bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cone-driven, geniculo-cortical responses in canine models of outer retinal disease
Authors: Taskin Huseyin O. , Wivel Jacqueline , Aguirre Gustavo D. , Beltran William A. , Aguirre Geoffrey K. 
Published: December 2023

AbstractPurposeCanine models of inherited retinal degeneration are used for proof-of-concept of emerging gene and cell-based therapies that aim to produce functional restoration of cone-mediated vision. We examined functional MRI measures of the post-retinal response to cone-directed stimulation in wild type (WT) dogs, and in three different retinal disease models.MethodsTemporal spectral modulation of a uniform field of light around a photopic background was used to target the canine L/M (hereafter “L”) and S cones and rods. Stimuli were designed to separately target the post-receptoral luminance (L+S) and chrominance (L–S) pathways, the rods, and all photoreceptors jointly (light flux). These stimuli were presented to WT, and mutantPDE6B-RCD1,RPGR-XLPRA2, andNPHP5-CRD2 dogs during pupillometry and fMRI.ResultsPupil responses in WT dogs to light flux, L+S, and rod-directed stimuli were consistent with responses being driven by cone signals alone. For WT animals, both luminance and chromatic (L–S) stimuli evoked fMRI responses in the lateral geniculate nucleus (LGN) or visual cortex; RCD1 animals with predominant rod loss had similar responses. Responses to cone-directed stimulation were reduced in XLPRA2 and absent in CRD2. NPHP5 gene augmentation restored the cortical response to luminance stimulation in a CRD2 animal.ConclusionsCone-directed stimulation during fMRI can be used to measure the integrity of luminance and chrominance responses in the dog visual system. TheNPHP5-CRD2 model is appealing for studies of recovered cone function.Translational RelevancefMRI assessment of cone driven cortical response provides a tool to translate cell/gene therapies for vision restoration.
A complex regulatory network governs the production of an antibiotic with unusual cell-density-dependence
Authors: Hindra  , Elliot Marie A. 
Published: December 2023

ABSTRACTStreptomycesbacteria are renowned both for their antibiotic production capabilities, and for their cryptic metabolic potential. Here, we leveraged the activity of an Lsr2 knockdown construct to enhance antibiotic production in the wildStreptomycesisolate WAC07094. We determined the new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media. This density-dependent control was exerted at the level of the cluster-situated regulatory genesqnRand was mediated in part through the activity of the PhoRP two component regulatory system; deletingphoRPled to both constitutive antibiotic production andsqnRexpression, suggesting that PhoP functions to repress the expression ofsqnRat high cell density. We further discovered that magnesium supplementation could also alleviate this cell density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. This unusual density-dependent production of saquayamycin was not unique to WAC07094; we found that saquayamycin production by another wild isolate was also density-dependent, suggesting this spatial control may serve an important ecological function in their native environments.IMPORTANCEStreptomycesspecialized metabolic gene clusters are subject to complex regulation, and their products are frequently not observed under standard laboratory growth conditions. For the wildStreptomycesisolate WAC07094, production of the angucycline-family compound saquayamycin is subject to a unique constellation of control factors. Notably, it is produced primarily at low cell density, in contrast to the high cell density production typical of most antibiotics. This unusual density dependence is conserved in other saquayamycin producers and is driven by the pathway-specific regulator SqnR, whose expression is influenced by both nutritional and genetic elements. Collectively, this work provides new insights into an intricate regulatory system governing antibiotic production and indicates there may be benefits to including low density cultures in antibiotic screening platforms.
In SilicoCharacterization of Intracellular Localization Signals and Structural Features of Mosquito Densovirus (MDV) Viral Proteins
Authors: Barik Tapan K , Swain Surya N , Sahu Sushil Kumar , Acharya Usha R , Metz Hillery C. , Rasgon Jason L 
Published: December 2023

