bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Airway Epithelial Response to SARS-CoV-2 Infection in Children is Critically Tuned by the Cross-Talk Between Immune and Epithelial Cells
Authors: Magalhães Vladimir G. , Lukassen Sören , Drechsler Maike , Loske Jennifer , Burkart Sandy S. , Wüst Sandra , Jacobsen Eva-Maria , Röhmel Jobst , Mall Marcus A. , Debatin Klaus-Michael , Eils Roland , Autenrieth Stella , Janda Aleš , Lehmann Irina , Binder Marco 
Published: May 2023

AbstractTo cope with novel virus infections to which no prior adaptive immunity exists, the body strongly relies on the innate immune system. In such cases, including infections with SARS-CoV-2, children tend to fair better than adults. In the context of COVID-19, it became evident that a rapid interferon response at the site of primary infection is key for successful control of the virus and prevention of severe disease. The airway epithelium of children was shown to exhibit a primed state already at homeostasis and to respond particularly well to SARS-CoV-2 infection. However, the underlying mechanism for this priming remained elusive. Here we show that interactions between airway mucosal immune cells and epithelial cells are stronger in children, and via cytokine-mediated signaling lead to IRF-1-dependent upregulation of the viral sensors RIG-I and MDA5. Based on a cellularin vitromodel we show that stimulated human peripheral blood mononuclear cells (PBMC) can induce a robust interferon-beta response towards SARS-CoV-2 in a lung epithelial cell line otherwise unresponsive to this virus. This is mediated by type I interferon, interferon-gamma and TNF, and requires induction of both, RIG-I and MDA5. In single cell-analysis of nasal swab samples the same cytokines are found to be elevated in mucosal immune cells of children, correlating with elevated epithelial expression of viral sensors.In vitroanalysis of PBMC derived from healthy adolescents and adults confirm that immune cells of younger individuals show increased cytokine production and potential to prime epithelial cells. In co-culture with SARS-CoV-2-infected A549 cells, PBMC from adolescents significantly enhance the antiviral response. Taken together, our study suggests that higher numbers and a more vigorous activity of innate immune cells in the airway mucosa of children tune the set-point of the epithelial antiviral system. This likely is a major contributor to the robust immune response to SARS-CoV-2 in children. Our findings shed light on the molecular underpinnings of the stunning resilience of children towards severe COVID-19, and may propose a novel concept for immunoprophylactic treatments.
Carrion converging: Skull shape is predicted by feeding ecology in vultures
Authors: Steinfield Katherine R , Felice Ryan N , Kirchner Mackenzie E , Knapp Andrew 
Published: May 2023

AbstractThe link between skull shape and dietary ecology in birds at macroevolutionary scales has recently been called into question by analyses of 3D shape that reveal that cranial anatomy is mainly influenced by other factors such as allometry. It is still unknown whether this form-function disconnect also exists at smaller evolutionary scales, for example within specialized ecological guilds. Vultures are a diverse guild of 23 extant species in two families (Accipitridae and Cathartidae) that exhibit phenotypic convergence as a result of highly-specialized feeding ecology. Vultures are the only known obligate scavengers among vertebrates and are usually grouped together under this single dietary category, but within this specialized diet there are three distinct, species-specific feeding strategies termed ripper, gulper, and scrapper. We use three-dimensional geometric morphometrics to quantify the relative contributions of feeding ecology, allometry, and phylogeny on vulture skull shape, along with several non-vulture raptors of similar size, range and ecology. Families show clear separation in shape, but phylogenetic signal is comparatively weak (Kmult= 0.33). Taking into account the influence of phylogeny, skull shape is not significantly correlated with either skull size or feeding type, but there are examples of strong, significant convergence and parallel shape evolution across feeding groups. Furthermore, skull shape performs strongly in predicting feeding ecology in a phylogenetic discriminant function analysis. These findings highlight the importance of detailed assessment of feeding behavior in studies of ecomorphology, rather than broader dietary categories alone, and reveal that ecology can be readily inferred from form given appropriate information.
Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2
Authors: Li Huanyu Z. , Pike Ashley C.W. , Chi Gamma , Hansen Jesper S. , Lee Sarah G. , Rödström Karin E.J. , Bushell Simon R. , Speedman David , Evans Adam , Wang Dong , He Didi , Shrestha Leela , Nasrallah Chady , Burgess-Brown Nicola A. , Dafforn Timothy R. , Carpenter Elisabeth P. , Sauer David B. 
Published: May 2023

