bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethanol down-regulates gastrula gene expression and cell movement, causing symptoms of foetal alcohol spectrum disorders
Authors: Alsakran Amena Ali , Wong Hoi Ying , Heaton Caitlin , Boreham Rebekah , Ball Jonathan , Kudoh Tetsuhiro 
Published: December 2024

AbstractFoetal alcohol spectrum disorders (FASDs) occur in embryos when they are exposed to maternally supplied alcohol. To study the mechanisms of FASDs, the zebrafish embryo can serve as an excellent model as ethanol exposed zebrafish embryos exhibit common symptoms of human FASDs including microcephaly, incomplete neural plate closure, eye defects, craniofacial disorders and many other defects. Here we investigated the embryo development at gastrula stage when three germ layers develop with specific gene expressions and undergo dynamic cell movement including extension, convergence and epiboly, establishing the platform to form the head and body axis in the later development. Gastrula cell movement analyses using fluorescent transgenic zebrafish embryos revealed that ethanol induced dose dependent delay of extension, convergence and epiboly cell movement and associated gene expressions in all three germ layers. Our results suggest multiple targets of ethanol including gene expression and cell movement, consequently delay the key gene expression and cell localisation, causing irreversible developmental defects in the head and body axis formation.
Phenotyping the hidden half: Combining UAV phenotyping and machine learning to predict barley root traits in the field
Authors: Alahmad Samir , Smith Daniel , Katsikis Christina , Aldiss Zachary , Meer Sarah V. , Meijer Lotus , Chenu Karine , Chapman Scott , Potgieter Andries B. , Wasson Anton , Baraibar Silvina , Godoy Jayfred , Moody David , Robinson Hannah , Hickey Lee T. 
Published: December 2024

AbstractImproving crop root systems for enhanced adaptation and productivity remains challenging due to limitations in scalable non-destructive phenotyping approaches, inconsistent translation of root phenotypes from controlled environment to the field, and a lack of understanding of the genetic controls. This study serves as a proof of concept, evaluating a panel of Australian barley breeding lines and cultivars (Hordeum vulgareL) in two field experiments. Integrated ground-based root and shoot phenotyping was performed at key growth stages. UAV-captured vegetation indices (VIs) were explored for their potential to predict root distribution and above-ground biomass. Machine learning models, trained on a subset of 20 diverse lines, with the most accurate model applied to predict traits across a broader panel of 395 lines. Unlike previous studies focusing on above-ground traits or indirect proxies, this research directly predicts root traits in field conditions using VIs, machine learning and root phenotyping. Root trait predictions for the broader panel enabled genomic analysis using a haplotype-based approach, identifying key genetic drivers, includingEGT1andEGT2which regulate root gravitropism. This approach offers the potential to advance root research across various crops and integrate root traits into breeding programs, fostering the development of varieties adapted to future environments.HighlightIntegrating UAV phenotyping and machine learning can be used to predict RSA traits non-destructively and offers a new approach to support root research and crop improvement.
Study on the mechanism of action of the Pt(IV) complex with lonidamine ligands by ultrafast chemical proteomics
Authors: Imaikina Ekaterina A. , Fedorov Ivan I. , Emekeeva Daria D. , Kazakova Elizaveta M. , Garibova Leila A. , Ivanov Mark V. , Shutkov Ilya A. , Nazarov Alexey A. , Gorshkov Mikhail V. , Tarasova Irina A. 
Published: December 2024

ABSTRACTPlatinum (II) complexes such as cisplatin among the few others are well-known and approved for clinical use as anticancer metal-based drugs. In spite of their successful and wide acceptance, the respective chemotherapy is associated with severe side effects and the ability of tumors to quickly develop resistance. To overcome these drawbacks the novel strategy is considered, which is based on the use of platinum complexes with bioactive ligands attached to act in synergy with platinum and further improve its pharmacological properties. Among the recently introduced such multi-action prodrugs is Pt(IV) complex with two lonidamine ligands, the latter selectively inhibiting hexokinase and, thus, the glycolysis in cancer cells. While platinum based multi-action prodrugs are exhibiting increased levels of activity towards cancer cells and, thus, considered as potent to overcome the resistance to cisplatin, there is a crucial need to uncover their mechanism of action by revealing all possibly affected processes and targets across the whole cellular proteomes. These are the challenging tasks in proteomics requiring high-throughput analysis of hundreds of samples for just a single drug-to-proteome system. In this work we performed these analyses for 8-azaguanine and experimental Pt(IV)-lonidamine complex applied to ovarian cancer cell line A2780, using both mechanism- and compound-centric chemical proteomics approaches based on ultrafast expression proteomics and thermal proteome profiling, respectively. Analysis of data obtained for Pt(IV)-lonidamine complex revealed regulation of proteins involved in glucose metabolic process associated with lonidamine further supporting the multi-action mechanism of this prodrug action.
Stable topical application of antimicrobials using plumbing rings in anex vivoporcine corneal infection model
Authors: Foulkes Daniel M. , Mclean Keri , Masharma Taruni , Fernig David G. , Kaye Stephen B. 
Published: December 2024

