bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of long-chain acyl-CoA dehydrogenase protects against acute kidney injury
Authors: Chiba Takuto , Oda Akira , Zhang Yuxun , Bons Joanna , Bharathi Sivakama S , Pfister Katherine E. , Zhang Bob B. , Richert Adam C. , Schilling Birgit , Goetzman Eric S. , Sims-Lucas Sunder
Published: October 2024

Proximal tubular epithelial cells (PTECs) are particularly vulnerable to acute kidney injury (AKI). While fatty acids are the preferred energy source for PTECs via fatty acid oxidation (FAO), FAO-mediated H2O2production in mitochondria has been shown to be a major source of oxidative stress. We have previously shown that a mitochondrial flavoprotein, long-chain acyl-CoA dehydrogenase (LCAD), which catalyzes a key step in mitochondrial FAO, directly produces H2O2in vitro. Further we have established that loss of a lysine deacylase, Sirtuin 5 (Sirt5−/−), induces hypersuccinylation and inhibition of mitochondrial FAO genes to stimulate peroxisomal FAO and to protect against AKI. However, the role of LCAD has yet to be determined.

Mass spectrometry data acquisition revealed that LCAD is hypersuccinylated inSirt5−/−kidneys after AKI. Following two distinct models of AKI, cisplatin treatment or renal ischemia/reperfusion (IRI), LCAD knockout mice (LCAD−/−) demonstrated renoprotection against AKI. Specifically,LCAD−/−kidneys displayed mitigated renal tubular injury, decreased oxidative stress, preserved mitochondrial function, enhanced peroxisomal FAO, and decreased ferroptotic cell death.

LCAD deficiency confers protection against two distinct models of AKI. This suggests a therapeutically attractive mechanism whereby preserved mitochondrial respiration as well as enhanced peroxisomal FAO by loss of LCAD mediates renoprotection against AKI.
K-mer analysis of long-read alignment pileups for structural variant genotyping
Authors: ENGLISH ADAM C. , Cunial Fabio , Metcalf Ginger A. , Gibbs Richard A. , Sedlazeck Fritz J.
Published: October 2024

Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes. We benchmark kanpig against the latest SV benchmarks and show single-sample genotyping concordance of 82.1%, which is higher than existing genotypers averaging 66.3%. We explore kanpig's applicability to multi-sample projects by benchmarking project-level VCFs containing 47 genetically diverse samples and find kanpig accurately genotypes complex loci (e.g. SVs neighboring other SVs), achieving much higher genotyping concordance than other tools. Kanpig requires only 43 seconds to process a single sample's 20x long-reads and can be run on PacBio or ONT long-reads.
Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species
Authors: Marín Alan , Alfaro Ruben , Reyes-Flores Lorenzo E. , Ingar Claudia , Santos-Rojas Luis E. , Alvarez-Jaque Irina B. , Rodríguez-Bernales Karen , Carbajal Cleila , Yon-Utrilla Angel , Zelada-Mázmela Eliana
Published: October 2024

Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide strong discriminatory power for fast and simultaneous differentiation between closely related species. In this study, we used interspecific variations detected in two mitochondrial genes to develop species-specific primers for eDNA monitoring and identifying 10 fish and shellfish species commercially available within the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to PCR, qPCR, and sequencing methods, coupled with robust validation assays that included a) an in-silico stage using self-generated and public DNA sequences, b) an in-vitro stage using target species belonging to vouchered specimens, fresh and cooked commercial samples, early life stages, and broad taxa of non-target species, and c) an in-situ stage using eDNA samples from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process with high efficiency and specificity in unequivocally identifying all target species with 100% accuracy and without cross-species amplifications, thereby making them valuable tools for eDNA monitoring, seafood authentication, and to identify and combat illegal, unreported and unregulated fishing. The identification assays presented herein can be used to support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species also occur or are available as imported commodities.
Biocontrol efficiency and mechanism of novelStreptomyces luomodiensisSCA4-21 against bananaFusariumwilt
Authors: Liu Qiao , Zou Liangping , Chen Yufeng , Feng Junting , Wei Yongzan , Miaoyi Zhang , Li Kai , Zhao Yankun , Zhou Dengbo , Wang Wei , Qi Dengfeng , Xie Jianghui
Published: October 2024

The soil-borne fungiFusarium oxysporumf. sp.cubensetropical race 4 (Foc TR4) causes bananaFusariumwilt, which seriously threats global banana production. Biocontrol has been considered viable alternative method to manage bananaFusariumwilt. In previous study, we found that novelS. luomodiensisSCA4-21 exhibited antifungal activity. Here, we revealed that the extracts of strain SCA4-21 significantly inhibited the growth of Foc TR4 hyphae and spore germination, severely disrupting the ultrastructure of Foc TR4 hyphal cells and spore morphology. These extracts also exhibited broad-spectrum antifungal activity against eight other phytopathogenic fungi. Furthermore, we demonstrated that strain SCA4-21 produce 32 volatile organic compounds, including five antifungal compounds. In a pot experiment, we discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, achieving a biocontrol efficiency of 59.3%, and promoted the growth of banana seedlings. Additionally, this inoculation significantly enhanced the abundances of beneficial bacterial generaStreptomyces,Bacillus,Sphingomonas, andMassilia, as well as fungal generaMortierella,Purpureocillium,Gibellulopsis, andXenomyrothecium, while significantly reduced the abundances of pathogenic bacteria genusPantoeaand fungal genusFusarium, in the banana rhizosphere soil. Moreover, the inoculation of strain SCA4-21 significantly increased the enrichment of pathways such as carbohydrate metabolism, amino acid metabolism, and metabolism of terpenoids and polyketides. Therefore, we postulated that strain SCA4-21 may synergistically combat bananaFusariumwilt by producing antifungal compounds and enriching beneficial bacteria and fungi. Our findings present a promising biocontrol agent for the management of bananaFusariumwilt.

