bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking
Authors: Jeppesen Mads , André Ingemar 
Published: June 2023

AbstractAlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 21 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.71. 15 had TM-scores of above 0.8 and were categorized as high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.
GDF15 is a Critical Renostat in the Defense Against Hypoglycemia
Authors: Li Zongyu , Zhang Xinyi , Zhu Wanling , Xu Qian , Yu Chuyue , Zhao Qiancheng , Siebel Stephan , Zhang Cuiling , Costa Lima Bruna Genisa , Li Xiruo , Israni-Winger Kavita , Nasiri Ali R. , Caplan Michael J. , Chang Rui B. , Wang Andrew , Belfort de Aguiar Renata , Hwang Janice J. , Perry Rachel J. 
Published: June 2023

SummaryEpisodic hypoglycemia is one of the best honed, evolutionary conserved phenomena in biology, because of the constant feast-fast cycles that have characterized most of history. The counterregulatory response to hypoglycemia, mobilizing substrate stores to produce glucose, is the primary adaptive mechanism to enable survival. Catecholamines and glucagon have long been considered the key hypoglycemia counterregulatory hormones, but here we identify a new hypoglycemia counterregulatory factor. We employed the insulin tolerance test (ITT) and hyperinsulinemic-hypoglycemic clamp to mimic the two common settings in which hypoglycemia can occur in patients: postprandial insulin overdose and elevated basal insulin administration, respectively. We found that Growth Differentiation Factor 15 (GDF15) production is induced in the S3 segment of the renal proximal tubules and its release increases hepatic gluconeogenesis by increasing intrahepatic lipolysis in a beta-adrenergic receptor-2 (Adrb2)-dependent manner. In addition, mice exposed to recurrent hypoglycemia and patients with T1D exhibit impaired GDF15 production in the setting of hypoglycemia. These data demonstrate that GDF15 acts acutely as a gluco-counterregulatory hormone and identify a critical role for kidney-derived GDF15 in glucose homeostasis under physiological and pathophysiological conditions.
Functional stress responses in Glaucophyta: evidence of ethylene and abscisic acid functions inCyanophora paradoxa
Authors: Genot Baptiste , Grogan Margaret , Yost Matthew , Iacono Gabriella , Archer Stephen D. , Burns John A. 
Published: June 2023

ABSTRACTGlaucophytes, an enigmatic group of freshwater algae, occupy a pivotal position within the Archaeplastida, providing insights into the early evolutionary history of plastids and their host cells. These algae possess unique plastids, known as cyanelles, that retain certain ancestral features, enabling a better understanding of the plastid transition from cyanobacteria. In this study, we investigated the role of ethylene, a potent hormone used by land plants to coordinate stress responses, in the glaucophyte algaCyanophora paradoxa.We demonstrate thatC. paradoxaproduces gaseous ethylene when supplied with exogenous 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor in land plants. In addition, we show that cells produce ethylene natively in response to abiotic stress, and that another plant hormone, abscisic acid (ABA), interferes with ethylene synthesis from exogenously supplied ACC, while positively regulating reactive oxygen species (ROS) accumulation. ROS synthesis also occurred following abiotic stress and ACC treatment, possibly acting as a second-messenger in stress responses. A physiological response ofC. paradoxato ACC treatment is growth inhibition. Using transcriptomics, we reveal that ACC treatment induces the upregulation of senescence-associated proteases, consistent with the observation of growth inhibition. This is the first report of hormone usage in a glaucophyte alga, extending our understanding of hormone-mediated stress response coordination into the Glaucophyta, with implications for the evolution of signaling modalities across Archaeplastida.
Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Safflower
Authors: Ren Chaoxiang , Xi Ziqing , Xian Bin , Chen Chao , Huang Xulong , Jiang Huajuan , Chen Jiang , Peng Cheng , Pei Jin 
Published: June 2023