AbstractMicrobial keratitis (MK) is a substantial cause of clinical blindness worldwide.Pseudomonas aeruginosais an opportunistic gram-negative bacterium and is the leading cause of MK. Infection models are vital tools in understanding host-pathogen interactions and the development of novel therapies. As well as ethical and practical advantages,ex vivoinfection models can allow researchers to better investigate host-pathogen interactions more accurately than traditional cell culture systems. The versatility of porcine cornealex vivomodels have been employed to study various pathogens (for exampleStaphylococcus aureusandAcanthamoeba) and has enabled innovation of novel MK therapies. Here, we describe an improved porcine cornealex vivoprotocol, which uses plumbing rings and medical adhesive to circumvent several distinct limitations and challenges. The application of a 10 mm plumbing ring to the center of the cornea allows localized inoculation of pathogens of interest, maintaining them at the site of infection, rather than running the risk of “run off” of topically added aqueous solutions. The second important advantage is that topically applied therapeutic agents can be properly maintained on the cornea within the plumbing ring reservoir, allowing more accurate study of antimicrobial effects. In this contextualized protocol, we infected porcine corneas with theP. aeruginosastrain PA103 with topical treatments of moxifloxacin. PA103 colony forming unit (CFU) deduction, quantification of corneal opacity and histology analysis (hematoxylin and eosin staining), was used to assess infection over 48h, which was alleviated by moxifloxacin in a dose-dependent manner.
Vaccines for immunological defense against traumatic brain injury
Authors: Lintecum Kelly , Thumsi Abhirami , Dunn Kara , Druschel Lindsey , Chimene Sierra , Prieto David Flores , Simmons Amberlyn , Mantri Shivani , Esrafili Arezoo , Swaminathan Srivatsan J. , Trivedi Mytreyi , Manjre Shreya , Willingham Crystal , Kizeev Gabriele , Davila Alondra , Inamdar Sahil , Mangal Joslyn L. , Suresh Abhirami P. , Kasthuri Niveda M. , Jaggarapu Madan Mohan Chandra Sekhar , Appel Nicole , Khodaei Taravat , Ng Nathan D. , Sundem Alison , Pathak Sanmoy , Bjorklund George , Balmer Timothy , Newbern Jason , Capadona Jeffrey , Stabenfeldt Sarah E. , Acharya Abhinav P. 
Published: December 2024

AbstractTraumatic brain injury (TBI) and subsequent neurodegeneration is partially driven by chronic inflammation both locally and systemically. Yet, current clinical intervention strategies do not mitigate inflammation sequalae necessitating the development of innovative approaches to reduce inflammation and minimize deleterious effects of TBI. Herein, a subcutaneous formulation based on polymer of alpha-ketoglutarate (paKG) delivering glycolytic inhibitor PFK15 (PFKFB3 inhibitor, a rate limiting step in glycolysis), alpha-ketoglutarate (to fuel Krebs cycle) and peptide antigen from myelin proteolipid protein (PLP139-151) was utilized as the prophylactic immunosuppressive formulation in a mouse model of TBI.In vitro,the paKG(PFK15+PLP) vaccine formulation stimulated proliferation of immunosuppressive regulatory T cells and induced generation of T helper-2 cells. When given subcutaneously in the periphery to two weeks prior to mice sustaining a TBI, the active vaccine formulation increased frequency of immunosuppressive macrophages and dendritic cells in the periphery and the brain at day 7 post- TBI and by 28 days post-TBI enhanced PLP-specific immunosuppressive cells infiltrated the brain. While immunohistology measurements of neuroinflammation were not altered 28 days post-TBI, the vaccine formulation improved motor function and enhanced autophagy mediated genes in a spatial manner in the brain. Overall, these data suggest that the TBI vaccine formulation successfully induced an anti-inflammatory profile and decreased TBI-associated inflammation.TeaserIn this study, a vaccine formulation was generated to develop central nervous specific immunosuppressive responses for TBI.
High-throughput synapse profiling reveals cell-type-specific spatial configurations in the fly brain
Authors: Wu Hongyang , Maekawa Yoh , Eno Sayaka , Kondo Shu , Yamagata Nobuhiro , Tanimoto Hiromu 
Published: December 2024

