bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Mechanism of Huanglian Jiedu Decoction in Treatment of Alzheimer’s Disease based on Network Pharmacology
Authors: Ye Qiuyan , Li Xue , Gao Wei , Zhang Yutong , Zhang Miao-miao , Zheng Liping , Li Honglin 
Published: May 2024

AbstractPurposeThe aim of this study was to investigate the pharmacological mechanism of Huanglian Jiedu Decoction (HLJDD) in treating Alzheimer’s disease through network pharmacology. HLJDD is a classic Chinese medicine prescription that is recommended in the Chinese Alzheimer’s disease diagnosis and treatment guidelines. However, the mechanism of HLJDD treatment for Alzheimer’s disease (AD) remains unclear because of its complicated components.MethodsThe related ingredients and targets of HLJDD in treating AD were screened by Traditional Chinese Medicine Systems Pharmacology Database and Analysis platform (TCMSP), TTD, OMIM, GeneCards, and DrugBank. The data of the protein-protein interaction (PPI) network was constructed using STRING. The Metascape database was adopted for Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. AutoDockTools was used for molecular docking verification.ResultsIn the treatment of AD, HLJDD demonstrated strong efficacy with its core active components including were quercetin, β-sitosterol, stigmasterol, targeting key proteins such as AKT1, TNF, and IL6. Molecular docking tests confirmed the significant binding affinity between these components and the aforementioned targets. The biological pathway of HLJDD in treating AD primarily involves the modulation of IL-17, TNF, and other inflammatory cytokines to regulate their impact on nerve functions.ConclusionsHLJDD may treat AD by inhibiting neuroinflammation through a comprehensive, multi-component, multi-target, and multi-pathway method.
Mature adipocytes inhibit differentiation of myogenic cells but stimulate proliferation of fibro-adipogenic precursors derived from trout musclein vitro
Authors: Goffette Valentine , Sabin Nathalie , Bugeon Jerôme , Jagot Sabrina , Hue Isabelle , Gabillard Jean-Charles 
Published: May 2024

AbstractInteractions between tissues and cell types, mediated by cytokines or direct cell-cell exchanges, regulate growth. To determine whether mature adipocytes influence thein vitrodevelopment of trout mononucleated muscle cells, we developed an indirect coculture system, and showed that adipocytes (5×106cells/well) derived from perivisceral adipose tissue increased the proliferation (BrdU+) of the mononucleated muscle cells (26%versus39%; P<0.001) while inhibiting myogenic differentiation (myosin+) (25%versus15%; P<0.001). Similar effects were obtained with subcutaneous adipose tissue-derived adipocytes, although requiring more adipocytes (3×107cells/wellversus5×106cells/well). Conditioned media recapitulated these effects, stimulating proliferation (31%versus39%; p<0.001) and inhibiting myogenic differentiation (32%versus23%; p<0.001). Adipocytes began to reduce differentiation after 24 hours, whereas proliferation stimulation was observed after 48 hours. While adipocytes did not changepax7+andmyoD1/2+percentages, they reducedmyogenin+cells showing inhibition from early differentiation stage. Finally, adipocytes increased BrdU+cells in thePdgfrα+population but not in themyoD+one. Collectively, our results demonstrate that trout adipocytes promote fibro-adipocyte precursor proliferation while inhibiting myogenic cells differentiationin vitro, suggesting the key role of adipose tissue in regulating fish muscle growth.
Autofluorescence lifetime flow cytometry with time‐correlated single photon counting
Authors: Samimi Kayvan , Pasachhe Ojaswi , Guzman Emmanuel Contreras , Riendeau Jeremiah , Gillette Amani A. , Pham Dan L. , Wiech Kasia J. , Moore Darcie L. , Skala Melissa C. 
Published: May 2024

