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This study investigated the mechanism of the extracellular matrix-mimicking hydrogel-mediated TGFB1/Nrf2 signaling pathway in osteoarthritis using bone marrow mesenchymal stem cell-derived exosomes (BMSCs-Exos). A GMOCS-Exos hydrogel was synthesized and evaluated for its impact on chondrocyte viability and neutrophil extracellular traps (NETs) formation. In an OA rat model, GMOCS-Exos promoted cartilage regeneration and inhibited NETs formation. Transcriptome sequencing identified TGFB1 as a key gene, with GMOCS-Exos activating Nrf2 signaling through TGFB1. Depletion of TGFB1 hindered the cartilage-protective effect of GMOCS-Exos. This study sheds light on a promising therapeutic strategy for osteoarthritis through GMOCS-Exos-mediated TGFB1/Nrf2 pathway modulation.
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Condrocitos , Exosomas , Hidrogeles , Células Madre Mesenquimatosas , Osteoartritis , Ratas Sprague-Dawley , Factor de Crecimiento Transformador beta1 , Animales , Osteoartritis/terapia , Células Madre Mesenquimatosas/metabolismo , Ratas , Hidrogeles/química , Factor de Crecimiento Transformador beta1/metabolismo , Condrocitos/metabolismo , Exosomas/metabolismo , Masculino , Transducción de Señal , Factor 2 Relacionado con NF-E2/metabolismo , Trampas Extracelulares/metabolismo , Modelos Animales de Enfermedad , Humanos , Supervivencia Celular/efectos de los fármacos , Células CultivadasRESUMEN
Metal-organic frameworks (MOFs) with fit ligands and metals can be integrated into electrochemical biosensors for the detection of various biomolecules. In this study, we have synthesized novel magnetic MOF composites as electrocatalysts and constructed a novel biosensor for electrochemical detection of dopamine. The composites named Fe3O4@ZIF-8@AuNPs-COOH are synthesized through layer-by-layer assembly. They exhibit excellent stability and cooperative catalytic activity. In addition, green recycling is readily achieved through magnetizing/demagnetizing the electrode. The large specific surface area and ordered porous structures of the magnetic MOFs ensure good dispersion of gold nanoparticles, while the carboxyl group efficiently shields other redox-active interfering substances. The proposed electrochemical biosensor accomplishes the sensitive detection of dopamine in human serums and living cells. This study broadens the application of MOFs in electrochemical biosensing, validates the feasibility of biosensors for in vivo analysis, and provides new insights into green sensing.
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Técnicas Biosensibles , Dopamina , Técnicas Electroquímicas , Estructuras Metalorgánicas , Dopamina/análisis , Dopamina/sangre , Dopamina/química , Técnicas Biosensibles/métodos , Estructuras Metalorgánicas/química , Humanos , Catálisis , Oro/química , Tamaño de la Partícula , Propiedades de Superficie , Nanopartículas del Metal/química , ElectrodosRESUMEN
Exposure to environmental BaP or its metabolite BPDE causes trophoblast cell dysfunctions to induce miscarriage (abnormal early embryo loss), which might be generally regulated by lncRNAs. IL1B, a critical inflammatory cytokine, is closely associated with adverse pregnancy outcomes. However, whether IL1B might cause dysfunctions of BaP/BPDE-exposed trophoblast cells to induce miscarriage, as well as its specific epigenetic regulatory mechanisms, is completely unexplored. In this study, we find that BPDE-DNA adducts, trophoblast cell dysfunctions, and miscarriage are closely associated. Moreover, we also identify a novel lnc-HZ06 and IL1B, both of which are highly expressed in BPDE-exposed trophoblast cells, in villous tissues of recurrent miscarriage patients, and in placental tissues of BaP-exposed mice with miscarriage. Both lnc-HZ06 and IL1B suppress trophoblast cell migration/invasion and increase apoptosis. In mechanism, lnc-HZ06 promotes STAT4-mediated IL1B mRNA transcription, enhances IL1B mRNA stability by promoting the formation of METTL3/HuR/IL1B mRNA ternary complex, and finally up-regulates IL1B expression levels. BPDE exposure promotes TBP-mediated lnc-HZ06 transcription, and thus up-regulates IL1B levels. Knockdown of either murine lnc-hz06 (which down-regulates Il1b levels) or murine Il1b could alleviate miscarriage in BaP-exposed mice. Collectively, this study not only discovers novel biological mechanisms and pathogenesis of unexplained miscarriage but also provides novel potential targets for treatment against BaP/BPDE-induced miscarriage.