AbstractSafflower (Carthamus tinctoriusL.) flowers are used as a traditional Chinese medicine for a long history. Flavonoids are the main bioactive components in safflower flowers, and most of them exist in the form of flavonoid glycosides. Only few glycosyltransferases have been identified in safflower. To reveal the uridine diphosphate glycosyltransferase (UGT) involved in flavonoid glycosides biosynthesis in safflower, a metabolomics and transcriptome analysis was performed by using the flowers under different light qualities treatments. Three differentially expressedUGTgenes were screened, and their expressions were significantly related with concentrations of 9 flavonoidO-glycosides. Safflower corolla protoplasts were further used to confirm flavonoidO-glycosylation ability of UGT candidates. The astragalin (kaempferol 3-O-glucoside) content was only significantly increased when CtUGT3 was overexpressed in protoplasts. The biochemical properties and kinetic parameters of CtUGT3 were determined. CtUGT3 also showed flavonoid 3-OH and 7-OH glycosylation activitiesin vitro. Molecular modeling and site-directed mutagenesis revealed that E384 and S276 were critical catalytic residues for the 3-OH glycosylation of CtUGT3. These results demonstrate that CtUGT3 has a flavonoid 3-OH glycosylation function and is involved in the biosynthesis of astragalin in safflower. This study provides insights into the catalytic mechanisms of flavonoidO-glycosyltransferases, and makes a reference for flavonoid biosynthesis genes research in medicinal plants.
CRISPR/Cas9 gene editing to generateDrosophilaLexA lines in secondary school classes
Authors: Rankin Anne E. , Fox Elizabeth , Chisholm Townley , Lantz Nicole , Rajan Arjun , Phillips William , Griffin Elizabeth , Harper Jaekeb , Suhr Christopher , Tan Max , Wang Jason , Yang Alana , Kim Ella S. , Ankrah Naa Kwama A. , Chakraborty Praachi , Lam Alistair C. K. , Laws Madeleine E. , Lee Jackson , Park Kyle , Wesel Emily , Covert Peter H. , Kockel Lutz , Park Sangbin , Kim Seung K. 
Published: June 2023

ABSTRACTGenome editingin vivowith CRISPR/Cas9 generates powerful tools to study gene regulation and function. We developed CRISPR-based methods that permitted secondary school student scientists to convertDrosophilaGAL4 lines to LexA lines. Our novel curricula implement a new donor strain optimizing Homology-assisted CRISPR knock-in (HACK) that simplifies screening using light microscopy. Successful curricula adoption by a consortium of schools led to the generation and characterization of 16 novel LexA lines. This includes extensive comparative tissue expression analysis between the parental Gal4 and derived LexA lines. From this collaboration, we established a workflow to systematically generate LexA lines from frequently-used GAL4 lines. Modular courses developed from this effort can be tailored to specific secondary school scheduling needs, and serve as a template for science educators to innovate courses and instructional goals. Our unique collaborations highlight that resources and expertise harnessed by university-based research laboratories can transform experiential science instruction in secondary schools while addressing research needs for the community of science.
α-tubulin regulation by 5’ introns inS. cerevisiae
Authors: Wethekam Linnea C. , Moore Jeffrey K. 
Published: June 2023

AbstractAcross eukaryotic genomes, multiple α- and β-tubulin genes require regulation to ensure sufficient production of tubulin heterodimers. Features within these gene families that regulate expression remain underexplored. Here we investigate the role of the 5’ intron in regulating α-tubulin expression inS. cerevisiae. We find that the intron in the α-tubulin,TUB1, promotes α-tubulin expression and cell fitness during microtubule stress. The role of theTUB1intron depends on proximity to theTUB1promoter and sequence features that are distinct from the intron in the alternative α-tubulin isotype,TUB3. These results lead us to perform a screen to identify genes that act with theTUB1intron. We identified several genes involved in chromatin remodeling, α/β-tubulin heterodimer assembly, and the spindle assembly checkpoint. We propose a model where theTUB1intron promotes expression from the chromosomal locus, and that this may represent a conserved mechanism for tubulin regulation under conditions that require high levels of tubulin production.Article Summaryα and β-tubulin proteins are encoded by families of genes that must be coordinately regulated to supply the αβ heterodimers that form microtubules. This study by Wethekam and Moore identifies a role for the early intron in the budding yeast α-tubulin, TUB1, in promoting gene function. A genetic screen reveals new tubulin regulators that act through the TUB1 intron. The results establish new layers of α-tubulin regulation that may be conserved across eukaryotes.
Overexpression of MUC1 influences the anti-proliferative effect of STAT3-inhibitor Napabucasin in epithelial cancers
Authors: Bose Mukulika , Sanders Alexa , Handa Aashna , Vora Aabha , Brouwer Cory , Mukherjee Pinku 
Published: June 2023