AbstractAutofluorescence lifetime imaging microscopy (FLIM) is sensitive to metabolic changes in single cells based on changes in the protein-binding activities of the metabolic co-enzymes NAD(P)H. However, FLIM typically relies on time-correlated single-photon counting (TCSPC) detection electronics on laser-scanning microscopes, which are expensive, low-throughput, and require substantial post-processing time for cell segmentation and analysis. Here, we present a fluorescence lifetime-sensitive flow cytometer that offers the same TCSPC temporal resolution in a flow geometry, with low-cost single-photon excitation sources, a throughput of tens of cells per second, and real-time single-cell analysis. The system uses a 375nm picosecond-pulsed diode laser operating at 50MHz, alkali photomultiplier tubes, an FPGA-based time tagger, and can provide real-time phasor-based classification (i.e., gating) of flowing cells. A CMOS camera produces simultaneous brightfield images using far-red illumination. A second PMT provides two-color analysis. Cells are injected into the microfluidic channel using a syringe pump at 2-5 mm/s with nearly 5ms integration time per cell, resulting in a light dose of 2.65 J/cm2that is well below damage thresholds (25 J/cm2at 375 nm). Our results show that cells remain viable after measurement, and the system is sensitive to autofluorescence lifetime changes in Jurkat T cells with metabolic perturbation (sodium cyanide), quiescent vs. activated (CD3/CD28/CD2) primary human T cells, and quiescent vs. activated primary adult mouse neural stem cells, consistent with prior studies using multiphoton FLIM. This TCSPC-based autofluorescence lifetime flow cytometer provides a valuable label-free method for real-time analysis of single-cell function and metabolism with higher throughput than laser-scanning microscopy systems.
A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato
Authors: Rosenkranz Remus RE , Vraggalas Stavros , Keller Mario , Sankaranarayanan Srimeenakshi , McNicoll François , Löchli Karin , Bublak Daniela , Benhamed Moussa , Crespi Martin , Berberich Thomas , Bazakos Christos , Feldbrügge Michael , Schleiff Enrico , Müller-McNicoll Michaela , Zarnack Kathi , Fragkostefanakis Sotirios 
Published: May 2024

AbstractHigh temperatures cause heat stress (HS), which has negative effects on plant growth and development and affects many cellular processes including pre-mRNA splicing. In tomato plants the splicing profile of many of genes is altered under HS, including that ofHSFA2, a central transcriptional regulator of thermotolerance. To identify the core splicing regulators of HS-sensitive alternative splicing, we usedHSFA2as bait and identified two plant-specific members of the serine/arginine-rich family of splicing factors, namely RS2Z35 and RS2Z36, that inhibitHSFA2intron splicing. Single and double CRISPR mutants of these proteins show dysregulated splicing of many genes and exhibit lower basal and acquired thermotolerance. Individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) of tomato leaves revealed that the majority of HS-sensitive alternatively spliced RNAs are bound by RS2Z35 and RS2Z36 and this interaction occurs at purine-rich RNA motifs. Phenotypic and transcriptome analyses revealed that RS2Z35 and RS2Z36 are important players in the stress response and thermotolerance in plants that mitigate the negative effects of HS on RNA splicing homeostasis.
Physiological role and mechanisms of action for a long noncoding haplotype region
Authors: Xue Hong , Mishra Manoj K. , Liu Yong , Liu Pengyuan , Grzybowski Michael , Pandey Rajan , Usa Kristie , Vanden Avond Mark A. , Bala Niharika , Alli Abdel A. , Cowley Allen W. , Qiu Qiongzi , Greene Andrew S. , Rao Sridhar , O’Meara Caitlin C. , Geurts Aron M. , Liang Mingyu 
Published: May 2024

ABSTRACTMost common sequence variants associated with human traits are in noncoding regions of the genome, form haplotypes with other noncoding variants, and exhibit small effect sizes in the general population. Determining the physiological roles and mechanisms of action for these noncoding variants, particularly large haplotypes containing multiple variants, is both critical and challenging. To address this challenge, we developed an approach that integrates physiological studies in genetically engineered and phenotypically permissive animal models, precise editing of large haplotypes in human induced pluripotent stem cells (hiPSCs), and targeted chromatin conformation analysis. We applied this approach to examine the blood pressure associated rs1173771 locus, which includes a haplotype containing 11 single nucleotide polymorphisms (SNPs) spanning 17.4 kbp. Deleting the orthologous noncoding region in the genome of the Dahl salt-sensitive rat attenuated the salt-induced increase in systolic blood pressure by nearly 10 mmHg. This attenuation of hypertension appeared to be mediated by upregulation of the adjacent geneNpr3(natriuretic peptide receptor 3) in arteries, enhancing vasodilation. The blood pressure-elevating and -lowering haplotypes were precisely reconstituted in hiPSCs using an efficient, two-step genome editing technique. The blood pressure-elevating haplotype decreased NPR3 expression in endothelial cells and vascular smooth muscle cells derived from the edited, isogenic hiPSCs. The influence of the haplotype was partially recapitulated by the sentinel SNP rs1173771. Additionally, the blood pressure-elevating haplotype showed significantly greater chromatin interactions with theNPR3promoter region. This study illustrates the feasibility of ascertaining the physiological roles and mechanisms of action for large noncoding haplotypes. Our efficient, integrated, and targeted approach can be applied to investigate other noncoding variants.
Catechol acetylglucose: A newly identified benzoxazinoid-regulated defensive metabolite in maize
Authors: Richter Annett , Schroeder Allen F. , Marcon Caroline , Hochholdinger Frank , Jander Georg , Negin Boaz 
Published: May 2024