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Interleucina-1beta , ARN Largo no Codificante , Trofoblastos , Animales , Femenino , Humanos , Ratones , Embarazo , Aborto Habitual/genética , Aborto Habitual/metabolismo , Aborto Espontáneo , Apoptosis/efectos de los fármacos , Línea Celular , Movimiento Celular/efectos de los fármacos , Interleucina-1beta/metabolismo , Interleucina-1beta/genética , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Trofoblastos/metabolismo , Trofoblastos/efectos de los fármacos , Regulación hacia ArribaRESUMEN
In this study, juvenile crayfish hatched from the same population were cultured in different growing environments: pond (D1), paddy field (D2), and aquaculture barrel (D3), and fed for 60 days. Crayfishes were selected randomly, females and males, 50 tails each from six groups (D1-â, D1-â, D2-â, D2-â, D3-â, D3-â) to measure the following morphological traits: full length (X1), body length (X2), chelicerae length (X3), chelicerae weight (X4), cephalothorax length (X5), cephalothorax width (X6), cephalothorax height (X7), eye spacing (X8), caudal peduncle length (X9), and caudal peduncle weight (X10). We found that the coefficient of variation (CV) of X4 was the largest in each culture mode, and males (28.58%~38.67%) were larger than females (37.76%~66.74%). The CV of X4 of crayfish cultured in D1 and D2 was larger than that of D3. All traits except X8 were positively correlated with body weight (p < 0.05). After pathway analysis, we found that X4, X5, X7, and X10 were significantly correlated with the body weight of D1-â; the equation was YD1-â = -29.803 + 1.249X4 + 0.505X5 + 0.701X7 + 1.483X10 (R2 = 0.947). However, X2, X4, and X6 were significantly correlated with the body weight of D1-â; the equation was YD1-â = -40.881 + 0.39X2 + 0.845X4 + 1.142X6 (R2 = 0.927). In D2-â, X1, X4, X5, and X10 were significantly correlated with body weight; the equation was YD2-â = -12.248 + 0.088X1 + 1.098X4 + 0.275X5 + 0.904X10 (R2 = 0.977). X4 and X5 played a major role in the body weight of D2-â with the equation: YD2-â = -24.871 + 1.177X4 + 0.902X5 (R2 = 0.973). X3 and X10 mainly contributed to the body weight of D3-â with the equation: YD3-â = -22.476 + 0.432X3 + 3.153X10 (R2 = 0.976). X1 and X4 mainly contributed to the body weight of D3-â with the equation: YD3-â = -34.434 + 0.363X1 + 0.669X4 (R2 = 0.918). Comparing the pathway analysis with the gray relation analysis, we could conclude that the traits most correlated with body weight in D1-â were X10 and X7; in D1-â, X6; in D2-â, X10, X1, and X5; in D2-â, X5; in D3-â, X10; and in D3-â, X4 and X1.
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Abnormal expression of long non-coding RNAs (lncRNAs) is associated with the dysfunctions of human trophoblast cells and the occurrence of miscarriage (abnormal early embryo loss). BBC3/PUMA (BCL2 binding component 3) plays significant roles in regulation of cell apoptosis. However, whether specific lncRNAs might regulate BBC3 in trophoblast cells and further induce apoptosis and miscarriage remains completely unclear. Through screening, we identified a novel lnc-HZ12, which was significantly highly expressed in villous tissues of recurrent miscarriage (RM) patients relative to their healthy control (HC) group. Lnc-HZ12 suppressed chaperone-mediated autophagy (CMA) degradation of BBC3, promoted trophoblast cell apoptosis, and was associated with miscarriage. In mechanism, lnc-HZ12 downregulated the expression levels of chaperone molecules HSPA8 and LAMP2A in trophoblast cells. Meanwhile, lnc-HZ12 (mainly lnc-HZ12-SO2 region in F2 fragment) and HSPA8 competitively bound with the 169RVLYNL174 patch on BBC3, which prevented BBC3 from interactions with HSPA8 and impaired the formation of BBC3-HSPA8-LAMP2A complex for CMA degradation of BBC3. Thus, lnc-HZ12 upregulated the BBC3-CASP9-CASP3 pathway and induced trophoblast cell apoptosis. In villous tissues, lnc-HZ12 was highly expressed, CMA degradation of BBC3 was suppressed, and the apoptosis levels were higher in RM vs HC villous tissues, all of which were associated with miscarriage. Interestingly, knockdown of murine Bbc3 could efficiently suppress placental apoptosis and alleviate miscarriage in a mouse miscarriage model. Taken together, our results indicated that lnc-HZ12 and BBC3 played important roles in trophoblast cell apoptosis and miscarriage and might act as attractive targets for miscarriage treatment.Abbreviation: 7-AAD: 7-aminoactinomycin D; BaP: benzopyrene; BBC3/PUMA: BCL2 binding component 3; ChIP: chromatin immunoprecipitation; CHX: cycloheximide; CMA: chaperone-mediated autophagy; CQ: chloroquine; DMSO: dimethyl sulfoxide; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HC: healthy control; HSPA8: heat shock protein family A (Hsp70) member 8; IP: immunoprecipitation; LAMP2A: lysosomal associated membrane protein 2; LncRNA: long non-coding RNA; mRNA: messenger RNA; MT: mutant-type; NC: negative control; NSO: nonspecific oligonucleotide; PARP1: poly(ADP-ribose) polymerase 1; RIP: RNA immunoprecipitation; RM: recurrent miscarriage; TBP: TATA-box binding protein; WT: wild-type.