AbstractMUC1 is a transmembrane glycoprotein that is overexpressed and aberrantly glycosylated in epithelial cancers. The cytoplasmic tail of MUC1 (MUC1 CT) aids in tumorigenesis by upregulating the expression of multiple oncogenes. Signal transducer and activator of transcription 3 (STAT3) plays a crucial role in several cellular processes and is aberrantly activated in many cancers. In this study, we focus on recent evidence suggesting that STAT3 and MUC1 regulate each other’s expression in cancer cells in an auto-inductive loop and found that their interaction plays a prominent role in mediating epithelial-to-mesenchymal transition (EMT) and drug resistance. The STAT3 inhibitor Napabucasin was in clinical trials but was discontinued due to futility. We found that higher expression of MUC1 increased the sensitivity of cancer cells to Napabucasin. Therefore, high-MUC1 tumors may have a better outcome to Napabucasin therapy. We report how MUC1 regulates STAT3 activity and provide a new perspective on repurposing the STAT3-inhibitor Napabucasin to improve clinical outcome of epithelial cancer treatment.
Stereoscopic RNA Analysis of Transcriptional and Post-transcriptional Regulation
Authors: Lee Seungha Alisa , Kwak Hojoong 
Published: June 2023

SUMMARYRegulation of gene expression takes place at multiple stages of RNA synthesis, processing, and decay. The dynamics of RNA processing is an essential layer of RNA regulation, required for a deeper understanding of gene expression. Here, we present a streamlined analysis combining nascent RNA sequencing and poly(A) tail length sequencing methods, named Stereoscopic Analysis of Transcriptome (STOAT). Using this analysis, we were able to redefine known and unknown transcripts with high precision, and quantitatively assess RNA expression and stability. We also investigated poly(A) tail processing and their linkage to post-transcriptional features in different cell lines and identified the diversity of microRNA networks in RNA stability and opposing effects of HuR-TTP on poly(A) processing among human cell lines. This method can effectively measure promoter activity, RNA synthesis, poly(A) processing, stability, and decay, providing a comprehensive perspective of the dynamic transcriptome as well as discovering diverse transcript isoforms.MOTIVATIONRNA sequencing (RNA-seq) enables transcriptome-wide mapping and quantitative analysis, but it only provides a static view of the transcriptome. Also, due to its lack of standardization between sequencing platforms and read depth, it compromises reproducibility, and the cost remains prohibitive. To improve these limitations, we are presenting the minimal combination of two methods, nascent RNA sequencing and poly(A) tail length sequencing, which can effectively measure promoter activity, RNA synthesis, abundance, poly(A) processing, stability, and decay, and can discover diverse undefined transcript isoforms. This streamlined analysis of transcription rate and polyadenylation status will provide a comprehensive perspective of the dynamic transcriptome.
Essential Function of Transmembrane Transcription Factor MYRF in Promoting Transcription of miRNAlin-4duringC. elegansDevelopment
Authors: Xu Zhimin , Wang Zhao , Wang Lifang , Qi Yingchuan B. 
Published: June 2023