IMPORTANCE

Banana (Musaspp.) is one of the most popular fruit crops and the fourth largest food crop in developing countries within tropical and subtropical regions. However, the emergence and rapid spread of strain Foc TR4 seriously hinder the development of banana industry. Currently, there is no effective control measure available. Biological control holds potential due to its safety and effectiveness. Here, we found that the extracts ofS. luomodiensisSCA4-21 exhibited significant inhibitory effects on the hyphal growth and spore germination of Foc TR4, as well as severe destructive effects on its cell morphology and ultrastructure, and broad-spectrum antifungal activity. We also discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, reduced the incidence index of bananaFusariumwilt, promoted the growth of banana seedlings, and enhances beneficial microbes and metabolic pathways, suggesting that strain SCA4-21 is a promising biocontrol agent.
The genome assembly of the duckweed fern,Azolla caroliniana
Authors: Song Michael J. , Li Fay-Wei , Freund Forrest , Escalona Merly , Toffelmier Erin , Miller Courtney , Shaffer H. Bradley , Nguyen Oanh , Marimuthu Mohan P.A. , Chumchim Noravit , Tribble Carrie , Fairbairn Colin W. , Seligmann William , Rothfels Carl J.
Published: October 2024

Azolla is a genus of freshwater ferns that is economically important as a nitrogen-fixing biofertilizer, biofuel, bioremediator, and for potential carbon sequestration, but also contains weedy invasive species. In California, only two species are currently recognized but there may be up to six putative species, with the discrepancy being due to the difficulty in identifying taxa, hybridization, and the introduction of non-native species. Here, we report a new haplotype-resolved, chromosome-level assembly of Azolla caroliniana as part of the California Conservation Genomics Project (CCGP), using a combination of PacBio HiFi and Omni-C sequencing technologies. The assembly is 521 Mb in length, with a contig N50 of 1.6 Mb, and is scaffolded into 22 pseudo-chromosomes. The BUSCO completeness score is 87.5%, making it the most complete and most contiguous Azolla assembly to date. In combination with the previously published A. filiculoides genome, this A. caroliniana genome will be a powerful tool for understanding the population genetics and taxonomy of one of the most cryptic, economically important, and poorly circumscribed fern taxa, and for facilitating land plant genomics more broadly.
Type-I IFNs induce GBPs and lysosomal defense in hepatocytes to control malaria
Authors: Marques-da-Silva Camila , Schmidt-Silva Clyde , Bowers Carson , Charles-Chess Essel , Shiau Justine C. , Park Eui-Soon , Yuan Zhongyu , Kim Bae-Hoon , Kyle Dennis E. , Harty John T. , MacMicking John D. , Kurup Samarchith P.
Published: October 2024

Plasmodiumparasites undergo development and replication within the hepatocytes before infecting the erythrocytes and initiating clinical malaria. Although type-I interferons (IFNs) are known to hinderPlasmodiuminfection within the liver, the underlying mechanisms remain unclear. Here, we describe two IFN-I-driven hepatocyte antimicrobial programs controlling liver-stage malaria. First, oxidative defense by NADPH oxidases 2 and 4 triggers a pathway of lysosomal fusion with the parasitophorous vacuole (PV) to help clearPlasmodium. Second, guanylate-binding protein (GBP) 1 disruption of the PV activates caspase-1 inflammasome, inducing pyroptosis to remove the infected host cells. Remarkably, both human and mouse hepatocytes enlist these cell-autonomous immune programs to eliminatePlasmodium; their pharmacologic or genetic inhibition led to profound malarial susceptibility, and are essentialin vivo. In addition to identifying the IFN-I-mediated cell-autonomous immune circuits controllingPlasmodiuminfection in the hepatocytes, this study extends our understanding of how non-immune cells are integral to protective immunity against malaria.
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression
Authors: Sink Warren J. , Fling Russell , Yilmaz Ali , Nault Rance , Goniwiecha Delanie , Harkema Jack R. , Graham Stewart F. , Zacharewski Timothy
Published: October 2024

Epidemiological evidence suggests an association between dioxin and dioxin-like compound (DLC) exposure and human liver disease. The prototypical DLC, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), has been shown to induce the progression of reversible hepatic steatosis to steatohepatitis with periportal fibrosis and biliary hyperplasia in mice. Although the effects of TCDD toxicity are mediated by aryl hydrocarbon receptor (AHR) activation, the underlying mechanisms of TCDD-induced hepatotoxicity are unresolved. In the present study, male C57BL/6NCrl mice were gavaged every 4 days for 28 days with 0.03 - 30 μg/kg TCDD and evaluated for liver histopathology and gene expression as well as complementary 1-dimensional proton magnetic resonance (1D-1H NMR) urinary metabolic profiling. Urinary trimethylamine (TMA), trimethylamineN-oxide (TMAO), and 1-methylnicotinamide (1MN) levels were altered by TCDD at doses ≤ 3 μg/kg; other urinary metabolites, like glycolate, urocanate, and 3-hydroxyisovalerate, were only altered at doses that induced moderate to severe steatohepatitis. Bulk liver RNA-seq data suggested altered urinary metabolites correlated with hepatic differential gene expression corresponding to specific metabolic pathways. In addition to evaluating whether altered urinary metabolites were liver-dependent, published single-nuclear RNA-seq (snRNA-seq), AHR ChIP-seq, and AHR knockout gene expression datasets provide further support for hepatic cell-type and AHR-regulated dependency, respectively. Overall, TCDD-induced liver effects were preceded by and occurred with changes in urinary metabolite levels due to AHR-mediated changes in hepatic gene expression.
When to Trust Epigenetic Clocks: Avoiding False Positives in Aging Interventions
Authors: Borrus Daniel S. , Sehgal Raghav , Armstrong Jenel Fraij , Kasamoto Jessica , Gonzalez John , Higgins-Chen Albert
Published: October 2024

