bluuebunny/crossref_metadata_2025_split huggingface dataset:
FluoroTensor: identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning
Authors: Wills Max F.K. , Alejo Carlos Bueno , Hundt Nikolas , Hudson Andrew J. , Eperon Ian C. 
Published: November 2023

AbstractThe identification of photobleaching steps in single molecule fluorescence imaging is a well-established procedure for analysing the stoichiometries of molecular complexes. Nonetheless, the method is challenging with protein fluorophores because of the high levels of noise, rapid bleaching and very variable signal intensities, all of which complicate methods based on statistical analyses of intensities to identify bleaching steps. It has recently been shown that deep learning by convolutional neural networks can yield an accurate analysis with a relatively short computational time. We describe here an improved use of such an approach that detects bleaching events even in the first time point of observation, and we have included this within an integrated software package incorporating fluorescence spot detection, colocalisation, tracking, FRET and photobleaching step analyses of single molecules or complexes. This package, known as FluoroTensor, is written in Python with a self-explanatory user interface.
Real-Time Structural Biology of DNA and DNA-Protein Complexes on an Optical Microscope
Authors: Szalai Alan M. , Ferrari Giovanni , Richter Lars , Hartmann Jakob , Kesici Merve-Zeynep , Ji Bosong , Coshic Kush , Jaeger Annika , Aksimentiev Aleksei , Tessmer Ingrid , Kamińska Izabela , Vera Andrés M. , Tinnefeld Philip 
Published: November 2023

AbstractThe intricate interplay between DNA and proteins is key for biological functions such as DNA replication, transcription, and repair. To better understand these interactions, it is crucial to develop tools to study DNA-protein complexes with high spatial and temporal resolution. Here, we use the vertical orientation that DNA adopts on graphene and investigate its interactions with proteins via energy transfer from a probe dye to graphene, achieving spatial resolution down to the Ångström scale. We measured the bending angle of DNA induced by adenine tracts, bulges, abasic sites and the binding of Escherichiacoliendonuclease IV with unprecedented precision and millisecond time resolution. Additionally, we observed the translocation of the O6-alkylguanine DNA alkyltransferase along double-stranded DNA, reaching single-base pair resolution and detecting an affinity for adenine tracts. Overall, we foresee that this method will become a widespread tool for the dynamical study of nucleic acid and nucleic acid-protein interactions.
Spatially explicit sampling frameworks to identify regions of increased mosquito abundance
Authors: Kemei Brigid , Ochomo Eric , Ombok Maurice , Midega Janet , Lucas Eric R. , Donnelly Martin J , Sedda Luigi , McDermott Daniel P. 
Published: November 2023

AbstractVector control interventions often lack comprehensive information on vector population distribution and dynamics. This knowledge gap poses challenges in targeting interventions effectively, especially in areas with heterogeneous transmission and where complementary vector control tools may be required to achieve sustained impact on disease transmission. In this study, we implemented a spatially explicit sampling framework for improved vector surveillance in coastal Kenya. Our stratified lattice with close pair sampling design aimed to characterise the vector dynamics of the primary malaria-transmitting species in the area and assess the ecotype classification’s effectiveness at identifying clear population patterns. The study collected 3,621 mosquitoes, withAn. funestuss.l. being the most abundant malaria vector. The inclusion of the ecotype classification significantly improved spatial abundance model estimates forAn. gambiaeandCulexspp. Wetlands, topographic wetness index, and proximity to rivers were associated with increased mosquito abundance. Spatial modelling revealed high abundance regions near the Galana-Sabaki River. Our study demonstrates the applicability of a reproducible spatial sampling approach to identify areas with high vector abundance and inform targeted vector control strategies. The study highlights the importance of ecological stratification and a spatial explicit sampling approach for predicting mosquito presence when prior data is limited and underscores the potential for refining future sampling for control efforts.
First isolate ofOrientia tsutsugamushifrom Vellore, South India
Authors: Kumaraswamy Janaki , Kirubanandan Agilandeeswari , Nagarajan Lakshmi Surya , Gunasekaran Karthik , Abhilash KPP , Jude Prakash John Antony 
Published: November 2023

