bluuebunny/crossref_metadata_2025_split huggingface dataset:
eIF1 and eIF5 dynamically control translation start site fidelity
Authors: Grosely Rosslyn , Alvarado Carlos , Ivanov Ivaylo P. , Nicholson Oliver B. , Puglisi Joseph D. , Dever Thomas E. , Lapointe Christopher P. 
Published: July 2024

ABSTRACTTranslation initiation defines the identity of a synthesized protein through selection of a translation start site on a messenger RNA. This process is essential to well-controlled protein synthesis, modulated by stress responses, and dysregulated in many human diseases. The eukaryotic initiation factors eIF1 and eIF5 interact with the initiator methionyl-tRNAiMeton the 40S ribosomal subunit to coordinate start site selection. Here, using single-molecule analysis of in vitro reconstituted human initiation combined with translation assays in cells, we examine eIF1 and eIF5 function. During translation initiation on a panel of RNAs, we monitored both proteins directly and in real time using single-molecule fluorescence. As expected, eIF1 loaded onto mRNAs as a component of the 43S initiation complex. Rapid (∼ 2 s) eIF1 departure required a translation start site and was delayed by alternative start sites and a longer 5’ untranslated region (5’UTR). After its initial departure, eIF1 rapidly and transiently sampled initiation complexes, with more prolonged sampling events on alternative start sites. By contrast, eIF5 only transiently bound initiation complexes late in initiation immediately prior to association of eIF5B, which allowed joining of the 60S ribosomal subunit. eIF5 association required the presence of a translation start site and was inhibited and destabilized by alternative start sites. Using both knockdown and overexpression experiments in human cells, we validated that eIF1 and eIF5 have opposing roles during initiation. Collectively, our findings demonstrate how multiple eIF1 and eIF5 binding events control start-site selection fidelity throughout initiation, which is tuned in response to changes in the levels of both proteins.
Defining a Muscle Stem Cell matrisome signature: from transcriptome data to extracellular matrix niche topology
Authors: Guillon Emilie , Hisoilat Bacar , Sasaki Takako , Mourikis Philippos , Ruggiero Florence 
Published: July 2024

ABSTRACTAlthough intensively investigated, the regulation of skeletal muscle stem cells (MuSCs) by their niche remains an open question. The extracellular matrix (ECM) components of the niche represent a dynamic microenvironment that undoubtedly participates in MuSCs behavior. We used bioinformatics analysis of transcriptomic data to define the matrisome profile of skeletal muscle resident cells, comprising genes encoding ECM and ECM-associated proteins. We identified quiescent MuSCs as key ECM producers of the niche, notably through the expression of specific basement membrane genes asCol19a1andLama3and regulators of ECM assembly,Thsd4 and Aebp1. Unexpectedly, quiescent MuSCs also expressed matrisome neurogenesis-related genes. Immunofluorescence staining of selected ECM components showed their organization in isolated murine myofiber bundles. Upon activation, MuSCs strikingly downregulated the niche-related ECM genes and instead expressed genes involved in basement membrane disruption and matrisome genes linked to cell motility. This study identified distinct matrisome signatures of quiescent and activated MuSCs that are consistent with their function in homeostasis and repair of damaged skeletal muscle.
MDRepo – an open environment for data warehousing and knowledge discovery from molecular dynamics simulations
Authors: Roy Amitava , Ward Ethan , Choi Illyoung , Cosi Michele , Edgin Tony , Hughes Travis S. , Islam Md. Shafayet , Khan Asif M. , Kolekar Aakash , Rayl Mariah , Robinson Isaac , Sarando Paul , Skidmore Edwin , Swetnam Tyson L. , Wall Mariah , Xu Zhuoyun , Yung Michelle L. , Merchant Nirav , Wheeler Travis J. 
Published: July 2024

BackgroundMolecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. This enables advances in drug discovery and the design of therapeutic interventions. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more.A needIdeally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols.A solutionHere, we introduce MDRepo, a robust infrastructure that supports a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyberinfrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.
ABCA1 and apoA-I dependent 12-hydroxyeicosatetraenoic acid efflux regulates macrophage inflammatory signaling
Authors: Harsch Brian A. , Borkowski Kamil , Walker Rachel E. , Pedersen Theresa L. , Newman John W. , Shearer Gregory C. 
Published: July 2024