AbstractCharacterization of intracellular synapse heterogeneity aides to understand the intricate computational logic of neuronal circuits. Despite recent advances in connectomics, the spatial patterns of synapses and their inter-individual variability remain largely unknown. Using directed split-GFP reconstitution, we achieved visualization of endogenous Bruchpilot (Brp) proteins, the presynaptic active zone (AZ) scaffold, in a cell-type-specific manner. By developing a high-throughput quantification pipeline, we profiled AZ structures in identified neurons of the mushroom body circuit, where intracellular synaptic pattern is crucial due to its compartmentalized connectivity. Quantitative characterization of the pattern of Brp clusters across multiple individuals revealed cell-type-dependent synapse heterogeneity and stereotypy. Furthermore, we discovered previously unidentified sub-compartmental synapse configuration and its regulation by cAMP signaling. These results of synapse profiling uncovered multi-layered organizations of AZs, ranging from neighboring synapses to consistent patterns across individuals.TeaserHigh-throughput profiling of single active zones revealed previously unidentified multi-layered synaptic organizations.
Octopamine signals coordinate the spatial pattern of presynaptic machineries within individualDrosophilamushroom body neurons
Authors: Wu Hongyang , Eno Sayaka , Jinnai Kyoko , Maekawa Yoh , Saito Kokoro , Abe Ayako , Williams Darren W , Yamagata Nobuhiro , Kondo Shu , Tanimoto Hiromu 
Published: December 2024

SUMMARYNeurons need to adjust synaptic output according to the targets. However, the target-specific synaptic structures within individual neurons in the central nervous system remains unresolved. Applying the CRISPR/Cas9-mediated split-GFP tagging, we visualized the endogenous active zone scaffold protein, Bruchpilot (Brp), in specific cells. This technology enabled the spatial characterization of presynaptic machineries only within the Kenyon cells (KCs) of theDrosophilamushroom bodies. We found the patterned accumulation of Brp among the compartments of axon terminals, where a KC synapses onto different postsynaptic neurons. Mechanistically, the localized octopaminergic modulation along γ KC terminals regulate this compartmental Brp heterogeneity via Octβ2R and cAMP signaling. We further found that acute food deprivation reorganizes this spatial pattern in an octopamine-dependent manner. Such coordinated regulation of local synaptic machineries thus explains how the mushroom bodies integrate changing physiological states. This subcellular information processing represents an elegant solution to expand computational capacity of the circuit.
The mouth of America: the oral microbiome profile of the US population
Authors: Chaturvedi Anil K. , Vogtmann Emily , Shi Jianxin , Yano Yukiko , Blaser Martin J. , Bokulich Nicholas A. , Caporaso J. Gregory , Gillison Maura L. , Graubard Barry I. , Hua Xing , Hullings Autumn G. , Kahle Lisa , Knight Rob , Li Shilan , McLean Jody , Purandare Vaishnavi , Wan Yunhu , Freedman Neal D. , Abnet Christian C. 
Published: December 2024

