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1.
Mol Cell ; 82(10): 1821-1835.e6, 2022 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-35381197

RESUMEN

GLS1 orchestrates glutaminolysis and promotes cell proliferation when glutamine is abundant by regenerating TCA cycle intermediates and supporting redox homeostasis. CB-839, an inhibitor of GLS1, is currently under clinical investigation for a variety of cancer types. Here, we show that GLS1 facilitates apoptosis when glutamine is deprived. Mechanistically, the absence of exogenous glutamine sufficiently reduces glutamate levels to convert dimeric GLS1 to a self-assembled, extremely low-Km filamentous polymer. GLS1 filaments possess an enhanced catalytic activity, which further depletes intracellular glutamine. Functionally, filamentous GLS1-dependent glutamine scarcity leads to inadequate synthesis of asparagine and mitogenome-encoded proteins, resulting in ROS-induced apoptosis that can be rescued by asparagine supplementation. Physiologically, we observed GLS1 filaments in solid tumors and validated the tumor-suppressive role of constitutively active, filamentous GLS1 mutants K320A and S482C in xenograft models. Our results change our understanding of GLS1 in cancer metabolism and suggest the therapeutic potential of promoting GLS1 filament formation.


Asunto(s)
Glutaminasa , Glutamina , Apoptosis , Asparagina/genética , Glutaminasa/genética , Glutaminasa/metabolismo , Glutamina/metabolismo , Humanos , Especies Reactivas de Oxígeno
2.
Plant Cell ; 34(12): 4816-4839, 2022 11 29.
Artículo en Inglés | MEDLINE | ID: mdl-36040191

RESUMEN

Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of VLCFAs and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level.


Asunto(s)
Giberelinas , Gossypium , Gossypium/genética , Gossypium/metabolismo , Giberelinas/metabolismo , Regulación de la Expresión Génica de las Plantas , Fibra de Algodón , Pared Celular/metabolismo , Celulosa/metabolismo
3.
Mol Cell Proteomics ; 22(2): 100490, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36566904

RESUMEN

Aspergillus flavus is a common saprophytic and pathogenic fungus, and its secondary metabolic pathways are one of the most highly characterized owing to its aflatoxin (AF) metabolite affecting global economic crops and human health. Different natural environments can cause significant variations in AF synthesis. Succinylation was recently identified as one of the most critical regulatory post-translational modifications affecting metabolic pathways. It is primarily reported in human cells and bacteria with few studies on fungi. Proteomic quantification of lysine succinylation (Ksuc) exploring its potential involvement in secondary metabolism regulation (including AF production) has not been performed under natural conditions in A. flavus. In this study, a quantification method was performed based on tandem mass tag labeling and antibody-based affinity enrichment of succinylated peptides via high accuracy nano-liquid chromatography with tandem mass spectrometry to explore the succinylation mechanism affecting the pathogenicity of naturally isolated A. flavus strains with varying toxin production. Altogether, 1240 Ksuc sites in 768 proteins were identified with 1103 sites in 685 proteins quantified. Comparing succinylated protein levels between high and low AF-producing A. flavus strains, bioinformatics analysis indicated that most succinylated proteins located in the AF biosynthetic pathway were downregulated, which directly affected AF synthesis. Versicolorin B synthase is a key catalytic enzyme for heterochrome B synthesis during AF synthesis. Site-directed mutagenesis and biochemical studies revealed that versicolorin B synthase succinylation is an important regulatory mechanism affecting sclerotia development and AF biosynthesis in A. flavus. In summary, our quantitative study of the lysine succinylome in high/low AF-producing strains revealed the role of Ksuc in regulating AF biosynthesis. We revealed novel insights into the metabolism of AF biosynthesis using naturally isolated A. flavus strains and identified a rich source of metabolism-related enzymes regulated by succinylation.