AbstractProline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes which link substrate release and opening of the cytoplasmic gate, and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.
Cytomegalovirus-induced inactivation of TSC2 disrupts the coupling of fatty acid biosynthesis to glucose availability resulting in a vulnerability to glucose limitation
Authors: Raymonda Matthew H. , Rodríguez-Sánchez Irene , Schafer Xenia L. , Smorodintsev-Schiller Leonid , Harris Isaac S. , Munger Joshua 
Published: May 2023

AbstractHuman cytomegalovirus (HCMV) modulates cellular metabolism to support productive infection, and the HCMV UL38 protein drives many aspects of this HCMV-induced metabolic program. However, it remains to be determined whether virally-induced metabolic alterations might induce novel therapeutic vulnerabilities in virally infected cells. Here, we explore how HCMV infection and the UL38 protein modulate cellular metabolism and how these changes alter the response to nutrient limitation. We find that expression of UL38, either in the context of HCMV infection or in isolation, sensitizes cells to glucose limitation resulting in cell death. This sensitivity is mediated through UL38’s inactivation of the TSC complex subunit 2 (TSC2) protein, a central metabolic regulator that possesses tumor-suppressive properties. Further, expression of UL38 or the inactivation of TSC2 results in anabolic rigidity in that the resulting increased levels of fatty acid biosynthesis are insensitive to glucose limitation. This failure to regulate fatty acid biosynthesis in response to glucose availability sensitizes cells to glucose limitation, resulting in cell death unless fatty acid biosynthesis is inhibited. These experiments identify a regulatory circuit between glycolysis and fatty acid biosynthesis that is critical for cell survival upon glucose limitation and highlight a metabolic vulnerability associated with viral infection and the inactivation of normal metabolic regulatory controls.ImportanceViruses modulate host cell metabolism to support the mass production of viral progeny. For Human Cytomegalovirus, we find that the viral UL38 protein is critical for driving these pro-viral metabolic changes. However, our results indicate that these changes come at a cost, as UL38 induces an anabolic rigidity that leads to a metabolic vulnerability. We find that UL38 decouples the link between glucose availability and fatty acid biosynthetic activity. Normal cells respond to glucose limitation by down-regulating fatty acid biosynthesis. Expression of UL38 results in the inability to modulate fatty acid biosynthesis in response to glucose limitation, which results in cell death. We find this vulnerability in the context of viral infection, but this linkage between fatty acid biosynthesis, glucose availability, and cell death could have broader implications in other contexts or pathologies that rely on glycolytic remodeling, for example, oncogenesis.
A Novel Pan-RAS Inhibitor with a Unique Mechanism of Action Blocks Tumor Growth in Mouse Models of GI Cancer
Authors: Foote Jeremy B. , Mattox Tyler E. , Keeton Adam B. , Chen Xi , Smith Forrest , Berry Kristy L. , Holmes Thomas , Wang Junwei , Huang Chung-Hui , Ward Antonio B. , Mitra Amit K. , Ramirez-Alcantara Veronica , Hardy Cherlene , Fleten Karrianne G. , Flatmark Kjersti , Yoon Karina J. , Sarvesh Sujith , Nagaraju Ganji Purnachandra , Bandi Dhana Sekhar Reddy , Maxuitenko Yulia Y. , Valiyaveettil Jacob , Carstens Julienne L. , Buchsbaum Donald J. , Yang Jennifer , Zhou Gang , Nurmemmedov Elmar , Babic Ivan , Gaponenko Vadim , Abdelkarim Hazem , Boyd Michael R. , Gorman Gregory S. , Manne Upender , Bae Sejong , El-Rayes Bassel F. , Piazza Gary A. 
Published: May 2023

ABSTRACTHere, we describe a novel pan-RAS inhibitor, ADT-007, that potently inhibited the growth of RAS mutant cancer cells irrespective of the RAS mutation or isozyme. RASWTcancer cells with GTP-activated RAS from upstream mutations were equally sensitive. Conversely, RASWTcancer cells harboring downstream BRAF mutations and normal cells were essentially insensitive to ADT-007. Sensitivity of cancer cells to ADT-007 required activated RAS and dependence on RAS for proliferation, while insensitivity was attributed to metabolic deactivation by UDP-glucuronosyltransferases expressed in RASWTand normal cells but repressed in RAS mutant cancer cells. ADT-007 binds nucleotide-free RAS to block GTP activation of effector interactions and MAPK/AKT signaling, resulting in mitotic arrest and apoptosis. ADT-007 displayed unique advantages over mutant-specific KRAS and pan-KRAS inhibitors, as well as other pan-RAS inhibitors that could impactin vivoantitumor efficacy by escaping compensatory mechanisms leading to resistance. Local administration of ADT-007 showed robust antitumor activity in syngeneic immune-competent and xenogeneic immune-deficient mouse models of colorectal and pancreatic cancer. The antitumor activity of ADT-007 was associated with the suppression of MAPK signaling and activation of innate and adaptive immunity in the tumor immune microenvironment. Oral administration of ADT-007 prodrug also inhibited tumor growth, supporting further development of this novel class of pan-RAS inhibitors for RAS-driven cancers.SIGNIFICANCEADT-007 has unique pharmacological properties with distinct advantages over other RAS inhibitors by circumventing resistance and activating antitumor immunity. ADT-007 prodrugs and analogs with oral bioavailability warrant further development for RAS-driven cancers.
Studying stochastic systems biology of the cell with single-cell genomics data
Authors: Gorin Gennady , Vastola John J. , Pachter Lior 
Published: May 2023

