bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis for surface activation of the classical complement cascade by the short pentraxin C-reactive protein
Authors: Noone Dylan P. , Isendoorn Marjolein M. E. , Hamers Sebastiaan M. W. R. , Keizer Mariska E. , Wulffelé Jip , van der Velden Tijn T. , Dijkstra Douwe J. , Trouw Leendert A. , Filippov Dmitri V. , Sharp Thomas H. 
Published: March 2024

AbstractHuman C-reactive protein (CRP) is a pentameric complex involved in defence against pathogens and regulation of autoimmunity. CRP is also a therapeutic target, with both administration and depletion of serum CRP being pursued as a possible treatment for autoimmune and cardiovascular diseases, among others. CRP binds to phosphocholine (PC) moieties on membranes in order to activate the complement system via the C1 complex, but it is unknown how CRP, or any pentraxin, binds to C1. Here, we present a cryo-electron tomography (cryoET)-derived structure of CRP bound to PC ligands and the C1 complex. To gain control of CRP binding, a synthetic mimotope of PC was synthesised and used to decorate cell-mimetic liposome surfaces. Structure-guided mutagenesis of CRP yielded a fully-active complex able to bind PC-coated liposomes that was ideal for cryoET and subtomogram averaging. In contrast to antibodies, which form Fc-mediated hexameric platforms to bind and activate the C1 complex, CRP formed rectangular platforms assembled from four laterally-associated CRP pentamers that bind only four of the six available globular C1 head groups. Potential residues mediating lateral association of CRP were identified from interactions between unit cells in existing crystal structures, which rationalised previously unexplained mutagenesis data regarding CRP-mediated complement activation. The structure also enabled interpretation of existing biochemical data regarding interactions mediating C1 binding, and identified additional residues for further mutagenesis studies. These structural data therefore provide a possible mechanism for regulation of complement by CRP, which limits complement progression and has consequences for how the innate immune system influences autoimmunity.Significance statementHuman C-reactive protein (CRP) activates the complement system to protect us from infections, but can also contribute towards progression of cardiovascular and autoimmune diseases when erroneously activated. To understand these processes, the authors used cryo-electron tomography to solve thein situstructure of surface-bound CRP interacting with the complement C1 complex. The structure revealed new interfaces that explain previous, sometimes contradictory, biochemical data. Comparisons with existing structures of antibody-mediated C1 activation revealed distinct structural differences that may explain how CRP modulates complement activity. Together, these structural data identify residues for mutagenesis to gain control over CRP functions, and provide new routes for future therapeutic developments.
Classification and analysis of retinal interneurons by computational structure under natural scenes
Authors: Lee Dongsoo , Kim Juyoung , Baccus Stephen A. 
Published: March 2024

AbstractInhibitory neurons are diverse across the brain, but for the visual system we lack the ability to functionally classify these neurons under complex natural stimuli. Here we take the approach of classifying retinal amacrine cell responses to natural scenes using optical recording and an interpretable neural network model. We fit mouse amacrine cell responses to a two-layer convolutional neural network model of a class shown previously to accurately capture salamander ganglion cell responses to natural scenes. Using an approach from interpretable machine learning, we determined for each stimulus the model interneurons that generated each amacrine response, analogous to the set of bipolar cells that target the amacrine population. From this analysis we clustered amacrine cells not by their natural scene responses, but by the model presynaptic neurons that constructed those responses, conservatively finding approximately seven groups by this approach. By analyzing the set of model presynaptic input neurons for each amacrine cluster, we find that distributed rather than dedicated inputs generate natural scene responses for different amacrine cell types. Additional analyses revealed distinct transient and sustained modes exhibited by the network during the response to simple flashes. These results give insight into the computational structure of how the diverse amacrine cell population responds to natural scenes, and generate multiple quantitative hypotheses for how synaptic inputs generate those responses.
Mutating the arginine residue within the FRNK motif of HC-Pro yield highly attenuated strains that confer complete cross protection against telosma mosaic virus (TelMV) in passion fruit (Passiflora edulis)
Authors: Wang Linxi , Shi Wei , Aziz Asma , Wang Xiaoqing , Liu Haobin , Shen Wentao , Wang Aiming , Cui Hongguang , Dai Zhaoji 
Published: March 2024