Asunto(s)
Aflatoxinas , Aspergillus flavus , Humanos , Aspergillus flavus/metabolismo , Lisina/metabolismo , Proteómica , Aflatoxinas/metabolismo , Procesamiento Proteico-Postraduccional
4.
J Am Chem Soc ; 146(7): 4455-4466, 2024 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-38335066

RESUMEN

Cytochrome c (cyt c) is a multifunctional protein with varying conformations. However, the conformation of cyt c in its native environment, mitochondria, is still unclear. Here, we applied NMR spectroscopy to investigate the conformation and location of endogenous cyt c within intact mitochondria at natural isotopic abundance, mainly using widespread methyl groups as probes. By monitoring time-dependent chemical shift perturbations, we observed that most cyt c is located in the inner mitochondrial membrane and partially unfolded, which is distinct from its native conformation in solution. When suffering oxidative stress, cyt c underwent oxidative modifications due to increasing reactive oxygen species (ROS), weakening electrostatic interactions with the membrane, and gradually translocating into the inner membrane spaces of mitochondria. Meanwhile, the lethality of oxidatively modified cyt c to cells was reduced compared with normal cyt c. Our findings significantly improve the understanding of the molecular mechanisms underlying the regulation of ROS by cyt c in mitochondria. Moreover, it highlights the potential of NMR to monitor high-concentration molecules at a natural isotopic abundance within intact cells or organelles.


Asunto(s)
Citocromos c , Mitocondrias , Citocromos c/química , Especies Reactivas de Oxígeno/metabolismo , Mitocondrias/metabolismo , Oxidación-Reducción , Membranas Mitocondriales/metabolismo
5.
J Biomol NMR ; 78(2): 87-94, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38530516

RESUMEN

The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S2 to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite complex and lengthy. In this paper, we present a machine learning approach for predicting backbone 1H-15N order parameters based on protein NMR structure ensemble. A random forest model is used to learn the relationship between order parameters and structural features. Our method achieves high accuracy in predicting backbone 1H-15N order parameters for a test dataset of 10 proteins, with a Pearson correlation coefficient of 0.817 and a root-mean-square error of 0.131.


Asunto(s)
Aprendizaje Automático , Resonancia Magnética Nuclear Biomolecular , Conformación Proteica , Proteínas , Proteínas/química , Resonancia Magnética Nuclear Biomolecular/métodos
6.
Anal Chem ; 2024 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-39263786

RESUMEN

Herbal extracts are rich sources of active compounds that can be used for drug screening due to their diverse and unique chemical structures. However, traditional methods for screening these compounds are notably laborious and time-consuming. In this manuscript, we introduce a new high-throughput approach that combines nuclear magnetic resonance (NMR) spectroscopy with a tailored database and algorithm to rapidly identify bioactive components in herbal extracts. This method distinguishes characteristic signals and structural motifs of active constituents in the raw extracts through a relaxation-weighted technique, particularly utilizing the perfect echo Carr-Purcell-Meiboom-Gill (peCPMG) sequence, complemented by precise 2D spectroscopic strategies. The cornerstone of our approach is a customized database designed to filter potential compounds based on defined parameters, such as the presence of CHn segments and unique chemical shifts, thereby expediting the identification of promising compounds. This innovative technique was applied to identifying substances interacting with choline kinase α (ChoKα1), resulting in the discovery of four new inhibitors. Our findings demonstrate a powerful tool for unraveling the complex chemical landscape of herbal extracts, considerably facilitating the search for new pharmaceutical candidates. This approach offers an efficient alternative to traditional methods in the quest for drug discovery from natural sources.

7.
Anal Chem ; 2024 Feb 09.
Artículo en Inglés | MEDLINE | ID: mdl-38334355

RESUMEN

Abnormal fatty acid metabolism is recognized as a key driver of tumor development and progression. Although numerous inhibitors have been developed to target this pathway, finding drugs with high specificity that do not disrupt normal cellular metabolism remains a formidable challenge. In this paper, we introduced a novel real-time NMR-based drug screening technique that operates within living cells. This technique provides a direct way to putatively identify molecular targets involved in specific metabolic processes, making it a powerful tool for cell-based drug screening. Using 2-13C acetate as a tracer, combined with 3D cell clusters and a bioreactor system, our approach enables real-time detection of inhibitors that target fatty acid metabolism within living cells. As a result, we successfully demonstrated the initial application of this method in the discovery of traditional Chinese medicines that specifically target fatty acid metabolism. Elucidating the mechanisms behind herbal medicines remains challenging due to the complex nature of their compounds and the presence of multiple targets. Remarkably, our findings demonstrate the significant inhibitory effect of P. cocos on fatty acid synthesis within cells, illustrating the potential of this approach in analyzing fatty acid metabolism events and identifying drug candidates that selectively inhibit fatty acid synthesis at the cellular level. Moreover, this systematic approach represents a valuable strategy for discovering the intricate effects of herbal medicine.