ABSTRACTRecent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
Abcg2a is the functional homolog of human ABCG2 expressed at the zebrafish blood-brain barrier
Authors: Thomas Joanna R. , Frye William J. E. , Robey Robert W. , Warner Andrew C. , Butcher Donna , Matta Jennifer L. , Morgan Tamara C. , Edmondson Elijah F. , Salazar Paula B. , Ambudkar Suresh V. , Gottesman Michael M. 
Published: May 2023

AbstractBackgroundA principal protective component of the mammalian blood-brain barrier (BBB) is the high expression of the multidrug efflux transporters P-glycoprotein (P-gp, encoded byABCB1) and ABCG2 (encoded byABCG2) on the lumenal surface of endothelial cells. The zebrafish P-gp homolog Abcb4 is expressed at the BBB and phenocopies human P-gp. Comparatively little is known about the four zebrafish homologs of the humanABCG2gene:abcg2a,abcg2b,abcg2c, andabcg2d. Here we report the functional characterization and brain tissue distribution of zebrafish ABCG2 homologs.MethodsTo determine substrates of the transporters, we stably expressed each in HEK-293 cells and performed cytotoxicity and fluorescent efflux assays with known ABCG2 substrates. To assess the expression of transporter homologs, we used a combination of RNAscopein situhybridization probes and immunohistochemistry to stain paraffin-embedded sections of adult and larval zebrafish.ResultsWe found Abcg2a had the greatest substrate overlap with ABCG2, and Abcg2d appeared to be the least functionally similar. We identifiedabcg2aas the only homolog expressed at the adult and larval zebrafish BBB, based on its localization to claudin-5 positive brain vasculature.ConclusionsThese results demonstrate the conserved function of zebrafish Abcg2a and suggest that zebrafish may be an appropriate model organism for the studying the role of ABCG2 at the BBB.
Human Herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: Network analysis Identifies Interacting Pathways
Authors: Webber Chelsea J , Murphy Caroline N. , Rondón-Ortiz Alejandro N. , van der Spek Sophie J.F. , Kelly Elena X. , Lampl Noah M. , Chiesa Giulio , Khalil Ahmad S. , Emili Andrew , Wolozin Benjamin 
Published: May 2023

AbstractAggregation of TAR DNA-binding protein 43kDa (TDP-43) is thought to drive the pathophysiology of ALS and some Frontotemporal dementias. TDP-43 is normally a nuclear protein that in neurons translocates to the cytoplasm and forms insoluble aggregates upon activation of the integrated stress response (ISR). Viruses evolved to control the ISR. In the case of Herpesvirus 8, the protein ORF57 acts to bind protein kinase R, inhibit phosphorylation of eIF2α and reduce activation of the ISR. We hypothesized that ORF57 might also possess the ability to inhibit aggregation of TDP-43. ORF57 was expressed in the neuronal SH-SY5Y line and its effects on TDP-43 aggregation characterized. We report that ORF57 inhibits TDP-43 aggregation by 55% and elicits a 2.45-fold increase in the rate of dispersion of existing TDP-43 granules. These changes were associated with a 50% decrease in cell death. Proteomic studies were carried out to identify the protein interaction network of ORF57. We observed that ORF57 directly binds to TDP-43 as well as interacts with many components of the ISR, including elements of the proteostasis machinery known to reduce TDP-43 aggregation. We propose that viral proteins designed to inhibit a chronic ISR can be engineered to remove aggregated proteins and dampen a chronic ISR.
Sequencing, fast and slow: profiling microbiomes in human samples with nanopore sequencing
Authors: Park Yunseol , Lee Jeesu , Shim Hyunjin 
Published: May 2023