AbstractTelosma mosaic virus (TelMV,Potyvirus, Potyviridae) is an emerging viral pathogen causing a major global threat to passion fruit plantations. However, an efficient strategy for controlling such viruses is not yet available. Cross protection is a phenomenon in which pre-infection of a plant with one virus prevents or delays superinfection with the same or closely related virus. HC-Pro is the potyviral encoded multifunctional protein involved in several steps of viral infection, including multiplication, movement, transmission and RNA silencing suppression. The main hypothesis we tested in this study was whether it is possible to generate attenuated viral strains capable of conferring protection against severe TelMV infection by manipulating theHC-Progene. By introducing point mutation into the potyviral conserved motif FRNK of HC-Pro, we have successfully obtained three highly attenuated mutants of TelMV (R181K, R181D and R181E, respectively) that can systemically infect passion fruit plants without any noticeable symptoms. Importantly, these mutants confer complete protection against subsequent infection of severe recombinant virus TelMV-GFP, evidenced by no detection of viral RNA or protein of the superinfection virus in the systemic leaves of passion fruit plants in both early and late stages. Lastly, we demonstrated that the HC-Pros harbored by the highly attenuated mutants exhibited reduced RNA silencing suppression activity inNicotiana benthamianaleaves. Altogether, this study provides the first demonstration of the generation of highly attenuated strains for TelMV and highlights key amino acid residue involved in complete cross protection against TelMV, opening a new avenue to fight TelMV in the field.
Variational inference for microbiome survey data with application to global ocean data
Authors: Mishra Aditya , McNichol Jesse , Fuhrman Jed , Blei David , Müller Christian L. 
Published: March 2024

AbstractLinking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (VariationalInference forMIcrobiome surveyDAta analysiS), that enablesjointestimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling which can incorporate spatio-temporal informationandtaxon-taxon interactions. We leverage mean-field variational inference for posterior VI-MIDAS model parameter estimation and illustrate model building and analysis using Tara Ocean Expedition survey data. Using VI-MIDAS’ latent embedding model and tools from network analysis, we show that marine microbial communities can be broadly categorized into five modules, including SAR11-, Nitrosopumilus-, and Alteromondales-dominated communities, each associated with specific environmental and spatiotemporal signatures. VI-MIDAS also finds evidence for largely positive taxon-taxon associations in SAR11 or Rhodospirillales clades, and negative associations with Alteromonadales and Flavobacteriales classes. Our results indicate that VI-MIDAS provides a powerful integrative statistical analysis framework for discovering broad patterns of associations between microbial taxa and context-specific covariate data from microbiome survey data.
Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenileThuja plicatain UK Woodlands
Authors: Guillardín Laura , Glover Ella , Kerr Gary , MacKay John J. 
Published: March 2024

AbstractThuja plicatais a conifer tree that is appreciated for its cultural, ecological and wood quality features in its natural range in western North America. It is also used in Europe and the UK for timber production. SomeT. Plicataplantations in the UK are converted to Continuous Cover Forestry (CCF) management which uses natural regeneration and concerns have been raised about the genetic diversity in both the adult trees and the offspring. We studied species diversity, stand structure, and genetic diversity in four UK woodlands planted withT. plicatawhich contained both adults and naturally regenerated individuals. We discovered 61,104 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 504 SNPs for analysis. We selected 67 SNPs for PCR-based genotyping of 163 adults and 176 juveniles. We found a large number of monomorphic sites (40.3%) most of which were restricted to adults in a single woodland, indicative of a high genetic differentiation among woodlands. The effective population size (Ne) was very low across all sites (Ne< 100), varied between adults and juveniles, and was lowest in the most diverse woodland in terms of species and structure. In contrast, heterozygosity was high overall (Ho= 0.38), except in the divergent woodland (Ho= 0.26), and did not vary between adults and juveniles. Our findings and genotyping methods provide insights into the ability of CCF-managed woodlands, including instances of low genetic diversity inT. plicata, to face environmental shifts and disease threats.
Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis
Authors: Palma Alessandro , Ballarino Monica 
Published: March 2024

AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which a comprehensive knowledge about the pathological mechanisms is still lacking. A multitude of dysregulated cellular processes and pathways have been linked to ALS so far, including the recent focus directed toward the implication of several classes of non-coding (nc)RNAs. Within this context, the class of long ncRNAs (lncRNAs), may provide an important contribution to the onset and the severity of ALS pathogenesis, due to their high tissue specificity and their function as gene expression regulators. Nevertheless, their identification in humans often relies on differential expression analyses from bulk RNA-seq, which limits their targeting in the cellular contexts where they may be primarily involved.Here we apply dedicated pipelines to single-nucleus nuclei datasets to study lncRNA from non-pathological and pre-frontal ALS human cortex. We found that in brain, distinct cell subtypes express very different pattern of lncRNAs to suggest possible roles in cellular processes found dysregulated in ALS patients. Moreover, we show the lncRNA involvement in important gene regulatory networks that result differentially regulated in pathological conditions and dissect the genomic organization of differentially expressed lncRNAs.
Presynaptic Rac1 in the hippocampus selectively regulates working memory
Authors: Kim Jaebin , Bustamante Edwin , Sotonyi Peter , Maxwell Nicholas D. , Parameswaran Pooja , Kent Julie K. , Wetsel William C. , Soderblom Erik J. , Rácz Bence , Soderling Scott H. 
Published: March 2024

AbstractOne of the most extensively studied members of the Ras superfamily of small GTPases, Rac1 is an intracellular signal transducer that remodels actin and phosphorylation signaling networks. Previous studies have shown that Rac1-mediated signaling is associated with hippocampal-dependent working memory and longer-term forms of learning and memory and that Rac1 can modulate forms of both pre- and postsynaptic plasticity. How these different cognitive functions and forms of plasticity mediated by Rac1 are linked, however, is unclear. Here, we show that spatial working memory is selectively impaired following the expression of a genetically encoded Rac1-inhibitor at presynaptic terminals, while longer-term cognitive processes are affected by Rac1 inhibition at postsynaptic sites. To investigate the regulatory mechanisms of this presynaptic process, we leveraged new advances in mass spectrometry to identify the proteomic and post-translational landscape of presynaptic Rac1 signaling. We identified serine/threonine kinases and phosphorylated cytoskeletal signaling and synaptic vesicle proteins enriched with active Rac1. The phosphorylated sites in these proteins are at positions likely to have regulatory effects on synaptic vesicles. Consistent with this, we also report changes in the distribution and morphology of synaptic vesicles and in postsynaptic ultrastructure following presynaptic Rac1 inhibition. Overall, this study reveals a previously unrecognized presynaptic role of Rac1 signaling in cognitive processes and provides insights into its potential regulatory mechanisms.
Establishing synthetic ribbon-type active zones in a heterologous expression system
Authors: Kapoor Rohan , Schwenzer Niko , Dresbach Thomas , Lehnart Stephan E. , Moser Tobias 
Published: March 2024

AbstractEncoding of several sensory modalities into neural signals is mediated by ribbon synapses. The synaptic ribbon tethers synaptic vesicles at the presynaptic active zone (AZ) and might act as a super-scaffold organizing AZ topography. Here we employed a synthetic biology approach to reconstitute ribbon-type AZs in HEK293 cells for probing their minimal molecular requirements and studying presynaptic Ca2+channel clustering. Co-expressing a membrane-targeted version of the AZ-protein Bassoon and the ribbon core protein RIBEYE, we observed structures recapitulating basic aspects of ribbon-type AZs, which we callsyntheticribbons orSyRibbons.SyRibbonswith Ca2+channel clusters formed upon additional expression of CaV1.3 Ca2+channels and RIM-binding protein 2 (RBP2), known to promote presynaptic Ca2+channel clustering. Confocal and super-resolution microscopy along with functional analysis by patch-clamp and Ca2+-imaging revealed striking similarities and interesting differences ofSyRibbonsin comparison to native IHC ribbon-type AZs. In summary, we identify Ca2+channels, RBP, membrane-anchored Bassoon, and RIBEYE as minimal components for reconstituting a basic ribbon-type AZ.SyRibbonsmight complement animal studies on molecular interactions of AZ proteins.Significance StatementEncoding of sensory information in our eyes and ears builds on specialized ribbon synapses of sensory cells. Elucidating the molecular underpinning of their fascinating structure and function is an ongoing effort to which we add a bottom-up reconstitution approach in cultured cells. Aiming to recapitulate basic properties of ribbon-type presynaptic active zones of cochlear inner hair cells, we identified a minimal set of proteins that assemble in cellular nanodomains, structurally and functionally alike active zones. While not yet reconstituting synaptic vesicle exocytosis, we consider the established synthetic ribbon-type active zones a valuable platform for studying molecular interactions of active zone proteins. We expect the approach to complement, refine, and reduce experiments on native ribbon synapses asserted from animals.
GPCR surface creates a favorable pathway for membrane permeation of drug molecules
Authors: Herrero Cristina Gil , Thallmair Sebastian 
Published: March 2024

