultures with either yeast- or hyphal-formC. albicans, indicating the impact of differingC. albicanscell morphotypes in biofilm-associated medical device colonization on silicone elastomers. Quantification of biofilm formation by crystal violet staining provided further validation of the system. These findings underscore the importance of developing tools for biofilm study which more closely resemble the infectious microenvironment, with our work detailing such a system which can be employed in further study to improve strategies against device-related HAIs.
A secreted helminth microRNA suppresses gastrointestinal cell differentiation
required for innate immunity
Authors: Perez Matias G. , Gillan Victoria , Anderson William M. , Gerbe François , Herbert Fabien , McNeilly Tom N. , Maizels Rick M. , Jay Philippe , Devaney Eileen , Britton Collette 
Published: January 2025

Summary
Pathogens have developed multiple strategies to modulate host immune defense
mechanisms. Understanding how this is achieved has potential to inform novel
therapeutics for diseases caused by immune dysfunction. Parasitic helminths are
masters of immune evasion, via release of secreted products, resulting in
chronic infection. Helminths secrete small regulatory microRNA (miRNAs), which
can interact with host cells. Here we show that a single parasite miRNA
(miR-5352), conserved across gastrointestinal (GI) nematodes, suppresses
IL-13-induced GI epithelial cell differentiation and cytokine responses, and
promotes stem cell maintenance. Mechanistically, this is achieved through
targeted repression of critical host factors, including Klf-4 and the IL-22
receptor, together with modulation of Wnt and Notch signalling pathways.
Nematode miR-5352 shows seed sequence conservation with mammalian miR-92a family
members, indicating that through convergent evolution, GI nematodes exploit a
host miRNA regulatory network to suppress host innate responses, promote tissue
regeneration and establish a favourable environment for chronic
infection.
Genomic feature of filled regions of telomere-to-telomere genomes in five model species
Authors: Xiong Chu , Zheng Jun , Zhang Hui , Zhang Yunpeng , Hao Lihong , Wang Min , Liang Zhen 
Published: January 2025

AbstractT2T genome is a telomere-to-telomere high-quality genome with exceptional accuracy, continuity and integrity. It significantly filled some gaps of chromosome. However, the genomic features unique to the filled regions assembled in the T2T genome across species remain unclear. Here, we collected and compared T2T genomes with their older version from human (Homo sapiens), animal (Mus musculus), and plants (Arabidopsis thaliana,Musa acuminata, andFragaria vesca). We explored the newly filled regions generated by the T2T genome in comparison to the old one, and focused on: (1) the comparison of their locations, (2) the distribution of genomic features, and (3) gene annotation and gene function for filled regions. Research indicated that the filled regions of the T2T genome ordinarily appear in the centromere and telomere regions, contain a great number of repetitive sequences. The T2T genome revealed the identification of a certain number of newly annotated genes, alongside significant variations in common annotated genes. Interestingly, the genomic features of filled regions exhibit distinct patterns between plants and human/animal. T2T genomes feature analysis serves as a crucial resource for studying pattern characteristics across diverse species and advancing the in-depth development of genomics.
Molecular mechanisms underlying p62-dependent secretion of the Alzheimer-associated ubiquitin variant, UBB+1
Authors: Wagh Ajay R. , Glickman Michael H. 
Published: January 2025