AbstractRapid and accurate pathogen identification is crucial in effectively combating infectious diseases. However, the current diagnostic tools for bacterial infections predominantly rely on century-old culture-based methods. Furthermore, recent research highlights the significance of host-microbe interactions within the host microbiota in influencing the outcome of infection episodes. As our understanding of science and medicine continues to advance, there is a pressing need for innovative diagnostic methods that can identify pathogens and also rapidly and accurately profile the microbiome landscape in human samples. In clinical settings, such diagnostic tools will become a powerful predictive instrument in directing the diagnosis and prognosis of infectious diseases by providing comprehensive insights into the patient’s microbiota. Here, we explore the potential of long-read sequencing in profiling the microbiome landscape from various human samples in terms of speed and accuracy. Using nanopore sequencers, we generate native DNA sequences from saliva and stool samples rapidly, from which each long-read is basecalled in real-time to provide downstream analyses such as taxonomic classification and antimicrobial resistance through the built-in software (< 12 hours). Subsequently, we utilize the nanopore sequence data for in-depth analysis of each microbial species in terms of host-microbe interaction types and deep learning-based classification of unidentified reads. We find that the nanopore sequence data encompass complex information regarding the microbiome composition of the host and its microbial communities, and also shed light on the unexplored human mobilome including bacteriophages. In this study, we use two different systems of long-read sequencing to give insights into human microbiome samples in the ‘slow’ and ‘fast’ modes, which raises additional inquiries regarding the precision of this novel technology and the feasibility of extracting native DNA sequences from other human microbiomes.
Activating M1 muscarinic cholinergic receptors induces destabilization of resistant contextual fear memories in rats
Authors: Abouelnaga Karim H. , Huff Andrew E. , Messer William S. , Winters Boyer D. 
Published: May 2023

AbstractDestabilization of previously consolidated memories places them in a labile state in which they are open to modification. However, strongly encoded fear memories tend to be destabilization-resistant and the conditions required to destabilize such memories remain poorly understood. Our lab has previously shown that exposure to salient novel contextual cues during memory reactivation can destabilize strongly encoded object location memories and that activity at muscarinic cholinergic receptors is critical for this effect. In the current study, we similarly targeted destabilization-resistant fear memories, hypothesizing that exposure to salient novelty at the time of reactivation would induce destabilization of strongly encoded fear memories in a muscarinic receptor-dependent manner. First, we show that contextual fear memories induced by 3 context-shock pairings readily destabilize upon memory reactivation, and that this destabilization is blocked by systemic (ip) administration of the muscarinic receptor antagonist scopolamine (0.3mg/kg) in male rats. Next, we demonstrate that more strongly encoded fear memories (induced with 5 context-shock pairings) resist destabilization. Consistent with our previous work, however, we report that salient novelty (a change in floor texture) presented during the reactivation session promotes destabilization of resistant contextual fear memories in a muscarinic receptor-dependent manner. Finally, the effect of salient novelty on memory destabilization was mimicked by stimulating muscarinic receptors with the selective M1 agonist CDD-0102A (ip, 0.3mg/kg). These findings reveal further generalizability of our previous results implicating novel cues and M1 muscarinic signaling in promoting destabilization of resistant memories and suggest possible therapeutic options for disorders characterized by persistent, maladaptive fear memories such as PTSD and phobias.
Dynamic nuclear polarization illuminates key protein-lipid interactions in the native bacterial cell envelope
Authors: Kent James E. , Ackermann Bryce E. , Debelouchina Galia T. , Marassi Francesca M. 
Published: May 2023

ABSTRACTElucidating the structure and interactions of proteins in native environments has become a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway ofYersinia pestis. We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.
Music Affects State Anxiety and Brain Connectivity
Authors: Pedersen Mangor , Shepherd Daniel , Vashista Geet , Kercher Amy , Hautus Michael. J. 
Published: May 2023

AbstractStress, anxiety, and depressive symptoms can be reduced by listening to music, but the underlying mechanisms remain unclear. To address this gap, we measured brain connectivity while participants listened to songs of different genres: ambient, pop, and metal. Additionally, affective ratings were obtained while participants (n= 30) listened to the six different songs, and subjective ratings of state anxiety were solicited at the terminus of each song. Electroencephalography (EEG) connectivity combining weighted Phase Lag Index and graph theory was utilised to document brain activity during listening. Repeated-measures ANOVA indicated that listening to more pleasant and less arousing songs was associated with lower self-reported state anxiety levels than songs rated unpleasant and highly arousing. Of interest, EEG alpha connectivity differed across two ambient songs, particularly in the frontal lobes, despite being from the same genre and rated as highly pleasant and low in arousal. We also observed a sex effect on EEG results, where female participants (n= 18) displayed stronger connectivity than male participants (n= 12). Combined, these results suggest that ambient songs reduce state anxiety but have divergent brain responses, possibly reflecting the complex nature of music listening, including sensory processing, emotion and cognition.