bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emerin deficiency drives MCF7 cells to an invasive phenotype
Authors: Hansen Emily , Rolling Christal , Wang Matthew , Holaska James M. 
Published: February 2024

AbstractDuring metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer cells showed similar results. Supporting the clinical relevance of emerin reduction in cancer progression, our analysis of 192 breast cancer patient samples showed emerin expression inversely correlates with cancer invasiveness. We conclude emerin loss is an important driver of invasive transformation and has utility as a biomarker for tumor progression.
Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH
Authors: Troyer Zach , Gololobova Olesia , Koppula Aakash , Liao Zhaohao , Horns Felix , Elowitz Michael B , Tosar Juan Pablo , Batish Mona , Witwer Kenneth W. 
Published: February 2024

AbstractInterest in using nanoparticles for delivery of therapeutic RNA has been steadily growing, provoking a need to precisely understand their structure and contents. Single-particle and single-molecule analysis techniques provide snapshots of single biological nanoparticles, including viruses, liposomes, and extracellular vesicles (EVs). While existing methods primarily focus on protein detection, RNA delivery is becoming increasingly prevalent. A method to simultaneously detect protein and internal RNA in the same particle would reveal variability in size, structure, and RNA packaging efficiency, enabling optimization of nanoparticle delivery. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor (SP-IRIS) with single-molecule fluorescence in-situ hybridization (smFISH). Using SPIRFISH, we detect HIV-1 envelope protein and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNA within EVs. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles.Teaser:A new single particle analysis technique simultaneously detects specific RNA and protein in biological nanoparticles.
ConcurrentAscarisinfection modulates host immunity resulting in impaired control ofSalmonellainfection in pigs
Authors: Midha Ankur , Oser Larissa , Schlosser-Brandenburg Josephine , Laubschat Alexandra , Mugo Robert M. , Musimbi Zaneta D. , Höfler Philipp , Kundik Arkadi , Hayani Rima , Adjah Joshua , Groenhagen Saskia , Tieke Malte , Elizalde-Velázquez Luis E. , Kühl Anja A. , Klopfleisch Robert , Tedin Karsten , Rausch Sebastian , Hartmann Susanne 
Published: February 2024

AbstractAscarisis one of the most widespread helminth infections of humans and pigs, leading to chronic morbidity in humans and considerable economic losses in pig farming. Additionally, pigs are an important reservoir for the zoonotic bacterial pathogenSalmonella,where pigs can serve as asymptomatic carriers. Here, we investigated the impact of an ongoingAscarisinfection on the immune response toSalmonellain pigs. We observed higher bacterial burdens in experimentally coinfected pigs compared to pigs infected withSalmonellaalone.Ascaris-infected pigs exhibited numerous hallmarks of a type 2 immune response in organs impacted by larval migration, including increased Th2 cells, increased IL-4 production, eosinophilia, and increased expression of CD206, a marker for alternatively activated macrophages. While we observed only mild changes in frequencies of CD4+Treg,Ascaris-infected pigs had increased frequencies of CD8α+Treg. We show that type 2 immune signals enhance susceptibility of macrophages toSalmonellainfectionin vitro. Furthermore,AscarisimpairedSalmonella-induced monocytosis and TNF-α production by myeloid cells. Hence, our data demonstrate widespread immunomodulation during an acuteAscarisinfection that facilitates the microbial spread into gut-associated lymphoid tissue in aSalmonellacoinfection.ImportanceIn experimentally infected pigs we show that an ongoing infection with the parasitic wormAscaris suummodulates host immunity to render pigs more susceptible to invadingSalmonella.Both infections are widespread in pig production and the prevalence ofSalmonellais high in endemic regions of human Ascariasis, indicating that this is a clinically meaningful coinfection. We observed a type 2 immune response to be induced during anAscarisinfection correlating with an increased susceptibility of pigs to the concurrent bacterial infection.
Differential functions of the dorsal and intermediate regions of the hippocampus for optimal goal-directed navigation in VR space
Authors: Hwang Hyeri , Jin Seung-Woo , Lee Inah 
Published: February 2024