AbstractUBB⁺¹, a ubiquitin variant protein arising from a frameshift in the ubiquitin-B gene, is a pathological marker in the brains of Alzheimer disease (AD) patients. At the cellular level, UBB⁺¹ disrupts the ubiquitin-proteasome system while simultaneously activating autophagy. UBB⁺¹ is itself secreted in autophagosome-like vesicles. Secretory autophagy mediates the release of cytosolic proteins via the fusion of autophagosomes with the plasma membrane, bypassing lysosomal degradation. We demonstrate that SQSTM1/p62 plays a pivotal role in UBB⁺¹ secretion by acting as a ubiquitin receptor for its ubiquitin domain thereby facilitating UBB⁺¹ loading into autophagosome-like vesicles. Gain- and loss-of-function studies reveal that SQSTM1/p62 is critical for regulating both intracellular and extracellular UBB⁺¹ levels. Knockout of SQSTM1/p62 resulted in the accumulation of UBB⁺¹ in insoluble aggregates, while its overexpression promoted the formation of p62-UBB⁺¹ bodies. Notably, under both conditions, UBB⁺¹ secretion was suppressed, leading to its intracellular retention. This study reveals distinct roles for SNARE-mediated membrane fusion in degradative and secretory autophagy pathways. Specifically, SEC22B (an R-SNARE) and Syntaxin-4 (STX4) (a Q-SNARE) are identified as key mediators of UBB⁺¹ exocytosis. Disruption of these SNAREs impaired the fusion of UBB⁺¹-containing autophagosomes with the plasma membrane, significantly reducing UBB⁺¹ secretion while leaving intracellular turnover unaffected. This study highlights a dual role for autophagy in managing neurotoxic proteins, with SQSTM1/p62 serving as a critical ubiquitin receptor for UBB⁺¹ trafficking and secretion. These findings offer new insights into the cellular mechanisms underlying the clearance of misfolded proteins in neurodegenerative diseases.
Resolving vs. Non-resolving Sphingolipid Dynamics During Macrophage Activation: A Time-resolved Metabolic Analysis
Authors: Chiappa Nathan A. , Lal Nidhi , Botchwey Edward A. 
Published: January 2025

AbstractSphingolipids are increasingly recognized as critical regulators of inflammation and cell fate decisions, with metabolites such as ceramide and sphingosine 1-phosphate exerting contrasting effects on survival and pro-inflammatory signaling. In macrophages, this balance is especially important, given their central role in host defense, pathogenesis and wound healing. Here, we present a time-resolved model of sphingolipid metabolism in RAW 264.7 macrophages stimulated with KdO₂–Lipid A. By integrating measured metabolite concentrations with flux balance analysis and established enzyme kinetics, we systematically map dynamic changes in the sphingolipid network during inflammation. Our results reveal a three-phase pattern of sphingolipid remodeling that correlates with distinct functional states of the cell. Moreover, metabolites can be classified into “resolving” or “non-resolving” lipids based on whether they return to basal levels or remain dysregulated through the later phases of the inflammatory response. This partitioning suggests that targeted modulation of specific metabolic nodes may influence the resolution of inflammation. Importantly, our computational approach can assist in the rational design of experimental studies by pinpointing putative drug targets with maximal impact on sphingolipid homeostasis. Such targeted interventions may prevent the pathological amplification of inflammatory signals without globally suppressing essential sphingolipid functions. These findings highlight the utility of an integrative systems-level analysis for elucidating sphingolipid dynamics in macrophages and underscore its potential to guide therapeutic strategies against conditions involving dysregulated inflammation.
Pushing the limits of structure prediction in regions of disorder using ColabFold: Progress and insights
Authors: Rieth Monica D. 
Published: January 2025

ABSTRACTUnderstanding the impact of amino acid substitutions on protein structure is critical for unraveling mechanisms of protein function and disease. ColabFold, a user-friendly implementation of AlphaFold2, offers an efficient and accessible platform for high-accuracy protein structure predictions. In this study, we explore the utility of ColabFold in predicting structural changes arising from specific amino acid substitutions. Using a structurally well-characterized model protein, mutations were selectively introduced and resulting structural deviations compared to the wild-type conformations. By employing a confidence score embedded in the program called the predicted local distance difference test (pLDDT), which is used to assess a model’s accuracy, together with what is known about the protein’s structure, we identify mutation-induced alterations and determine their potential implications on structural integrity. The results reported here demonstrate that ColabFold is capable of capturing subtle structural perturbations, offering insights into structural stability and the propensity for specific amino acid residues to induce or disrupt secondary structure conformations. We anticipate these studies and others like it will pave the way for high-throughput mutation screening and provide a valuable tool for protein engineering along with hypothesis-driven experimental studies to facilitate our understanding of the behavior of disease-associated mutations.
PicornaviridaeandCaliciviridaediversity in Madagascar fruit bats is driven by cross-continental genetic exchange
Authors: Kettenburg Gwenddolen , Ranaivoson Hafaliana C. , Andrianianina Angelo , Andry Santino , Henry Amy R. , Davis Rachel L. , Laboune Farida , Longtine Elizabeth R. , Godbole Sucheta , Horigan Sophia , Ruhs Emily Cornelius , Raharinosy Vololoniaina , Randriambolamanantsoa Tsiry Hasina , Lacoste Vincent , Heraud Jean-Michel , Dussart Philippe , Douek Daniel C. , Brook Cara E. 
Published: January 2025

