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1.
Proc Natl Acad Sci U S A ; 121(41): e2313098121, 2024 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-39312679

RESUMO

One of the remaining issues regarding the Anthropocene is the lack of stratigraphic evidence indicating when the cumulative human pressure from the early Holocene began to fundamentally change the Earth system. Herein, we compile anthropogenic fingerprints from various high-precision-dated proxy records for 137 global sites to determine the age of the unprecedented surge in these records over the last 7700 y. The cumulative number of fingerprints revealed an unprecedented surge in diverse anthropogenic fingerprints starting in 1952 ± 3 CE, corresponding to the onset of the Great Acceleration. Notably, the period from 1953 to 1958 CE saw a nearly simultaneous surge in fingerprints across all regions, including Antarctica, the Arctic, East Asia, Europe, North America, and Oceania. This synchronous upsurge reflects the moment when human impacts led to rapid transformations in various natural processes and cycles, with humans becoming a geological force capable of inscribing abundant and diverse anthropogenic fingerprints in global strata. Following this global fingerprint explosion, profound planetary-scale changes, including deviations from the established natural climatic conditions, begin. This unprecedented surge in anthropogenic signals worldwide suggests that human influences started to match many natural forces controlling the processes and cycles and overwhelm some of the functioning of the Earth system around 1952.


Assuntos
Efeitos Antropogênicos , Humanos , Geologia , Planeta Terra , Arquivos
2.
Methods ; 221: 18-26, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38040204

RESUMO

Drug-induced liver injury (DILI) is a significant issue in drug development and clinical treatment due to its potential to cause liver dysfunction or damage, which, in severe cases, can lead to liver failure or even fatality. DILI has numerous pathogenic factors, many of which remain incompletely understood. Consequently, it is imperative to devise methodologies and tools for anticipatory assessment of DILI risk in the initial phases of drug development. In this study, we present DMFPGA, a novel deep learning predictive model designed to predict DILI. To provide a comprehensive description of molecular properties, we employ a multi-head graph attention mechanism to extract features from the molecular graphs, representing characteristics at the level of compound nodes. Additionally, we combine multiple fingerprints of molecules to capture features at the molecular level of compounds. The fusion of molecular fingerprints and graph features can more fully express the properties of compounds. Subsequently, we employ a fully connected neural network to classify compounds as either DILI-positive or DILI-negative. To rigorously evaluate DMFPGA's performance, we conduct a 5-fold cross-validation experiment. The obtained results demonstrate the superiority of our method over four existing state-of-the-art computational approaches, exhibiting an average AUC of 0.935 and an average ACC of 0.934. We believe that DMFPGA is helpful for early-stage DILI prediction and assessment in drug development.


Assuntos
Doença Hepática Induzida por Substâncias e Drogas , Modelos Químicos , Humanos , Doença Hepática Induzida por Substâncias e Drogas/etiologia , Desenvolvimento de Medicamentos , Aprendizado Profundo
3.
Proc Natl Acad Sci U S A ; 119(12): e2122245119, 2022 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-35302894

RESUMO

High-performance metabolic analysis is emerging in the diagnosis and prognosis of breast cancer (BrCa). Still, advanced tools are in demand to deliver the application potentials of metabolic analysis. Here, we used fast nanoparticle-enhanced laser desorption/ionization mass spectrometry (NPELDI-MS) to record serum metabolic fingerprints (SMFs) of BrCa in seconds, achieving high reproducibility and low consumption of direct serum detection without treatment. Subsequently, machine learning of SMFs generated by NPELDI-MS functioned as an efficient readout to distinguish BrCa from non-BrCa with an area under the curve of 0.948. Furthermore, a metabolic prognosis scoring system was constructed using SMFs with effective prediction performance toward BrCa (P < 0.005). Finally, we identified a biomarker panel of seven metabolites that were differentially enriched in BrCa serum and their related pathways. Together, our findings provide an efficient serum metabolic tool to characterize BrCa and highlight certain metabolic signatures as potential diagnostic and prognostic factors of diseases including but not limited to BrCa.