AbstractAs entomopathogenic viruses, mosquito densoviruses (MDVs) are widely studied for their potential as biocontrol agents and molecular laboratory tools for mosquito manipulation. The nucleus of the mosquito cell is the site for MDV genome replication and capsid assembly, however the nuclear localization signals (NLSs) and nuclear export signals (NES) for MDV proteins have not yet been identified. We carried out anin silicoanalysis to identify putative NLSs and NESs in the viral proteins of densoviruses that infect diverse mosquito genera (Aedes, Anopheles, andCulex) and identified putative phosphorylation and glycosylation sites on these proteins. These analyses lead to a more comprehensive understanding of how MDVs are transported into and out of the nucleus and lay the foundation for the potential use of densoviruses in mosquito control and basic research.Data summaryData used in this article were obtained from the GenBank database using accession numbers AYH52680, AYH52678, AYH52679, ABX83665, ABX83663, ABX83664, ABU95013, ABU95011, ABU95012, and AXQ04861.Impact statementMosquito densoviruses (MDVs) are of interest as mosquito biocontrol agents and as laboratory research tools. The trafficking of viral proteins to the cell nucleus is a critical step in viral replication. We usedin silicoapproaches to identify putative nuclear localization signals and nuclear export signals for MDVs that infect the three major genera of pathogen-transmitting mosquitoes (Aedes, Anopheles, andCulex). These analyses lead a more comprehensive understanding of how MDVs are transported into and out of the nucleus and lay the foundation for the potential use of densoviruses in mosquito control and basic research.
Natural reversal of cavefish heart asymmetry is controlled by Sonic Hedgehog effects on the left-right organizer
Authors: Ng Mandy , Ma Li , Shi Janet , Jeffery William R. 
Published: December 2023

AbstractThe direction of left-right (L-R) visceral asymmetry is conserved in vertebrates. Deviations of the asymmetric pattern are rare, and the underlying mechanisms are not understood. Here we use the teleostAstyanax mexicanus, a single species consisting of surface fish with normal left-oriented heart asymmetry and cavefish with high levels of reversed right-oriented heart asymmetry, to explore natural changes in L-R determination. We show that Sonic Hedgehog (Shh) signaling is increased at the posterior midline, Kupffers Vesicle (KV), the teleost L-R Organizer (LRO), is enlarged and contains longer cilia, and the number of dorsal forerunner cells, the KV precursors, is increased in cavefish. Furthermore, Shh overexpression in surface fish induces KV modifications and changes in heart asymmetry resembling the cavefish phenotype. Asymmetric expression of the Nodal antagonistdand5is equalized or reversed in the cavefish KV, and Shh overexpression in surface fish mimics changes in cavefish L-Rdand5asymmetry and shifts Nodal laterality in the lateral plate mesoderm. Our results show that naturally occurring modifications in cavefish heart asymmetry are controlled by the effects of enhanced Shh signaling on LRO function.SummaryNatural reversal of cavefish heart asymmetry is controlled by enhanced Sonic Hedgehog signaling at the posterior midline, which modifies left-right organizer function and subsequent Nodal laterality.
Arabidopsis actin-binding protein WLIM2A links PAMP-triggered immunity and cytoskeletal organization
Authors: Manickam Prabhu , Abulfaraj Aala A , Alhoraibi Hanna M , Veluchamy Alaguraj , Almeida-Trapp Marilia , Hirt Heribert , Rayapuram Naganand 
Published: December 2023

AbstractMAPKs are a family of highly conserved serine/threonine protein kinases that link upstream receptors to their downstream targets which can be localized in the cytoplasm or the nucleus. Pathogens produce pathogen-associated molecular patterns (PAMPs) that trigger the activation of MAPK cascades in plants. Phosphoproteomic analysis of PAMP-inducedArabidopsisplants led to the identification of several putative MAPK targets, WLIM2A. Here, we investigated the role of WLIM2A in plant immunity via a reverse-genetics approach generatingwlim2aknockout lines using CRISPR-Cas9, as well as complementation and phosphosite mutatedWLIM2Aexpression lines in thewlim2abackground. Thewlim2alines were compromised in their response toPstDC3000 but showed enhanced resistance to fungal infection byBotrytis cinereae. Transcriptome analyses revealed that immune hormone signaling and biosynthesis genes of salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) are differentially regulated in thewlim2aknockout lines. Pathogen assays withPst DC3000showed altered stomatal phenotypes inwlim2amutants. Importantly,WLIM2Aphosphomutants had opposing stomatal behaviour and resistance phenotypes in response toPstDC3000 infection. Overall, these data show that phosphorylation of WLIM2A by MAPKs regulatesArabidopsisstomatal immunity.
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma
Authors: Benitz Simone , Steep Alec , Nasser Malak , Preall Jonathan , Mahajan Ujjwal M. , McQuithey Holly , Loveless Ian , Davis Erick T. , Wen Hui-Ju , Long Daniel W. , Metzler Thomas , Zwernik Samuel , Louw Michaela , Rempinski Donald , Salas-Escabillas Daniel , Brender Sydney , Song Linghao , Huang Ling , Zhang Zhenyu , Steele Nina G. , Regel Ivonne , Bednar Filip , Crawford Howard C. 
Published: December 2023