AbstractGoal-directed navigation requires the hippocampus to process spatial information in a value-dependent manner, but its underlying mechanism needs to be better understood. Here, we investigated whether the dorsal (dHP) and intermediate (iHP) regions of the hippocampus differentially function in processing place and its associated value information. Rats were trained in a place-preference task involving reward zones with different values in a visually rich VR environment where two-dimensional navigation was possible. Rats learned to use distal visual scenes effectively to navigate to the reward zone associated with a higher reward. Inactivation of both dHP and iHP with muscimol altered the efficiency and precision of wayfinding behavior, but iHP inactivation induced more severe damage, including impaired place preference. Our findings suggest that the iHP is more critical for value-dependent navigation toward higher-value goal locations.
Changes in bird migration phenology over six decades, a perspective from the Neotropical non-breeding grounds
Authors: Gutiérrez-Carrillo Daniel A. , Mateus-Aguilar Bryam , Gómez Camila , Cadena Carlos Daniel 
Published: February 2024

SummaryChanges in the migration phenology of birds linked to global change are extensively documented. Longitudinal studies from temperate breeding grounds have mostly shown earlier arrivals in the spring and a variety of patterns during fall migration1,2, yet no studies have addressed whether and how migration phenology has changed using data from the tropical non-breeding grounds. Understanding whether changes in migratory phenology are also evident in non-breeding sites is essential to determine the underlying causes of patterns documented in breeding areas. Using data from historical scientific collections and modern repositories of community-science records, we assessed changes in migration phenology of 12 Nearctic-Neotropical long-distance migratory birds in Colombia over six decades. We also explored whether shared breeding and non-breeding climatic niches explained variation in phenological patterns observed among species. All species showed shifts in spring (range −37 – 9 days from peak passage date) or fall (range −26 – 36 days) migration, but patterns differed among species in ways partly attributable to shared breeding or wintering climatic niches. Our results, although not yet broadly generalizable, suggest that birds use cues to time their migration at their non-breeding grounds which are most likely different to those they use on their breeding grounds. To better understand the effects of global change on biodiversity, exploring the underlying drivers of phenological changes with further research integrating more long-term datasets available through scientific collections and community science platforms should be a priority.
The GPI sidechain ofToxoplasma gondiiprevents parasite pathogenesis
Authors: Alvarez Julia A , Gas-Pascual Elisabet , Malhi Sahil , Njume Ferdinand Ngale , Sánchez-Arcila Juan C , van der Wel Hanke , Zhao Yanlin , Ceron Gabriella , Posada Jasmine , Souza Scott P , Yap George S , West Christopher M , Jensen Kirk D C 
Published: February 2024

ABSTRACTGlycosylphosphatidylinositols (GPIs) are highly conserved anchors for eukaryotic cell surface proteins. The apicomplexan parasite,Toxoplasma gondii, is a widespread intracellular parasite of warm-blooded animals whose plasma membrane is covered with GPI-anchored proteins, and free GPIs called GIPLs. While the glycan portion is conserved, species differ in sidechains added to the triple mannose core. The functional significance of the Glcα1,4GalNAcβ1-sidechain reported inToxoplasma gondiihas remained largely unknown without an understanding of its biosynthesis. Here we identify and disrupt two glycosyltransferase genes and confirm their respective roles by serology and mass spectrometry. Parasites lacking the sidechain on account of deletion of the first glycosyltransferase, PIGJ, exhibit increased virulence during primary and secondary infections, suggesting it is an important pathogenesis factor. Cytokine responses, antibody recognition of GPI-anchored SAGs, and complement binding to PIGJ mutants are intact. In contrast, the scavenger receptor CD36 shows enhanced binding to PIGJ mutants, potentially explaining a subtle tropism for macrophages detected early in infection. Galectin-3, which bind GIPLs, exhibits a slight enhancement of binding to PIGJ mutants, and the protection of galectin-3 knockout mice from lethality suggests thatΔpigjparasite virulence in this context is sidechain dependent. Parasite numbers are not affected byΔpigjearly in the infection in wildtype mice, suggesting a breakdown of tolerance. However, increased tissue cysts in the brains of mice infected withΔpigjparasites indicate an advantage over wildtype strains. Thus, the GPI sidechain ofT. gondiiplays a crucial and diverse role in regulating disease outcome in the infected host.SummaryThe functional significance of sidechain modifications to the GPI anchor is yet to be determined because the glycosyltransferases responsible for these modifications have not been identified. Here we present identification and characterization of bothT.gondiiGPI sidechain-modifying glycosyltransferases. Removal of the glycosyltransferase that adds the first GalNAc to the sidechain results in parasites without a sidechain on the GPI, and increased parasite virulence. Loss of the second glycosyltransferase results in a sidechain with GalNAc alone, and no glucose added, and has negligible effect on parasite virulence. This indicates GPI sidechains as fundamental to host-parasite interactions.
Symplasmic phloem loading and subcellular transport in storage roots are key factors for carbon allocation in cassava
Authors: Rüscher David , Vasina Viktoriya V. , Knoblauch Jan , Bellin Leo , Pommerrenig Benjamin , Alseekh Saleh , Fernie Alisdair R. , Neuhaus H. Ekkehard , Knoblauch Michael , Sonnewald Uwe , Zierer Wolfgang 
Published: February 2024

