bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potent GST ketosteroid isomerase activity relevant to ecdysteroidogenesis in the malaria vectorAnopheles gambiae
Authors: Musdal Yaman , Ismail Aram , Sjödin Birgitta , Mannervik Bengt 
Published: March 2023

AbstractNobo is a glutathione transferase (GST) crucially contributing to ecdysteroid biosynthesis in insects of the ordersDipteraandLepidoptera. Ecdysone is a vital steroid hormone in insects, which governs larval molting and metamorphosis, and suppression of its synthesis has potential as a novel approach to insect growth regulation and combatting vectors of disease. In general, GSTs catalyze detoxication, whereas the specific function of Nobo in ecdysteroidogenesis is unknown. We report that Nobo from the malaria-spreading mosquitoAnopheles gambiaeis a highly efficient ketosteroid isomerase catalyzing double-bond isomerization in the steroids 5-androsten-3,17-dione and 5-pregnen-3,20-dione. These mammalian ketosteroids are unknown in mosquitoes, but the discovered prominent catalytic activity with these compounds suggests that the unknown Nobo substrate in insects has a ketosteroid functionality. Nobo Asp111 is essential for activity with the steroids, but not for conventional GST substrates. Further characterization of Nobo may guide the development of new insecticides to prevent malaria.
Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts
Authors: Nelson Anders R. , Christiansen Steven L. , Naegle Kristen M. , Saucerman Jeffrey J. 
Published: March 2023

AbstractFibroblasts are essential regulators of extracellular matrix deposition following cardiac injury. These cells exhibit highly plastic responses in phenotype during fibrosis in response to environmental stimuli. Here, we test whether and how candidate anti-fibrotic drugs differentially regulate measures of cardiac fibroblast phenotype, which may help identify treatments for cardiac fibrosis. We conducted a high content microscopy screen of human cardiac fibroblasts treated with 13 clinically relevant drugs in the context of TGFβ and/or IL-1β, measuring phenotype across 137 single-cell features. We used the phenotypic data from our high content imaging to train a logic-based mechanistic machine learning model (LogiMML) for fibroblast signaling. The model predicted how pirfenidone and Src inhibitor WH-4-023 reduce actin filament assembly and actin-myosin stress fiber formation, respectively. Validating the LogiMML model prediction that PI3K partially mediates the effects of Src inhibition, we found that PI3K inhibition reduces actin-myosin stress fiber formation and procollagen I production in human cardiac fibroblasts. In this study, we establish a modeling approach combining the strengths of logic-based network models and regularized regression models, apply this approach to predict mechanisms that mediate the differential effects of drugs on fibroblasts, revealing Src inhibition acting via PI3K as a potential therapy for cardiac fibrosis.SignificanceCardiac fibrosis is a dysregulation of the normal wound healing response, resulting in excessive scarring and cardiac dysfunction. As cardiac fibroblasts primarily regulate this process, we explored how candidate anti-fibrotic drugs alter the fibroblast phenotype. We identify a set of 137 phenotypic features that change in response to drug treatments. Using a new computational modeling approach termed logic-based mechanistic machine learning, we predict how pirfenidone and Src inhibition affect the regulation of the phenotypic features actin filament assembly and actin-myosin stress fiber formation. We also show that inhibition of PI3K reduces actin-myosin stress fiber formation and procollagen I production in human cardiac fibroblasts, supporting a role for PI3K as a mechanism by which Src inhibition may suppress fibrosis.
CTLA-4 antibody-drug conjugate reveals autologous destruction of B-lymphocytes associated with regulatory T cell impairment
Authors: Muthana Musleh M. , Du Xuexiang , Liu Mingyue , Wang Xu , Wu Wei , Ai Chunxia , Su Lishan , Zheng Pan , Liu Yang 
Published: March 2023