AbstractBackgroundScrub typhus a common cause of acute febrile illness in India caused byOrientia tsutsugamushian obligate intracellular bacterium requiring cell culture for isolation. Cell lines like Vero and L929 are most suitable for isolating and maintaining this organism. This study was undertaken to isolate and characterize ofOrientia tsutsugamushifrom whole blood samples at a tertiary care centre in Southern India.MethodsThe PBMCs (peripheral blood mononuclear cells) collected from scrub typhus positive (47kDa qPCR positive) patients were inoculated into Vero and L929 cell line at 80% confluence for primary isolation. The inoculated flasks were incubated at 37°C with 5% CO2for 30 days and examined for presence ofOrientia tsutsugamushion the day 10, 15, 20 post-inoculation and everyday thereafter for a maximum of 30 days post inoculation. The scrapings were subjected to Giemsa staining, IFA, 47kDa qPCR and transmission electron microscopy (TEM). The isolates were passaged 3-4 times to ensure viability and then stored in DMEM with 10% FBS (-80°C). Genotyping of the isolates was performed by amplifying a 650 bp segment of the TSA 56 (type specific antigen 56) gene.ResultsAmongst the 50 samples inoculated, three were culture positive as confirmed by 47 kDa qPCR at 24thday of inoculation. This was further confirmed by Giemsa, IFA staining and TEM. The 650bp amplicons showed 99.5 to 100% homology withOrientia tsutsugamushiMW604716, MH003839, MW604718, MW604717, MH922787 and MH003838 strains. Phylogenetic analysis revealed that 2 isolates belong to TA763 genotype and one belongs to Gilliam genotype.ConclusionsWe have successfully isolated and characterised theOrientia tsutsugamushifor the first time at our centre from PBMCs. Based on the partial TSA56 gene sequence our isolates belongs to TA763 and Gilliam genotype. More number of samples are being processed for identifying further isolates followed by genomic analysis.
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads
Authors: Han Seong Woo , Jewell San , Thomas-Tikhonenko Andrei , Barash Yoseph 
Published: November 2023

AbstractMapping transcriptomic variations using either short or long reads RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, while short reads still provides improved coverage and error rates. Yet how to quantitatively compare the technologies, can we combine those, and what may be the benefit of such a combined view remain open questions. We tackle these questions by first creating a pipeline to assess matched long and short reads data using a variety of transcriptome statistics. We find that across datasets, algorithms and technologies, matched short reads data detects roughly 50% more splice junctions, with 10-30% of the splice junctions included at 20% or more are missed by long reads. In contrast, long reads detect many more intron retention events, pointing to the benefit of combining the technologies. We introduce MAJIQ-L, an extension of the MAJIQ software to enable a unified view of transcriptome variations from both technologies and demonstrate its benefits. Our software can be used to assess any future long reads technology or algorithm, and combine it with short reads data for improved transcriptome analysis.
Host-derived oxidized phospholipids initiate effector-triggered immunity fostering lethality upon microbial encounter
Authors: Di Gioia Marco , Poli Valentina , Tan Piao J , Spreafico Roberto , Chu Anne , Cuenca Alex G , Gordts Philip LSM , Pandolfi Laura , Meloni Federica , Witztum Joseph L , Chou Janet , Springstead James R , Zanoni Ivan 
Published: November 2023

AbstractMacrophages detect invading microorganisms via pattern recognition receptors that recognize pathogen-associated molecular patterns, or via sensing the activity of virulence factors that initiates effector-triggered immunity (ETI). Tissue damage that follows pathogen encounter leads to the release of host-derived factors that participate to inflammation. How theseself-derived molecules are sensed by macrophages and their impact on immunity remain poorly understood. Here we demonstrate that, in mice and humans, host-derived oxidized phospholipids (oxPLs) are formed upon microbial encounter. oxPL blockade restricts inflammation and prevents the death of the host, without affecting pathogen burden. Mechanistically, oxPLs bind and inhibit AKT, a master regulator of immunity and metabolism. AKT inhibition potentiates the methionine cycle, and epigenetically dampensIl10, a pluripotent anti-inflammatory cytokine. Overall, we found that host-derived inflammatory cues act as “self” virulence factors that initiate ETI and that their activity can be targeted to protect the host against excessive inflammation upon microbial encounter.
Neuroinfectiology of an atypical anthrax-causing pathogen in wild chimpanzees
Authors: Gräßle Tobias , Jäger Carsten , Kirilina Evgeniya , Jaffe Jenny E. , Carlier Penelope , Pizarro Andrea , Jauch Anna , Reimann Katja , Lipp Ilona ,   EBC consortium, Wittig Roman M. , Crockford Catherine , Weiskopf Nikolaus , Leendertz Fabian H. , Morawski Markus 
Published: November 2023