AbstractAberrant high-density lipoprotein (HDL) function is implicated in inflammation-associated pathologies. While HDL ABCA1-mediated reverse cholesterol and phospholipid transport are well described, the movement of pro-/anti-inflammatory lipids has not been explored. HDL phospholipids are the largest reservoir of circulating arachidonic acid-derived oxylipins. Endotoxin-stimulation activates inflammatory cells leading to hydroxyeicosatetraenoic acid (HETE) production, oxylipins which are involved in inflammatory response coordination. Active signaling in the non-esterified (NE) pool is terminated by sequestration of HETEs as esterified (Es) forms and degradation. We speculate that an ABCA1-apoA-I-dependent efflux of HETEs from stimulated cells could regulate intracellular HETE availability. Here we test this hypothesis both in vitro and in vivo. In endotoxin-stimulated RAW-264.7 macrophages preloaded with d8-arachidonic acid we use compartmental tracer modeling to characterize the formation of HETEs, and their efflux into HDL. We found that in response to endotoxin: I) Cellular NE 12-HETE is positively associated with MCP-1 secretion (p<0.001); II) HETE transfer from NE to Es pools is ABCA1-depedent (p<0.001); III) Cellular Es HETEs are transported into media when both apoA-I and ABCA1 are present (p<0.001); IV) The stimulated efflux of HETEs >> arachidonate (p<0.001). Finally, in endotoxin challenged humans (n=17), we demonstrate that intravenous lipopolysaccharide (0.6 ng/kg body weight) resulted in accumulation of 12-HETE in HDL over a 168-hour follow-up. Therefore, HDL can suppress inflammatory responses in macrophages by regulating intracellular HETE content in an apoA-I/ABCA1 dependent manner. The described mechanism may apply to other oxylipins and explain anti-inflammatory properties of HDL. This newly defined HDL property opens new doors for the study of lipoprotein interactions in metabolic diseases.
Maturation of Human Intestinal Epithelial Cell Layers Fortifies the Apical Surface againstSalmonellaAttack
Authors: van Rijn Jorik M. , Lopes Ana C. C. , Ceylan Merve , Eriksson Jens , Bergholtz Alexandra , Ntokaki Angelika , Hammar Rebekkah , Sundbom Magnus , Skogar Martin , Graf Wilhelm , Webb Dominic-Luc , Hellström Per M. , Artursson Per , Pelaseyed Thaher , Di Martino Maria Letizia , Sellin Mikael E. 
Published: July 2024

AbstractThe active invasion of intestinal epithelial cells (IECs) represents a key event in the infection cycle of many gut pathogens. Studies of howSalmonella entericaTyphimurium (S.Tm) bacteria enter transformed cell lines have shaped the paradigm for swift type-three-secretion-system-1 (TTSS-1)-driven IEC invasion, fueled by expansive membrane ruffles. However, comparative studies suggest that non-transformed IECs in the intact gut context comprise a much more challenging target for the attack. The molecular and cellular features that explain these discrepancies remain undefined. By live-cell imaging in human enteroid-and colonoid-derived IEC layers, we demonstrate that the maturation state of gut epithelia dramatically impacts permissiveness toS.Tm invasion. IEC layers kept under immature progenitor-cell-promoting conditions are permissive to the bacterial invasion, whereas maturation towards an enterocyte/colonocyte fate reduces the frequency ofS.Tm-induced epithelial entry structures, and lowers the invasion efficiency by up to tenfold. This phenotypic shift during IEC maturation couples to an altered expression of actin regulatory proteins implicated in the invasion process, and an increased dependence on theS.Tm TTSS-1 effector SipA for successful entry. In addition, IEC maturation involves upregulation of cell surface mucins, e.g. MUC13, and shifts in glycocalyx composition, as revealed by multiple lectin stainings. Enzymatic treatment of the apical surface with the StcE mucinase converts maturing IEC layers back to theS.Tm-invasion-permissive state of their immature counterparts. Taken together, these results showcase how the maturation state of human IECs dictates the susceptibility to invasion by a prototype enterobacterium.
Long-term single-molecule tracking in living cells using weak-affinity protein labeling
Authors: Catapano Claudia , Dietz Marina S. , Kompa Julian , Jang Soohyen , Freund Petra , Johnsson Kai , Heilemann Mike 
Published: July 2024

AbstractSingle-particle tracking (SPT) has become a powerful tool to monitor the dynamics of membrane proteins in living cells. However, permanent labeling strategies for SPT suffer from photobleaching as a major limitation, restricting observation times, and obstructing the study of long-term cellular processes within single living cells. Here, we use exchangeable HaloTag Ligands (xHTLs) as an easy-to-apply labeling approach for live-cell SPT and demonstrate extended observation times of individual live cells of up to 30 minutes. Using the xHTL/HT7 labeling system, we measure the ligand-induced activation kinetics of the epidermal growth factor receptor (EGFR) in single living cells. Furthermore, we generate spatial maps of receptor diffusion in cells, report non-uniform distributions of receptor activation, and the formation of spatially confined ‘hot spots’ of EGFR activation. This approach represents a general strategy to monitor protein dynamics in a functional context and for extended observation times in single living cells.
Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake
Authors: Olmsted Charles N. , Gahler Mark , Roden Eric , Peterson Ben , Lazarcik James , Tran Patricia Q. , Berg Maureen , Bryant Donald A. , Goudeau Danielle , Malmstrom Rex R. , Qin Mohan , McMahon Katherine D. 
Published: July 2024