AbstractAn enormous diversity of specialized metabolites is produced in the plant kingdom, with each individual plant synthesizing thousands of these compounds. Previous research showed that benzoxazinoids, the most abundant class of specialized metabolites in maize, also function as signaling molecules by regulating the production callose as a defense response. In this study, we identified catechol acetylglucose (CAG) as a benzoxazinoid-regulated metabolite that is produced from salicylic acid via catechol and catechol-glucoside. Genome wide association studies of CAG abundance identified a gene encoding a predicted acetyltransferase. Knockout of this gene resulted in maize plants that lack CAG and over-accumulate catechol glucoside. Upon tissue disruption, maize plants accumulate catechol, which inhibitsSpodoptera frugiperda(fall armyworm) growth. Analysis of caterpillar frass showed thatS. frugiperdadetoxifies catechol by glycosylation, and the efficiency of catechol glycosylation was correlated withS. frugiperdagrowth on a catechol-containing diet. Thus, the success ofS. frugiperdaas an agricultural pest may depend partly on its ability to detoxify catechol, which is produced as a defensive metabolite by maize plants.
Expanding the Triangle of U: The genome assembly ofHirschfeldia incanaprovides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits
Authors: Hoang Nam V. , Walden Nora , Caracciolo Ludovico , Luoni Sofia Bengoa , Retta Moges , Li Run , Wolters Felicia C. , Woldu Tina , Becker Frank F. M. , Verbaarschot Patrick , Harbinson Jeremy , Driever Steven M. , Struik Paul C. , Amerongen Herbert van , de Ridder Dick , Aarts Mark G.M. , Schranz M. Eric 
Published: May 2024

ABSTRACTThe Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ∼15.9 million years ago), different lineages and species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention and loss (fractionation). Lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. The C3speciesHirschfeldia incanais studied as it displays high photosynthetic rates under high-light conditions. We present an improved chromosome-level genome assembly forH. incana(Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation allowed to investigate the WGT history ofH. incanain a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops.Hirschfeldia incana(x=7) shares extensive genome collinearity withRaphanus sativus(x=9). These two species share some commonalities withBrassica rapaandB. oleracea(A genome, x=10 and C genome, x=9, respectively) and other similarities withB. nigra(B genome, x=8). Phylogenetic analysis revealed thatH. incanaandR. sativusform a monophyletic clade in between theBrassicaA/C and B genomes. We postulate thatH. incanaandR. sativusgenomes are results of reciprocal hybridization combinations of theBrassicaA/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement ofH. incanaandR. sativusin relation to the “Triangle of U” species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed inH. incanawhich likely facilitate its high-photosynthesis traits under high light.
Impact of flagellated and elongated morphological phenotypes on the focusing behaviours of biological cells in inertial microfluidic devices
Authors: Howell Jessie , Hall Nicole , Omwenga Sulochana , Hammarton Tansy C. , Jimenez Melanie 
Published: May 2024