ABSTRACTImportanceThe oral microbiome is increasingly recognized to play key roles in human health and disease; yet, population-representative characterizations are lacking.ObjectiveCharacterize the composition, diversity, and correlates of the oral microbiome among US adults.DesignCross-sectional population-representative survey.SettingThe National Health and Nutrition Examination Survey (NHANES, 2009-2012), a stratified multistage probability sample of the US population.ParticipantsNHANES participants aged 18-69 years (n=8,237, representing 202,314,000 individuals).ExposuresDemographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics.Main outcomesOral microbiome, characterized through 16S rRNA sequencing. Microbiome metrics were alpha diversity (number of observed Amplicon Sequence Variants [ASV], Faith’s Phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); beta diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at taxonomic levels (phylum through genus). Analyses accounted for the NHANES complex sample design.ResultsAmong US adults aged 18-69 years, the oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1,219 genera. Five phyla—Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria,andFusobacteriaand six genera—Veillonella, Streptococcus, Prevotella7, Rothia, Actinomyces, and Gemella, were present in nearly all US adults (weighted-prevalence >99%). These genera also were the most abundant, accounting for 65.7% of abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), was similar by sex, significantly lower among non-Hispanic White individuals, and increased with higher body mass index (BMI) categories, alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability, as measured by beta diversity (unweighted UniFrac=8.7%, weighted UniFrac=7.2%, and Bray-Curtis=6.3%). By contrast, relative abundance of a few genera explained a high percentage of variability in beta diversity (weighted UniFrac:Aggregatibacter=22.4%,Lactococcus=21.6%,Haemophilus=18.4%). Prevalence and relative abundance of numerous genera were significantly associated (Bonferroni-corrected Wald-p<0.0002) with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity.ConclusionsWe provide a contemporary reference standard for the oral microbiome of the US adult population. Our results indicate that a few genera were universally present in US adults and a different set of genera explained a high percentage of oral microbiome diversity across the population.
Diagnostic and prognostic value of alpha-synuclein seed amplification assay in Parkinson’s disease: a longitudinal cohort study
Authors: Orrú Christina D , Vaughan David P , Vijiaratnam Nirosen , Real Raquel , Carrasco Alejandro Martinez , Fumi Riona , Jensen Marte Theilmann , Hodgson Megan , Girges Christine , Gil-Martinez Ana-Luisa , Stafford Eleanor J. , Wu Lesley , Groveman Bradley R , Hughson Andrew G , Ansorge Olaf , Quaegebeur Annelies , Allinson Kieren SJ , Warner Thomas T , Jaunmuktane Zane , Misbahuddin Anjum , Leigh P Nigel , Ghosh Boyd CP , Bhatia Kailash P , Church Alistair , Kobylecki Christopher , Hu Michele TM , Rowe James B , Foltynie Thomas , Morris Huw R , Caughey Byron , Jabbari Edwin 
Published: December 2024

SummaryBackgroundAlpha-synuclein seed amplification assay (a-syn SAA) has been proposed to be a diagnostic biomarker for Parkinson’s disease (PD). Here, we have explored the diagnostic and prognostic value of cerebrospinal fluid (CSF) a-syn SAA status and seeding kinetics in PD.MethodsBaseline CSF a-syn SAA data and longitudinal clinical data were collected and analysed between 1stJanuary 2010 and 1stApril 2022 for the Parkinson’s Progression Markers Initiative (PPMI) and UK parkinsonism cohorts respectively. We calculated the sensitivity and specificity of a-syn SAA in PD and controls, used linear regression to analyse a-syn SAA positive vs. negative group comparisons, and used time-to-event analyses to assess the ability of a-syn SAA seeding kinetic measures to predict clinical decline in PD.FindingsWe studied 1,402 participants: publicly available data from the PPMI cohort, n=1275 (PD, n=1,036; controls, n=239); newly generated data from the UK parkinsonism cohort, n=127 (PD, n=66; progressive supranuclear palsy (PSP), n=52; controls n=9). Over 2-5 years of follow-up, the sensitivity of a-syn SAA in PD was 87.7% and the specificity in controls was 91.9%. A-syn SAA was positive in 8/52 (15.4%) PSP samples with distinct ‘low and slow’ kinetics. A-syn SAA negative LRRK2-PD participants (n=57) had an older mean (SD) age at symptom onset (63.0 (7.6) vs. 55.4 (9.9) years) and higher mean (SD) baseline serum neurofilament light chain levels (20.4 (13.2) vs. 13.8 (8.6) pg/ml), p<0.05, vs. a-syn SAA positive LRRK2-PD participants (n=110). The baseline seeding kinetic measure, time to threshold, predicted cognitive decline in PD, defined as MoCA ≤21 (HR 2.51, 95% CI 1.50-4.20, p=0.001).InterpretationIn PD, a-syn SAA may have value as a diagnostic and prognostic biomarker in clinical practice and as a stratification tool in clinical trials. Furthermore, we have highlighted the presence of pathological heterogeneity in LRRK2-PD.FundingMedical Research Council, PSP Association.
High-throughput discovery and deep characterization of cyclin-CDK docking motifs
Authors: Örd Mihkel , Winters Matthew J. , Subbanna Mythili S. , de Martin Garrido Natalia , Cushing Victoria I. , Kliche Johanna , Benz Caroline , Ivarsson Ylva , Greber Basil J. , Pryciak Peter M. , Davey Norman E. 
Published: December 2024