Recent human studies have suggested that aging interventions can reduce aging biomarkers related to morbidity and mortality risk. Such biomarkers may potentially serve as early, rapid indicators of effects on healthspan. An increasing number of studies are measuring intervention effects on epigenetic clocks, commonly used aging biomarkers based on DNA methylation profiles. However, with dozens of clocks to choose from, different clocks may not agree on the effect of an intervention. Furthermore, changes in some clocks may simply be the result of technical noise causing a false positive result. To address these issues, we measured the variability between 6 popular epigenetic clocks across a range of longitudinal datasets containing either an aging intervention or an age-accelerating event. We further compared them to the same clocks re-trained to have high test-retest reliability. We find the newer generation of clocks, trained on mortality or rate-of-aging, capture aging events more reliably than those clocks trained on chronological age, as these show consistent effects (or lack thereof) across multiple clocks including high-reliability versions, and including after multiple testing correction. In contrast, clocks trained on chronological age frequently show sporadic changes that are not replicable when using high-reliability versions of those same clocks, or when using newer generations of clocks and these results do not survive multiple-testing correction. These are likely false positive results, and we note that some of these clock changes were previously published, suggesting the literature should be re-examined. This work lays the foundation for future clinical trials that aim to measure aging interventions with epigenetic clocks, by establishing when to attribute a given change in biological age to abona fidechange in the aging process.
Learning antibody sequence constraints from allelic inclusion
Authors: Jagota Milind , Hsu Chloe , Mazumder Thomas , Sung Kevin , DeWitt William S. , Listgarten Jennifer , Matsen Frederick A. , Ye Chun Jimmie , Song Yun S.
Published: October 2024

Antibodies and B-cell receptors (BCRs) are produced by B cells, and are built of a heavy chain and a light chain. Although each B cell could express two different heavy chains and four different light chains, usually only a unique pair of heavy chain and light chain is expressed—a phenomenon known asallelic exclusion. However, a small fraction of naive-B cells violate allelic exclusion by expressing two productive light chains, one of which has impaired function; this has been calledallelic inclusion. We demonstrate that these B cells can be used to learn constraints on antibody sequence. Using large-scale single-cell sequencing data from humans, we find examples of light chain allelic inclusion in thousands of naive-B cells, which is an order of magnitude larger than existing datasets. We train machine learning models to identify the abnormal sequences in these cells. The resulting models correlate with antibody properties that they were not trained on, including polyreactivity, surface expression, and mutation usage in affinity maturation. These correlations are larger than what is achieved by existing antibody modeling approaches, indicating that allelic inclusion data contains useful new information. We also investigate the impact of similar selection forces on the heavy chain in mouse, and observe that pairing with the surrogate light chain significantly restricts heavy chain diversity.
Virtual staining from bright-field microscopy for label-free quantitative analysis of plant cell structures
Authors: Ichita Manami , Yamamichi Haruna , Higaki Takumi
Published: October 2024

The applicability of a deep learning model for the virtual staining of plant cell structures using bright-field microscopy was investigated. The training dataset consisted of microscopy images of tobacco BY-2 cells with the plasma membrane stained with the fluorescent dye PlasMem Bright Green and the cell nucleus labeled with Histone-red fluorescent protein. The trained models successfully detected the expansion of cell nuclei upon aphidicolin treatment and a decrease in the cell aspect ratio upon propyzamide treatment, demonstrating its utility in cell morphometry. The model also accurately documented the shape of Arabidopsis pavement cells in both wild type and thebpp125triple mutant, which has an altered pavement cell phenotype. Metrics such as cell area, circularity, and solidity obtained from virtual staining analyses were highly correlated with those obtained by manual measurements of cell features from microscopy images. Furthermore, the versatility of virtual staining was highlighted by its application to track chloroplast movement inEgeria densa. The method was also effective for classifying live and dead BY-2 cells using texture-based machine learning, suggesting that virtual staining can be applied beyond typical segmentation tasks. Although this method still has some limitations, its non-invasive nature and efficiency make it highly suitable for label-free, dynamic, and high-throughput analyses in quantitative plant cell biology.
Suregada multifloraRoot Fluro-PolyPhosphate-Glycoside (NU2) inhibits MDR Bacteria and Unicellular Parasites Targeting DNA Topoisomerase I
Authors: Chakraborty Asit Kumar
Published: October 2024

Background

Common antibiotics were useless now asmdrgenes were gradually accumulating in all environmental bacterial plasmids. Thus, development of alternate to synthetic antibiotics is great.

Objectives

Plants secrete ex-metabolites to prevent soil bacteria and thus a good source for new antibiotics. Our objective is to discover an abundant active phyto-chemical against MDR pathogens from household plants of West Bengal.

