RESUMEN
To evaluate the diagnostic accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry based on nucleotide (nucleotide MALDI-TOF MS) on bronchoalveolar lavage fluid (BALF) from suspected pulmonary tuberculosis (PTB) patients. A retrospective study was conducted on suspected PTB patients (total of 960) admitted to Chongqing Public Health Medical Center between May 2021 and January 2022. The sensitivity, specificity, positive predictive value, negative predictive value (NPV) and area under the curve values of nucleotide MALDI-TOF MS as well as smear microscopy, Mycobacterium Growth Indicator Tube 960 culture (MGIT culture), and Xpert MTB/RIF were calculated and compared. Total of 343 presumed PTB cases were enrolled. Overall, using the clinical diagnosis as reference, the sensitivity and NPV of nucleotide MALDI-TOF MS was 71.5% and 43.1%, respectively, significantly higher than smear microscopy (22.6%, 23.2%), MGIT culture (40.6%, 18.9%), Xpert MTB/RIF (40.8%, 27.9%). Furthermore, nucleotide MALDI-TOF MS also outperformed over Xpert MTB/RIF and MGIT culture on smear-negative BALFs. Approximately 50% and 30% of patients benefited from nucleotide MALDI-TOF MS compared with smear and MGIT culture or Xpert MTB/RIF, respectively. This study demonstrated that the analysis of BALF with nucleotide MALDI-TOF MS provided an accurate and promising tool for the early diagnosis of PTB.
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Líquido del Lavado Bronquioalveolar , Mycobacterium tuberculosis , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Tuberculosis Pulmonar , Humanos , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Líquido del Lavado Bronquioalveolar/microbiología , Líquido del Lavado Bronquioalveolar/química , Estudios Retrospectivos , Tuberculosis Pulmonar/diagnóstico , Tuberculosis Pulmonar/microbiología , Femenino , Masculino , Persona de Mediana Edad , Adulto , Mycobacterium tuberculosis/aislamiento & purificación , Sensibilidad y Especificidad , Nucleótidos/análisis , AncianoRESUMEN
Cordyceps genus is entomopathogenic mushrooms that have traditionally been used in ethnomedicine in Asian countries. Nucleosides (Ns), nucleotide(Nt), Nucleobases (Nb) and their analogues play a critically physiological role and have a great potential in drug development, such as pentostatin and cordycepin (COR). Due to their significance bioactivity, several Nt/Ns were used as markers for quality evaluation for medicinal Cordyceps, including adenosine, inosine, guanosine, uridine and COR. Among them, COR is the most considerable adenosine analogue, exhibiting significant therapeutic potential and has many intracellular targets. Nt/Ns contains polar compounds and the phosphate groups of Nt deprotonate and carry negative charges with a broad range of pH values. Recent years, various advanced methods of extraction and separation, and nanomaterials have been developed to extract, isolate and determine these molecules, such as ultrasound-assisted extraction (UAE), Supercritical fluid extraction (SFE) and pressurized liquid extraction (PLE) for the extraction, the solid phase extraction (SPE) methods (microextraction SPE (SPME), magnetic SPE (MSPE), and unique SPE materials based on the boronate affinity for the separation, and chromatography methods employing ultraviolet (UV), fluorescence, MS detection and electrospray ionization (ESI), along with matrix-assisted laser desorption/ ionization (MALDI) for the determination. COR derived from adenosine and its structure is very similar to that of 2'-deoxyadenosine (2'-dA) and adenosine, resulting in an incorrect identification, which will influence its therapeutic effects. Therefore, this review primarily focused on the characteristics of Nt/Ns, the advanced methods, strategies, nanomaterials for extracting and determining Nt/Ns (COR in particular) in Cordyceps spp, as well as the methods for distinguishing COR from its structure analogs.
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Cordyceps , Nucleósidos , Nucleótidos , Cordyceps/química , Nucleósidos/análisis , Nucleósidos/aislamiento & purificación , Nucleótidos/análisis , Nucleótidos/aislamiento & purificación , Nucleótidos/química , DesoxiadenosinasRESUMEN
BACKGROUND: Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging. MATERIALS AND METHODS: We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences. RESULTS: The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation. CONCLUSIONS: We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.