AbstractCyclin-CDKs are master regulators of cell division. In addition to directly activating the CDK, the cyclin subunit regulates CDK specificity by binding short peptide “docking” motifs in CDK substrates. Here, we measure the relative binding strength of ∼100,000 peptides to 11 human cyclins from five cyclin families (D, E, A, B and F). Using a quantitative intracellular binding assay and large-scale tiled peptide screening, we identified a range of non-canonical binders that unveil a broader than anticipated repertoire of cyclin docking motif types. Structural and saturation mutagenesis studies revealed distinct binding modes and sequence features that govern motif recognition, binding strength, and cyclin preference. Docking motifs vary from highly selective to pan-cyclin, thereby fine-tuning the timing of CDK phosphorylation during cell cycle progression. Overall, these findings provide an unprecedented depth of understanding about the rules encoding specificity and affinity within a group of related but distinct protein domains.
In and out of replication stress: PCNA/RPA1-based dynamics of fork stalling and restart in the same cell
Authors: Dyankova-Danovska Teodora , Uzunova Sonya , Danovski Georgi , Stamatov Rumen , Kanev Petar-Bogomil , Atemin Aleksandar , Ivanova Aneliya , Stoynov Stoyno 
Published: December 2024

AbstractReplication forks encounter various impediments which induce fork stalling and threaten genome stability, yet the precise dynamics of fork stalling and restart at the single-cell level remain elusive. Herein, we devise a live-cell microscopy-based approach to follow hydroxyurea-induced fork stalling and subsequent restart at 30-s resolution. We measure two distinct processes during fork stalling. One is rapid PCNA removal, which reflects the drop in DNA synthesis. The other is gradual RPA1 accumulation on up to 2400 nt of ssDNA per fork despite an active intra-S checkpoint. Restoring the nucleotide pool enables prompt restart without post-replicative ssDNA and a smooth cell cycle progression. ATR, but not ATM inhibition, accelerates hydroxyurea-induced RPA1 accumulation nine-fold, leading to RPA1 exhaustion within 20 min. Fork restart under ATR inhibition led to the persistence of ∼600 nt ssDNA per fork after S-phase, which reached 2500 nt under ATR/ATM co-inhibition, with both scenarios leading to mitotic catastrophe. MRE11 inhibition had no effect on PCNA/RPA1 dynamics regardless of ATR activity. E3 ligase RAD18 was recruited at stalled replication forks in parallel to PCNA removal. Our results shed light on fork dynamics during nucleotide depletion and provide a valuable tool for interrogating the effects of replication stress-inducing anti-cancer agents.
Extracellular HDAC6 ZnF UBP domain enhances podosome-mediated neuronal migration
Authors: Qureshi Tazeen , Desale Smita Eknath , Sonawane Shweta Kishor , Balmik Abhishek Ankur , Chidambaram Hariharakrishnan , Chinnathambi Subashchandrabose 
Published: December 2024

ABSTRACTThe increasing prevalence of Alzheimer’s disease demands research into therapeutic strategies that go beyond Amyloid and Tau. Synaptic loss, neuritic loss, and microtubule destabilization due to misfolded Tau and dysfunctional signalling in the AD-affected neuron, all point toward understanding and targeting cytoskeletal dysregulation in AD. Here we present, an extensive study on the novel role of the ZnF UBP (Zinc Finger Ubiquitin Binding Protein) domain of HDAC6 (Histone Deacetylase 6) in actin remodelling in neurons. We have demonstrated this function through immunofluorescence colocalization analysis in actin-rich podosome structures. We have found that this HDAC6 domain induces increased localization of the actin polymerization proteins, Arp2 and WASP and the adaptor protein TKS5 in the podosome structures. We have also extended our work to understand the potential of this domain in enhancing the podosome-mediated migration of neuronal cells. It was thus established that HDAC6 ZnF UBP induces increased association of cytoskeletal proteins within the podosomes, conferring enhanced migration potential to neurons and presenting an interesting strategy to improve neuronal health.