AbstractBacillus cereusbiovaranthracis(Bcbva) is an atypical anthrax-causing bacterium, inflicting wildlife fatalities across African rainforest ecosystems. The pathogen’s virulence in one of our closest living relatives, the chimpanzee, together with human serological evidence, suggestsBcbvais zoonotic. While classicalB. anthracis-induced anthrax has been described to affect the central nervous system at a progressive disease-state, the neuroinfectiology ofBcbvais yet unknown. Here we characterised the pathogen’s neuro-invasiveness via gross pathological assessment, ultra-high resolution quantitative Magnetic Resonance Imaging and histological analysis on four brains, which were extracted from naturally deceased wild chimpanzees in Taï National Park, Côte d’Ivoire.Based on macroscopically evident pial vessel congestion and haemorrhages as well as cortical siderosis detected via MRI, we concluded thatBcbvainduced meningitis analogous toB. anthracis. Further, histological visualisation of bacteria and leukocytes in the subarachnoid space evidenced the bacterium’s capability to breach the arachnoid barrier.Bcbvawas detected in the brain parenchyma of all four cases. This indicates a higher ability to transgress the glia limitans and therefore exhibits a higher neuroinvasiveness compared toB. anthracisthat predominantly stays confined to the meninges. Heightened glial fibrillary acidic protein (GFAP) expression but little morphological gliosis suggest a rapid disease progression leading to host-death within hours to a few days after central nervous system invasion.Overall our results revealBcbva’s ability to breach blood-brain barriers which results in a pronounced neuropathogenicity.Bcbvacauses extensive damage to the meninges and the brain parenchyma, as well as rapid and massive digestion of brain extracellular matrix in chimpanzees and potentially so in humans in case of zoonotic spillover.
Human leukocyte antigen HLA-DR-expressing fibroblast-like synoviocytes are inducible antigen presenting cells that present autoantigens in Lyme arthritis
Authors: Rouse Joseph R , Danner Rebecca , Wahhab Amanda , Pereckas Michaela , McClune Mecaila E , Steere Allen C , Strle Klemen , Jutras Brandon L , Lochhead Robert B 
Published: November 2023

ABSTRACTBackgroundHLA-DR-expressing fibroblast-like synoviocytes (FLS) are a prominent cell type in synovial tissue in chronic inflammatory forms of arthritis. We recently showed that peptides from several extracellular matrix (ECM) proteins, including fibronectin-1 (FN1), contained immunogenic CD4+ T cell epitopes in patients with postinfectious Lyme arthritis (LA). However, the role of FLS in presentation of these T cell epitopes remains uncertain.MethodsPrimary LA FLS and primary murine FLS stimulated with interferon gamma (IFNγ),Borrelia burgdorferi, and/orB. burgdorferipeptidoglycan (PG) were assessed for properties associated with antigen presentation. HLA-DR-presented peptides from stimulated LA FLS were identified by immunopeptidomics analysis. OT-II T cells were cocultured with stimulated murine FLS in the presence of cognate ovalbumin antigen to determine the potential of FLS to act as inducible antigen presenting cells (APC).ResultsFLS expressed HLA-DR molecules within inflamed synovial tissue and tendons from patients with post-infectious LA patientsin situ.MHC class II and costimulatory molecules were expressed by FLS followingin vitrostimulation with IFNγ andB. burgdorferiand presented both foreign and self MHC-II peptides, including T cell epitopes derived from two Lyme autoantigens fibronectin-1 (FN1) and endothelial cell growth factor (ECGF). Stimulated murine FLS induced proliferation of naïve OT-II CD4+ T cells, particularly when FLS were stimulated with both IFNγ and PG.ConclusionsMHC-II+ FLS are inducible APCs that can induce CD4+ T cell activation and can present Lyme autoantigens derived from ECM proteins, thereby amplifying tissue-localized autoimmune CD4+ T cell responses in LA.AUTHORS’ SUMMARYThis study demonstrates that IFNγ-activated MHC-II+ fibroblast-like synoviocytes (FLS) stimulated withBorrelia burgdorferipresent foreign and self MHC-II antigens, including Lyme autoantigens. Furthermore, IFNγ-activated MHC-II+ FLS stimulated withB. burgdorferipeptidoglycan can induce activation and proliferation of naïve CD4+ T cells in an MHC-II antigen-dependent manner, demonstrating that activated MHC-II+ FLS are inducible antigen presenting cells.
HAMLET, a human milk protein-lipid complex, modulates amoxicillin-induced changes in anex vivobiofilm model of the oral microbiome
Authors: Brar NK , Dhariwal A , Shekhar S , Junges R , Hakansson AP , Petersen FC 
Published: November 2023

ABSTRACTChallenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work synergistically with antibiotics and minimize resistance risk. In this study we investigated the potential synergistic effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using anex-vivooral biofilm model. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination group promoted a most remarkable shift in overall microbial composition compared to the untreated samples. Up to 90% of the bacterial species in the combined treatment wereLactobacillus crispatus, a species with probiotic effects, whereas it was detected in minor fraction in untreated samples. Resistome analysis indicated no major shifts on alpha-diversity, while beta-diversity revealed distinct clustering patterns for each treatment group, signifying that each treatment group harbors a unique resistome. TEM beta-lactamase genes were detected in low proportions in all treated samples but absent in untreated samples. Our study highlights the potential of HAMLET to synergize with amoxicillin in anex-vivomodel of the oral microbiome and modulate the proportion of probiotic bacteria. The findings extend the knowledge on the synergistic effects of HAMLET and antibiotics from single-species studies to polymicrobial biofilms of human origin.ImportancePolymicrobial infections are challenging to treat and prevent, requiring the use of antibiotics that exhibit reduced efficacy due to biofilm formation. HAMLET has recently emerged as an antimicrobial agent that can synergize with antibiotics while limiting microbial resistance. We investigated the effects of HAMLET, alone and combined with low concentrations of amoxicillin, onex vivooral biofilms to simulate complex microbial interactions observed in the oral cavity. The combination of HAMLET and amoxicillin effectively targeted polymicrobial biofilms and led to an increase inLactobacillus crispatus. The potency of this combination appears to be due to the synergistic effect of HAMLET and amoxicillin. These findings underscore the potential of combining antimicrobials with different modes of action for the development of more effective strategies for preventing and treating polymicrobial infections.
Tumorigenesis driven by the BRAFV600Eoncoprotein requires secondary mutations that overcome its feedback inhibition of migration and invasion
Authors: Gadal Sunyana , Boyer Jacob A. , Roy Simon F. , Outmezguine Noah A. , Sharma Malvika , Li Hongyan , Fan Ning , Chan Eric , Romin Yevgeniy , Barlas Afsar , Chang Qing , Pancholi Priya , Timaul Neilawattie. Merna , Overholtzer Michael , Yaeger Rona , Manova-Todorova Katia , Stanchina Elisa de , Bosenberg Marcus , Rosen Neal 
Published: November 2023

AbstractBRAFV600Emutation occurs in 46% of melanomas and drives high levels of ERK activity and ERK-dependent proliferation. However,BRAFV600Eis insufficient to drive melanoma in GEMM models, and 82% of human benign nevi harborBRAFV600Emutations. We show here that BRAFV600Einhibits mesenchymal migration by causing feedback inhibition of RAC1 activity. ERK pathway inhibition induces RAC1 activation and restores migration and invasion. In cells withBRAFV600E, mutant RAC1, overexpression of PREX1, PREX2, or PTEN inactivation restore RAC1 activity and cell motility. Together, these lesions occur in 48% of BRAFV600Emelanomas. Thus, although BRAFV600Eactivation of ERK deregulates cell proliferation, it prevents full malignant transformation by causing feedback inhibition of cell migration. Secondary mutations are, therefore, required for tumorigenesis. One mechanism underlying tumor evolution may be the selection of lesions that rescue the deleterious effects of oncogenic drivers.Statement of significanceBRAFV600Eactivation of ERK causes feedback inhibition of cell migration and invasion and thus blocks tumorigenesis. Secondary genetic lesions are required to rescue these processes and enable tumor development. Thus, oncogenic feedback can shape the details of tumor progression and, in doing so, selects for new mutations that may be therapeutic targets.
High Frequency Longitudinal RNAseq Reveals Temporally Varying Genes and Recovery Trajectories in Rats
Authors: Chen Wei , Chai Yi , Jiang Qi , Miao Eva Y. , Gopinath Ashwin , Zhang David Yu 
Published: November 2023

AbstractWhen living organisms are exposed to potentially toxic chemicals, they respond via changes in gene expression. Traditional differentially expressed gene analysis based on before/after blood samples does not reveal the response’s temporal dynamics, and often produces false positives and negatives. Here, we performed longitudinal daily RNA sequencing on rats dosed with tetracycline, isoniazid, carbon tetrachloride, or valproate. We identified 4,302 temporally variable genes (TVGs) with statistically strong change in expression following dosing. Projecting TVG expressions into a 3-dimensional principal component (PC) space reveals consistent trajectories for recovery following dosing, and enables separation of healthy from recovering states with 91% to 99% area under the receiver operator curve. Finally, we observed that Fast Recovery vs. Slow Recovery rats exhibited distinct temporal expression patterns in the TVGs, suggesting that individual variations could be potentially captured via longitudinal RNAseq analysis.
New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)
Authors: Singh Rachit Pratap , Weng Yi-Ming , Sondhi Yash , Plotkin David , Frandsen Paul B. , Kawahara Akito Y. 
Published: November 2023

AbstractNearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.