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Código de Barras del ADN Taxonómico , ADN de Plantas , ADN de Plantas/genética , Código de Barras del ADN Taxonómico/métodos , Medicamentos Herbarios Chinos/normas , Apiaceae/genética , Apiaceae/clasificación , Medicina Tradicional China/normas , ADN Espaciador Ribosómico/genética , Contaminación de Medicamentos , Plantas Medicinales/genética , Filogenia , Análisis de Secuencia de ADN/métodos , Reacción en Cadena de la Polimerasa/métodos , Nucleótidos/genética , Nucleótidos/análisisRESUMEN
Oligonucleotides have emerged as important therapeutic options for inherited diseases. In recent years, RNA therapeutics, especially mRNA, have been pushed to the market. Analytical methods for these molecules have been published extensively in the last few years. Notably, mass spectrometry has proven as a state-of-the-art quality control method. For RNA based therapeutics, numerous methods are available, while DNA therapeutics lack of suitable MS-based methods when it comes to molecules exceeding approximately 60 nucleotides. We present a method which combines the use of common restriction enzymes and short enzyme-directing oligonucleotides to generate DNA digestion products with the advantages of high-resolution tandem mass spectrometry. The instrumentation includes ion pair reverse phase chromatography coupled to a time-of-flight mass spectrometer with a collision induced dissociation (CID) for sequence analysis. Utilizing this approach, we increased the sequence coverage from 23.3% for a direct CID-MS/MS experiment of a 100 nucleotide DNA molecule to 100% sequence coverage using the restriction enzyme mediated approach presented in this work. This approach is suitable for research and development and quality control purposes in a regulated environment, which makes it a versatile tool for drug development.
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Enzimas de Restricción del ADN , ADN , Oligonucleótidos , Espectrometría de Masas en Tándem , Espectrometría de Masas en Tándem/métodos , ADN/química , ADN/genética , Enzimas de Restricción del ADN/metabolismo , Oligonucleótidos/química , Nucleótidos/análisis , Nucleótidos/química , Cromatografía de Fase Inversa/métodos , Control de Calidad , Análisis de Secuencia de ADN/métodosRESUMEN
Nucleotide sugars (NS) fulfil important roles in all living organisms and in humans, related defects result in severe clinical syndromes. NS can be seen as the "activated" sugars used for biosynthesis of a wide range of glycoconjugates and serve as substrates themselves for the synthesis of other nucleotide sugars. NS analysis is complicated by the presence of multiple stereoisomers without diagnostic transition ions, therefore requiring separation by liquid chromatography. In this paper, we explored weak anion-exchange/reversed-phase chromatography on a hybrid column for the separation of 17 nucleotide sugars that can occur in humans. A robust and reproducible method was established with intra- and inter-day coefficients of variation below 10% and a linear range spanning three orders of magnitude. Application to patient fibroblasts with genetic defects in mannose-1-phosphate guanylyltransferase beta, CDP-L-ribitol pyrophosphorylase A, and UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase showed abnormal levels of guanosine-5'-diphosphate-α-D-mannose (GDP-Man), cytidine-5'-diphosphate-L-ribitol (CDP-ribitol), and cytidine-5'-monophosphate-N-acetyl-ß-D-neuraminic acid (CMP-Neu5Ac), respectively, in consonance with expectations based on the diagnosis. In conclusion, a novel, semi-quantitative method was established for the analysis of nucleotide sugars that can be applied to diagnose several genetic glycosylation disorders in fibroblasts and beyond.