AbstractCellular plasticity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) starting from the conversion of normal cells into precancerous lesions to the progression of carcinoma subtypes associated with aggressiveness and therapeutic response. We discovered that normal acinar cell differentiation, maintained by the transcription factor Pdx1, suppresses a broad gastric cell identity that is maintained in metaplasia, neoplasia, and the classical subtype of PDAC in mouse and human. We have identified the receptor tyrosine kinase Ror2 as marker of a gastric metaplasia (SPEM)-like identity in the pancreas. Ablation ofRor2in a mouse model of pancreatic tumorigenesis promoted a switch to a gastric pit cell identity that largely persisted through progression to the classical subtype of PDAC. In both human and mouse pancreatic cancer, ROR2 activity continued to antagonize the gastric pit cell identity, strongly promoting an epithelial to mesenchymal transition, conferring resistance to KRAS inhibition, and vulnerability to AKT inhibition.SignificanceWe discovered the receptor tyrosine kinase ROR2 as an important regulator of cellular identity in pancreatic precancerous lesions and pancreatic cancer. ROR2 drives an aggressive PDAC phenotype and confers resistance to Kras inhibitors, suggesting that targeting ROR2 will enhance sensitivity to this new generation of targeted therapies.
Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer’s disease
Authors: Moon Hae Sol , Mahzarnia Ali , Stout Jacques , Anderson Robert J , Badea Cristian T. , Badea Alexandra 
Published: December 2023

ABSTRACTAlzheimer’s disease (AD) remains one of the most extensively researched neurodegenerative disorders due to its widespread prevalence and complex risk factors. Age is a crucial risk factor for AD, which can be estimated by the disparity between physiological age and estimated brain age. To model AD risk more effectively, integrating biological, genetic, and cognitive markers is essential. Here, we utilized mouse models expressing the major APOE human alleles and human nitric oxide synthase 2 to replicate genetic risk for AD and a humanized innate immune response. We estimated brain age employing a multivariate dataset that includes brain connectomes, APOE genotype, subject traits such as age and sex, and behavioral data. Our methodology used Feature Attention Graph Neural Networks (FAGNN) for integrating different data types. Behavioral data were processed with a 2D Convolutional Neural Network (CNN), subject traits with a 1D CNN, brain connectomes through a Graph Neural Network using quadrant attention module. The model yielded a mean absolute error for age prediction of 31.85 days, with a root mean squared error of 41.84 days, outperforming other, reduced models. In addition, FAGNN identified key brain connections involved in the aging process. The highest weights were assigned to the connections between cingulum and corpus callosum, striatum, hippocampus, thalamus, hypothalamus, cerebellum, and piriform cortex. Our study demonstrates the feasibility of predicting brain age in models of aging and genetic risk for AD. To verify the validity of our findings, we compared Fractional Anisotropy (FA) along the tracts of regions with the highest connectivity, the Return-to-Origin Probability (RTOP), Return-to-Plane Probability (RTPP), and Return-to-Axis Probability (RTAP), which showed significant differences between young, middle-aged, and old age groups. Younger mice exhibited higher FA, RTOP, RTAP, and RTPP compared to older groups in the selected connections, suggesting that degradation of white matter tracts plays a critical role in aging and for FAGNN’s selections. Our analysis suggests a potential neuroprotective role of APOE2, relative to APOE3 and APOE4, where APOE2 appears to mitigate age-related changes. Our findings highlighted a complex interplay of genetics and brain aging in the context of AD risk modeling.
Bacteriophage cocktail shows no toxicity and improves the survival ofGalleria mellonellainfected withKlebsiellaspp.
Authors: Kelly Lucy , Jameson Eleanor 
Published: December 2023