AbstractGermline CTLA-4 deficiency causes severe autoimmune diseases characterized by dysregulation of Foxp3+Tregs, hyper-activation of effector memory T cells, and variable forms autoimmune cytopenia including gradual loss of B cells. Cancer patients with severe immune-related adverse events (irAE) after receiving anti-CTLA-4/PD-1 combination immunotherapy also have markedly reduced peripheral B cells. The immunological basis for B cell loss remains unexplained. Here we probe the decline of B cells in human CTLA-4 knock-in mice by using anti-human CTLA-4 antibody Ipilimumab conjugated to a drug payload emtansine (Anti-CTLA-4 ADC). The anti-CTLA-4 ADC-treated mice have T cell hyper-proliferation and their differentiation into effector cells which results in B cell depletion. B cell depletion is mediated by both CD4 and CD8 T cells and at least partially rescued by anti-TNF-alpha antibody. These data revealed an unexpected antagonism between T and B cells and the importance of regulatory T cells in preserving B cells.
Combining high-resolution imaging, deep learning, and dynamic modelling to separate disease and senescence in wheat canopies
Authors: Anderegg Jonas , Zenkl Radek , Walter Achim , Hund Andreas , McDonald Bruce A. 
Published: March 2023

AbstractMaintenance of sufficient healthy green leaf area after anthesis is key to ensuring an adequate assimilate supply for grain filling. Tightly regulated age-related physiological senescence and various biotic and abiotic stressors drive overall greenness decay dynamics under field conditions. Besides direct effects on green leaf area in terms of leaf damage, stressors often anticipate or accelerate physiological senescence, which may multiply their negative impact on grain filling. Here, we present an image processing methodology that enables the monitoring of chlorosis and necrosis separately for ears and shoots (stems + leaves) based on deep learning models for semantic segmentation and color properties of vegetation. A vegetation segmentation model was trained using semi-synthetic training data generated using image composition and generative adversarial neural networks, which greatly reduced the risk of annotation uncertainties and annotation effort. Application of the models to image time-series revealed temporal patterns of greenness decay as well as the relative contributions of chlorosis and necrosis. Image-based estimation of greenness decay dynamics was highly correlated with scoring-based estimations (r ≈ 0.9). Contrasting patterns were observed for plots with different levels of foliar diseases, particularly septoria tritici blotch. Our results suggest that tracking the chlorotic and necrotic fractions separately may enable (i) a separate quantification of the contribution of biotic stress and physiological senescence on overall green leaf area dynamics and (ii) investigation of the elusive interaction between biotic stress and physiological senescence. The potentially high-throughput nature of our methodology paves the way to conducting genetic studies of disease resistance and tolerance.
Actin-microtubule crosstalk imparts stiffness to the contractile ring in fission yeast
Authors: Bellingham-Johnstun Kimberly , Tyree Zoe L. , Martinez-Baird Jessica , Thorn Annelise , Laplante Caroline 
Published: March 2023

ABSTRACTActin-microtubule interactions are critical for cell division yet how these networks of polymers mutually influence their mechanical properties and functions in live cells remains unknown. In fission yeast, the post-anaphase array (PAA) of microtubules assembles in the plane of the contractile ring and its assembly relies on the Myp2p-dependent recruitment of Mto1p, a component of equatorial microtubule organizing centers (eMTOCs). The general organization of this array of microtubule and the impact on their physical attachment to the contractile ring remain unclear. We found that Myp2p facilitates the recruitment of Mto1p to the inner face of the contractile ring where the eMTOCs polymerize microtubules without their direct interaction. The PAA microtubules form a dynamic polygon of Ase1p crosslinked microtubules inside the contractile ring. The specific loss of PAA microtubules affects the mechanical properties of the contractile ring of actin by lowering its stiffness. This change in the mechanical properties of the ring has no measurable impact on cytokinesis or on the anchoring of the ring. Our work proposes that the PAA microtubules exploit the contractile ring for their assembly and function during cell division while the contractile ring may receive no benefit from these interactions.
Medium depth influences O2availability and metabolism in cultured RPE cells
Authors: Hass Daniel T. , Zhang Qitao , Autterson Gillian A. , Bryan Richard A. , Hurley James B. , Miller Jason ML. 
Published: March 2023