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Cromatografía de Fase Inversa , Fibroblastos , Espectrometría de Masas en Tándem , Humanos , Fibroblastos/metabolismo , Espectrometría de Masas en Tándem/métodos , Cromatografía por Intercambio Iónico/métodos , Cromatografía de Fase Inversa/métodos , Nucleótidos/análisis , Nucleótidos/metabolismo , Aniones/análisis , Cromatografía Líquida con Espectrometría de MasasRESUMEN
Aging affects tissue glycan profiles, which may alter cellular functions and increase the risk of age-related diseases. Glycans are biosynthesized by glycosyltransferases using the corresponding nucleotide sugar, and the availability of nucleotide sugars affects glycosylation efficiency. However, the effects of aging on nucleotide sugar profiles and contents are yet to be elucidated. Therefore, this study aimed to investigate the effects of aging on nucleotide sugars using a new LC-MS/MS method. Specifically, the new method was used to determine the nucleotide sugar contents of various tissues (brain, liver, heart, skeletal muscle, kidney, lung, and colon) of male C57BL/6NCr mice (7- or 26-month-old). Characteristic age-associated nucleotide sugar changes were observed in each tissue sample. Particularly, there was a significant decrease in UDP-glucuronic acid content in the kidney of aged mice and a decrease in the contents of several nucleotide sugars, including UDP-N-acetylgalactosamine, in the brain of aged mice. Additionally, there were variations in nucleotide sugar profiles among the tissues examined regardless of the age. The kidneys had the highest concentration of UDP-glucuronic acid among the seven tissues. In contrast, the skeletal muscle had the lowest concentration of total nucleotide sugars among the tissues; however, CMP-N-acetylneuraminic acid and CDP-ribitol were relatively enriched. Conclusively, these findings may contribute to the understanding of the roles of glycans in tissue aging.
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Envejecimiento , Ratones Endogámicos C57BL , Nucleótidos , Animales , Ratones , Masculino , Envejecimiento/metabolismo , Nucleótidos/metabolismo , Nucleótidos/análisis , Riñón/metabolismo , Riñón/química , Músculo Esquelético/metabolismo , Músculo Esquelético/química , Espectrometría de Masas en Tándem , Hígado/metabolismo , Hígado/química , Encéfalo/metabolismoRESUMEN
Rapid and effective separation of nucleotides (NTs) and their derivatives is crucial for studying their physiological functions. In this work, we comprehensively evaluated the separation ability of a zwitterionic hydrophilic monolith, i.e., poly(N,N-dimethyl-N-(3-methacrylamidopropyl)-N-(3-sulfopropyl)ammonium betaine-co-N,N'-methylenebisacrylamide) (poly(SPP-co-MBA)) for NTs analysis, including its selectivity, chemical stability under extremely basic condition and compatibility with hydrophilic interaction liquid chromatography (HILIC) coupled with mass spectrometry (HILIC-MS). The poly(SPP-co-MBA) monolith exhibited excellent chemical stability, as evidenced by the low relative standard deviation of retention time (0.16-1.05%) after 4000 consecutive injections over one month under strong alkaline elution condition (pH 10). After optimizing the separation conditions, including buffer pH and concentration, organic solvent content and column temperature, four nucleoside triphosphates, five nucleoside diphosphates and five nucleoside monophosphates were baseline separated within 7 min. Additionally, the mixtures containing one nucleoside and its corresponding mono-, di-, and triphosphates were baseline separated within only 3 min, respectively. It is good HILIC-MS compatibility was also confirmed by the satisfactory peak shape and high response of nine NTs. Overall, the proposed poly(SPP-co-MBA) monolith exhibited good mechanical stability and compatibility of HILIC-MS, making it a promising technique for NTs analysis.
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Nucleósidos , Nucleótidos , Nucleótidos/análisis , Nucleósidos/análisis , Nucleósidos/química , Cromatografía Liquida/métodos , Betaína/química , Interacciones Hidrofóbicas e HidrofílicasRESUMEN
OBJECTIVE: To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS). BACKGROUND: The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date. MATERIALS AND METHODS: Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS. RESULTS: Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary. CONCLUSION: The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.
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Nucleósidos , Periodontitis , Humanos , Nucleósidos/análisis , Espectrometría de Masas en Tándem , Cromatografía Liquida/métodos , Nucleótidos/análisis , Periodontitis/diagnóstico , ARN/análisis , Citidina/análisis , Uridina , Biomarcadores/análisis , Saliva/químicaRESUMEN
Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.
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Nanoporos , Secuencia de Bases , ADN/genética , Nucleótidos/análisis , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Aprendizaje AutomáticoRESUMEN
Almost 40 years since the discovery of microtubule dynamic instability, the molecular mechanisms underlying microtubule dynamics remain an area of intense research interest. The "standard model" of microtubule dynamics implicates a "cap" of GTP-bound tubulin dimers at the growing microtubule end as the main determinant of microtubule stability. Loss of the GTP-cap leads to microtubule "catastrophe," a switch-like transition from microtubule growth to shrinkage. However, recent studies, using biochemical in vitro reconstitution, cryo-EM, and computational modeling approaches, challenge the simple GTP-cap model. Instead, a new perspective on the mechanisms of microtubule dynamics is emerging. In this view, highly dynamic transitions between different structural conformations of the growing microtubule end - which may or may not be directly linked to the nucleotide content at the microtubule end - ultimately drive microtubule catastrophe.