AbstractCassava is a deciduous woody perennial shrub that stores large amounts of carbon and water in its storage roots. Previous studies have shown that assimilate unloading into storage roots happens symplasmically once secondary anatomy is established. However, mechanisms controlling phloem loading and overall carbon partitioning to different cassava tissues remain unclear. Here we used a combination of histological, transcriptional, and biochemical analyses on different cassava tissues and timepoints to better understand source-sink carbon allocation. We find that cassava likely utilizes a predominantly passive symplasmic phloem loading strategy, indicated by the lack of expression of genes coding for key players of sucrose transport, the existence of branched plasmodesmata in the companion cell/bundle sheath interface of minor leaf veins, and very high leaf sucrose concentrations. Furthermore, we show that tissue-specific changes in anatomy and NSC contents are associated with tissue-specific modification in gene expression for sucrose cleavage/synthesis, as well as subcellular compartmentalization of sugars. Overall, our data suggest that carbon allocation during storage root filling is mostly facilitated symplasmically, and is likely mostly regulated by local tissue demand and subcellular compartmentalization.
Mutational Analysis of an Antimalarial Drug TargetPfATP4
Authors: Rachuri Swaksha , Nepal Binod , Shukla Anurag , Ramanathan Aarti , Morrisey Joanne M. , Daly Thomas , Mather Michael W. , Bergman Lawrence W. , Kortagere Sandhya , Vaidya Akhil B. 
Published: February 2024

AbstractAmong new antimalarials discovered over the past decade are multiple chemical scaffolds that targetPlasmodium falciparumP-type ATPase (PfATP4). This essential protein is a Na+pump responsible for the maintenance of Na+homeostasis.PfATP4 belongs to the type 2D subfamily of P-type ATPases, for which no structures have been determined. To gain better insight into the structure/function relationship of this validated drug target, we generated a homology model ofPfATP4 based on SERCA, a P2A-type ATPase, and refined the model using molecular dynamics in its explicit membrane environment. This model predicted several residues inPfATP4 critical for its function, as well as those that impart resistance to variousPfATP4 inhibitors. To validate our model, we developed a genetic system involving merodiploid states ofPfATP4 in which the endogenous gene was conditionally expressed, and the second allele was mutated to assess its effect on the parasite. Our model predicted residues involved in Na+coordination as well as the phosphorylation cycle ofPfATP4. Phenotypic characterization of these mutants involved assessment of parasite growth, localization of mutatedPfATP4, response to treatment with knownPfATP4 inhibitors, and evaluation of the downstream consequences of Na+influx. Our results were consistent with modeled predictions of the essentiality of the critical residues. Additionally, our approach confirmed the phenotypic consequences of resistance-associated mutations as well as a potential structural basis for the fitness cost associated with some mutations. Taken together, our approach provides a means to explore the structure/function relationship of essential genes in haploid organisms.Significance StatementPlasmodium falciparumATP4 (PfATP4) is a Na+efflux pump and represents an important target for antimalarial drugs with nanomolar potency. However, the structure ofPfATP4 is unknown, prompting the development of new methodologies to investigate the structure/function relationship. Here, we introduce a dynamic homology modeling approach to (a) identify key residues essential forPfATP4 function and (b) provide a structural basis to understand resistance-associated mutations. To validate these predictions, we developed a genetic system to manipulate the PfATP4 gene to assess the phenotypic consequences of such changes. Our results support the utility of combining homology modeling and genetics to gain functional insights into an antimalarial drug target.
Mutations iniclRincrease evolvability by facilitating compensation that exposes cryptic beneficial mutations in experimental populations ofEscherichia coli
Authors: Staples Rachel K , Cooper Tim F. 
Published: February 2024