Methods

Suregada multifloraplant was grown in clay pot. Root ethanol extract was made for overnight at RT and concentrated. Preparative TLC was performed to isolate major active component by UV-shadow method and was further purified by HPLC. NU2 Inhibitory assays on MDREscherichia coliKT-1,Leishmania donovanipromastigotes,Plasmodium falciparumin human RBC culture were performed as described previously. Biochemical assays, elementary and spectral analyses (MASS, FTIR, NMR) were performed to validate chemical nature of NU2. DNA Topoisomerase I, RNA polymerase and DNA polymerase assays were performed to find modes of action. The structures of NU2 were drawn using Stacher and NU2 binding to DNA topoisomerase I was performed using SwissDock server [Bugnon et al. 2024].

Results

Well cultivatedS. multifloraroot extract was 18fold active than bark extract and further enhanced 2.8fold in MS media root culture. The four times TLC purified active principle (NU2) was eluted at 10.2min in HPLC C18column. NU2 inhibits MDR bacteria as well as unicellular parasitesPlasmodium falciparum,Leishmania donovaniand Trypanosoma brucei. Spectral analyses suggested NU2 was a glycoside-polyphosphate with molecular mass 454mu and molecular formula C4H7P4O16F. FT-IR gave broad band at 3000-3600cm-1for -OH including at 1559cm-1 for -OH bending. The distinct phosphate -PO4-3group absorption was confirmed at 1021.4cm-1including 928.7cm-1for C-O-P and skeleton minor phosphate group vibration at 525cm-1. Proton-NMR demonstrated huge absorption at δ=2.16ppm for C-O-H, at δ=1.52ppm for -POH while Carbon-NMR at 30.1ppm for C-H and at 207.01ppm for -HC=O. NU2 actively inhibited the DNA topoisomerase I but DNA polymerase and RNA polymerase ofEscherichia coliwere not inhibited. The AI-guided computer simulation suggested that NU2.1, NU2.2 and NU2.3 were better inhibitors for topoIII than topoI ofE. coli,M. tuberculosisandL. donovani. We postulate that NU2 prevent the DNA nicking, strand passing and ligase activities after specific binding to the domain-2 active sites.

Conclusion

Thus, NU2 cyclic glycoside-fluoropolyphosphate may be a versatile type-I DNA topoisomerase inhibitor and could be studied further for drug design against bacterial and parasite drug-resistant pathogenesis.

Graphical Abstract
Gardenia duerrii(Gardenieae : Rubiaceae), a new species from India and Neotypification ofGardenia resiniferaRoth
Authors: Raja Kullayiswamy K , Sarojini Devi N
Published: October 2024

Gardenia duerriisp. nov. is described and illustrated from middle parts of Central Peninsula Plateau, India. This new species is allied toGardenia resiniferain flower (corolla tube, lobes and anther) and somewhat in leaf and stipule, but it differs in leaf texture, venation, fruit and calyx nature. Distribution of the new species is under the canopy of dry deciduous forests of Telangana, Andhra Pradesh, Odisha and Maharashtra states of India. Allied speciesGardenia resiniferaRoth type specimen is missing or likely destroyed during WW-II at the Botanic Garden and Botanical Museum Berlin, Germany. Consequently, we designate herein a neotype forGardenia resinifera.
Biomimic opto-nanobiointerface enables multiscale biomodulation
Authors: Müller Christoph Alexander , Zhang Yuge , Meng Lingyuan , Kalatanova Anna , Madsen Jesper Guldsmed , Klompmaker Kjeld Kaj , Jakobsen Thomas Stax , Jørgensen Asbjørn C. , Askou Anne Louise , Huang Ge , Li Wen , Davidsen Rasmus Schmidt , Bek Toke , Hatzakis Nikos S. , Corydon Thomas J. , Leinonen Henri , Tian Bozhi , Dong Mingdong , Chen Menglin
Published: October 2024

Virtually all organic material on Earth has been produced converting solar energy through photosynthesis in chloroplasts, a sack-like, double membrane organelle in plants and algae, where transmembrane electron transfer occurs from lumen to stroma. Although animals hardly harness the power of photosynthesis, their bioelectrical signals extensively regulate complex electrophysiological behaviors, rendering it a superior target for biomedical innovation. Here a crude structural mimicry of chloroplast has led us to discover that hollow sphere graphitic carbon nitride nanoparticles (hg-C3N4NPs) endowed non-genetic, subcellular and intercellular photo-modulation of various excitable and non-excitable cells, accumulatively achieving modulation at tissue/organ function level. The homogeneous hg-C3N4NPs showed photo-responsiveness via photoelectrochemical and photothermal mechanisms under photocurrent measurement. The hg-C3N4NPs can be spontaneously internalized with excellent cytocompatibility. Using a focusing laser, the hg-C3N4NPs enable intracellular optical stimulation with subcellular resolution, inducing calcium transient release in multiple cells and propagation in primary cardiomyocytes and cardiac fibroblasts. At multicellular scale, optical pacing and synchronization of cardiomyocyte beating is achieved facilely by LED. Further, we demonstrate that hg-C3N4NPs can be safely injected into mouse eyes, restoring light sensitivity in blind mice. Finally, application of hg-C3N4NPs to porcine retinal tissueex vivoconfirmed their modulation capability to reactivate RGCs activity under LED photostimulation. Taken together, these nanostructured biomimic semiconductor NPs offer high resolution, leadless optical probing, non-invasive delivery and great biocompatibility, serving as a versatile tool for addressing a range of complex biomedical challenges through subcellular, intercellular and tissue-level photo-modulation across a broad spectrum of scales.
Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists
Authors: Vince Matthew J. K. , Hughes Kristin A. , Buzuk Anastasiya , Perlstein Deborah L. , Viarengo-Baker Lauren A. , Whitty Adrian
Published: October 2024

