bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dopamine-dependent cerebellar dysfunction enhances beta oscillations and disrupts motor learning in a multiarea model
Authors: Gambosi Benedetta , Sheiban Francesco Jamal , Biasizzo Marco , Antonietti Alberto , D’Angelo Egidio , Mazzoni Alberto , Pedrocchi Alessandra 
Published: July 2023

AbstractParkinson’s disease (PD) is a chronic degenerative disorder of the central nervous system that affects the motor system. The discovery that PD motor symptoms result from the death of dopaminergic cells in the substantia nigra led to focus most of PD research on the basal ganglia. However, recent findings point to an active involvement of the cerebellum in PD. Here, we have developed a multiscale computational model of the rodent brain’s basal ganglia-cerebellar network. Simulations showed that a direct effect of dopamine depletion on the cerebellum must be taken into account to reproduce the alterations of PD neural activity, particularly the increased beta oscillations widely reported in PD patients. Moreover, dopamine depletion indirectly impacted spike-time-dependent plasticity at the parallel fiber-Purkinje cell synapses, degrading associative motor learning as observed in PD. Overall, these results suggest a relevant involvement of cerebellum in PD motor symptoms.Significance StatementThis study highlights the role of cerebellum in Parkinson’s disease (PD). While most studies on PD concentrate on dopaminergic mechanisms in the basal ganglia, here we show that dopamine depletion impacts also on the cerebellum, generating a complex dysfunctional interaction between the two subcortical circuits. To investigate this interaction, we developedde novoa multiarea multiscale network model that mechanistically addresses the effects of dopamine depletionon the cerebellum. Our study demonstrates that this aspect is crucial to reproduce experimental data, particularly the increased beta wave activity. Moreover, alterations in spike-time-dependent plasticity at the parallel fibre – Purkinje cell synapse of cerebellum can explain the link between dopamine depletion to motor learning impairment. These simulations indicate that the cerebellum warrants more attention in future PD research.
Mitochondrial variation inAnopheles gambiaeandAn. coluzzii: phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides
Authors: Romero Jorge E. Amaya , Chenal Clothilde , Chehida Yacine Ben , Miles Alistair , Clarkson Chris S. , Pedergnana Vincent , Wertheim Bregje , Fontaine Michael C. 
Published: July 2023

AbstractMitochondrial DNA (mtDNA) has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mtDNA variation inAn. gambiaeandAn. coluzzii, in perspective with other species in theAnopheles gambiaecomplex (AGC), by assembling the mitogenomes of 1219 mosquitoes across Africa. The mtDNA phylogeny of the AGC was consistent with a previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, An. arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three salt-water tolerant species (An. merus, An. melas, An. bwambae) in the AGC also suggested that introgression and possibly selection shaped mtDNA evolution. MtDNA variation inAn. gambiaeandAn. coluzziiacross Africa revealed significant partitioning among populations and species. A peculiar mtDNA lineage found predominantly inAn. coluzziiand in the hybrid taxon of the African “far-west”exhibited divergence comparable to the inter-species divergence in the AGC, with a geographic distribution matching closelyAn. coluzzii’s geographic range. This phylogeographic relict of theAn. coluzziiandAn. gambiaesplit was associated with population and species structuration, but not withWolbachiaoccurrence. The lineage was significantly associated with SNPs in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline the mito-nuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticide inAnopheles.
Adaptation of theMycobacterium tuberculosistranscriptome to biofilm growth
Authors: Youngblom Madison A. , Smith Tracy M. , Pepperell Caitlin S. 
Published: July 2023