ABSTRACTThe genetic potential for extracellular electron transfer (EET)-based metabolism has been shown to be a prevailing feature of humic lakes where bacterioplankton may be able to use EET to cycle dissolved organic matter (DOM) extracellularly between oxidized and reduced states, but measurable abiotic features resulting from this phenomenon have yet to be demonstrated. We observed an anoxygenic photosyntheticChlorobiumsp. bloom each summer in Trout Bog Lake in northern WI, USA. Given this bloom’s characteristics, we hypothesized that EET-based metabolisms ofChlorobiumsp. and accompanying bacteria cycle DOM between oxidized and reduced states with seasonal or diel-timescale oscillations; therefore, we anticipated this could be measured by weekly and subdaily sampling. We collected vertical profiles on these timescales using a multiparameter sonde, including oxidation-reduction potential measurement, and we assayed for inorganic electron donors. We also developed and deployed a buoy to measure electric current flow between many pairs of electrodes simultaneously. Using metagenomics analyses, we examined the EET genes and other oxidoreductases of bacteria from water column samples at select depths and from biofilms that developed on electrodes at similar depths. Our results indicate the occurrence of diel electron cycling between phototrophic oxidation (electrotrophic metabolism) and anaerobic respiration (electrogenic metabolism), likely involving DOM. We also observed a gradual seasonal increase in hypolimnion oxidation-reduction potential. These diel and seasonal patterns have implications for carbon emissions and the ecology of electroactive bacteria in lakes.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.
Surviving the Storm: Exploring the Role of Natural Transformation in Nutrition and DNA Repair of StressedDeinococcus radiodurans
Authors: Sharma Dhirendra Kumar , Soni Ishu , Gupta Gagan D. , Rajpurohit Yogendra Singh 
Published: July 2024

AbstractDeinococcus radiodurans, a natural transformation (NT) enabled bacterium renowned for its exceptional radiation resistance, employs unique DNA repair and oxidative stress mitigation mechanisms as a strategic response to DNA damage. This study excavate into the intricate roles of NT machinery in the stressedD. radiodurans, focusing on the genescomEA,comEC,endA,pilTanddprA, which are instrumental in the uptake and processing of extracellular DNA (eDNA). Our data reveals that NT not only supports the nutritional needs ofD. radioduransunder stress but also have roles in DNA repair. The study findings establish that NT-specific proteins (ComEA, ComEC, and EndA) might contribute to support the nutritional requirements in unstressed and heavily DNA-damaged cells while DprA contribute differently and in a context-dependent manner to navigating through the DNA damage storm. Thus, this dual functionality of NT-specific genes is proposed to be one of factor inD. radioduransremarkable ability to survive and thrive in environments characterized by high levels of DNA-damaging agents.Author Summary:Deinococcus radiodurans, a bacterium known for its extraordinary radiation resistance. This study explores the roles of natural transformation (NT) machinery in the radiation-resistant bacteriumDeinococcus radiodurans, focusing on the genescomEA,comEC,endA,pilT, anddprA. These genes are crucial for the uptake and processing of extracellular DNA (eDNA) and contribute to the bacterium nutritional needs and DNA repair under stress. The findings suggest that the NT-specific proteins ComEA, ComEC, and EndA may help meet the nutritional needs of unstressed and heavily DNA-damaged cells, whereas DprA plays a distinct role that varies depending on the context in aiding cells to cope with DNA damage. The functionality of NT genes is proposed to enhanceD. radioduranssurvival in environments with high levels of DNA-damaging agents.
A conserved code for anatomy: Neurons throughout the brain embed robust signatures of their anatomical location into spike trains
Authors: Tolossa Gemechu B. , Schneider Aidan M. , Dyer Eva L. , Hengen Keith B. 
Published: July 2024