Machine learning (ML) is rapidly gaining traction in many areas of experimental molecular science for elucidating relationships and patterns in large or complex data sets. Historically, ML was largely the preserve of those with specialized training in fields such as statistics or cheminformatics. Increasingly, however, ML methodologies are becoming part of the standard toolkit for experimental scientists across a range of disciplines. Lowering the barrier of entry to these ML techniques, for scientists without a significant background in computer science or statistics, is important to broadening access to these powerful methods. Here we provide detailed, step by step tutorials for performing four ML methods that are particularly useful for applications in biochemistry, cell biology, and drug discovery: hierarchical clustering, Principal Component Analysis (PCA), Partial Least-Squares Discriminant Analysis (PLSDA), and Partial Least-Squares Regression (PLSR). The protocols are written for the widely used software MATLAB, but no prior experience with MATLAB is required to use them. We include an explanation of each step, pitched at a level to be understood by investigators without any prior experience with ML, MATLAB, or any kind of coding. We also highlight the scientific issues pertaining to selecting and scaling the data to be analyzed, and describe controls to test the validity of the results obtained. Throughout, we emphasize the relationship between the scientific question and how to choose data and methods that will allow it to be addressed in a meaningful way. Our aim is to provide a basic introduction that will equip experimental chemical biologists and other chemical and biomedical scientists with the knowledge required to use ML to aid in the design of experiments, the formulation and data-driven testing of hypotheses, and the analysis of experimental data.

Basic Protocol 1

Clustering

Basic Protocol 2

Principal Component Analysis (PCA)

Basic Protocol 3

Partial Least Squares Discriminant Analysis (PLSDA)

Basic Protocol 4

Partial Least Squares Regression (PLSR)
T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.
Authors: Bozkus Cansu Cimen , Brown Matthew , Velazquez Leandra , Thomas Marcus , Wilson Eric A. , O'Donnell Timothy , Ruchnewitz Denis , Geertz Douglas , Bykov Yonina , Kodysh Julia , Oguntuyo Kasopefoluwa Y , Roudko Vladimir , Hoyos David , Srivastava Komal , Kleiner Giulio , Alshammary Hala , Karekar Neha , McClain Christopher , Gopal Ramya , Nie Kai , Del Valle Diane , Delbeau-Zagelbaum Daniela , Rodriguez Denise , Setal Jessica ,   The Mount Sinai COVID-19 Biobank Team, Carroll Emily , Wiesendanger Margrit , Gulko Percio , Charney Alexander , Merad Miriam , Kim-Schulze Seunghee , Lee Benhur , Wajnberg Ania , Simon Viviana , Greenbaum Benjamin D. , Chowell Diego , Vabret Nicolas , Luksza Marta , Bhardwaj Nina
Published: October 2024

As SARS-CoV-2 variants continue to emerge capable of evading neutralizing antibodies, it has become increasingly important to fully understand the breadth and functional profile of T cell responses to determine their impact on the immune surveillance of variant strains. Here, sampling healthy individuals, we profiled the kinetics and polyfunctionality of T cell immunity elicited by mRNA vaccination. Modeling of anti-spike T cell responses against ancestral and variant strains of SARS-CoV-2 suggested that epitope immunodominance and cross-reactivity are major predictive determinants of T cell immunity. To identify immunodominant epitopes across the viral proteome, we generated a comprehensive map of CD4+ and CD8+ T cell epitopes within non-spike proteins that induced polyfunctional T cell responses in convalescent patients. We found that immunodominant epitopes mainly resided within regions that were minimally disrupted by mutations in emerging variants. Conservation analysis across historical human coronaviruses combined with in silico alanine scanning mutagenesis of non-spike proteins underscored the functional importance of mutationally-constrained immunodominant regions. Collectively, these findings identify immunodominant T cell epitopes across the mutationally-constrained SARS-CoV-2 proteome, potentially providing immune surveillance against emerging variants, and inform the design of next-generation vaccines targeting antigens throughout SARS-CoV-2 proteome for broader and more durable protection.
Grey Matter Volume and Fractional Anisotropy as Correlates of Cognitive Improvement in Traumatic Brain Injury Over a 6-Month Period
Authors: Zhang Ben , Fulmer Niko , Dunn Sarah , Zheng Zhong Sheng , Schnakers Caroline , Rosario Emily R.
Published: October 2024

Objective

In this study we explored how neuroimaging and blood biomarkers relate to cognitive recovery in traumatic brain injury (TBI) patients.

Methods

Sixteen participants with moderate to severe traumatic brain injury (TBI) were enrolled, with blood samples, MRI, and diffusion tensor imaging (DTI) collected at enrollment and six months. The Repeatable Battery for the Assessment of Neuropsychological Status (RBANS), Disability Rating Scale, and Montreal Cognitive Assessment (MoCA) were also administered at both time points to evaluate neuropsychological and functional outcomes.