Assuntos
Neoplasias da Mama , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/metabolismo , Feminino , Humanos , Espectrometria de Massas/métodos , Prognóstico , Reprodutibilidade dos Testes
4.
J Proteome Res ; 23(8): 2805-2814, 2024 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-38171506

RESUMO

Triacylglycerols and wax esters are two lipid classes that have been linked to diseases, including autism, Alzheimer's disease, dementia, cardiovascular disease, dry eye disease, and diabetes, and thus are molecules worthy of biomarker exploration studies. Since triacylglycerols and wax esters make up the majority of skin-surface lipid secretions, a viable sampling method for these potential biomarkers would be that of groomed latent fingerprints. Currently, however, blood-based sampling protocols predominate in the field. The invasiveness of a blood draw limits its utility to protected populations, including children and the elderly. Herein we describe a noninvasive means for sample collection (from fingerprints) paired with fast MS data-acquisition (MassIVE data set MSV000092742) and efficient data analysis via machine learning. Using both supervised and unsupervised classification, we demonstrate the usefulness of this method in determining whether a variable of interest imparts measurable change within the lipidomic data set. As a proof-of-concept, we show that the method is capable of distinguishing between the fingerprints of different individuals as well as between anatomical sebum collection regions. This noninvasive, high-throughput approach enables future lipidomic biomarker researchers to more easily include underrepresented, protected populations, such as children and the elderly, thus moving the field closer to definitive disease diagnoses that apply to all.


Assuntos
Biomarcadores , Lipidômica , Aprendizado de Máquina , Humanos , Lipidômica/métodos , Biomarcadores/sangue , Biomarcadores/análise , Espectrometria de Massas/métodos , Triglicerídeos/sangue , Triglicerídeos/análise , Dermatoglifia , Idoso , Criança , Masculino , Feminino , Sebo/metabolismo , Sebo/química , Lipídeos/sangue , Lipídeos/análise , Manejo de Espécimes/métodos
5.
BMC Genomics ; 25(1): 818, 2024 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-39210290

RESUMO

BACKGROUND: Cannabis sativa is seeing a global resurgence as a food, fiber and medicinal crop for industrial hemp and medicinal Cannabis industries respectively. However, a widespread moratorium on the use and research of C. sativa throughout most of the 20th century has seen the development of improved cultivars for specific end uses lag behind that of conventional crops. While C. sativa research and development has seen significant investments in the recent past, resulting in a suite of publicly available genomic resources and tools, a versatile and cost-effective mid-density genotyping platform for applied purposes in breeding and pre-breeding is lacking. Here we report on a first mid-density fixed-target SNP platform for C. sativa. RESULTS: The High-throughput Amplicon-based SNP-platform for medicinal Cannabis and industrial Hemp (HASCH) was designed using a combination of filtering and Integer Linear Programming on publicly available whole-genome sequencing and RNA sequencing data, supplemented with in-house generated genotyping-by-sequencing (GBS) data. HASCH contains 1,504 genome-wide targets of high call rate (97% mean) and even distribution across the genome, designed to be highly informative (> 0.3 minor allele frequency) across both medicinal cannabis and industrial hemp gene pools. Average numbers of mismatch SNP between any two accessions were 251 for medicinal cannabis (N = 116) and 272 for industrial hemp (N = 87). Comparing HASCH data with corresponding GBS data on a collection of diverse C. sativa accessions demonstrated high concordance and resulted in comparable phylogenies and genetic distance matrices. Using HASCH on a segregating F2 population derived from a cross between a tetrahydrocannabinol (THC)-dominant and a cannabidiol (CBD)-dominant accession resulted in a genetic map consisting of 310 markers, comprising 10 linkage groups and a total size of 582.7 cM. Quantitative Trait Locus (QTL) mapping identified a major QTL for CBD content on chromosome 7, consistent with previous findings. CONCLUSION: HASCH constitutes a versatile, easy to use and cost-effective genotyping solution for the rapidly growing Cannabis research community. It provides consistent genetic fingerprints of 1504 SNPs with wide applicability genetic resource management, quantitative genetics and breeding.