AbstractMycobacterium tuberculosis(M. tb), the causative agent of tuberculosis (TB), is a leading global cause of death from infectious disease. Biofilms are increasingly recognized as a relevant growth form duringM. tbinfection and may impede treatment by enabling bacterial drug and immune tolerance.M. tbhas a complicated regulatory network that has been well-characterized for many relevant disease states, including dormancy and hypoxia. However, despite its importance, our knowledge of the genes and pathways involved in biofilm formation is limited. Here we characterize the biofilm transcriptomes of fully virulent clinical isolates and find that the regulatory systems underlying biofilm growth vary widely between strains and are also distinct from regulatory programs associated with other environmental cues. We used experimental evolution to investigate changes to the transcriptome during adaptation to biofilm growth and found that the application of a uniform selection pressure resulted in loss of strain-to-strain variation in gene expression, resulting in a more uniform biofilm transcriptome. The adaptive trajectories of transcriptomes were shaped by the genetic background of theM. tbpopulation leading to convergence on a sub-lineage specific transcriptome. We identified widespread upregulation of non-coding RNA (ncRNA) as a common feature of the biofilm transcriptome and hypothesize that ncRNA function in genome-wide modulation of gene expression, thereby facilitating rapid regulatory responses to new environments. These results reveal a new facet of theM. tbregulatory system and provide valuable insight into howM. tbadapts to new environments.ImportanceUnderstanding mechanisms of resistance and tolerance inMycobacterium tuberculosis(M. tb) can help us develop new treatments that capitalize onM. tb’s vulnerabilities. Here we used transcriptomics to study both the regulation of biofilm formation in clinical isolates as well as how those regulatory systems adapt to new environments. We find that closely related clinical populations have diverse strategies for growth under biofilm conditions, and that genetic background plays a large role in determining the trajectory of evolution. These results have implications for future treatment strategies that may be informed by our knowledge of the evolutionary constraints on strain(s) from an individual infection. This work provides new information about the mechanisms of biofilm formation inM. tband outlines a framework for population level approaches for studying bacterial adaptation.
Regulation of BCR-mediated Ca2+mobilization by MIZ1-TIMBIM4 safeguards IgG1+GC B cell positive selection
Authors: Zhang Lingling , Toboso-Navasa Amparo , Gunawan Arief , Camara Abdouramane , Nakagawa Rinako , Finsterbusch Katja , Chakravarty Probir , Newman Rebecca , Zhang Yang , Eilers Martin , Andreas Wack , Tolar Pavel , Toellner Kai-Michael , Calado Dinis Pedro 
Published: July 2023

SummaryThe transition from IgM to affinity-matured IgG antibodies is vital for effective humoral immunity. This is facilitated by germinal centers (GCs) through affinity maturation and preferential accumulation of IgG+B cells over IgM+B cells. However, it is not known whether the positive selection of the different immunoglobulin isotypes within GCs varies in its dependency on specific transcriptional mechanisms. Here, we identified IgG1+GC B cell transcription factor dependency using CRISPR-Cas9 and conditional mouse genetics. We found that MIZ1 was specifically required for IgG1+GC B cell survival during positive selection, whereas IgM+GC B cells were largely independent. Mechanistically, MIZ1 induced TMBIM4, an ancestral anti-apoptotic protein that regulated inositol trisphosphate receptor mediated Ca2+mobilization downstream of IgG1. The MIZ1-TMBIM4 axis prevented mitochondrial dysfunction-induced IgG1+GC cell death caused by excessive Ca2+accumulation. This study uncovers a unique immunoglobulin isotype-specific dependency, on a hitherto unidentified mechanism in GC positive selection.
Smooth muscle-derived adventitial progenitor cells promote key cell type transitions controlling plaque stability in atherosclerosis in a Klf4-dependent manner
Authors: Dubner Allison M , Lu Sizhao , Jolly Austin J , Strand Keith A , Mutryn Marie F , Hinthorn Tyler , Noble Tysen , Nemenoff Raphael A , Moulton Karen S , Majesky Mark W , Weiser-Evans Mary CM 
Published: July 2023

ABSTRACTWe previously established that vascular smooth muscle-derived adventitial progenitor cells (AdvSca1-SM) preferentially differentiate into myofibroblasts and contribute to fibrosis in response to acute vascular injury. However, the role of these progenitor cells in chronic atherosclerosis has not been defined. Using an AdvSca1-SM lineage tracing model, scRNA-Seq, flow cytometry, and histological approaches, we confirmed that AdvSca1-SM cells localize throughout the vessel wall and atherosclerotic plaques, where they primarily differentiate into fibroblasts, SMCs, or remain in a stem-like state. Klf4 knockout specifically in AdvSca1-SM cells induced transition to a more collagen-enriched myofibroblast phenotype compared to WT mice. Additionally, Klf4 depletion drastically modified the phenotypes of non-AdvSca1-SM-derived cells, resulting in more contractile SMCs and atheroprotective macrophages. Functionally, overall plaque burden was not altered with Klf4 depletion, but multiple indices of plaque vulnerability were reduced. Collectively, these data support that modulating the AdvSca1-SM population confers increased protection from the development of unstable atherosclerotic plaques.
Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation
Authors: Smith Tanya M. , Arora Manish , Austin Christine , Ávila Janaína N. , Duval Mathieu , Lim Tze Tshen , Piper Philip J. , Vaiglova Petra , Vos John de , Williams Ian S. , Zhao Jian-xin , Green Daniel R. 
Published: July 2023