Results

Fractional anisotropy (FA) in the genu (rs= 0.937, p = 0.002) and splenium of the corpus callosum (rs= 0.955, p < 0.001) was strongly correlated with changes in RBANS - Attention scores. Fornix FA was correlated with changes in RBANS - Total (rs= 0.928, p = 0.008), and left tapetum FA was correlated with changes in RBANS - Visuospatial scores (rs= 0.964, p < 0.001). Right temporal fusiform cortex grey matter (GM) volume was correlated with changes in RBANS - Attention scores (rs= 0.975, p = 0.005). Blood biomarkers did not show significance.

Conclusion

Imaging markers like FA and GM volume appear to help predict cognitive recovery in TBI, supporting the potential use of neuroimaging to guide rehabilitation strategies.
The global burden of chikungunya virus and the potential benefit of vaccines
Authors: Ribeiro dos Santos Gabriel , Jawed Fariha , Mukandavire Christinah , Deol Arminder , Scarponi Danny , Mboera Leonard E.G. , Seruyange Eric , Poirier Mathieu J.P. , Bosomprah Samuel , Udeze Augustine O. , Dellagi Koussay , Hozé Nathanael , Chilongola Jaffu , Nasrallah Gheyath K. , Saathof Elmar , Cauchemez Simon , Salje Henrik
Published: October 2024

The first chikungunya virus (CHIKV) vaccine has now been licensed, however, its potential to reduce disease burden remains unknown due to a poor knowledge of the underlying global burden. We use data from seroprevalence studies, observed cases and mosquito distributions to quantify the underlying burden in 190 countries and territories, and explore the potential impact of the vaccine. We estimate that 104 countries have experienced transmission, covering 2.8 billion individuals and that in epidemic settings, the mean duration between outbreaks is 6.2 years, with 8.4% of the susceptible population infected per outbreak. Globally there are 33.7 million annual infections, driven by countries in Southeast Asia, Africa and the Americas. Assuming a vaccine efficacy against disease of 70% a protection against infection of 40%, vaccinating 50% of individuals over 12 years old in places and times where the virus circulates would avert 3,718 infections, 2.8 deaths and 158 DALYs per 100,000 doses used. These findings highlight the global burden and the significant potential of the vaccine.
Predicting the 10-year risk of cardiomyopathy in long-term survivors of childhood cancer: a report from the St. Jude Lifetime Cohort and the Childhood Cancer Survivor Study
Authors: Petrykey Kateryna , Chen Yan , Neupane Achal , French Jennifer , Wang Huiqi , Xiang Haoxue , Dixon Stephanie B. , Vukadinovich Chris , Im Cindy , Ehrhardt Matthew J. , Mulrooney Daniel A. , Sharafeldin Noha , Wang Xuexia , Howell Rebecca M. , Jefferies John L. , Burridge Paul W. , Oeffinger Kevin C. , Gramatges M. Monica , Bhatia Smita , Robison Leslie L. , Ness Kirsten K. , Hudson Melissa M. , Chow Eric J. , Armstrong Gregory T. , Yasui Yutaka , Sapkota Yadav
Published: October 2024

Purpose

Considering the heightened risk of cancer treatment-related cardiomyopathy and cardiac death in long-term survivors of childhood cancer, we aimed to develop and validate a clinically-applicable risk prediction model for cardiomyopathy.

Patients and Methods

Childhood cancer survivors from St. Jude Lifetime Cohort, (SJLIFE, model-development; n=3,479; median age 32.3 years, IQR 24.4-40.9) and Childhood Cancer Survivor Study (CCSS, model-validation; n=6,875; median age 33.2 years, IQR 27.9-38.9) were assessed for demographic and cardiovascular risk factors, treatment exposures, and polygenic risk scores (PRSs) for cardiomyopathy, heart failure, cardiac structure and function, and anthracycline-related cardiomyopathy risk. Multivariable Poisson regression predicted the 10-year risk of cardiomyopathy (CTCAE grade ≥3: requiring heart failure medications or heart transplantation or leading to death) following baseline visit/survey. Model performance was assessed by area under the receiver operating characteristic curve (AUC).

Results

Cardiomyopathy was clinically identified in 75 (2.2%, SJLIFE) and self-reported in 87 (1.3%, CCSS) survivors within 10 years of the baseline assessment. AUC of a clinical model with sex, age at cancer diagnosis, cumulative anthracycline and mean heart radiation doses was 0.833 (SJLIFE) and 0.812 (CCSS). Age at baseline, hypertension and genetic ancestry showed associations with higher cardiomyopathy rates in SJLIFE but did not increase AUC in CCSS (0.812). Adding PRSs for hypertrophic cardiomyopathy and left ventricular end-systolic volume improved AUC in CCSS (0.822;P=0.016). Compared to existing survivorship-care guidelines, the PRS model classified fewer survivors as high-risk or moderate-risk, while identifying survivors in those categories as having 1.5-times greater risk.