Assuntos
Cannabis , Técnicas de Genotipagem , Maconha Medicinal , Polimorfismo de Nucleotídeo Único , Cannabis/genética , Técnicas de Genotipagem/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Genoma de Planta , Genótipo
6.
Neuroimage ; 285: 120480, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38061689

RESUMO

The knowledge that brain functional connectomes are unique and reliable has enabled behaviourally relevant inferences at a subject level. However, whether such "fingerprints" persist under altered states of consciousness is unknown. Ayahuasca is a potent serotonergic psychedelic which produces a widespread dysregulation of functional connectivity. Used communally in religious ceremonies, its shared use may highlight relevant novel interactions between mental state and functional connectome (FC) idiosyncrasy. Using 7T fMRI, we assessed resting-state static and dynamic FCs for 21 Santo Daime members after collective ayahuasca intake in an acute, within-subject study. Here, connectome fingerprinting revealed FCs showed reduced idiosyncrasy, accompanied by a spatiotemporal reallocation of keypoint edges. Importantly, we show that interindividual differences in higher-order FC motifs are relevant to experiential phenotypes, given that they can predict perceptual drug effects. Collectively, our findings offer an example of how individualised connectivity markers can be used to trace a subject's FC across altered states of consciousness.


Assuntos
Banisteriopsis , Conectoma , Humanos , Encéfalo/fisiologia , Estado de Consciência , Imageamento por Ressonância Magnética
7.
Hum Brain Mapp ; 45(1): e26561, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38096866

RESUMO

Non-negligible idiosyncrasy due to interindividual differences is an ongoing issue in resting-state functional MRI (rfMRI) analysis. We show that a deep neural network (DNN) can be employed for individual identification by learning important features from the time-varying functional connectivity (FC) of rfMRI in the Human Connectome Project. We employed the trained DNN to identify individuals from an independent dataset acquired at our institution. The results revealed that the DNN could successfully identify 300 individuals with an error rate of 2.9% using 15 s time-window and 870 individuals with an error rate of 6.7%. A trained DNN with nonlinear hidden layers led to the proposal of the "fingerprint of FC" (fpFC) as representative edges of individual FC. The fpFCs for individuals exhibited commonly important and individual-specific edges across time-window lengths (from 5 min to 15 s). Furthermore, the utility of our model for another group of subjects was validated, supporting the feasibility of our technique in the context of transfer learning. In conclusion, our study offers an insight into the discovery of the intrinsic mode of the human brain using whole-brain resting-state FC and DNNs.


Assuntos
Conectoma , Imageamento por Ressonância Magnética , Humanos , Imageamento por Ressonância Magnética/métodos , Redes Neurais de Computação , Encéfalo/diagnóstico por imagem , Conectoma/métodos
8.
Brief Bioinform ; 23(5)2022 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-36002937

RESUMO

The ability of a compound to permeate across the blood-brain barrier (BBB) is a significant factor for central nervous system drug development. Thus, for speeding up the drug discovery process, it is crucial to perform high-throughput screenings to predict the BBB permeability of the candidate compounds. Although experimental methods are capable of determining BBB permeability, they are still cost-ineffective and time-consuming. To complement the shortcomings of existing methods, we present a deep learning-based multi-model framework model, called Deep-B3, to predict the BBB permeability of candidate compounds. In Deep-B3, the samples are encoded in three kinds of features, namely molecular descriptors and fingerprints, molecular graph and simplified molecular input line entry system (SMILES) text notation. The pre-trained models were built to extract latent features from the molecular graph and SMILES. These features depicted the compounds in terms of tabular data, image and text, respectively. The validation results yielded from the independent dataset demonstrated that the performance of Deep-B3 is superior to that of the state-of-the-art models. Hence, Deep-B3 holds the potential to become a useful tool for drug development. A freely available online web-server for Deep-B3 was established at http://cbcb.cdutcm.edu.cn/deepb3/, and the source code and dataset of Deep-B3 are available at https://github.com/GreatChenLab/Deep-B3.