AbstractPrecise developmental timing control is essential for organism formation and function, but its mechanisms are unclear. InC. elegans, the microRNAlin-4critically regulates developmental timing by post-transcriptionally downregulating the larval-stage-fate controller LIN-14. However, the mechanisms triggering the activation oflin-4expression toward the end of the first larval stage remain unknown. We demonstrate that the transmembrane transcription factor MYRF-1 is necessary forlin-4activation. MYRF-1 is initially localized on the cell membrane, and its increased cleavage and nuclear accumulation coincide withlin-4expression timing. MYRF-1 regulateslin-4expression cell-autonomously and hyperactive MYRF-1 can prematurely drivelin-4expression in embryos and young first-stage larvae. The tandemlin-4promoter DNA recruits MYRF-1GFPto form visible loci in the nucleus, suggesting that MYRF-1 directly binds to thelin-4promoter. Our findings identify a crucial link in understanding developmental timing regulation and establish MYRF-1 as a key regulator oflin-4expression.
Retrospective Evaluation of the Eye Irritation Potential of Agrochemical Formulations
Authors: Choksi Neepa , Latorre Andreia , Catalano Shadia , Grivel Arthur , Baldassari James , Pires Janaina , Corvaro Marco , Silva Mariana , Ogasawara Maryanne , Inforzato Monique , Habe Priscila , Murata Rosana , Stinchcombe Stefan , Kolle Susanne , Masinja W. , Perjessy Gisele , Daniel Amber , Allen David 
Published: June 2023

AbstractWhile multiplein vitroeye irritation methods have been developed and adopted as OECD health effects test guidelines, only one is considered a complete replacement for thein vivorabbit eye test for classification and labelling for eye irritation hazard. Additionally, for most of the adopted methods there is a data gap on the applicability to predict the ocular irritation potential of agrochemical formulations. To overcome this data gap, a retrospective evaluation of 192 agrochemical formulations within vivo(OECD TG 405) orin vitro(OECD TG 437, 439, or 492) data was conducted to determine if thein vitromethods could accurately assign United Nations Globally Harmonized System for Classification and Labelling of Chemicals (GHS) eye irritation hazard classifications. In addition, for each of the final formulations and their individual components, we also conducted an evaluation of the GHS concentration threshold (CT) approach. The results herein suggest that the four individual methods and GHS CT approach were highly predictive of formulations that would not require classification for eye irritation hazard. Given most agrochemical formulations fall into this category, methods that accurately identify not classified mixtures could significantly reduce the use of animals for this endpoint.
hnRNPM and ELAVL1 control type I interferon induction by promoting IRF3 phosphorylation downstream of both cGAS and RIG-I
Authors: Kirchhoff Alexander , Herzner Anna-Maria , Urban Christian , Piras Antonio , Düster Robert , Wegner Julia , Grünewald Agathe , Schlee-Guimarães Thais M. , Ciupka Katrin , Leka Petro , Bootz Robert J. , de Regt Ann Kristin , Kümmerer Beate M. , Christensen Maria Hønholt , Schmidt Florian I. , Günther Claudia , Kato Hiroki , Bartok Eva , Hartmann Gunther , Geyer Matthias , Pichlmair Andreas , Schlee Martin 
Published: June 2023

ABSTRACTRIG-I and cGAS are crucial sensors of viral nucleic acids and induce type I IFNs via TBK1/IKK and IRF3. Here, we have identified hnRNPM as a novel positive regulator of IRF3 phosphorylation and type I IFN induction downstream of both cGAS and RIG-I. Combining interactome analysis and genome editing, we further identified ELAVL1 as an immune-relevant interactor of hnRNPM. Depletion of hnRNPM or ELAVL1 impaired type I IFN induction by HSV-1 and SeV. In addition, we found that hnRNPM and ELAVL1 interact with TBK1 and NF-kB p65. Confocal microscopy revealed cytosolic and perinuclear interactions between hnRNPM, ELAVL1, and TBK1. To our knowledge, hnRNPM and ELAVL1 represent the first non-redundant signaling components merging the cGAS-STING and RIG-I-MAVS pathways, thus representing a novel platform that fuels antiviral defense.
Interactive effects of salinity, temperature and food web configuration on performance and harmfulness of the raphidophyteHeterosigma akashiwo
Authors: Giesler Jakob Karl , Lemley Daniel Alan , Adams Janine Barbara , Moorthi Stefanie Devi 
Published: June 2023