Conclusion

We developed and validated a model with highest-to-date performance for estimating the 10-year risk of cardiomyopathy in survivors of childhood cancer. Results could enhance identification of at-risk survivors beyond current guidelines.
Construction of a macrophage-tropic subtype C HIV-1 mGreenLantern reporter virus for studies on HIV-1 replication and the impact of methamphetamine
Authors: Mofed Dina , Mandarino Angelo , Wu Xuhong , Lang Yuekun , Gowripalan Anjali , Kalpana Ganjam V. , Prasad Vinayaka R.
Published: October 2024

HIV-1 subtype C viruses are responsible for 50% of global HIV burden. However, nearly all currently available reporter viruses widely used in HIV research are based on subtype B. We constructed and characterized a replication competent HIV-1 subtype C reporter virus expressing mGreenLantern. mGreenLantern sequences were inserted in-frame withnefATG in HIV-1IndieC1. As controls, we employed HIV-1IndieC1, HIV-1ADA,and HIV-1NLAD8-GFP-Nefviruses. HIV-1IndieC1-mGreenLantern(HIV-1IndieC1-mGL) exhibited characteristics of the parental HIV-1IndieC1virus, including its infectivity in TZMbl reporter cells and replication competence in macrophages. To further characterize HIV-1IndieC1-mGLvirus, we tested its responsiveness to CCL2 levels, a characteristic feature of subtype B HIV-1 that is missing in subtype C. CCL2 immunodepletion inhibited the production of HIV-1ADAand HIV-1NLAD8-GFP-Nefas expected, but not that of HIV-1IndieC1-mGLas previously reported. We also tested the effect of Methamphetamine, as its effect is mediated by NF-κB and since subtype C viruses carry an additional copy of NFκB. We found that methamphetamine increased the replication of all viruses tested in macrophages, however, its effect was much more robust for HIV-1IndieC1and HIV-1IndieC1-mGL. Our studies established that HIV-1IndieC1-mGLretains all the characteristics of the parental HIV-1IndieC1and can be a useful tool for HIV-1 subtype C investigations.
Optical control of sphingolipid biosynthesis using photoswitchable sphingosines
Authors: Kol Matthijs , Novak Alexander J.E. , Morstein Johannes , Schröer Christian , Sokoya Tolulope , Mensing Svenja , Korneev Sergei M. , Trauner Dirk , Holthuis Joost C.M.
Published: October 2024

Sphingolipid metabolism comprises a complex interconnected web of enzymes, metabolites and modes of regulation that influence a wide range of cellular and physiological processes. Deciphering the biological relevance of this network is challenging as numerous intermediates of sphingolipid metabolism are short-lived molecules with often opposing biological activities. Here, we introduce clickable, azobenzene-containing sphingosines, termedcaSphs, as light-sensitive substrates for sphingolipid biosynthesis. Photo-isomerization of the azobenzene moiety enables reversible switching between a straighttrans- and curvedcis-form of the lipid’s hydrocarbon tail. Combiningin vitroenzyme assays with metabolic labeling studies, we demonstrate thattrans-to-cisisomerization ofcaSphs profoundly stimulates their metabolic conversion by ceramide synthases and downstream sphingomyelin synthases. These light-induced changes in sphingolipid production rates are acute, reversible, and can be implemented with great efficiency in living cells. Our findings establishcaSphs as versatile tools with unprecedented opportunities to manipulate sphingolipid biosynthesis and function with the spatiotemporal precision of light.
Cortical norepinephrine-astrocyte signaling critically mediates learned behavior
Authors: Drummond Gabrielle T. , Natesan Arundhati , Celotto Marco , Shih Jennifer , Ojha Prachi , Osako Yuma , Park Jiho , Sipe Grayson O. , Jenks Kyle R. , Breton-Provencher Vincent , Simpson Paul C. , Panzeri Stefano , Sur Mriganka
Published: October 2024

Updating behavior based on feedback from the environment is a crucial means by which organisms learn and develop optimal behavioral strategies1–3. Norepinephrine (NE) release from the locus coeruleus (LC) has been shown to mediate learned behaviors4–6such that in a task with graded stimulus uncertainty and performance, a high level of NE released after an unexpected outcome causes improvement in subsequent behavior7. Yet, how the transient activity of LC-NE neurons, lasting tens of milliseconds, influences behavior several seconds later, is unclear. Here, we show that NE acts directly on cortical astrocytes via Adra1a adrenergic receptors to elicit sustained increases in intracellular calcium. Chemogenetic blockade of astrocytic calcium elevation prevents the improvement in behavioral performance. NE-activated calcium invokes purinergic pathways in cortical astrocytes that signal to neurons; pathway-specific astrocyte gene expression is altered in mice trained on the task, and blocking neuronal adenosine-sensitive A1 receptors also prevents post-reinforcement behavioral gain. Finally, blocking either astrocyte calcium dynamics or A1 receptors alters encoding of the task in prefrontal cortex neurons, preventing the post-reinforcement change in discriminability of rewarded and unrewarded stimuli underlying behavioral improvement. Together, these data demonstrate that astrocytes, rather than indirectly reflecting neuronal drive, play a direct, instrumental role in representing task-relevant information and signaling to neurons to mediate a fundamental component of learning in the brain.
Surface display of proximity labeling enzymes on extracellular vesicles for surfaceome and target cell mapping
Authors: Zheng Wenyi , Mowoe Metoboroghene , Hou Wenqing , Hagey Daniel W. , Imami Koshi , Andaloussi Samir EL
Published: October 2024

Extracellular vesicles (EV) surface proteins have important extracellular functions and determine cellular tropism; however, characterizing the EV surfaceome remains challenging with available methods. EV-mediated intercellular communication takes place primarily through interactions at the recipient cell membrane, underscoring the importance of methodological advances to map this interplay. Here, we leverage the proximity labeling enzyme APEX2 (Apurinic/Apyrimidinic Endodeoxyribonuclease 2) for high-fidelity analysis of the EV surfaceome and cellular tropism. Surface display of APEX2 on EVs is achieved through its genetic fusion with EV-sorting domains, such as CD63 and TSPAN2. Upon adding the substrates biotin-phenol and hydrogen peroxide, vesicle surface APEX2 enables biotinylation of EV integral and corona proteins as well as target cells in vitro. Further data mining of the EV surfaceome reveals potential scaffolds for the bioengineering of EVs. Altogether, we introduce a robust tool for EV surfaceome and target cell mapping and uncover novel EV-sorting domains for bioengineering.
Topological rearrangements activate the HerA-DUF anti-phage defense system
Authors: Rish Anthony D. , Fosuah Elizabeth , Shen Zhangfei , Marathe Ila A. , Wysocki Vicki H. , Fu Tian-Min
Published: October 2024