AbstractStudies of climate variation commonly rely on chemical and isotopic changes recorded in sequentially-produced growth layers, such as in corals, shells and tree rings, as well as in accretionary deposits—ice and sediment cores, and speleothems. Oxygen isotopic compositions (δ18O) of tooth enamel are a direct method of reconstructing environmental variation experienced by an individual animal. Here we utilize long-forming orangutan dentitions (Pongospp.) to probe recent and ancient rainfall trends on a weekly basis over ∼ 3–11 years per individual. We first demonstrate the lack of any consistent isotopic enrichment effect during exclusive nursing, supporting the use of primate first molar teeth as environmental proxies. Comparisons of δ18O values (n = 2016) in twelve molars from six modern Bornean and Sumatran orangutans reveal a high degree of overlap, with more consistent annual and bimodal rainfall patterns in the Sumatran individuals. Comparisons with fossil orangutan δ18O values (n = 955 measurements from six molars) reveal similarities between modern and late Pleistocene fossil Sumatran individuals, but differences between modern and late Pleistocene/early Holocene Bornean orangutans. These suggest drier and more open environments with reduced monsoon intensity during this earlier period in northern Borneo, consistent with other Niah Caves studies and long-term speleothem δ18O records in the broader region. This approach can be extended to test hypotheses about the paleoenvironments that early humans encountered in southeast Asia.
A Plant Flavonol Rescues a Pathogenic Mutation Associated with Kinesin in Neurons
Authors: Chai Yongping , Li Dong , Gong Weibin , Ke Jingyi , Tian Dianzhe , Chen Zhe , Guo Angel , Guo Zhengyang , Li Wei , Feng Wei , Ou Guangshuo 
Published: July 2023

AbstractKIF1A, a microtubule-based motor protein responsible for axonal transport, is linked to a group of neurological disorders known as KIF1A-associated neurological disorder (KAND). Current therapeutic options for KAND are limited. Here, we introduced the clinically relevant KIF1A(R11Q) variant into theC. eleganshomolog UNC-104, resulting in uncoordinated animal behaviors. Through genetic suppressor screens, we identified intragenic mutations in UNC-104’s motor domain that rescued synaptic vesicle localization and coordinated movement. We showed that two suppressor mutations partially recovered motor activity in vitro by counteracting the structural defect caused by R11Q at KIF1A’s nucleotide-binding pocket. We found that supplementation with fisetin, a plant flavonol, improved KIF1A(R11Q) worms’ movement and morphology. Notably, our biochemical and single-molecule assays revealed that fisetin directly restored the ATPase activity and processive movement of human KIF1A(R11Q) without affecting wild-type KIF1A. These findings suggest fisetin as a potential intervention for enhancing KIF1A(R11Q) activity and alleviating associated defects in KAND.
A global, integrated view of the ubiquitylation site occupancy and dynamics
Authors: Prus Gabriela , Satpathy Shankha , Weinert Brian T. , Narita Takeo , Choudhary Chunaram 
Published: July 2023

SummaryUbiquitylation regulates virtually all proteins and biological processes in a cell. However, the global site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have never been quantified. Here, we present the first integrated picture of ubiquitylation site occupancy and half-life. Ubiquitylation occupancy spans four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and the regulation of sites by proteasome inhibitors show strong interrelationships. These properties can discriminate signaling-relevant sites from the sites involved in proteasomal degradation. The sites strongly upregulated by proteasome inhibitors have a longer half-life, and the half-life increases with increasing protein length. Importantly, a previously unknown surveillance mechanism rapidly deubiquitylates all ubiquitin-specific E1 and E2 enzymes and protects them against bystander ubiquitylation accumulation. This work reveals general principles of ubiquitylation-dependent governance and offers conceptual insights into the dynamic regulation of the cell.HighlightsUbiquitylation site occupancy is 3 orders of magnitude lower than phosphorylationThe highest 80% and the lowest 20% occupancy sites have distinct propertiesHigh occupancy sites are concentrated in the cytoplasmic domains of SLC proteinsA dedicated mechanism prevevents ubiquitylation accumulation in E1s and E2s
Towards Modular Engineering of Cell Signalling: Topographically-Textured Microparticles Induce Osteogenesis via Activation of Canonical Hedgehog Signalling
Authors: Ghuloum Fatmah I. , Stevens Lee A. , Johnson Colin A. , Riobo-Del Galdo Natalia A. , Amer Mahetab H. 
Published: July 2023