8.
J Gene Med ; 26(1): e3654, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38282153

RESUMEN

BACKGROUND: The present study aimed to explore the biological role and underlying mechanism of the long non-coding RNA actin filament-associated protein 1-antisense RNA1 (lncRNA AFAP1-AS1) in the progression of tongue squamous cell carcinoma (TSCC). METHODS: A quantitative reverse transcriptase-PCR (RT-qPCR) was conducted to assess relative levels of the miR-133a-5p, lncRNAs AFAP1-AS1 and zinc finger family member 2 (ZIC2) in TSCC cell lines and specimens, whereas ZIC2 protein levels were measured using western blotting. After modifying the levels of expression of lncRNA AFP1-AS1, miR-133a-5p and ZIC2 using lentivirus or plasmid transfection, we examined AKT/epithelial-mesenchymal transition signaling pathway alterations, in vivo carcinogenesis of TSCC in nude mice and in vitro malignant phenotypes. A dual-luciferase reporter assay was conducted to confirm the targeting relationship between ZIC2 and miR-133a-5p, as well as between miR-133a-5p and lncRNA AFAP1-AS1. Based on The Cancer Genome Atlas (TCGA) database, we additionally validated AFP1-AS1. The potential biological pathway for AFP1-AS1 was investigated using gene set enrichment analysis (GSEA). We also evaluated the clinical diagnostic capacities of AFP1-AS1 and clustered the most potential biomarkers with the Mfuzz expression pattern. Finally, we also made relevant drug predictions for AFP1-AS1. RESULTS: In TSCC cell lines and specimens, lncRNA AFAP1-AS1 was upregulated. ZIC2 was upregulated in TSCC cells as a result of lncRNA AFAP1-AS1 overexpression, which also promoted TSCC cell migration, invasion, viability, and proliferation. Via the microRNA sponge effect, it was found that lncRNA AFAP1-AS1 could upregulate ZIC2 by competitively inhibiting miR-133a-5p. Interestingly, knockdown of ZIC2 reversed the biological roles of lncRNA AFAP1-AS1 with respect to inducing malignant phenotypes in TSCC cells. In addition, in vivo overexpression of lncRNA AFAP1-AS1 triggered subcutaneous tumor growth in nude mice implanted with TSCC cells and upregulated ZIC2 in the tumors. The TCGA database findings revealed that AFAP1-AS1 was significantly upregulated in TSCC specimens and had good clinical diagnostic value. The results of GSEA showed that peroxisome proliferator-activated receptor signaling pathway was significantly correlated with low expression of AFP1-AS1. Finally, the results of drug prediction indicated that the group with high AFAP1-AS1 expression was more sensitive to docetaxel, AZD4547, AZD7762 and nilotinib. CONCLUSIONS: The upregulation of lncRNA AFAP1-AS1, which increases TSCC cell viability, migration, proliferation and invasion via the AFAP1-AS1/miR-133a-5p/ZIC2 axis, aids in the progression of TSCC.


Asunto(s)
Carcinoma de Células Escamosas , MicroARNs , ARN sin Sentido , ARN Largo no Codificante , Neoplasias de la Lengua , Animales , Ratones , Citoesqueleto de Actina/metabolismo , Carcinoma de Células Escamosas/genética , Línea Celular Tumoral , Proliferación Celular/genética , Regulación Neoplásica de la Expresión Génica , Ratones Desnudos , Proteínas de Microfilamentos/genética , MicroARNs/genética , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Neoplasias de la Lengua/genética , ARN sin Sentido/genética
9.
Radiology ; 310(2): e231710, 2024 02.
Artículo en Inglés | MEDLINE | ID: mdl-38319165