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Microtúbulos , Tubulina (Proteína) , Tubulina (Proteína)/química , Simulación por Computador , Guanosina Trifosfato , Nucleótidos/análisisRESUMEN
The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.
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Eucariontes , ARN Ribosómico , Animales , Eucariontes/genética , Mamíferos/genética , Ratones , Conformación de Ácido Nucleico , Nucleótidos/análisis , Filogenia , ARN Ribosómico/química , Ribosomas/química , Ribosomas/genéticaRESUMEN
Jujube (Ziziphus jujuba Mill.) is a popular fruit with health benefits ascribed to its various metabolites. These metabolites determine the flavors and bioactivities of the fruit, as well as their desirability. However, the dynamics of the metabolite composition and the underlying gene expression that modulate the overall flavor and accumulation of active ingredients during fruit development remain largely unknown. Therefore, we conducted an integrated metabolomic and transcriptomic investigation covering various developmental stages in the jujube cultivar Z. jujuba cv. Jinsixiaozao, which is famous for its nutritional and bioactive properties. A total of 407 metabolites were detected by non-targeted metabolomics. Metabolite accumulation during different jujube developmental stages was examined. Most nucleotides and amino acids and their derivatives accumulated during development, with cAMP increasing notably during ripening. Triterpenes gradually accumulated and were maintained at high concentrations during ripening. Many flavonoids were maintained at relatively high levels in early development, but then rapidly decreased later. Transcriptomic and metabolomic analyses revealed that chalcone synthase (CHS), chalcone isomerase (CHI), flavonol synthase (FLS), and dihydroflavonol 4-reductase (DFR) were mainly responsible for regulating the accumulation of flavonoids. Therefore, the extensive downregulation of these genes was probably responsible for the decreases in flavonoid content during fruit ripening. This study provide an overview of changes of active components in 'Jinsixiaozao' during development and ripening. These findings enhance our understanding of flavor formation and will facilitate jujube breeding for improving both nutrition and function.
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Triterpenos , Ziziphus , Aminoácidos/metabolismo , Flavonoides/metabolismo , Frutas , Nucleótidos/análisis , Nucleótidos/metabolismo , Oxidorreductasas/metabolismo , Fitomejoramiento , Transcriptoma , Triterpenos/metabolismo , Ziziphus/genéticaRESUMEN
The biochemical properties and microstructural changes of freeze-dried Japanese scallop (Patinopecten yessoensis) striated muscle during room temperature storage and rehydration were investigated. The results showed that the content of ATP in freeze-dried scallop muscle remained stable with no significant difference (p > 0.05). However, ATP was rapidly decomposed and AMP accumulated within 1.5 min of rehydration, and HxR and Hx were gradually produced from AMP decomposition with the extension of rehydration time. Besides, the results of chymotryptic digestion patterns demonstrated that the rod of myosin was unstable after dehydration, reflecting lower salt solubility than that of frozen-thawed scallop. In contrast, the myosin subfragment-1 (S-1) was stable, as indicated by the constant of Ca2+-ATPase activity of freeze-dried scallops throughout the storage and rehydration (p > 0.05). Furthermore, the microstructural analysis revealed that the Z line of the freeze-dried scallop was broken after dehydration process. This study might be useful for developing high-quality dehydrated scallops in the future.