ABSTRACTPolymer microparticles possess great potential as functional building blocks for advanced bottom-up engineering of complex tissues. Tailoring the three-dimensional architectural features of culture substrates has been shown to induce osteogenesis in mesenchymal stem cellsin vitro, but the molecular mechanisms underpinning this remain unclear. This study proposes a mechanism linking the activation of Hedgehog signalling to the osteoinductive effect of surface-engineered, topographically-textured polymeric microparticles. In this study, mesenchymal progenitor C3H10T1/2 cells were cultured on smooth and dimpled poly(D,L-lactide) microparticles to assess differences in viability, cellular morphology, proliferation, and expression of a range of Hedgehog signalling components and osteogenesis-related genes. Dimpled microparticles induced osteogenesis and activated the Hedgehog signalling pathway relative to smooth microparticles and 2D-cultured controls without the addition of exogenous biochemical factors. We observed upregulation of the osteogenesis markersRunt-related transcription factor2(Runx2) andbone gamma-carboxyglutamate protein 2(Bglap2), as well as the Hedgehog signalling components,glioma associated oncogene homolog 1(Gli1),Patched1(Ptch1), andSmoothened(Smo). Treatment with the Smo antagonist KAAD-cyclopamine confirmed the involvement of Smo inGli1target gene activation, with a significant reduction in the expression ofGli1,Runx2andBglap2(p≤0.001) following KAAD-cyclopamine treatment. Overall, our study demonstrates the role of the topographical microenvironment in the modulation of Hedgehog signalling, highlighting the potential for tailoring substrate topographical design to offer cell-instructive 3D microenvironments. Topographically-textured microparticles allow the modulation of Hedgehog signallingin vitrowithout adding exogenous biochemical agonists, thereby eliminating potential confounding artefacts in high-throughput drug screening applications.Graphical Abstract
Chemically Induced Degradation of Native Proteins by Direct Recruitment to the 26S Proteasome
Authors: Balzarini Madeline , Gui Weijun , Jayalath Isuru M. , Schell Bin-Bin , Tong Joel , Kodadek Thomas 
Published: July 2023

AbstractTargeted protein degradation (TPD) is a promising strategy for drug development. Most degraders function by forcing the association of the target protein (TP) with an E3 Ubiquitin ligase, which in favorable cases results in the poly-Ubiquitylation of the TP and its subsequent degradation by the 26S proteasome. Here we explore the feasibility of a different TPD strategy in which the TP is recruited directly to the proteasome without the requirement for poly-Ubiquitylation. Using an engineered cell line in which the HaloTag protein is fused to one of the Ubiquitin receptors, we show that native protein targets can be degraded in this fashion when the cells are exposed to a chemical dimerizer containing a chloroalkane and a TP ligand. The potential advantages and disadvantages of Ubiquitin-independent degraders vs. traditional proteolysis-targeting chimeras are discussed.
Identification ofLactuca sativatranscription factors impacting resistance toBotrytis cinereathrough predictive network inference
Authors: Pink Harry , Talbot Adam , Carter Ryan , Hickman Richard , Cooper Oliver , Law Rebecca , Higgins Gillian , Yao Chenyi , Gawthrop Frances , Hand Paul , Pink David , Clarkson John , Denby Katherine 
Published: July 2023

AbstractLettuce is susceptible to a wide range of plant pathogens including the fungal pathogensBotrytis cinereaandSclerotinia sclerotiorum, causal agents of grey mould and lettuce drop, respectively. Chemical control is routinely used but there is an urgent need to develop varieties with enhanced resistance given the economic and environmental costs of preventative pesticide sprays, the prevalence of fungicide-resistant isolates of both pathogens in the field, and the increasing withdrawal of approved fungicides through legislation. Resistance againstBotrytis cinereaandSclerotinia sclerotiorumis quantitative, governed by multiple small-medium impact loci, with plant responses involving large-scale transcriptional reprogramming. The elucidation of the gene regulatory networks (GRNs) mediating these responses will not only identify key transcriptional regulators but also interactions between regulators and show how the defence response is fine-tuned to a particular pathogen. We generated high-resolution (14 time points) time series expression data from lettuce leaves following mock-inoculation or inoculation withB. cinerea, capturing the dynamics of the transcriptional response to infection. Integrating this data with a time series dataset fromS. sclerotioruminfection of lettuce identified a core set of 4362 genes similarly differentially expressed in response to both pathogens. Using the expression data for these core genes (with additional single time point data from 21 different lettuce accessions) we inferred a GRN underlying the lettuce defence response to these pathogens. Using the GRN, we have predicted and validated key regulators of lettuce immunity, identifying both positive (LsBOS1) and negative (LsNAC53) regulators of defence againstB. cinerea, as well as downstream target genes. These data provide a high level of detail on defence-induced transcriptional change in a crop species and a GRN with the ability to predict transcription factors mediating disease resistance both in lettuce and other species.
A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Authors: Du Ze-Zhen , He Jia-Bao , Jiao Wen-Biao 
Published: July 2023

AbstractBackgroundAlthough sequencing technologies have boosted the measurement of the sequencing diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes, however, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes.ResultsHere we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and read data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotype concordances without increasing resource consumption. EVG can achieve comparably higher genotyping recall and precision even using 5× reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of variants, especially for insertion and deletion.ConclusionsOur study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.