RESUMEN

Background Preoperative recognition of irreversible bowel necrosis is important, as it provides valuable guidance for surgical strategy selection but also may inform perioperative risk assessment and communication. Few studies have focused on the association between CT signs and bowel necrosis. Purpose To assess the diagnostic accuracy of CT signs to predict bowel necrosis in patients with closed-loop small bowel obstruction (CL-SBO). Materials and Methods This retrospective single-center study included patients who were surgically confirmed to have CL-SBO caused by adhesion or internal hernia between January 2016 and May 2022. Necrosis was determined based on surgical exploration and postoperative pathologic examination. Two radiologists independently reviewed CT signs by both subjective visual assessment and objective measurement. Disagreements were resolved in consensus with a third gastrointestinal radiologist. Univariable and multivariable analyses were used to assess the association between CT signs and bowel necrosis, and Cohen κ was used to assess interobserver agreement. Sensitivity and specificity were calculated for each CT sign. Results This study included 145 patients: 61 (42.1%) in the necrotic group (median age, 62 years [IQR, 51-71.5 years]; 37 [60.7%] women) and 84 (57.9%) in the nonnecrotic group (median age, 61.5 years [IQR, 51-68.8 years]; 51 [60.7%] women). Univariable analysis and multivariable analysis showed that increased attenuation of intestinal contents and increased attenuation of intestinal wall were independent predictors for bowel necrosis (odds ratio = 45.3 and 15.1; P = .001 and P < .001, respectively). Increased attenuation of intestinal contents and increased attenuation of intestinal wall had similar sensitivity (64% and 67%, respectively) and specificity (99% and 92%, respectively) for predicting bowel necrosis. However, interobserver agreement was better for assessing the contents than the wall (κ = 0.84 and 0.59, respectively). Conclusion Increased attenuation of intestinal contents was a highly specific CT sign with good reproducibility to predict bowel necrosis in CL-SBO. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Taourel and Zins in this issue.


Asunto(s)
Contenido Digestivo , Obstrucción Intestinal , Humanos , Femenino , Persona de Mediana Edad , Masculino , Reproducibilidad de los Resultados , Estudios Retrospectivos , Obstrucción Intestinal/diagnóstico por imagen , Obstrucción Intestinal/cirugía , Necrosis/diagnóstico por imagen , Tomografía Computarizada por Rayos X
10.
Radiology ; 313(1): e240137, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39404632

RESUMEN

Background Clinical outcome prediction based on acute-phase ischemic stroke data is valuable for planning health care resources, designing clinical trials, and setting patient expectations. Existing methods require individualized features and often involve manually engineered, time-consuming postprocessing activities. Purpose To predict the 90-day modified Rankin Scale (mRS) score with a deep learning (DL) model fusing noncontrast-enhanced CT (NCCT) and clinical information from the acute phase of stroke. Materials and Methods This retrospective study included data from six patient datasets from four multicenter trials and two registries. The DL-based imaging and clinical model was trained by using NCCT data obtained 1-7 days after baseline imaging and clinical data (age; sex; baseline and 24-hour National Institutes of Health Stroke Scale scores; and history of hypertension, diabetes, and atrial fibrillation). This model was compared with models based on either NCCT or clinical information alone. Model-specific mRS score prediction accuracy, mRS score accuracy within 1 point of the actual mRS score, mean absolute error (MAE), and performance in identifying unfavorable outcomes (mRS score, >2) were evaluated. Results A total of 1335 patients (median age, 71 years; IQR, 60-80 years; 674 female patients) were included for model development and testing through sixfold cross validation, with distributions of 979, 133, and 223 patients across training, validation, and test sets in each of the six cross-validation folds, respectively. The fused model achieved an MAE of 0.94 (95% CI: 0.89, 0.98) for predicting the specific mRS score, outperforming the imaging-only (MAE, 1.10; 95% CI: 1.05, 1.16; P < .001) and the clinical information-only (MAE, 1.00; 95% CI: 0.94, 1.05; P = .04) models. The fused model achieved an area under the receiver operating characteristic curve (AUC) of 0.91 (95% CI: 0.89, 0.92) for predicting unfavorable outcomes, outperforming the clinical information-only model (AUC, 0.88; 95% CI: 0.87, 0.90; P < .001) and the imaging-only model (AUC, 0.85; 95% CI: 0.84, 0.87; P < .001). Conclusion A fused DL-based NCCT and clinical model outperformed an imaging-only model and a clinical-information-only model in predicting 90-day mRS scores. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Lee in this issue.


Asunto(s)
Aprendizaje Profundo , Accidente Cerebrovascular Isquémico , Tomografía Computarizada por Rayos X , Humanos , Femenino , Masculino , Accidente Cerebrovascular Isquémico/diagnóstico por imagen , Estudios Retrospectivos , Anciano , Tomografía Computarizada por Rayos X/métodos , Persona de Mediana Edad , Anciano de 80 o más Años , Valor Predictivo de las Pruebas
11.
Mol Carcinog ; 63(11): 2237-2253, 2024 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-39150096