AbstractEvolvability describes the potential of a population to generate beneficial variation. Several mechanisms that increase evolvability have been demonstrated, including the action of systems that reveal accumulated beneficial variants following an environmental shift. We examine the basis of an increase in the evolvability ofEscherichia colilines that were first selected in an environment supplemented with glucose as sole carbon source and then transferred to an otherwise identical lactose supplemented environment. These lines increased in fitness significantly more quickly in the lactose environment, and reached a higher final fitness, than did naïve ancestral lines. In four of six lines this increased evolvability can be explained by mutations iniclRthat were selected in glucose but were significantly deleterious in lactose, masking the effect of other generally beneficial mutations. Secondary mutations that compensated for this cost resulted in large fitness increases. We did not detect any consistent genetic signature associated with the compensation, suggesting that different pathways were responsible and, therefore, that it can occur at a relatively high rate. That mutations selected in one environment will become deleterious following an environmental shift, so that compensation provides potential for a large subsequent fitness increase represents a potentially common and general mechanism of evolvability in changing environments.
Development of novel tools for dissection of central versus peripheral dopamine D2-like receptor signaling in dysglycemia
Authors: Bonifazi Alessandro , Ellenberger Michael , Farino Zachary J. , Aslanoglou Despoina , Rais Rana , Pereira Sandra , Mantilla-Rivas José O. , Boateng Comfort A. , Eshleman Amy J. , Janowsky Aaron , Hahn Margaret K. , Schwartz Gary J. , Slusher Barbara S. , Newman Amy Hauck , Freyberg Zachary 
Published: February 2024

AbstractDopamine (DA) D2-like receptors in both the central nervous system (CNS) and the periphery are key modulators of metabolism. Moreover, disruption of D2-like receptor signaling is implicated in dysglycemia. Yet, the respective metabolic contributions of CNS versus peripheral D2-like receptors including D2(D2R) and D3(D3R) receptors remain poorly understood. To address this, we developed new pharmacological tools, D2-like receptor agonists with diminished and delayed blood-brain barrier capability, to selectively manipulate D2R/D3R signaling in the periphery. We designated bromocriptine methiodide (BrMeI), a quaternary methiodide analogue of D2/3R agonist and diabetes drug bromocriptine, as our lead compound based on preservation of D2R/D3R binding and functional efficacy. We then used BrMeI and unmodified bromocriptine to dissect relative contributions of CNS versus peripheral D2R/D3R signaling in treating dysglycemia. Systemic administration of bromocriptine, with unrestricted access to CNS and peripheral targets, significantly improved both insulin sensitivity and glucose tolerance in obese, dysglycemic micein vivo. In contrast, metabolic improvements were attenuated when access to bromocriptine was restricted either to the CNS through intracerebroventricular administration or delayed access to the CNS via BrMeI. Our findings demonstrate that the coordinated actions of both CNS and peripheral D2-like receptors are required for correcting dysglycemia. Ultimately, the development of a first-generation of drugs designed to selectively target the periphery provides a blueprint for dissecting mechanisms of central versus peripheral DA signaling and paves the way for novel strategies to treat dysglycemia.
A doubly stochastic renewal framework for partitioning spiking variability
Authors: Aghamohammadi Cina , Chandrasekaran Chandramouli , Engel Tatiana A. 
Published: February 2024