AbstractG protein-coupled receptors (GPCRs) play a crucial role in modulating physiological responses and serve as the main drug target. Specifically, salmeterol and salbutamol which are used for the treatment of pulmonary diseases, exert their effects by activating the GPCR β2-adrenergic receptor (β2AR). In our study, we employed coarse-grained molecular dynamics simulations with the Martini 3 force field to investigate the dynamics of drug molecules in membranes in presence and absence of β2AR. Our simulations reveal that in more than 50% of theflip-flopevents the drug molecules use the β2AR surface to permeate the membrane. The pathway along the GPCR surface is significantly more energetically favorable for the drug molecules, which was revealed by umbrella sampling simulations along spontaneousflip-floppathways. Furthermore, we assessed the behavior of drugs with intracellular targets, such as kinase inhibitors, whose therapeutic efficacy could benefit from this observation. In summary, our results show that β2AR surface interactions can significantly enhance membrane permeation of drugs, emphasizing their potential for consideration in future drug development strategies.
miR-146a-5p mediates inflammation-induced β cell mitochondrial dysfunction and apoptosis
Authors: Krishnan Preethi , Branco Renato Chaves Souto , Weaver Staci A. , Chang Garrick , Lee Chih-Chun , Syed Farooq , Evans-Molina Carmella 
Published: March 2024

ABSTRACTWe previously showed that miR-146a-5p is upregulated in pancreatic islets treated with pro-inflammatory cytokines. Others have reported that miR-146a-5p overexpression is associated with β cell apoptosis and impaired insulin secretion. However, the molecular mechanisms mediating these effects remain elusive. To investigate the role of miR-146a-5p in β cell function, we developed stable MIN6 cell lines to either overexpress or inhibit the expression of miR-146a-5p. Monoclonal cell populations were treated with pro-inflammatory cytokines (IL-1β, IFNγ, and TNFα) to model type 1 diabetes (T1D)in vitro. We found that overexpression of miR-146a-5p increased cell death under conditions of inflammatory stress and led to mitochondrial membrane depolarization, whereas inhibition of miR-146a-5p reversed these effects. Additionally, inhibition of miR-146a-5p increased insulin secretion, mitochondrial DNA copy number, respiration rate, and ATP production Further, RNA sequencing data showed enrichment of pathways related to insulin secretion, apoptosis, and mitochondrial function when the expression levels of miR-146a-5p were altered. Finally, a temporal increase in miR-146a-5p expression levels and a decrease in mitochondria function markers was observed in islets derived from NOD mice. Collectively, these data suggest that miR-146a-5p may promote β cell dysfunction and death during inflammatory stress by suppressing mitochondrial function.
Malaria-derived hemozoin alters chromatin remodelling and skews dendritic cell responses to subsequent bacterial infections
Authors: Lasaviciute Gintare , Tariq Kanwal , Sugathan Anaswara , Quin Jaclyn , Bujila Ioana , Skorokhod Oleksii , Troye-Blomberg Marita , Sverremark-Ekström Eva , Farrants Ann-Kristin Östlund 
Published: March 2024