RESUMEN

C1R has been identified to have a distinct function in cutaneous squamous cell carcinoma that goes beyond its role in the complement system. However, it is currently unknown whether C1R is involved in the progression of hepatocellular carcinoma (HCC). HCC tissues were used to examine C1R expression in relation to clinical and pathological factors. Malignant characteristics of HCC cells were assessed through in vitro and in vivo experiments. The mechanism underlying the role of C1R in HCC was explored through RNA-seq, methylation-specific PCR, immuno-precipitation, and dual-luciferase reporter assays. This study found that the expression of C1R decreased as the malignancy of HCC increased and was associated with poor prognosis. C1R promoter was highly methylated through DNMT1 and DNMT3a, resulting in a decrease in C1R expression. Downregulation of C1R expression resulted in heightened malignant characteristics of HCC cells through the activation of HIF-1α-mediated glycolysis. Additionally, decreased C1R expression was found to promote xenograft tumor formation. We found that C-reactive protein (CRP) binds to C1R, and the free CRP activates the NF-κB signaling pathway, which in turn boosts the expression of HIF-1α. This increase in HIF-1α leads to higher glycolysis levels, ultimately promoting aggressive behavior in HCC. Methylation of the C1R promoter region results in the downregulation of C1R expression in HCC. C1R inhibits aggressive behavior in HCC in vitro and in vivo by inhibiting HIF-1α-regulated glycolysis. These findings indicate that C1R acts as a tumor suppressor gene during HCC progression, opening up new possibilities for innovative therapeutic approaches.


Asunto(s)
Carcinoma Hepatocelular , Metilación de ADN , Regulación hacia Abajo , Regulación Neoplásica de la Expresión Génica , Glucólisis , Subunidad alfa del Factor 1 Inducible por Hipoxia , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/patología , Carcinoma Hepatocelular/metabolismo , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patología , Neoplasias Hepáticas/metabolismo , Glucólisis/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Animales , Ratones , Regiones Promotoras Genéticas , Masculino , Línea Celular Tumoral , Ratones Desnudos , Femenino , Pronóstico , Proliferación Celular , Proteína C-Reactiva/genética , Proteína C-Reactiva/metabolismo , Transducción de Señal , ADN Metiltransferasa 3A/metabolismo , ADN Metiltransferasa 3A/genética , Ratones Endogámicos BALB C
12.
J Antimicrob Chemother ; 79(7): 1606-1613, 2024 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-38804142

RESUMEN

BACKGROUND: The efficacy of current drugs against hookworms at a single dose is highly variable across regions, age groups and infection intensity. Extensive and repeated use of these drugs also leads to potential drug resistance. Therefore, novel drugs are required for sustained disease control. OBJECTIVES: Novel aromatic heterocycle substituted aminamidine derivatives (AADs) were synthesized based on tribendimine (TBD), and their in vivo potency against Necator americanus was tested. METHODS: The efficacy of the AADs was tested in male hamsters. Oral and IV pharmacokinetic parameters were determined in male Sprague-Dawley rats. The proteomic profiles of N. americanus samples treated with AADs were compared using tandem mass tag-based quantitative proteomic analyses. RESULTS: Most AADs exhibited better anthelmintic activity than TBD at a single oral dose. Compound 3c exhibited improved solubility (>50×), and the curative dose was as low as 25 mg/kg. Similar to TBD, 3c was rapidly metabolized after oral administration and transformed into p-(1-dimethylamino ethylimino)aniline (dADT), an active metabolite against intestinal nematodes. dADT from 3c had better pharmacokinetic profiles than that from TBD and achieved an oral bioavailability of 99.5%. Compound 3c possessed rapid anthelmintic activity, clearing all worms within 24 h after an oral dose of 50 mg/kg. Quantitative proteomic analysis indicated that it might be related to ATP metabolism and cuticle protein synthesis. CONCLUSIONS: Compound 3c is a novel and promising compound against N. americanus in vivo.


Asunto(s)
Antihelmínticos , Necator americanus , Ratas Sprague-Dawley , Animales , Masculino , Antihelmínticos/farmacología , Antihelmínticos/farmacocinética , Necator americanus/efectos de los fármacos , Amidinas/farmacología , Amidinas/farmacocinética , Administración Oral , Cricetinae , Ratas , Compuestos Heterocíclicos/farmacología , Compuestos Heterocíclicos/farmacocinética , Compuestos Heterocíclicos/química , Proteómica
13.
Brief Bioinform ; 23(6)2022 11 19.
Artículo en Inglés | MEDLINE | ID: mdl-36094083