AbstractKlebsiellaspp. are causative agents of healthcare associated infections in patients who are immunocompromised and use medical devices. The antibiotic resistance crisis has led to an increase in infections caused by these bacteria, which can develop into potentially life-threatening illness if not treated swiftly and effectively. Thus, new treatment options forKlebsiellaare urgently required. Phage therapy can offer an alternative to ineffective antibiotic treatments for antibiotic-resistant bacteria infections. The aim of the present study was to produce a safe and effective phage cocktail treatment againstK. pneumoniaeandK. oxytoca, both in liquidin vitroculture and anin vivo Galleria mellonellainfection model. The phage cocktail was significantly more effective at killingK. pneumoniaeandK. oxytocastrains compared with monophage treatments. Preliminary phage cocktail safety was demonstrated through application in thein vivo G. mellonellamodel: where the phage cocktail induced no toxic side effects inG. mellonella. In addition, the phage cocktail significantly improved the survival ofG. mellonellawhen administered as a prophylactic treatment, compared with controls. In conclusion, our phage cocktail was demonstrated to be safe and effective againstKlebsiellaspp. in theG. mellonellainfection model. This provides a strong case for future treatment forKlebsiellainfections, either as an alternative, or adjunct to, antibiotics.
Integrin Mechanosensing relies on Pivot-clip Mechanism to Reinforce Cell Adhesion
Authors: Montes Andre R. , Barroso Anahi , Wang Wei , O’Connell Grace D. , Tepole Adrian B. , Mofrad Mohammad R.K. 
Published: December 2023

ABSTRACTCells intricately sense mechanical forces from their surroundings, driving biophysical and biochemical activities. This mechanosensing phenomenon occurs at the cell-matrix interface, where mechanical forces resulting from cellular motion, such as migration or matrix stretching, are exchanged through surface receptors, primarily integrins, and their corresponding matrix ligands. A pivotal player in this interaction is theα5β1integrin and fibronectin (FN) bond, known for its role in establishing cell adhesion sites for migration. However, upregulation of theα5β1-FN bond is associated with uncontrolled cell metastasis. This bond operates through catch bond dynamics, wherein the bond lifetime paradoxically increases with greater force. The mechanism sustaining the characteristic catch bond dynamics ofα5β1-FN remains unclear. Leveraging molecular dynamics simulations, our approach unveils a pivot-clip mechanism. Two key binding sites on FN, namely the synergy site and the RGD (arg-gly-asp) motif, act as active points for structural changes inα5β1integrin. Conformational adaptations at these sites are induced by a series of hydrogen bond formations and breaks at the synergy site. We disrupt these adaptations through a double mutation on FN, known to reduce cell adhesion. A whole-cell finite element model is employed to elucidate how the synergy site may promote dynamicα5β1-FN binding, resisting cell contraction. In summary, our study integrates molecular and cellular-level modeling to propose that FN’s synergy site reinforces cell adhesion through enhanced binding dynamics and a mechanosensitive pivot-clip mechanism. This work sheds light on the interplay between mechanical forces and cell-matrix interactions, contributing to our understanding of cellular behaviors in physiological and pathological contexts.SIGNIFICANCEα5β1integrin serves as a mediator of cell-matrix adhesion and has garnered attention as a target for impeding cancer metastasis. Despite its importance, the mechanism underlying the formation of a catch bond betweenα5β1integrin and its primary ligand, fibronectin, has remained elusive. Our study aims to address this gap by proposing a pivot-clip mechanism. This mechanism elucidates howα5β1integrin and fibronectin collaboratively reinforce cell adhesion through conformational changes induced by the dynamic interaction of a key binding motif known as the synergy site.
Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors
Authors: Johnston Adrian C. , Alicea Gretchen M. , Lee Cameron C. , Patel Payal V. , Hanna Eban A. , Vaz Eduarda , Forjaz André , Wan Zeqi , Nair Praful R. , Lim Yeongseo , Chen Tina , Du Wenxuan , Kim Dongjoo , Nichakawade Tushar D. , Rebecca Vito W. , Bonifant Challice L. , Fan Rong , Kiemen Ashley L. , Wu Pei-Hsun , Wirtz Denis 
Published: December 2023