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Músculo Estriado , Pectinidae , Adenosina Monofosfato/análisis , Adenosina Monofosfato/metabolismo , Adenosina Trifosfato/análisis , Adenosina Trifosfato/metabolismo , Animales , Deshidratación/metabolismo , Fluidoterapia , Músculo Esquelético/química , Nucleótidos/análisis , Pectinidae/química , Proteínas/análisisRESUMEN
The effects of hot air drying (HAD), vacuum hot air drying (VHAD), microwave drying (MWD), and vacuum freeze drying (VFD) on free amino acids (FAAs) and flavor nucleotides in scallop adductor muscle (SAM) were studied. The liquid chromatography and multidimensional infrared spectroscopy (MM-IR) were used. Compared with fresh SAM, the main FAAs were glycine, alanine, arginine, and glutamic acid in dried SAM. The total FAAs content in VFD group was 1.40-1.90 times of the other group. The umami taste nucleotides (IMP and AMP) content in the VFD and MWD groups was significantly higher than that in HAD and VHAD groups. Equivalent umami concentrations were found: VFD > MWD > VHAD > HAD. MM-IR analysis was an efficient method for identifying taste components. The results revealed FAAs and flavor nucleotides and the mutual adjustment of compounds were related to drying method, and VFD was preferred for taste substance retention in scallops.
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Aminoácidos , Pectinidae , Aminoácidos/análisis , Animales , Liofilización/métodos , Músculo Esquelético/química , Nucleótidos/análisisRESUMEN
Donkeys are indispensable livestock in China because they have transport function and medicinal value. With the popularization of artificial insemination on donkeys, semen cryopreservation technology has gradually become a research hotspot. Seminal plasma is a necessary medium for transporting sperm and provides energy and nutrition for sperm. Seminal plasma metabolites play an important role in the process of sperm freezing, and also have an important impact on sperm motility and fertilization rate after freezing and thawing. In this study, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to compare the metabolic characteristics of seminal plasma of high freezability (HF) and low freezability (LF) male donkeys. We identified 672 metabolites from donkey seminal plasma, of which 33 metabolites were significantly different between the two groups. Metabolites were identified and categorized according to their major chemical classes, including homogeneous non-metal compounds, nucleosides, nucleotides, and analogues, organosulphur compounds, phenylpropanoids and polyketide, organoheterocyclic compounds, organic oxygen compounds, benzenoids, organic acids and derivatives, lipids and lipid-like molecules, organooxygen compounds, alkaloids and derivatives, organic nitrogen compounds. The results showed that the contents of phosphatidylcholine, piceatannol and enkephalin in donkey semen of HF group were significantly higher than those of LF group (p < .05), while the contents of taurocholic and lysophosphatidic acid were significantly lower than those of LF group (p < .05). The different metabolites were mainly related to sperm biological pathway response and oxidative stress. These metabolites may be considered as candidate biomarkers for different fertility in jacks.
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Policétidos , Preservación de Semen , Animales , Biomarcadores/análisis , Cromatografía Liquida/veterinaria , Criopreservación/métodos , Criopreservación/veterinaria , Encefalinas/análisis , Equidae , Lisofosfolípidos/análisis , Masculino , Compuestos de Nitrógeno/análisis , Nucleótidos/análisis , Fosfatidilcolinas/análisis , Policétidos/análisis , Semen/fisiología , Preservación de Semen/métodos , Preservación de Semen/veterinaria , Motilidad Espermática , Espermatozoides/fisiología , Espectrometría de Masas en Tándem/veterinariaRESUMEN
This protocol describes necessary steps to isolate and quantify nucleotides and nucleosides from plant samples. Proper sample preparation in combination with liquid chromatography coupled to mass spectrometry enables the sensitive detection and quantification of metabolites of low abundance. Utilizing a liquid-liquid extraction in combination with a weak anion-exchange solid phase extraction enables the separation of negatively charged molecules from uncharged metabolites or cations.
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Nucleósidos , Nucleótidos , Cromatografía Líquida de Alta Presión/métodos , Cromatografía Liquida , Espectrometría de Masas , Nucleótidos/análisis , Plantas , Extracción en Fase Sólida/métodosRESUMEN
The ribosome CAR interaction surface behaves as an extension of the decoding center A site and has H-bond interactions with the +1 codon, which is next in line to enter the A site. Through molecular dynamic simulations, we investigated the codon sequence specificity of this CAR-mRNA interaction and discovered a strong preference for GCN codons, suggesting that there may be a sequence-dependent layer of translational regulation dependent on the CAR interaction surface. Dissection of the CAR-mRNA interaction through nucleotide substitution experiments showed that the first nucleotide of the +1 codon dominates over the second nucleotide position, consistent with an energetically favorable zipper-like activity that emanates from the A site through the CAR-mRNA interface. Moreover, the CAR/+1 codon interaction is affected by the identity of nucleotide 3 of +1 GCN codons, which influences the stacking of G and C. Clustering analysis suggests that the A-site decoding center adopts different neighborhood substates that depend on the identity of the +1 codon.