RESUMEN

Short open reading frames (sORFs) refer to the small nucleic fragments no longer than 303 nt in length that probably encode small peptides. To date, translatable sORFs have been found in both untranslated regions of messenger ribonucleic acids (RNAs; mRNAs) and long non-coding RNAs (lncRNAs), playing vital roles in a myriad of biological processes. As not all sORFs are translated or essentially translatable, it is important to develop a highly accurate computational tool for characterizing the coding potential of sORFs, thereby facilitating discovery of novel functional peptides. In light of this, we designed a series of ensemble models by integrating Efficient-CapsNet and LightGBM, collectively termed csORF-finder, to differentiate the coding sORFs (csORFs) from non-coding sORFs in Homo sapiens, Mus musculus and Drosophila melanogaster, respectively. To improve the performance of csORF-finder, we introduced a novel feature encoding scheme named trinucleotide deviation from expected mean (TDE) and computed all types of in-frame sequence-based features, such as i-framed-3mer, i-framed-CKSNAP and i-framed-TDE. Benchmarking results showed that these features could significantly boost the performance compared to the original 3-mer, CKSNAP and TDE features. Our performance comparisons showed that csORF-finder achieved a superior performance than the state-of-the-art methods for csORF prediction on multi-species and non-ATG initiation independent test datasets. Furthermore, we applied csORF-finder to screen the lncRNA datasets for identifying potential csORFs. The resulting data serve as an important computational repository for further experimental validation. We hope that csORF-finder can be exploited as a powerful platform for high-throughput identification of csORFs and functional characterization of these csORFs encoded peptides.


Asunto(s)
Sistemas de Lectura Abierta , ARN Largo no Codificante , Animales , Ratones , Drosophila melanogaster/genética , Aprendizaje Automático , Péptidos/genética , ARN Largo no Codificante/genética , ARN Mensajero/genética , Humanos
14.
Opt Express ; 32(1): 313-324, 2024 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-38175058

RESUMEN

Magnetic-free nonreciprocal optical devices have attracted great attention in recent years. Here, we investigated the magnetic-free polarization rotation of light in an atom vapor cell. Two mechanisms of magnetic-free nonreciprocity have been realized in ensembles of hot atoms, including electromagnetically induced transparency and optically-induced magnetization. For a linearly polarized input probe light, a rotation angle up to 86.4° has been realized with external control and pump laser powers of 10 mW and is mainly attributed to the optically-induced magnetization effect. Our demonstration offers a new approach to realize nonreciprocal devices, which can be applied to solid-state atom ensembles and may be useful in photonic integrated circuits.

15.
Cardiovasc Diabetol ; 23(1): 45, 2024 01 28.
Artículo en Inglés | MEDLINE | ID: mdl-38282013

RESUMEN

BACKGROUND: This study used a bidirectional 2-sample Mendelian randomization study to investigate the potential causal links between mtDNA copy number and cardiometabolic disease (obesity, hypertension, hyperlipidaemia, type 2 diabetes [T2DM], coronary artery disease [CAD], stroke, ischemic stroke, and heart failure). METHODS: Genetic associations with mtDNA copy number were obtained from a genome-wide association study (GWAS) summary statistics from the UK biobank (n = 395,718) and cardio-metabolic disease were from largest available GWAS summary statistics. Inverse variance weighting (IVW) was conducted, with weighted median, MR-Egger, and MR-PRESSO as sensitivity analyses. We repeated this in the opposite direction using instruments for cardio-metabolic disease. RESULTS: Genetically predicted mtDNA copy number was not associated with risk of obesity (P = 0.148), hypertension (P = 0.515), dyslipidemia (P = 0.684), T2DM (P = 0.631), CAD (P = 0.199), stroke (P = 0.314), ischemic stroke (P = 0.633), and heart failure (P = 0.708). Regarding the reverse directions, we only found that genetically predicted dyslipidemia was associated with decreased levels of mtDNA copy number in the IVW analysis (ß= - 0.060, 95% CI - 0.044 to - 0.076; P = 2.416e-14) and there was suggestive of evidence for a potential causal association between CAD and mtDNA copy number (ß= - 0.021, 95% CI - 0.003 to - 0.039; P = 0.025). Sensitivity and replication analyses showed the stable findings. CONCLUSIONS: Findings of this Mendelian randomization study did not support a causal effect of mtDNA copy number in the development of cardiometabolic disease, but found dyslipidemia and CAD can lead to reduced mtDNA copy number. These findings have implications for mtDNA copy number as a biomarker of dyslipidemia and CAD in clinical practice.