Structured AbstractPurposeRPE oxidative metabolism is critical for normal retinal function and is often studied in cell culture systems. Here, we show that conventional culture media volumes dramatically impact O2availability, limiting oxidative metabolism. We suggest optimal conditions to ensure cultured RPE is in a normoxic environment permissive to oxidative metabolism.MethodsWe altered the availability of O2to human primary RPE cultures directly via a hypoxia chamber or indirectly via the amount of medium over cells. We measured oxygen consumption rates (OCR), glucose consumption, lactate production,13C6-glucose flux, hypoxia inducible factor (HIF-1α) stability, intracellular lipid droplets after a lipid challenge, trans-epithelial electrical resistance, cell morphology, and pigmentation.ResultsMedium volumes commonly employed during RPE culture limit diffusion of O2to cells, triggering hypoxia, activating HIF-1α, limiting OCR, and dramatically altering cell metabolism, with only minor effects on typical markers of RPE health. Media volume effects on O2availability decrease acetyl-CoA utilization, increase glycolysis, and alter the size and number of intracellular lipid droplets under lipid-rich conditions.ConclusionsDespite having little impact on visible and typical markers of RPE culture health, media volume dramatically affects RPE physiology “under the hood”. As RPE-centric diseases like age-related macular degeneration (AMD) involve oxidative metabolism, RPE cultures need to be optimized to study such diseases. We provide guidelines for optimal RPE culture volumes that balance ample nutrient availability from larger media volumes with adequate O2availability seen with smaller media volumes.
Polychaetoid/ZO-1 strengthens cell junctions under tension while localizing differently than core adherens junction proteins
Authors: Schmidt Anja , Finegan Tara , Häring Matthias , Kong Deqing , Fletcher Alexander G , Alam Zuhayr , Grosshans Jörg , Wolf Fred , Peifer Mark 
Published: March 2023

AbstractDuring embryonic development dramatic cell shape changes and movements re-shape the embryonic body plan. These require robust but dynamic linkage between the cell-cell adherens junctions and the force-generating actomyosin cytoskeleton. Our view of this linkage has evolved, and we now realize linkage is mediated by a mechanosensitive multiprotein complex assembled via multivalent connections. Here we combine genetic, cell biological and modeling approaches to define the mechanism of action and functions of an important player,DrosophilaPolychaetoid, homolog of mammalian ZO-1. Our data reveal that Pyd reinforces cell junctions under elevated tension, and facilitates cell rearrangements. Pyd is important to maintain junctional contractility and in its absence cell rearrangements stall. We next use structured illumination microscopy to define the molecular architecture of cell-cell junctions during these events. The cadherin-catenin complex and Cno both localize to puncta along the junctional membrane, but are differentially enriched in different puncta. Pyd, in contrast, exhibits a distinct localization to strands that extend out from the region occupied by core junction proteins. We then discuss the implications for the protein network at the junction-cytoskeletal interface, suggesting different proteins localize and function in distinct ways but combine to produce robust connections.
NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples
Authors: Wang Wanli , Ma Li-Hua , Maletic-Savatic Mirjana , Liu Zhandong 
Published: March 2023

AbstractNuclear Magnetic Resonance is a powerful platform that reveals the metabolomics profiles within biofluids or tissues and contributes to personalized treatments in medical practice. However, data volume and complexity hinder the exploration of NMR spectra. Besides, the lack of fast and accurate computational tools that can handle the automatic identification and quantification of essential metabolites from NMR spectra also slows the wide application of these techniques in clinical. We present NMRQNet, a deep-learning-based pipeline for automatic identification and quantification of dominant metabolite candidates within human plasma samples. The estimated relative concentrations could be further applied in statistical analysis to extract the potential biomarkers. We evaluate our method on multiple plasma samples, including species from mice to humans, curated using three anticoagulants, covering healthy and patient conditions in neurological disorder disease, greatly expanding the metabolomics analytical space in plasma. NMRQNet accurately reconstructed the original spectra and obtained significantly better quantification results than the earlier computational methods. Besides, NMRQNet also proposed relevant metabolites biomarkers that could potentially explain the risk factors associated with the condition. NMRQNet, with improved prediction performance, highlights the limitations in the existing approaches and has shown strong application potential for future metabolomics disease studies using plasma samples.
Cat LCA-CRXmodel, homozygous for an antimorphic mutation has a unique phenotype
Authors: Occelli Laurence M. , Tran Nicholas M. , Chen Shiming , Petersen-Jones Simon M. 
Published: March 2023