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Simulación de Dinámica Molecular , Ribosomas , Codón/genética , Nucleótidos/análisis , ARN Mensajero/química , Ribosomas/química , Ribosomas/genéticaRESUMEN
Nucleotides are released from all cells through regulated pathways or as a result of plasma membrane damage or cell death. Outside the cell, nucleotides act as signalling molecules triggering multiple responses via specific plasma membrane receptors of the P2 family. In the nervous system, purinergic signalling has a key function in neurotransmission. Outside the nervous system, purinergic signalling is one of the major modulators of basal tissue homeostasis, while its dysregulation contributes to the pathogenesis of various disease, including inflammation and cancer. Pre-clinical and clinical evidence shows that selective P2 agonists or antagonists are effective treatments for many pathologies, thus highlighting the relevance of extracellular nucleotides and P2 receptors as therapeutic targets.
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Nucleótidos/metabolismo , Transducción de Señal , Animales , Enfermedades Cardiovasculares/metabolismo , Enfermedades Cardiovasculares/patología , Membrana Celular/metabolismo , Humanos , Enfermedades Pulmonares/metabolismo , Enfermedades Pulmonares/patología , Neoplasias/metabolismo , Neoplasias/patología , Nucleótidos/análisis , Receptores Purinérgicos P2X/metabolismo , Receptores Purinérgicos P2Y/metabolismoRESUMEN
Nucleotides, which are important low-molecular-weight compounds present in organisms, are precursors of nucleic acids and participate in various regulatory and metabolic functions. Sensitive and valid methods for monitoring and determining nucleotides and nucleosides in different samples are urgently required. Due to the presence of numerous endogenous interferences in complex matrices and the high polarity of the molecules of the phosphate moiety, the determination of nucleotide content is challenging. This review summarizes the pretreatment and analysis methods of nucleotides in different samples. Advanced pretreatment methods, including different microextraction methods, solid-phase extraction based on novel materials, QuEChERS, are clearly displayed, and continuous progress which has been made in LC, LC-MS/MS and capillary electrophoresis methods are discussed. Moreover, the strengths and weaknesses of different methods are discussed and compared. Highlight:Advanced pretreatment and detection methods of nucleotides were critically reviewed.Microextraction technology was one of the trends of nucleotides pretreatment in the future.Applications of novel materials and supercritical fluid were highlighted.The evolution and advance of HRMS analyzers were in detailed.
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Ácidos Nucleicos , Nucleótidos , Cromatografía Liquida/métodos , Electroforesis Capilar , Nucleósidos/análisis , Nucleótidos/análisis , Nucleótidos/metabolismo , Fosfatos , Espectrometría de Masas en TándemRESUMEN
The aim was to unveil the generation and variation rule of the main taste components in braised broth for 10 quantitative repeated braising cycles. The major taste compounds of three groups (MS, broth cooked with meat and spices; M, broth cooked with meat; and S, broth cooked with spices) were systematically analyzed by the state-of-art chromatography and electronic sensory technology. As braising cycles progressed, contents of free 5'-nucleotides and amino acids were increased in MS and M, while those nucleotides were not detected in S. A significant discrimination of taste in MS and M was revealed by electronic tongue evaluation during the process. As the formation rates (FR) of taste compounds and the transformation rates (TR) of taste compounds to volatile compounds were mainly accounting for the generation and variation of flavor in broth, a hypothesis was proposed to illustrate the whole variation of taste compounds in the process integrally that the ratio of FR/TR dividing the process into three stages, Degradation, Balance, and Accumulation. PRACTICAL APPLICATIONS: The traditional braising process and formula are empirical and extensive, which impede the increase in meat products output. Nowadays, the industry of braising products is facing a problem of standardization and quality control, and needs to carry out scientific and quantitative process improvement efficiently. Therefore, the developed comprehensive approach demonstrates great potential for braised meat broth flavor monitoring and quality control in an objective and holistic manner. It provides data support and new ideas of technology development for quality control in the process of meat braising.