AbstractInertial microfluidics has demonstrated tremendous potential to impact biological - and notably medical - fields, by offering a highly versatile, portable and cost-effective approach to cell focusing and sorting. While the range of applications of inertial devices spans medical diagnostics, bioprocessing or water engineering to mention a few, translation is still impeded by the lack of clear understanding of cell interactions in such devices. This often leads to bespoke designs that take years of development and characterisation for one targeted application, and limited tools for informed optimisation. A more fundamental knowledge of inertial behaviours is key to future translational works and impact, by enabling a deeper understanding of inertial forces in biological systems. Towards this goal, this paper focuses on high-throughput morphological phenotyping of the single-celled, flagellated parasiteLeishmania mexicanato better understand how variations in cell body length, width and flagellated status impact the focusing patterns of highly non-spherical cells in curved inertial devices. Some of the key findings in this study include i) not all organelles, such as flagella, will alter focusing if the body shape is conserved, ii) the impact of cell shape is specific to a channel design and slight changes in e.g., cell confinement can completely change focusing patterns, iii) elongated prolate-like cells align in different orientations depending on their lateral position with a curved channel and iv) despite variabilities observed in focusing patterns for elongated versus rounder cell phenotypes, large morphological variations can be completely overcome at high Reynolds numbers so that all phenotypes tightly focus at a single position (here towards the channel outer wall). This last finding, in particular, may open new avenues for highly efficient cell enrichment processes, such as for the detection of pathogens in water.
Reduced beta-hydroxybutyrate disposal after ketogenic diet feeding in mice
Authors: Cousineau Cody M , Snyder Detrick , Redd JeAnna R. , Turner Sophia , Carr Treyton , Bridges Dave 
Published: May 2024

ABSTRACTThe ketogenic diet (KD) has garnered considerable attention due to its potential benefits in weight loss, health improvement, and performance enhancement. However, the phenotypic responses to KD vary widely between individuals. Skeletal muscle is a major contributor to ketone body (KB) catabolism, however, the regulation of ketolysis is not well understood. In this study, we evaluated how mTORC1 activation and a ketogenic diet modify ketone body disposal in muscle Tsc1 knockout (KO) mice, inbred A/J mice, and Diversity Outbred (DO) mice. Muscle Tsc1 KO mice demonstrated enhanced ketone body clearance. Contrary to expectations, KD feeding in A/J mice did not improve KB disposal, and in most strains disposal was reduced. Transcriptional analysis revealed reduced expression of important ketolytic genes in KD-fed A/J mice, suggesting impaired KB catabolism. Diversity Outbred (DO) mice displayed variable responses to KD, with most mice showing worsened KB disposal. Exploratory analysis on these data suggest potential correlations between KB disposal and cholesterol levels as well as weight gain on a KD. Our findings suggest that ketone body disposal may be regulated by both nutritional and genetic factors and these relationships may help explain interindividual variability in responses to ketogenic diets.
Protein CoAlation on TXNRD2 regulates mitochondrial thioredoxin system to protect against ferroptosis
Authors: Lin Chao-Chieh , Lin Yi-Tzu , Chen Ssu-Yu , Setayeshpour Yasaman , Chen Yubin , Dunn Denise E , Soderblom Erik J , Zhang Guo-Fang , Filonenko Valeriy , Jeong Suh Young , Floyd Scott , Hayflick Susan J , Gout Ivan , Chi Jen-Tsan 
Published: May 2024

AbstractThe Cystine-xCT transporter-Glutathione (GSH)-GPX4 axis is the canonical pathway to protect against ferroptosis. While not required for ferroptosis-inducing compounds (FINs) targeting GPX4, FINs targeting the xCT transporter require mitochondria and its lipid peroxidation to trigger ferroptosis. However, the mechanism underlying the difference between these FINs is still unknown. Given that cysteine is also required for coenzyme A (CoA) biosynthesis, here we show that CoA supplementation specifically prevents ferroptosis induced by xCT inhibitors but not GPX4 inhibitors. We find that, auranofin, a thioredoxin reductase inhibitor, abolishes the protective effect of CoA. We also find that CoA availability determines the enzymatic activity of thioredoxin reductase, but not thioredoxin. Importantly, the mitochondrial thioredoxin system, but not the cytosolic thioredoxin system, determines CoA-mediated ferroptosis inhibition. Our data show that the CoA regulates thein vitroenzymatic activity of mitochondrial thioredoxin reductase (TXNRD2) by covalently modifying the thiol group of cysteine (CoAlation) on Cys-483. Replacing Cys-483 with alanine on TXNRD2 abolishes itsin vitroenzymatic activity and ability to protect cells from ferroptosis. Targeting xCT to limit cysteine import and, therefore, CoA biosynthesis reduced CoAlation on TXNRD2, an effect that was rescued by CoA supplementation. Furthermore, the fibroblasts from patients with disrupted CoA metabolism demonstrate increased mitochondrial lipid peroxidation. In organotypic brain slice cultures, inhibition of CoA biosynthesis leads to an oxidized thioredoxin system, mitochondrial lipid peroxidation, and loss in cell viability, which were all rescued by ferrostatin-1. These findings identify CoA-mediated post-translation modification to regulate the thioredoxin system as an alternative ferroptosis protection pathway with potential clinical relevance for patients with disrupted CoA metabolism.
High-throughput screening of more than 30,000 compounds for anthelmintics against gastrointestinal nematode parasites
Authors: Elfawal Mostafa A. , Goetz Emily , Kim You-Mie , Chen Paulina , Savinov Sergey N. , Barasa Leonard , Thompson Paul R. , Aroian Raffi V. 
Published: May 2024