ABSTRACTBats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied.Picornaviralesare an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification ofPicornaviralesworldwide. DivergentCaliciviridaeandPicornaviridae(families within thePicornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum,Pteropus rufus, andRousettus madagascariensis), we recovered 13 full-length and 37 partial-length genomic sequences within the orderPicornavirales(36Picornaviridaeand 14Caliciviridaesequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar batPicornaviraleslikely shaped the diversification patterns of these novel sequences through recombination events between closely relatedPicornavirales; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.
Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases
Authors: Finney Joel , Kuraoka Masayuki , Song Shengli , Watanabe Akiko , Liang Xiaoe , Liao Dongmei , Moody M. Anthony , Walter Emmanuel B. , Harrison Stephen C. , Kelsoe Garnett 
Published: January 2025

ABSTRACTThe discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The membrane-anchored NAs are catalytically active and are compatible with established small-molecule catalytic activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.
Impact of Low-Dose Narrowband UV Radiation on Skin Tissue and Mast Cells in a Canine Model
Authors: Maeda Yusuke , Kubota Shota , Kawarai Shinpei , Kamimura Mai , Okuyama Hiroki , Ono Moeko , Nishida Moe , Moriya Shigeharu , Onoda Yushi , Tsurumoto Tomohiro , Nagata Koichi , Ansai Shin-ichi , Fujikawa Yasuo , Tsukamoto Atsushi 
Published: January 2025

AbstractNarrowband ultraviolet radiation (NB-UVR) therapy is widely utilized in dermatology worldwide. While the immunosuppressive effects of ultraviolet radiation are well-documented, its non-inflammatory effects remain poorly understood. This study evaluated the effects of sub-minimal erythema dose (MED) narrowband ultraviolet radiation using a canine model. The effects of narrowband-ultraviolet B (310 nm) and A2 wavelengths (320 and 330 nm) were compared. Initially, we demonstrated the therapeutic potential of NB-UVR in dogs with spontaneous atopic dermatitis (n = 6, p < 0.05). Following 300 mJ/cm² sub-MED ultraviolet radiation exposure, intradermal skin testing, skin mast cell counts, and RNA sequencing analysis were conducted. Additionally, cell viability (WST assay) and apoptosis (DAPI staining) were assessed in vitro using a canine mast cell line. Ultraviolet radiation exposure significantly reduced intradermal skin test scores across all wavelengths and decreased skin mast cell counts at 310 nm (n = 3, p < 0.05). In vitro, cell viability was significantly reduced at 310 and 320 nm (p < 0.05), and 310 nm irradiation specifically increased apoptotic cell numbers (p < 0.05). RNA sequencing identified 71 differentially expressed genes at 320 nm, with enrichment analysis highlighting muscle cell components and functions, potentially associated with arrector pili muscle activity. These findings suggest that 310 nm irradiation induces apoptosis, while 320 nm elicits non-inflammatory modulatory effects, highlighting distinct wavelength-specific therapeutic mechanisms of narrowband ultraviolet radiation.
REM sleep microstructure alterations in REM sleep behavior disorder: beyond muscle tone
Authors: Nicolas Judith , Comperat Louis , Fort Patrice , Cheylus Anne , Ricordeau François , Bastuji Hélène , Simor Péter , Leclair-Visonneau Laurène , Peter-Derex Laure 
Published: January 2025