AbstractThe cosmopolitan raphidophyteHeterosigma akashiwocommonly forms harmful algal blooms (HABs) in diverse estuaries discharging into Algoa Bay, South Africa, potentially leading to hypoxia, fish kills and a decline in key primary consumers. Despite the high environmental variability in these estuaries, little is known about how abiotic factors such as temperature and salinity constrain bloom formation and harmfulness ofH. akashiwo. The present study therefore investigates growth, competition, and grazing interactions of H. akashiwo in laboratory experiments in response to two naturally relevant levels of salinity (15, 30) and temperature (16, 22°C), respectively. Experiments were set up with the naturally co-occurring dinoflagellate competitorHeterocapsa rotundataand two estuarine microzooplankton consumers, i.e., nauplii of the copepodAcartia tonsaand the rotiferBrachionus plicatilis. In monoculture,H. akashiwogrowth was promoted at high temperature – low salinity conditions, whileH. rotundatathrived under low temperature – high salinity conditions. In polyculture,H. akashiwodominated at high temperature irrespective of the salinity regime, while at low temperature, it only dominated at low salinity and was suppressed byH. rotundataat high salinity. Grazing assays revealed highly negative effects ofH. akashiwoon copepod nauplii survival and growth as well as mucus-induced immobilization, especially at high temperatures in combination with low salinity, while the estuarine adapted rotifers showed highest mortalities at the higher salinity level. The presence ofH. rotundatasignificantly alleviated the harmful effects ofH. akashiwoon both grazers, and the selectively feeding copepod nauplii actively avoidedH. akashiwowhen non-harmful prey was present. Overall, this study demonstrates that population dynamics and harmful effects ofH. akashiwoare interactively determined by both abiotic conditions and food web configuration, implying competitor and consumer specific tolerances to the abiotic environment and their susceptibility to the harmful algaH. akashiwo.
The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genusCacajao)
Authors: Silva Felipe Ennes , Luna Leilton Willians , Batista Romina , Röhe Fabio , Gubili Chrysoula , Farias Izeni P. , Hrbek Tomas , do Amaral João Valsecchi , Ribas Camila C. , McDevitt Allan D. , Dellicour Simon , Flot Jean-François , Boubli Jean P. 
Published: June 2023

ABSTRACTAimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia.LocationWestern AmazoniaTaxonThe uakari monkey (genusCacajao)MethodsWe performed a continuous phylogeographic analysis using 77 cytochromebsequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution ofCacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in threeCacajaospecies that were impacted by river rearrangements.ResultsOur continuous phylogeographical reconstruction points that the ancestralCacajaolineage occupied the flooded forests of the Solimões River at ∼1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure inCacajao. The demographic analysis indicates thatC. calvus, C. amuna, andC. rubicunduswent through a population decline in the last 70 Kya and have a low effective population size.Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently divergedCacajaolineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated someCacajaopopulations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.
Mitochondrial fusion and altered beta-oxidation drive muscle wasting in aDrosophilacachexia model
Authors: Dark Callum , Ali Nashia , Golenkina Sofia , Blazev Ronnie , Parker Benjamin L , Murphy Katherine , Lynch Gordon , Senapati Tarosi , Millard S Sean , Judge Sarah M , Judge Andrew R , Cheng Louise Y 
Published: June 2023

AbstractCancer cachexia is a tumour-induced wasting syndrome, characterised by extreme loss of skeletal muscle. Defective mitochondria can contribute to muscle wasting; however, the underlying mechanisms remain unclear. Using aDrosophilalarval model of cancer cachexia, we observed enlarged and dysfunctional muscle mitochondria. Morphological changes were accompanied by upregulation of beta-oxidation proteins and depletion of muscle glycogen and lipid stores. Muscle lipid stores were also decreased in Colon-26 adenocarcinoma mouse muscle samples, and expression of the beta-oxidation geneCPT1Awas negatively associated with muscle quality in cachectic patients. Mechanistically, mitochondrial defects result from reduced muscle insulin signalling, downstream of tumour-secreted insulin growth factor binding protein (IGFBP) homolog ImpL2. Strikingly, muscle-specific inhibition of Forkhead box O (FOXO), mitochondrial fusion, or beta-oxidation in tumour-bearing animals preserved muscle integrity. Finally, dietary supplementation with nicotinamide or lipids, improved muscle health in tumour-bearing animals. Overall, our work demonstrates that muscle FOXO, mitochondria dynamics/beta-oxidation and lipid utilisation are key regulators of muscle wasting in cancer cachexia.