AbstractHemozoin (HZ), the malaria pigment, is released together with the with the parasite merozoites during the blood stage of the disease, which is connected with the pro-inflammatory response to induce T-cells and B-cells. Co-infections with bacteria lead to a more severe disease progression and the underlying mechanisms are poorly understood. Here, we investigated the impact of HZ on the early response of monocyte-derived dendritic cells (moDC) to a common bacterial component, LPS. A short-term HZ exposure for two hours did not induce an inflammatory response, but it did alter the transcriptional response to LPS. In moDC co-exposed to HZ and LPS, the induction of HLA-DR and PD-L1 gene expression was reduced and associated with decreased binding of RELA compared to LPS-stimulated cells. These gene promoters recruited the silencing chromatin remodelling complex NuRD upon co-exposure, instead of the PBAF complex at the promoter in LPS-stimulated cells. Further, HZ maintained transcription of C-type lectin receptors associated to an immature DC phenotype, DC-SIGN (CD209) and macrophage mannose receptor (MMR/CD206). Here, activated RELA and IRF3 were recruited in a PBAF and ncBAF dependent manner. Upon LPS co-exposure, NuRD was replacing these complexes to allow for a reduced transcriptional level of these immature markers. The association of chromatin remodelling complexes did not alter the chromatin state at the promoters, which was changed during differentiation to DCs or even at an earlier point. In conclusion, HZ exposure primes specific gene promoters at an early time point, which results in a different transcriptional response and may also lead to a changed immune reaction to bacterial co-infections.Graphical abstract
Transformation of the drug ibuprofen byPriestia megaterium: Reversible glycosylation and generation of hydroxylated metabolites
Authors: Hinzke Tjorven , Schlüter Rabea , Mikolasch Annett , Zühlke Daniela , Müller Patrick , Riedel Katharina , Lalk Michael , Becher Dörte , Sheikhany Halah , Schauer Frieder 
Published: March 2024

AbstractAs one of the most-consumed drugs worldwide, ibuprofen (IBU) reaches the environment in considerable amounts as environmental pollutant, necessitating studies of its further biotransformation as potential removal mechanism. Therefore, we screened bacteria with known capabilities to degrade aromatic environmental pollutants, belonging to the generaBacillus,Priestia(formerly alsoBacillus)Paenibacillus,Mycobacterium, andCupriavidus, for their ability to transform ibuprofen. We identified five transformation products, namely 2-hydroxyibuprofen, carboxyibuprofen, ibuprofen pyranoside, 2-hydroxyibuprofen pyranoside, and 4-carboxy-α-methylbenzene-acetic acid. Based on our screening results, we focused on ibuprofen biotransformation byPriestia megateriumSBUG 518 with regard to structure of transformation products and bacterial physiology. Biotransformation reactions by P. megaterium involved (A) the hydroxylation of the isobutyl side chain at two positions, and (B) conjugate formation via esterification with a sugar molecule of the carboxylic group of ibuprofen and an ibuprofen hydroxylation product. Glycosylation seems to be a detoxification process, since the ibuprofen conjugate (ibuprofen pyranoside) was considerably less toxic than the parent compound toP. megateriumSBUG 518. Based on proteome profile changes and inhibition assays, cytochrome P450 systems are likely crucial for ibuprofen transformation inP. megateriumSBUG 518. The toxic effect of ibuprofen appears to be caused by interference of the drug with different physiological pathways, including especially sporulation, as well as amino acid and fatty acid metabolism.ImportanceIbuprofen is a highly consumed drug, and, as it reaches the environment in high quantities, also an environmental pollutant. It is therefore of great interest how microorganisms transform this drug and react to it. Here, we screened several bacteria for their ability to transform ibuprofen.Priestia megateriumSBUG 518 emerged as highly capable and was therefore studied in greater detail. We show thatP. megateriumtransforms ibuprofen via two main pathways, hydrolyzation and reversible conjugation. These pathways bear resemblance to those in humans. Ibuprofen likely impacts the physiology ofP. megateriumon several levels, including spore formation. Taken together,P. megateriumSBUG 518 is well suited as a model organism to study bacterial ibuprofen metabolism.