ABSTRACTPURPOSEHuman mutations in theCRXtranscription factor are associated with dominant retinopathies often with more severe macular changes. TheCRX-mutant cat (Rdy-A182d2) is the only animal model with the equivalent of the critical retinal region for high acuity vision, the macula. Heterozygous cats (CRXRdy/+) have a severe phenotype modeling Leber congenital amaurosis. This study reports the distinct ocular phenotype of homozygous cats (CRXRdy/Rdy).METHODSGene expression changes were assessed at both mRNA and protein levels. Changes in globe morphology and retinal structure were analyzed.RESULTSCRXRdy/Rdycats had high levels of mutantCRXmRNA and protein. The expression of photoreceptor target genes was severely impaired while there were variable effects on the expression of other transcription factors. The photoreceptor cells remained immature and failed to elaborate outer segments consistent with the lack of retinal function. The retinal layers displayed a progressive remodeling with cell loss but maintained overall retinal thickness due to gliosis. Rapid photoreceptor loss largely occurred in the macula-equivalent retinal region. The homozygous cats developed markedly increased ocular globe length.CONCLUSIONSThe phenotype ofCRXRdy/Rdycats was more severe compared toCRXRdy/+cats by several metrics.TRANSLATIONAL RELEVANCETheCRX-mutant cat is the only model forCRX-retinopathies with a macula-equivalent region. A prominent feature of theCRXRdy/Rdycat phenotype not detectable in homozygous mouse models, was the rapid degeneration of the macula-equivalent retinal region highlighting the value of this large animal model and its future importance in the testing of translational therapies aiming to restore vision.
Widespread post-transcriptional regulation of co-transmission
Authors: Chen Nannan , Zhang Yunpeng , Rivera-Rodriguez Emmanuel J. , Yu Albert D. , Hobin Michael , Rosbash Michael , Griffith Leslie C. 
Published: March 2023

AbstractWhile neurotransmitter identity was once considered singular and immutable for mature neurons, it is now appreciated that one neuron can release multiple neuroactive substances (co-transmission) whose identities can even change over time. To explore the mechanisms that tune the suite of transmitters a neuron releases, we developed transcriptional and translational reporters for cholinergic, glutamatergic, and GABAergic signaling inDrosophila. We show that many glutamatergic and GABAergic cells also transcribe cholinergic genes, but fail to accumulate cholinergic effector proteins. Suppression of cholinergic signaling involves posttranscriptional regulation of cholinergic transcripts by the microRNA miR-190; chronic loss of miR-190 function allows expression of cholinergic machinery, reducing and fragmenting sleep. Using a “translation-trap” strategy we show that neurons in these populations have episodes of transient translation of cholinergic proteins, demonstrating that suppression of co-transmission is actively modulated. Posttranscriptional restriction of fast transmitter co-transmission provides a mechanism allowing reversible tuning of neuronal output.One-Sentence SummaryCholinergic co-transmission in large populations of glutamatergic and GABAergic neurons in theDrosophilaadult brain is controlled by miR-190.
CD8+ cells and small viral reservoirs facilitate post-ART control of SIV in Mauritian cynomolgus macaques
Authors: Harwood Olivia E. , Matschke Lea M. , Moriarty Ryan V. , Balgeman Alexis J. , Weaver Abigail J. , Ellis-Connell Amy L. , Weiler Andrea M. , Winchester Lee C. , Fletcher Courtney V. , Friedrich Thomas C. , Keele Brandon F. , O’Connor David H. , Lang Jessica D. , Reynolds Matthew R. , O’Connor Shelby L. 
Published: March 2023

AbstractSustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority for HIV treatment. We observed surprising PTC in an MHC-haplomatched cohort of MHC-M3+ SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). For six months after ART withdrawal, we observed undetectable or transient viremia in seven of eight MCMs. In vivo depletion of CD8α+ cells induced rebound in all animals, indicating the PTC was mediated, at least in part, by CD8α+ cells. We found that MCMs had smaller acute viral reservoirs than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. The mechanisms by which unusually small viral reservoirs and CD8α+ cell-mediated virus suppression enable PTC can be investigated using this MHC-haplomatched MCM model. Further, defining the immunologic mechanisms that engender PTC in this model may identify therapeutic targets for inducing durable HIV remission in humans.
Emotional memories are enhanced when reactivated in slow-wave sleep but impaired in REM
Authors: Yuksel Cagri , Denis Dan , Coleman James , Ren Boyu , Oh Angela , Cox Roy , Morgan Alexandra , Sato Erina , Stickgold Robert 
Published: March 2023

AbstractSleep supports memory consolidation. However, it is not completely clear how different sleep stages contribute to this process. While rapid eye movement sleep (REM) has traditionally been implicated in the processing of emotionally charged material, recent studies indicate a role for slow wave sleep (SWS) in strengthening emotional memories. Here, to directly examine which sleep stage is primarily involved in emotional memory consolidation, we used targeted memory reactivation (TMR) in REM and SWS during a daytime nap. Contrary to our hypothesis, reactivation of emotional stimuli during REM led to impaired memory. Consistent with this, REM% was correlated with worse recall in the group that took a nap without TMR. Meanwhile, cueing benefit in SWS was strongly correlated with the product of times spent in REM and SWS (SWS-REM product), and reactivation significantly enhanced memory in those with high SWS-REM product. Surprisingly, SWS-REM product was associated with better memory for reactivated items and poorer memory for non-reactivated items, suggesting that sleep both preserved and eliminated emotional memories, depending on whether they were reactivated. Notably, the emotional valence of cued items modulated both sleep spindles and delta/theta power. Finally, we found that emotional memories benefited from TMR more than did neutral ones. Our results suggest that emotional memories decay during REM, unless they are reactivated during prior SWS. Furthermore, we show that active forgetting complements memory consolidation, and both take place across SWS and REM. In addition, our findings expand upon recent evidence indicating a link between sleep spindles and emotional processing.
Oligomerization enhances huntingtin membrane activity but is suppressed by covalent crosslinking
Authors: Sedighi Faezeh , Skeens Adam , Adegbuyiro Adewale , Bard John , Siriwardhana Chathuranga , Donley Emily , Geldenhuys Werner J. , Legleiter Justin 
Published: March 2023

ABSTRACTHuntingtin disease (HD) is a neurodegenerative disease caused by expansion of a polyglutamine (polyQ) tract within the huntingtin (htt) protein, leading to aggregation into a variety of species ranging from small oligomers to large fibrils. A consensus concerning which of these aggregate states are primarily responsible for toxicity associated with mutant htt remains elusive. Htt directly binds and damages a variety of membranous surfaces within cells. Here, the ability of different aggregation states of htt to interact with and damage lipid membranes was determined. Oligomers represented the most active lipid binding species, whereas, fibril formation severely limited membrane binding. Thus, strategies to stabilize oligomers were implemented, and conformational flexibility appeared to play a key role in the oligomer/membrane interaction. In particular, stabilizing oligomers with covalent crosslinking with 1,5-difluoro-2,4-dinitrobenzene (DFDNB) effectively eliminated the ability of oligomers to bind lipid membranes and reduced their associated cellular toxicity.