Assuntos
Barreira Hematoencefálica , Aprendizado Profundo , Transporte Biológico , Fármacos do Sistema Nervoso Central/farmacologia , Permeabilidade
9.
J Comput Aided Mol Des ; 38(1): 24, 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-39014286

RESUMO

Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and analyzing MD simulations continues to be a multi-step process making it cumbersome to assess a library of ligands in a protein binding pocket using MD. We present an automated workflow that streamlines setting up, running, and analyzing Desmond MD simulations for protein-ligand complexes using machine learning (ML) models. The workflow takes a library of pre-docked ligands and a prepared protein structure as input, sets up and runs MD with each protein-ligand complex, and generates simulation fingerprints for each ligand. Simulation fingerprints (SimFP) capture protein-ligand compatibility, including stability of different ligand-pocket interactions and other useful metrics that enable easy rank-ordering of the ligand library for pocket optimization. SimFPs from a ligand library are used to build & deploy ML models that predict binding assay outcomes and automatically infer important interactions. Unlike relative free-energy methods that are constrained to assess ligands with high chemical similarity, ML models based on SimFPs can accommodate diverse ligand sets. We present two case studies on how SimFP helps delineate structure-activity relationship (SAR) trends and explain potency differences across matched-molecular pairs of (1) cyclic peptides targeting PD-L1 and (2) small molecule inhibitors targeting CDK9.


Assuntos
Aprendizado de Máquina , Simulação de Dinâmica Molecular , Ligação Proteica , Proteínas , Ligantes , Proteínas/química , Proteínas/metabolismo , Sítios de Ligação , Simulação de Acoplamento Molecular , Conformação Proteica , Fluxo de Trabalho , Humanos , Desenho de Fármacos , Software
10.
Environ Sci Technol ; 58(1): 727-738, 2024 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-38100713

RESUMO

High-resolution mass spectrometry (HRMS) provides extensive chemical data, facilitating the differentiation and quantification of contaminants of emerging concerns (CECs) in aquatic environments. This study utilizes liquid chromatography-HRMS for source apportionment in Chebei Stream, an urban water stream in Guangzhou, South China. Initially, 254 features were identified as potential CECs by the nontarget screening (NTS) method. We then established 1689, 1317, and 15,759 source-specific HRMS fingerprints for three distinct sources, the mainstream (C3), the tributary (T2), and the rain runoff (R1), qualitatively assessing the contribution from each source downstream. Subsequently, 32, 55, and 3142 quantitative fingerprints were isolated for sites C3, T2, and R1, respectively, employing dilution curve screening for source attribution. The final contribution estimates downstream from sites C3, T2, and R1 span 32-96, 12-23, and 8-23%, respectively. Cumulative contributions from these sources accurately mirrored actual conditions, fluctuating between 103 and 114% across C6 to C8 sites. Yet, with further tributary integration, the overall source contribution dipped to 52%. The findings from this research present a pioneering instance of applying HRMS fingerprints for qualitative and quantitative source tracking in real-world scenarios, which empowers the development of more effective strategies for environmental protection.


Assuntos
Monitoramento Ambiental , Poluentes Químicos da Água , Monitoramento Ambiental/métodos , Poluentes Químicos da Água/análise , Espectrometria de Massas , Espectrometria de Massa com Cromatografia Líquida , China
11.
Clin Chem Lab Med ; 62(5): 988-998, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38018477