Asunto(s)
Enfermedad de la Arteria Coronaria , Diabetes Mellitus Tipo 2 , Dislipidemias , Insuficiencia Cardíaca , Hipertensión , Accidente Cerebrovascular Isquémico , Accidente Cerebrovascular , Humanos , ADN Mitocondrial/genética , Variaciones en el Número de Copia de ADN , Diabetes Mellitus Tipo 2/diagnóstico , Diabetes Mellitus Tipo 2/epidemiología , Diabetes Mellitus Tipo 2/genética , Estudio de Asociación del Genoma Completo , Análisis de la Aleatorización Mendeliana , Hipertensión/diagnóstico , Hipertensión/epidemiología , Hipertensión/genética , Insuficiencia Cardíaca/diagnóstico , Insuficiencia Cardíaca/epidemiología , Insuficiencia Cardíaca/genética , Obesidad/diagnóstico , Obesidad/epidemiología , Obesidad/genética , Dislipidemias/diagnóstico , Dislipidemias/epidemiología , Dislipidemias/genética
16.
Microb Pathog ; 196: 106912, 2024 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-39250982

RESUMEN

Duck spleen marble-like necrosis disease (DSMND) has been prevalent in Chinese duck farms since 2016. The etiological study was carried out in this study using etiological detection, pathogen isolation, whole genome sequencing, and artificial infection test. A highly pathogenic Riemerella anatipestifer (RA) strain was determined as the etiologic agent. Phylogenomic analysis showed that this RA strain was closely related to duck origin RA strain RCAD0421 and chicken origin RA strain S63. The clinical symptoms and pathological changes of artificial infection ducks were similar to those of clinical cases. This is the first identification of RA as the pathogen of DSMND, which provides a theoretical basis for this disease' s prevention and control.


Asunto(s)
Patos , Infecciones por Flavobacteriaceae , Filogenia , Enfermedades de las Aves de Corral , Riemerella , Bazo , Secuenciación Completa del Genoma , Animales , Patos/microbiología , Riemerella/genética , Riemerella/patogenicidad , Riemerella/aislamiento & purificación , Riemerella/clasificación , Enfermedades de las Aves de Corral/microbiología , Enfermedades de las Aves de Corral/patología , China , Infecciones por Flavobacteriaceae/microbiología , Infecciones por Flavobacteriaceae/veterinaria , Bazo/patología , Bazo/microbiología , Genoma Bacteriano/genética , Necrosis/microbiología , Pollos
17.
Phys Rev Lett ; 133(3): 036203, 2024 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-39094165

RESUMEN

Accurate description of nonadiabatic dynamics of molecules at metal surfaces involving electron transfer has been a long-standing challenge for theory. Here, we tackle this problem by first constructing high-dimensional neural network diabatic potentials including state crossings determined by constrained density functional theory, then applying mixed quantum-classical surface hopping simulations to evolve coupled electron-nuclear motion. Our approach accurately describes the nonadiabatic effects in CO scattering from Au(111) without empirical parameters and yields results agreeing well with experiments under various conditions for this benchmark system. We find that both adiabatic and nonadiabatic energy loss channels have important contributions to the vibrational relaxation of highly vibrationally excited CO(v_{i}=17), whereas relaxation of low vibrationally excited states of CO(v_{i}=2) is weak and dominated by nonadiabatic energy loss. The presented approach paves the way for accurate first-principles simulations of electron transfer mediated nonadiabatic dynamics at metal surfaces.

18.
Chemistry ; 30(34): e202401006, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38625163

RESUMEN

Direct determination of the equilibrium adsorption and spectroscopic observation of adsorbent-adsorbate interaction is crucial to evaluate the olefin/paraffin separation performance of porous adsorbents. However, the experimental characterization of competitive adsorption of various adsorbates at atomic-molecular level in the purification of multicomponent gas mixtures is challenging and rarely conducted. Herein, solid-state NMR spectroscopy is employed to examine the effect of co-adsorbed guest adsorbates on the separation of ethylene/ethane mixtures on Mg-MOF-74, Zn-MOF-74 and UTSA-74. 1H MAS NMR facilitates the determination of equilibrium uptake and adsorption selectivity of ethylene/ethane in ternary mixtures. The co-adsorption of H2O and CO2 significantly leads to the degradation of ethylene uptake and ethylene/ethane selectivity. The detailed host-guest and guest-guest interactions are unraveled by 2D 1H-1H spin diffusion homo-nuclear correlation and static 25Mg NMR experiments. The experimental results verify H2O coordinated on open metal sites can supply a new adsorption site for ethylene and ethane. The effects of guest adsorbates on the adsorption capacity and adsorption selectivity of ethylene/ethane mixtures are in the following order: H2O>CO2>O2. This work provides a direct approach for exploring the equilibrium adsorption and detailed separation mechanism of multicomponent gas mixtures using MOFs adsorbents.