ABSTRACTChimeric antigen receptor (CAR) T cells express antigen-specific synthetic receptors, which upon binding to cancer cells, elicit T cell anti-tumor responses. CAR T cell therapy has enjoyed success in the clinic for hematological cancer indications, giving rise to decade-long remissions in some cases. However, CAR T therapy for patients with solid tumors has not seen similar success. Solid tumors constitute 90% of adult human cancers, representing an enormous unmet clinical need. Current approaches do not solve the central problem of limited ability of therapeutic cells to migrate through the stromal matrix. We discover that T cells at low and high density display low- and high-migration phenotypes, respectively. The highly migratory phenotype is mediated by a paracrine pathway from a group of self-produced cytokines that include IL5, TNFα, IFNγ, and IL8. We exploit this finding to “lock-in” a highly migratory phenotype by developing and expressing receptors, which we call velocity receptors (VRs). VRs target these cytokines and signal through these cytokines’ cognate receptors to increase T cell motility and infiltrate lung, ovarian, and pancreatic tumors in large numbers and at doses for which control CAR T cells remain confined to the tumor periphery. In contrast to CAR therapy alone, VR-CAR T cells significantly attenuate tumor growth and extend overall survival. This work suggests that approaches to the design of immune cell receptors that focus on migration signaling will help current and future CAR cellular therapies to infiltrate deep into solid tumors.
Towards Ecological Measurement of Complex Cognitive Processes: Functional-Near Infrared Spectroscopy of Brain Activity During Reading
Authors: Čeko Marta , Hirshfield Leanne , Doherty Emily , Southwell Rosy , D’Mello Sidney 
Published: December 2023

AbstractFunctional magnetic resonance imaging (fMRI) has provided unparalleled insights into the fundamental neural mechanisms governing human cognition, including complex processes such as reading. Here, we leverage the wealth of prior fMRI work to capture reading outside the MRI scanner using functional near infra-red spectroscopy (fNIRS). In a large sample of participants (n = 82) we observe significant prefrontal and temporal fNIRS activations during reading, which are largely reliable across participants, therefore providing a robust validation of prior fMRI work on reading-related language processing. These results lay the groundwork towards developing adaptive systems capable of assisting these higher-level processes, for example to support readers and language learners. This work also contributes to bridging the gap between laboratory findings and real-world applications in the realm of cognitive neuroscience.
Systemic Sclerosis dermal fibroblast exosomes trigger a Type 1 interferon response in keratinocytes through the TBK/JAK/STAT signalling axis
Authors: Bryon Jessica , Wasson Christopher W , Koeppen Katja , Chandler Francesca , Willis Leon F , Klein Elliott , Zeqiraj Elton , Ross Rebecca L , Del Galdo Francesco 
Published: December 2023

AbstractBackgroundActivation of Type I IFN response has been shown to correlates with disease activity in systemic sclerosis. It is currently unknown whether the tissue-specific Type I IFN activation is a consequence of the response observed in blood or rather its source. Exosomes from SSc fibroblasts were recently shown to activate macrophagesin vitro. Here, we aimed to determine the source of Type I IFN signature in SSc skin biopsies and the potential role of exosomes from SSc dermal fibroblasts in the process.MethodsSkin biopsies were obtained from healthy and SSc patients’ forearms and processed for dermal fibroblasts and keratinocytes. Exosomes were isolated from healthy and SSc dermal fibroblast supernatants by ultracentrifugation and added to human skin keratinocytes. Keratinocyte transcriptome was analysed by RNA-seq analysis. TANK-binding kinase (TBK) and JAK were inhibited using a small molecule inhibitor (GSK8612) and Tofacitinib, respectively.ResultsSSc skin biopsies showed highest levels of Type I IFN response in the epidermal layer. RNA-seq analysis of keratinocytes transcriptome following exposure to dermal fibroblast exosomes showed strong upregulation of IFN signature genes induced by SSc exosomes compared to Healthy control. Inhibition of TBK or JAK activity suppressed the upregulation of the IFN signature induced by SSc exosomes.ConclusionIFN activation of SSc keratinocytes is dependent on their crosstalk with dermal fibroblasts and inducible by extracellular exosomes. Our data indicates that SSc fibroblasts exosomes may carry the ‘‘signal zero’’ of local Type I IFN activation through activation of pattern recognition receptors upstream of TBK.Key MessagesSSc patient skin exhibit a type 1 IFN signature with keratinocytes being the major source of the signatureCross talk between the fibroblasts and keratinocytes through exosomes may be signal zero for the type 1 IFN signatureBlocking JAK in the keratinocytes with Tofacitinib disrupts the type 1 IFN signature