RESUMO

OBJECTIVES: To explore the metabolic fingerprints of diabetic retinopathy (DR) in individuals with type 2 diabetes using a newly-developed laser desorption/ionization mass spectrometry (LDI-MS) platform assisted by ferric particles. METHODS: Metabolic fingerprinting was performed using a ferric particle-assisted LDI-MS platform. A nested population-based case-control study was performed on 216 DR cases and 216 control individuals with type 2 diabetes. RESULTS: DR cases and control individuals with type 2 diabetes were comparable for a list of clinical factors. The newly-developed LDI-MS platform allowed us to draw the blueprint of plasma metabolic fingerprints from participants with and without DR. The neural network afforded diagnostic performance with an average area under curve value of 0.928 for discovery cohort and 0.905 for validation cohort (95 % confidence interval: 0.902-0.954 and 0.845-0.965, respectively). Tandem MS and Fourier transform ion cyclotron resonance MS with ultrahigh resolution identified seven specific metabolites that were significantly associated with DR in fully adjusted models. Of these metabolites, dihydrobiopterin, phosphoserine, N-arachidonoylglycine, and 3-methylhistamine levels in plasma were first reported to show the associations. CONCLUSIONS: This work advances the design of metabolic analysis for DR and holds the potential to promise as an efficient tool for clinical management of DR.


Assuntos
Diabetes Mellitus Tipo 2 , Retinopatia Diabética , Humanos , Retinopatia Diabética/diagnóstico , Estudos de Casos e Controles , Espectrometria de Massas/métodos , Lasers , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos
12.
J Fluoresc ; 2024 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-38514485

RESUMO

Latent fingerprints (LFPs) is one of the most important physical evidence in the criminal scene, playing an important role in forensic investigations. Therefore, developing highly sensitive and convenient materials for the visualization of LFPs is of great significance. We designed and synthesized an organic fluorescent molecule TP-PH with aggregation-induced enhanced emission (AIEE) activity. By simply soaking, blue fluorescent images with high contrast and resolution are readily developed on various surfaces including tinfoil, steel, glass and plastic. Remarkably, LFPs can be visualized within 5 min including the first-, second- and tertiary-level details. In addition, TP-PH exhibits interesting photoactivated fluorescence enhancement properties. Under irradiation of 365 nm UV light with a power density of 382 mW/cm2, the fluorescence quantum yield displays approximately 21.5-fold enhancement. Mechanism studies reveals that the photoactivated fluorescence is attributed to the irreversible cyclodehydrogenation reactions under UV irradiation. This work provides a guideline for the design of multifunctional AIEE fluorescent materials.

13.
Anal Bioanal Chem ; 416(24): 5255-5280, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-39160439

RESUMO

Forensic chemistry literature has grown exponentially, with many analytical techniques being used to provide valuable information to help solve criminal cases. Among them, matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), particularly MALDI MS imaging (MALDI MSI), has shown much potential in forensic applications. Due to its high specificity, MALDI MSI can analyze a wide variety of compounds in complex samples without extensive sample preparation, providing chemical profiles and spatial distributions of given analyte(s). This review introduces MALDI MS(I) to forensic scientists with a focus on its basic principles and the applications of MALDI MS(I) to the analysis of fingerprints, drugs of abuse, and their metabolites in hair, medicine samples, animal tissues, and inks in documents.


Assuntos
Ciências Forenses , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Ciências Forenses/métodos , Humanos , Animais , Cabelo/química , Dermatoglifia , Detecção do Abuso de Substâncias/métodos
14.
J Biomed Inform ; 151: 104602, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-38346530

RESUMO

OBJECTIVE: An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable algorithms, especially in healthcare. This integrating is usually resolved using meta-data such as feature names, which may be unavailable or ambiguous. Our goal is to design methods that create a mapping between structured tabular datasets derived from electronic health records independent of meta-data. METHODS: We evaluate methods in the challenging case of numeric features without reliable and distinctive univariate summaries, such as nearly Gaussian and binary features. We assume that a small set of features are a priori mapped between two datasets, which share unknown identical features and possibly many unrelated features. Inter-feature relationships are the main source of identification which we expect. We compare the performance of contrastive learning methods for feature representations, novel partial auto-encoders, mutual-information graph optimizers, and simple statistical baselines on simulated data, public datasets, the MIMIC-III medical-record changeover, and perioperative records from before and after a medical-record system change. Performance was evaluated using both mapping of identical features and reconstruction accuracy of examples in the format of the other dataset. RESULTS: Contrastive learning-based methods overall performed the best, often substantially beating the literature baseline in matching and reconstruction, especially in the more challenging real data experiments. Partial auto-encoder methods showed on-par matching with contrastive methods in all synthetic and some real datasets, along with good reconstruction. However, the statistical method we created performed reasonably well in many cases, with much less dependence on hyperparameter tuning. When validating feature match output in the EHR dataset we found that some mistakes were actually a surrogate or related feature as reviewed by two subject matter experts. CONCLUSION: In simulation studies and real-world examples, we find that inter-feature relationships are effective at identifying matching or closely related features across tabular datasets when meta-data is not available. Decoder architectures are also reasonably effective at imputing features without an exact match.