AbstractIsolated rapid eye movement (REM) sleep behavior disorder (iRBD) is characterized by dream enactment behaviors and loss of physiological atonia during REM sleep. It is considered a prodromal stage of alpha-synucleinopathies and may result from dysfunction of brainstem structures regulating muscle tone in REM sleep. Whether other REM sleep features are simultaneously affected remains unclear. Here, we investigated alterations in REM sleep microstructure, including phasic REM sleep, sawtooth waves (STW) and non-REM/REM sleep transitions, in iRBD and RBD associated with Parkinson’s disease (PD+RBD). We retrospectively included 20 patients with iRBD (85% male, 66.5[63–68]years), 20 patients with PD+RBD (75% male, 62.5[57.5-65]years) and 20 controls (75% male, 67[61–70]years). REM sleep without atonia (RSWA), bursts of REMs and STW bursts were manually scored. Phasic REM sleep proportion (derived from REMs), STW density/duration/frequency and the duration of NREM/REM transitions were compared between groups with a general linear mixed-effects model. Phasic REM sleep proportion was higher in the iRBD group (26.5[21–33]%) than in control (16.4[12.5-22.3]%, p-corrected=0.005) and PD+RBD (17.6[13.9-21.7]%, p-corrected=0.005) ones. Non-REM/REM transitions showed a duration gradient, increasing from controls (119.0[58.5-186.1]sec) to iRBD (212.1[68.5-391.4]sec, p-corrected=0.0038) and PD+RBD (375.8[217.6-514.6]sec, p-corrected<0.001) patients. STW density and duration were reduced in the PD+RBD group only (1.33[1.1-1.54]/min; 2.13[1.70-2.69]sec) vs controls (1.74[1.52-2.05]/min, p-corrected=0.005; 2.98[2.18-4.11], p-corrected<0.001), whereas altered STW spectral content was observed in both patient’s groups with a power shift toward higher frequencies (both p<0.001 vs controls). These results reinforce the hypothesis that REM sleep dysregulation in RBD extends to REM-specific electrophysiological features beyond loss of muscle atonia and dream enactments.Statement of SignificanceThis study compared rapid eye movement (REM) sleep microstructure between patients with isolated REM sleep behavior disorder (iRBD) or RBD associated with Parkinson’s disease (PD+RBD), and controls. We found some altered REM sleep features in patient groups versus controls, as increased phasic REM sleep proportion in iRBD and reduced sawtooth waves (STW) density and duration in PD+RBD. Both groups exhibited altered STW spectral characteristics with a shift toward higher frequencies. Additionally, we observed a gradient in the duration of NREM/REM sleep transitions, increasing from controls to patients with iRBD and peaking in patients with PD+RBD, who exhibited the longest transitions. These findings highlight that REM sleep anomalies in RBD extends beyond atonia loss and dream enactments, encompassing broader microstructural changes.
CLN5 deficiency impairs glucose uptake in Batten disease
Authors: Marchese Maria , Bernardi Sara , Vivarelli Rachele , Doccini Stefano , Santucci Lorenzo , Ogi Asahi , Licitra Rosario , Zang Jingjing , Soliymani Rabah , Mero Serena , Neuhauss Stephan CF , Signore Giovanni , Lalowski Maciej M. , Santorelli Filippo M. 
Published: January 2025

AbstractCLN5 disease, a form of juvenile dementia within the neuronal ceroid lipofuscinosis (NCL), is associated with mutations in theCLN5gene encoding the lysosomal bis(monoacylglycero)phosphate (BMP) synthase, essential for BMP production and lysosomal function. Limited knowledge of cellular mechanisms and unclear drug targets hinder translating this to children’s treatment, which remains symptomatic. We developed and characterized a newcln5knock-out zebrafish model that replicates key features and molecular signatures of the human disease. Loss of Cln5 functionin vivoaltered axonal growth of retinal ON-bipolar cells revealing new disease features. Additionally, multi-omic analyzes at different developmental stages, revealed an impaired glucose metabolism as an original finding in NCL. This work demonstrates the profound metabolic impact of CLN5 dysfunction, offering a promising avenue toward targeted therapies for juvenile dementia.