Leveraging the rich structural information provided by AlphaFold, we used integrated experimental approaches to characterize the HerA-DUF4297 (DUF) anti-phage defense system, in which DUF is of unknown function. To infer the function of DUF, we performed structure-guided genomic analysis and found that DUF homologs are universally present in bacterial immune defense systems. One notable homolog of DUF is Cap4, a universal effector with nuclease activity in CBASS, the most prevalent anti-phage system in bacteria. To test the inferred nuclease function of DUF, we performed biochemical experiments and discovered that the DUF only exhibits activity against DNA substrates when it is bound by HerA. To understand how HerA activates DUF, we determined the structures of DUF and the HerA-DUF complex. DUF forms large oligomeric assemblies with or without HerA, suggesting that oligomerization per se is not sufficient for DUF activation. Instead, DUF activation requires dramatic topological rearrangements that propagate from HerA to the entire HerA-DUF complex, leading to reorganization of DUF for effective DNA cleavage. We further validated these structural insights by structure- guided mutagenesis. Together, these findings reveal dramatic topological rearrangements throughout the HerA-DUF complex, challenge the long-standing dogma that protein oligomerization alone activates immune signaling, and may inform the activation mechanism of CBASS.
Generation of human iPSC-derived pancreatic organoids to study pancreas development and disease
Authors: Darrigrand Jean-Francois , Isaacson Abigail , Spagnoli Francesca M.
Published: October 2024

The pancreas has vital endocrine and exocrine functions that can be affected by life-threatening diseases such as diabetes and pancreatic cancer. While animal models have been essential for understanding pancreatic development and disease, they are limited by their low-throughput and major species-specific molecular and physiological differences. Generating 3D in vitro models, such as organoids, that are physiologically relevant is thus primordial for investigating pancreatic development and disease in the human context. However, producing human stem cell-derived pancreatic organoids with proper branched architecture and correct patterning of cell domains has remained challenging. Here, we successfully developed a protocol that efficiently and reproducibly generates such organoids from human induced pluripotent stem cells (hiPSCs) by optimising organoid culture format and media. Our differentiation protocol promotes acinar cell differentiation and generates organoids with branches patterned into central trunk and peripheral tip domains, without relying on animal-derived matrices for organoid culture. This platform opens the door to high-throughput investigations of human pancreas development in a system recapitulating the most important aspects of pancreatic tissue architecture. Lastly, we anticipate that this system will contribute to the partial replacement of animal models used to investigate diseases such as pancreatic cancer.
Fragmentation and Multithreading of Experience in the Default-Mode Network
Authors: Yazin Fahd , Majumdar Gargi , Bramley Neil , Hoffman Paul
Published: October 2024

Reliance on internal predictive models of the world is central to many theories of human cognition. Yet it is unknown whether humans acquired multiple separate internal models, each evolved for a specific domain, or maintain a globally unified representation. Using fMRI, we show that during naturalistic experiences (during movie watching or narrative listening), adult participants selectively engage three topographically distinct midline prefrontal cortical regions, for different forms of predictions. Regions responded selectively to abstract spatial, referential (social), and temporal domains during model updates implying separate representations for each. Prediction-error-driven neural transitions in these regions, indicative of model updates, preceded subjective belief changes in a domain-specific manner. We find these parallel top-down predictions are unified and selectively integrated with sensory streams in the Precuneus, shaping participants’ ongoing experience. Results generalized across sensory modalities and content, suggesting humans recruit abstract, modular predictive models for both vision and language. Our results highlight a key feature of human world modeling: fragmenting information into abstract domains before global integration.
The deubiquitinase Rpn11 functions as an allosteric ubiquitin sensor to promote substrate engagement by the 26S proteasome
Authors: Htet Zaw Min , Dong Ken C. , Martin Andreas
Published: October 2024

The 26S proteasome is the major compartmental protease in eukaryotic cells, responsible for the ATP-dependent turnover of obsolete, damaged, or misfolded proteins that are delivered for degradation through attached ubiquitin modifications. In addition to targeting substrates to the proteasome, ubiquitin was recently shown to promote degradation initiation by directly modulating the conformational switching of the proteasome, yet the underlying mechanisms are unknown. Here, we used biochemical, mutational, and single-molecule FRET-based approaches to show that the proteasomal deubiquitinase Rpn11 functions as an allosteric sensor and facilitates the early steps of degradation. After substrate recruitment to the proteasome, ubiquitin binding to Rpn11 interferes with conformation-specific interactions of the ubiquitin-receptor subunit Rpn10, thereby stabilizing the engagement-competent state of the proteasome and expediting substrate insertion into the ATPase motor for mechanical translocation, unfolding, and Rpn11-mediated deubiquitination. These findings explain how modifications with poly-ubiquitin chains or multiple mono-ubiquitins allosterically promote substrate degradation and allow up to four-fold faster turnover by the proteasome.