AbstractGastrointestinal nematodes (GINs) are amongst the most common parasites of humans, livestock, and companion animals. GIN parasites infect 1-2 billion people worldwide, significantly impacting hundreds of millions of children, pregnant women, and adult workers, thereby perpetuating poverty. Two benzimidazoles with suboptimal efficacy are currently used to treat GINs in humans as part of mass drug administrations, with many instances of lower-than-expected or poor efficacy and possible resistance. Thus, new anthelmintics are urgently needed. However, screening methods for new anthelmintics using human GINs typically have low throughput. Here, using our novel screening pipeline that starts with human hookworms, we screened 30,238 unique small molecules from a wide range of compound libraries, including ones with generic diversity, repurposed drugs, natural derivatives, known mechanisms of action, as well as multiple target-focused libraries (e.g., targeting kinases, GPCRs, and neuronal proteins). We identified 55 compounds with broad-spectrum activity against adult stages of two evolutionary divergent GINs, hookworms (Ancylostoma ceylanicum) and whipworms (Trichuris muris). Based on known databases, the targets of these 55 compounds were predicted in nematode parasites. One novel scaffold from the diversity set library, F0317-0202, showed good activity (high motility inhibition) against both GINs. To better understand this novel scaffold’s structure-activity relationships (SAR), we screened 28 analogs and created SAR models highlighting chemical and functional groups required for broad-spectrum activity. These studies validate our new and efficient screening pipeline at the level of tens of thousands of compounds and provide an important set of new GIN-active compounds for developing novel and broadly-active anthelmintics.
Homeodomain transcription factors in adipocyte thermogenesis: insights into the species-specific and conserved regulatory elements of human UCP1
Authors: B. Tóth Beáta , Hegedűs Géza , Virág Eszter , Pethő Gergely Tamás , Laczkó Levente , Fésüs László 
Published: May 2024

AbstractAdipocyte thermogenesis is a promising target for treating metabolic disorders, but its regulatory mechanisms remain unclear. This study investigates transcription factors (TFs) and regulatory elements that may control the humanUCP1gene, which is essential for thermogenesis and the formation of the adipocyte phenotype. Using the Eukaryota Promoter Database, we performed computational analyses of theUCP1, UCP2andUCP3promoter sequences in humans, mice and rats to identify conserved and species-specific elements. We also used transcriptome data from human neck-derived adipocytes and databases (Contra v3, ChiPBase, TFlink, AdipoNet, ISMARA, etc.) to narrow potential regulatory TFs. Our results show that mouse and ratUCP1enhancers lack large segments, primarily due to the insertion of repetitive elements that are already lost in some clades. We identified key TFs such as PPARA, PPARG, THR, RARE, RXR, JUN, TFAP2 and SREBF1 as general regulators ofUCPs.Additionally, human-specificUCP1regulatory hotspots (e.g. 5’-TCTAATTAGA-3’) recognised by homeodomain TFs (e.g. EN1, PAX4, HOXA5 and PRRX2) and NFIL3 were detected. Phylogenetically conserved regulatory elements suggest common TFs in humanUCP1paralogues (MAX, MYCN, MNT, HES1) and cross-species (POU6F1). These results improve our understanding of thermogenic adipocyte development and provide new therapeutic targets for metabolic diseases.Graphical Abstract