ABSTRACTThe firing rate is a prevalent concept used to describe neural computations, but estimating dynamically changing firing rates from irregular spikes is challenging. An inhomogeneous Poisson process, the standard model for partitioning firing rate and spiking irregularity, cannot account for diverse spike statistics observed across neurons. We introduce a doubly stochastic renewal point process, a flexible mathematical framework for partitioning spiking variability, which captures the broad spectrum of spiking irregularity from periodic to super-Poisson. We validate our partitioning framework using intracellular voltage recordings and develop a method for estimating spiking irregularity from data. We find that the spiking irregularity of cortical neurons decreases from sensory to association areas and is nearly constant for each neuron under many conditions but can also change across task epochs. A spiking network model shows that spiking irregularity depends on connectivity and can change with external input. These results help improve the precision of estimating firing rates on single trials and constrain mechanistic models of neural circuits.
A site-wise reliability analysis of the ABCD diffusion fractional anisotropy and cortical thickness: impact of scanner platforms
Authors: Pan Yezhi , Hong L. Elliot , Acheson Ashley , Thompson Paul M. , Jahanshad Neda , Zhu Alyssa H. , Yu Jiaao , Chen Chixiang , Ma Tianzhou , Liu Ho-Ling , Veraart Jelle , Fieremans Els , Karcher Nicole R. , Kochunov Peter , Chen Shuo 
Published: February 2024

AbstractThe Adolescent Brain and Cognitive Development (ABCD) project is the largest study of adolescent brain development. ABCD longitudinally tracks 11,868 participants aged 9-10 years from 21 sites using standardized protocols for multi-site MRI data collection and analysis. While the multi-site and multi-scanner study design enhances the robustness and generalizability of analysis results, it may also introduce non-biological variances including scanner-related variations, subject motion, and deviations from protocols. ABCD imaging data were collected biennially within a period of ongoing maturation in cortical thickness and integrity of cerebral white matter. These changes can bias the classical test-retest methodologies, such as intraclass correlation coefficients (ICC). We developed a site-wise adaptive ICC (AICC) to evaluate the reliability of imaging-derived phenotypes while accounting for ongoing brain development. AICC iteratively estimates the population-level age-related brain development trajectory using a weighted mixed model and updates age-corrected site-wise reliability until convergence. We evaluated the test-retest reliability of regional fractional anisotropy (FA) measures from diffusion tensor imaging and cortical thickness (CT) from structural MRI data for each site. The mean AICC for 20 FA tracts across sites was 0.61±0.19, lower than the mean AICC for CT in 34 regions across sites, 0.76±0.12. Remarkably, sites using Siemens scanners consistently showed significantly higher AICC values compared to those using GE/Philips scanners for both FA (AICC=0.71±0.12 vs 0.46±0.17, p<0.001) and CT (AICC=0.80±0.10 vs 0.69±0.11, p<0.001). These findings demonstrate site-and-scanner related variations in data quality and underscore the necessity for meticulous data curation in subsequent association analyses.
Metabolic Quadrivalency in RSeT Human Embryonic Stem Cells
Authors: Chen Kevin G. , Park Kyeyoon , Maric Dragan , Johnson Kory R. , Robey Pamela G. , Mallon Barbara S. 
Published: February 2024

ABSTRACTOne of the most important properties of human embryonic stem cells (hESCs) is related to their pluripotent states. In our recent study, we identified a previously unrecognized pluripotent state induced by RSeT medium. This state makes primed hESCs resistant to conversion to naïve pluripotent state. In this study, we have further characterized the metabolic features in these RSeT hESCs, including metabolic gene expression, metabolomic analysis, and various functional assays. The commonly reported metabolic modes include glycolysis or both glycolysis and oxidative phosphorylation (i.e., metabolic bivalency) in pluripotent stem cells. However, besides the presence of metabolic bivalency, RSeT hESCs exhibited a unique metabolome with additional fatty acid oxidation and imbalanced nucleotide metabolism. This metabolic quadrivalency is linked to hESC growth independent of oxygen tension and restricted capacity for naïve reprogramming in these cells. Thus, this study provides new insights into pluripotent state transitions and metabolic stress-associated hPSC growthin vitro.