Assuntos
Algoritmos , Registros Eletrônicos de Saúde , Simulação por Computador , Ciência de Dados , Motivação
15.
Environ Res ; 247: 118215, 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38253194

RESUMO

Identifying sediment phosphorus sources, the key to control eutrophication, is hindered in multi-source polluted urban rivers by the lack of appropriate methods and data resolution. Community-based microbial source tracking (MST) offers new insight, but the bacterial communities could be affected by environmental fluctuations during the migration with sediments, which might induce instability of MST results. Therefore, the effects of environmental-induced community succession on the stability of MST were compared in this study. Liangxi River, a highly eutrophic urban river, was selected as the study area where sediment phosphorus sources are difficult to track because of multi-source pollution and complicated hydrodynamic conditions. Spearman correlation analysis (P < 0.05) was conducted to recognize a close relationship between sediment, bacterial communities and phosphorus, verifying the feasibility of MST for identify sediment phosphorus sources. Two distinct microbial community fingerprints were constructed based on whether excluded 113 vulnerable species, which were identified by analyzing the differences of microorganisms across a concentration gradient of exogenous phosphorus input in microbial environmental response experiment. Because of the lower unknown proportion and relative standard deviations, MST results were more stable and reliable when based on the fingerprints excluding species vulnerable to phosphorus. This study presents a novel insight on how to identify sediment phosphorus sources in multi-source polluted urban river, and would help to develop preferential control strategies for eutrophication management.


Assuntos
Microbiota , Poluentes Químicos da Água , Rios , Monitoramento Ambiental/métodos , Sedimentos Geológicos , Fósforo/análise , Bactérias , China , Poluentes Químicos da Água/toxicidade , Poluentes Químicos da Água/análise
16.
Plant Cell Rep ; 43(10): 247, 2024 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-39347829

RESUMO

KEY MESSAGE: High-throughput next-generation sequencing of 161 olive germplas. 33 samples were selected as core olive germplasm and Fingerprints were constructed. After GWAS analysis of olive leaf shape, 14 candidate genes were localized. Olive (Olea europaea L.) has been introduced to China since the 1960s. After a prolonged period of variation and domestication, there is a lack of comprehensive research on its genetics. The olive oil directly extracted from Olea europaea L. is recognized as 'liquid gold', nevertheless, people constantly overlook the valuable wealth of olive leaves. High-throughput next-generation sequencing was performed on 161 olive germplasm to analyze the kinship, genetic structure and diversity of olives, and the core germplasm of olives were selected and fingerprints were constructed. Meanwhile, Genome-wide association analysis (GWAS) was performed to locate the gene for regulating olive leaf shape. Herein, the results parsed that most of the Chinese olive germplasm was more closely related to the Italian germplasm. A wealth of hybridized germplasm possessed high genetic diversity and had the potential to be used as superior parental material for olive germplasm. A total of 33 samples were selected and characterized as core germplasm of olive and Fingerprints were also constructed. A total of 14 candidate genes were localized after GWAS analysis of four olive leaf shape phenotypes, including leaf shape, leaf curvature shape, leaf tip and leaf base shape. Collectively, this study revealed the genetic basis of olives in China and also succeeded in constructing the core germplasm that stands for the genetic diversity of olives, which can contribute to the scientific and effective collection and preservation of olive germplasm resources, and provide a scientific basis for the in-depth excavation and utilization of genes regulating olive leaf shape.