AbstractNeurons in the brain are known to encode diverse information through their spiking activity, primarily reflecting external stimuli and internal states. However, whether individual neurons also embed information about their own anatomical location within their spike patterns remains largely unexplored. Here, we show that machine learning models can predict a neuron’s anatomical location across multiple brain regions and structures based solely on its spiking activity. Analyzing high-density recordings from thousands of neurons in awake, behaving mice, we demonstrate that anatomical location can be reliably decoded from neuronal activity across various stimulus conditions, including drifting gratings, naturalistic movies, and spontaneous activity. Crucially, anatomical signatures generalize across animals and even across different research laboratories, suggesting a fundamental principle of neural organization. Examination of trained classifiers reveals that anatomical information is enriched in specific interspike intervals as well as responses to stimuli. Within the visual isocortex, anatomical embedding is robust at the level of layers and primary versus secondary but does not robustly separate individual secondary structures. In contrast, structures within the hippocampus and thalamus are robustly separable based on their spike patterns. Our findings reveal a generalizable dimension of the neural code, where anatomical information is multiplexed with the encoding of external stimuli and internal states. This discovery provides new insights into the relationship between brain structure and function, with broad implications for neurodevelopment, multimodal integration, and the interpretation of large-scale neuronal recordings. Computational approximations of anatomy have potential to support in-vivo electrode localization.
Resolving a neonatal intensive care unit outbreak of methicillin-resistantStaphylococcus aureusto the SNV level using Oxford Nanopore simplex reads and HERRO error correction
Authors: Bloomfield Max , Bakker Sarah , Burton Megan , Castro M. Leticia , Dyet Kristin , Eustace Alexandra , Hutton Samantha , Macartney-Coxson Donia , Taylor William , White Rhys T. 
Published: July 2024

AbstractObjectivesOur laboratory began prospective genomic surveillance for healthcare-associated organisms in 2022 using Oxford Nanopore Technologies (ONT) sequencing as a standalone platform. This has permitted the early detection of outbreaks but has been insufficient for single-nucleotide variant (SNV)-level analysis due to lower read accuracy than Illumina sequencing. This study aimed to determine whether Haplotype-aware ERRor cOrrection (HERRO) of ONT data could permit high-resolution comparison of outbreak isolates.MethodsWe used ONT simplex reads from isolates involved in a recent outbreak of methicillin-resistantStaphylococcus aureus(MRSA) in our neonatal unit. The raw sequence data were re-basecalled and adapter-trimmed using Dorado v0.7.0. The simplex reads then underwent HERRO correction. The resulting genome assemblies and phylogenies were compared with previous analyses (using Dorado v0.3.4, no HERRO correction and data generated by Illumina sequencing).ResultsFive of nine outbreak isolates were included in the analysis. The remaining four isolates had insufficient read lengths (N50 values <10,000 bp) and did not provide complete chromosome coverage after HERRO correction. The average chromosome sequencing depth for nanopore data was 147× (range: 44–220×) with an average read N50 of 12,215 bp (interquartile range (IQR): 11,439–12,711 bp). The median pairwise SNV distance between outbreak isolates from the original investigation was 51 SNVs (range: 40–68), which decreased to 3 SNVs (range: 1–15) with HERRO correction. Illumina sequencing generated a median SNV distance of 2 (range: 0–13). The resulting standalone ONT HERRO-corrected phylogeny was almost indistinguishable from the standalone Illumina-generated phylogeny.ConclusionsThe addition of HERRO correction meant isolates from this MRSA outbreak could be resolved to a level on par with Illumina sequencing. ONT data following HERRO correction represents a viable standalone option for high-resolution genomic analysis of hospital outbreaks, provided sufficient read lengths can be generated.
HIV broadly neutralizing antibody escapability drives the therapeutic efficacy of vectored immunotherapy
Authors: Galvez Nicolas M.S. , Cao Yi , Nitido Adam D. , Deal Cailin E. , Boutros Christine L. , MacDonald Scott W. , Soto Albrecht Yentli E. , Lam Evan C. , Sheehan Maegan L. , Parsons Dylan , Lin Allen Z. , Deymier Martin J. , Brady Jacqueline M. , Moon Benjamin , Bullock Christopher B. , Tanno Serah , Pegu Amarendra , Chen Xuejun , Liu Cuiping , Koup Richard A. , Mascola John R. , Vrbanac Vladimir D. , Lingwood Daniel , Balazs Alejandro B. 
Published: July 2024

SUMMARYBroadly neutralizing antibodies (bNAbs) have shown great promise for prevention and treatment of HIV infection. Breadth of bNAb neutralization, measuredin vitroacross panels of diverse viral isolates, is often used as a predictor of clinical potential. However, recent prevention studies demonstrate that the clinical efficacy of a broad and potent bNAb (VRC01) is undermined by neutralization resistance of circulating strains. Using HIV-infected humanized mice, we find that therapeutic efficacy of bNAbs delivered as Vectored ImmunoTherapy (VIT) is a function of both the fitness cost and resistance benefit of mutations that emerge during viral escape, which we term ‘escapability’. Applying this mechanistic framework, we find that the sequence of the envelope V5-loop alters the resistance benefits of mutants that arise during escape, thereby impacting the therapeutic efficacy of VIT-mediated viral suppression. We also find that an emtricitabine-based antiretroviral drug regimen dramatically enhances the efficacy of VIT, by reducing the fitness of mutants along the escape path. Our findings demonstrate that bNAb escapability is a key determinant to consider in the rational design of antibody regimens with maximal efficacy and illustrates a tractable means of minimizing viral escape from existing bNAbs.