19.
Anesthesiology ; 140(3): 538-557, 2024 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-37651459

RESUMEN

BACKGROUND: Memory deficits are a common comorbid disorder in patients suffering from neuropathic pain. The mechanisms underlying the comorbidities remain elusive. The hypothesis of this study was that impaired lactate release from dysfunctional astrocytes in dorsal hippocampal CA1 contributed to memory deficits. METHODS: A spared nerve injury model was established to induce both pain and memory deficits in rats and mice of both sexes. von Frey tests, novel object recognition, and conditioned place preference tests were applied to evaluate the behaviors. Whole-cell recording, fiber photometry, Western blotting, and immunohistochemistry combined with intracranial injections were used to explore the underlying mechanisms. RESULTS: Animals with spared sciatic nerve injury that had displayed nociception sensitization or memory deficit comorbidities demonstrated a reduction in the intrinsic excitability of pyramidal neurons, accompanied by reduced Ca2+ activation in astrocytes (ΔF/F, sham: 6 ± 2%; comorbidity: 2 ± 0.4%) and a decrease in the expression of glial fibrillary acidic protein and lactate levels in the dorsal CA1. Exogenous lactate supply or increasing endogenous lactate release by chemogenetic activation of astrocytes alleviated this comorbidity by enhancing the cell excitability (129 ± 4 vs. 88 ± 10 for 3.5 mM lactate) and potentiating N-methyl-d-aspartate receptor-mediated excitatory postsynaptic potentials of pyramidal neurons. In contrast, inhibition of lactate synthesis, blocking lactate transporters, or chemogenetic inhibition of astrocytes resulted in comorbidity-like behaviors in naive animals. Notably, ß2-adrenergic receptors in astrocytes but not neurons were downregulated in dorsal CA1 after spared nerve injury. Microinjection of a ß2 receptor agonist into dorsal CA1 or activation of the noradrenergic projections onto the hippocampus from the locus coeruleus alleviated the comorbidity, possibly by increasing lactate release. CONCLUSIONS: Impaired lactate release from dysfunctional astrocytes, which could be rescued by activation of the locus coeruleus, led to nociception and memory deficits after peripheral nerve injury.


Asunto(s)
Neuralgia , Traumatismos de los Nervios Periféricos , Humanos , Masculino , Femenino , Ratas , Ratones , Animales , Roedores , Ácido Láctico , Astrocitos , Nocicepción , Neuralgia/metabolismo , Trastornos de la Memoria/metabolismo , Traumatismos de los Nervios Periféricos/metabolismo , Comorbilidad
20.
Pharmacol Res ; 202: 107145, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38492829

RESUMEN

In many neurodegenerative disorders, such as Alzheimer's disease (AD), glutamate-mediated neuronal excitotoxicity is considered the basis for cognitive impairment. The mRNA and protein expression of SERPINA4(Kallistatin) are higher in patients with AD. However, whether Kallistatin plays a regulatory role in glutamate-glutamine cycle homeostasis remains unclear. In this study, we identified impaired cognitive function in Kallistatin transgenic (KAL-TG) mice. Baseline glutamate levels were elevated and miniature excitatory postsynaptic current (mEPSC) frequency was increased in the hippocampus, suggesting the impairment of glutamate homeostasis in KAL-TG mice. Mechanistically, we demonstrated that Kallistatin promoted lysine acetylation and ubiquitination of glutamine synthetase (GS) and facilitated its degradation via the proteasome pathway, thereby downregulating GS. Fenofibrate improved cognitive memory in KAL-TG mice by downregulating serum Kallistatin. Collectively, our study findings provide insights the mechanism by which Kallistatin regulates cognitive impairment, and suggest the potential of fenofibrate to prevente and treat of AD patients with high levels of Kallistatin.


Asunto(s)
Enfermedad de Alzheimer , Disfunción Cognitiva , Fenofibrato , Serpinas , Humanos , Ratones , Animales , Glutamato-Amoníaco Ligasa/metabolismo , Enfermedad de Alzheimer/metabolismo , Ratones Transgénicos , Ácido Glutámico/metabolismo , Disfunción Cognitiva/tratamiento farmacológico , Cognición
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