Assuntos
Estudo de Associação Genômica Ampla , Olea , Folhas de Planta , Olea/genética , Folhas de Planta/genética , Folhas de Planta/anatomia & histologia , Sequenciamento de Nucleotídeos em Larga Escala , Variação Genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Melhoramento Vegetal/métodos , China
17.
Arch Toxicol ; 98(8): 2647-2658, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38619593

RESUMO

Cytochrome P450 enzymes are a superfamily of enzymes responsible for the metabolism of a variety of medicines and xenobiotics. Among the Cytochrome P450 family, five isozymes that include 1A2, 2C9, 2C19, 2D6, and 3A4 are most important for the metabolism of xenobiotics. Inhibition of any of these five CYP isozymes causes drug-drug interactions with high pharmacological and toxicological effects. So, the inhibition or non-inhibition prediction of these isozymes is of great importance. Many techniques based on machine learning and deep learning algorithms are currently being used to predict whether these isozymes will be inhibited or not. In this study, three different molecular or substructural properties that include Morgan, MACCS and Morgan (combined) and RDKit of the various molecules are used to train a distinct SVM model against each isozyme (1A2, 2C9, 2C19, 2D6, and 3A4). On the independent dataset, Morgan fingerprints provided the best results, while MACCS and Morgan (combined) achieved comparable results in terms of balanced accuracy (BA), sensitivity (Sn), and Mathews correlation coefficient (MCC). For the Morgan fingerprints, balanced accuracies (BA), Mathews correlation coefficients (MCC), and sensitivities (Sn) against each CYPs isozyme, 1A2, 2C9, 2C19, 2D6, and 3A4 on an independent dataset ranged between 0.81 and 0.85, 0.61 and 0.70, 0.72 and 0.83, respectively. Similarly, on the independent dataset, MACCS and Morgan (combined) fingerprints achieved competitive results in terms of balanced accuracies (BA), Mathews correlation coefficients (MCC), and sensitivities (Sn) against each CYPs isozyme, 1A2, 2C9, 2C19, 2D6, and 3A4, which ranged between 0.79 and 0.85, 0.59 and 0.69, 0.69 and 0.82, respectively.


Assuntos
Inibidores das Enzimas do Citocromo P-450 , Sistema Enzimático do Citocromo P-450 , Aprendizado de Máquina , Inibidores das Enzimas do Citocromo P-450/farmacologia , Sistema Enzimático do Citocromo P-450/metabolismo , Humanos , Isoenzimas/metabolismo , Interações Medicamentosas , Xenobióticos/toxicidade , Xenobióticos/metabolismo , Máquina de Vetores de Suporte
18.
Biomed Chromatogr ; 38(5): e5847, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38368628

RESUMO

Cnidii Fructus, derived from the dried ripe fruit of Cnidium monnieri (L.) Cuss, has the effect of warming kidneys and invigorating Yang. This study established the spectrum-effect relationships between ultra-high-performance liquid chromatography (UHPLC) fingerprints and the antitumor activities of Cnidii Fructus on human hepatocellular carcinoma (HepG2) cells. In UHPLC fingerprints, 19 common peaks were obtained, and 17 batches of herbs had similarity >0.948. In Cell Counting Kit-8 (CCK-8) test, 17 batches of Cnidii Fructus extract significantly inhibited the proliferation of HepG2 cells to different degrees, showing different half-maximal inhibitory concentration (IC50) values. Furthermore, gray correlation analysis, Pearson's analysis, and orthogonal partial least squares discriminant analysis were performed to screen out eight components. The analysis of mass spectrum data and a comparison with standards revealed that the eight components were methoxsalen, isopimpinellin, osthenol, imperatorin, osthole, ricinoleic acid, linoleic acid, and oleic acid. The verification experiments by testing single compounds indicated that these eight compounds were the major anti-hepatoma compounds in Cnidii Fructus. This work provides a model combining UHPLC fingerprints and antitumor activities to study the spectrum-effect relationships of Cnidii Fructus, which can be used to determine the principal components responsible for the bioactivity.


Assuntos
Proliferação de Células , Cnidium , Cromatografia Líquida de Alta Pressão/métodos , Humanos , Células Hep G2 , Proliferação de Células/efeitos dos fármacos , Cnidium/química , Frutas/química , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/química , Neoplasias Hepáticas/tratamento farmacológico , Carcinoma Hepatocelular/tratamento farmacológico , Extratos Vegetais/farmacologia , Extratos Vegetais/química , Reprodutibilidade dos Testes , Antineoplásicos Fitogênicos/farmacologia , Antineoplásicos Fitogênicos/química , Antineoplásicos Fitogênicos/análise , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/análise , Furocumarinas/farmacologia , Furocumarinas/análise , Furocumarinas/química
19.
Luminescence ; 39(5): e4760, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38738510

RESUMO

The present communication reports on the synthesis of a novel methyl-pyridone azo fluorescent tag (MPAFT) were proven through 1H (NMR), FT-IR, UV-vis, and high-resolution mass spectrometry. The quantum chemical parameters of MPAFT were evaluated using density functional theory (DFT) analysis. It was further investigated for its latent fingerprint (LFPs) in various surfaces and anticounterfeiting applications. By exposing Level I-Level III, ridge features to UV light with a wavelength of 365 nm, a bioimaging investigation has also demonstrated the potential of MPAFT's emission behaviour. The cyclic voltammetry (CV) and linear sweep voltammetry (LSV) at MPAFT/MGCE (modified glassy carbon electrode) were used to explore the electrochemical sensitivity and reliable detection of dopamine (DA) in neutral PBS (pH 7) electrolyte solution, and the results show good sensitivity and detection. The lower detection limit for LSV was 0.81 µM under optimum conditions.


Assuntos
Dopamina , Técnicas Eletroquímicas , Corantes Fluorescentes , Pirazóis , Piridonas , Piridonas/química , Dopamina/análise , Dopamina/química , Corantes Fluorescentes/química , Corantes Fluorescentes/síntese química , Pirazóis/química , Humanos , Estrutura Molecular , Teoria da Densidade Funcional , Imagem Óptica , Processos Fotoquímicos
20.
Phytochem Anal ; 2024 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-39103224

RESUMO

INTRODUCTION: Schisandrae Chinensis Fructus (SCF), a traditional Chinese medicine, has been used in treating virtual injury and strain since ancient times. The Chinese Pharmacopoeia reveals that SCF includes raw (RSCF) and vinegar-processed (VSCF) decoction pieces. OBJECTIVE: This study developed an effective method combining the electronic eye (e-eye), electronic tongue (e-tongue), and chemometrics to discriminate RSCF and VSCF from the perspective of chemical composition, color, and taste. MATERIAL AND METHODS: First, RSCF were collected and processed into VSCF, and their color parameters, e-tongue sensory properties, high-performance liquid chromatography (HPLC) and ultra-HPLC (UPLC) characteristic fingerprints, and nominal ingredients were determined. Multivariate statistical analyses, including principal component, linear discriminant, similarity, and partial least squares discriminant analyses, were conducted. RESULTS: HPLC and UPLC fingerprints were established, demonstrating a > 0.900 similarity. The content determination indicated increased schisantherin A, schisantherin B, and schisandrin A contents in VSCF. The e-eye data demonstrated a > 1.5 total color difference before and after processing ΔE*ab, indicating the significantly changed sample color and appearance before and after processing. The e-tongue technology was used to quantitatively characterize the taste of RSCF and VSCF. The t-test revealed significantly reduced sourness, aftertaste-bitter, and aftertaste-astringent values of SCF after vinegar processing. Principal component and partial least squares discriminant analyses indicated that e-eye and e-tongue realize the rapid RSCF and VSCF identification. CONCLUSION: The proposed comprehensive strategy of electronic eye and electronic tongue combined with chemometrics demonstrated satisfactory results with high efficiency, accuracy, and reliability. This can be developed into a novel and accurate method for discriminating RSCF and VSCF.

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