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Defects of human trophoblast cells may induce miscarriage (abnormal early embryo loss), which is generally regulated by lncRNAs. Ferroptosis is a newly identified iron-dependent programmed cell death. Hypoxia is an important and unavoidable feature in mammalian cells. However, whether hypoxia might induce trophoblast cell ferroptosis and then induce miscarriage, as well as regulated by a lncRNA, was completely unknown. In this work, we discovered at the first time that hypoxia could result in ferroptosis of human trophoblast cells and then induce miscarriage. We also identified a novel lncRNA (lnc-HZ06) that simultaneously regulated hypoxia (indicated by HIF1α protein), ferroptosis, and miscarriage. In mechanism, HIF1α-SUMO, instead of HIF1α itself, primarily acted as a transcription factor to promote the transcription of NCOA4 (ferroptosis indicator) in hypoxic trophoblast cells. Lnc-HZ06 promoted the SUMOylation of HIF1α by suppressing SENP1-mediated deSUMOylation. HIF1α-SUMO also acted as a transcription factor to promote lnc-HZ06 transcription. Thus, both lnc-HZ06 and HIF1α-SUMO formed a positive auto-regulatory feedback loop. This loop was up-regulated in hypoxic trophoblast cells, in RM villous tissues, and in placental tissues of hypoxia-treated mice, which further induced ferroptosis and miscarriage by up-regulating HIF1α-SUMO-mediated NCOA4 transcription. Furthermore, knockdown of either murine lnc-hz06 or Ncoa4 could efficiently suppress ferroptosis and alleviate miscarriage in hypoxic mouse model. Taken together, this study provided new insights in understanding the regulatory roles of lnc-HZ06/HIF1α-SUMO/NCOA4 axis among hypoxia, ferroptosis, and miscarriage, and also offered an effective approach for treatment against miscarriage.
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Aborto Espontáneo , Ferroptosis , ARN Largo no Codificante , Ratones , Femenino , Humanos , Embarazo , Animales , Ferroptosis/genética , ARN Largo no Codificante/genética , Placenta , Hipoxia de la Célula , Hipoxia/genética , Factores de Transcripción , Trofoblastos , Mamíferos , Coactivadores de Receptor NuclearRESUMEN
A 10-week growth experiment was conducted to assess the physiological response of spotted seabass (Lateolabrax maculatus) raised at moderate (27 °C) and high temperatures (33 °C) to different dietary available phosphorus (P) levels. Five diets with available P levels of 0.35, 0.55, 0.71, 0.82 and 0.92% were formulated, respectively. A water temperature of 33 °C significantly decreased growth performance and feed utilization, and increased oxidative stress and lipid deposition of spotted seabass compared with 27 °C. A second-order polynomial regression analysis based on weight gain (WG) showed that the available P requirement of spotted seabass raised at 27 °C and 33 °C was 0.72% and 0.78%, respectively. The addition of 0.71-0.82% P to the diet improved the growth performance, feed utilization, and antioxidant capacity of spotted seabass and alleviated the excessive lipid deposition compared with the low-P diet (0.35% P). Moreover, the addition of 0.71-0.92% P to diets increased the diversity of intestinal microbiota and the relative abundance of Lactococcus lactis and decreased the relative abundance of Plesiomonas compared with the low-P diet. Thus, dietary supplementation with 0.71-0.82% P improved the growth performance, antioxidant capacity and microbial composition of spotted seabass, and alleviated the disturbance of lipid metabolism caused by high temperature or low-P diet.
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Nano-impact electrochemistry (NIE) enables simple, rapid, and high-throughput biocoupling and biomolecular recognition. However, the low effective collision frequency limits the sensitivity. In this study, we propose a novel NIE sensing strategy amplified by the CRISPR-responsive DNA hydrogel and cascade DNA assembly. By controlling the phase transition of DNA hydrogel and the self-electrolysis of silver nanoparticles, we can obtain significant electrochemical responses. The whole process includes target miRNA-induced strand displacement amplification, catalytic hairpin assembly, and CRISPR/Cas trans-cutting. Thus, ultrahigh sensitivity is promised. This NIE biosensing strategy achieves a limit of detection as low as 4.21 aM for miR-141 and demonstrates a high specificity for practical applications. It may have wide applicability in nucleic acid sensing and shows great potential in disease diagnosis.
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Técnicas Biosensibles , Nanopartículas del Metal , MicroARNs , Hibridación de Ácido Nucleico , Nanopartículas del Metal/química , Hidrogeles , Técnicas Electroquímicas , Técnicas de Amplificación de Ácido Nucleico , Límite de Detección , Plata/química , ADN/química , MicroARNs/genéticaRESUMEN
Human infections caused by Brucella (called brucellosis) are among the most common zoonoses worldwide with an estimated 500,000 cases each year. Since chronic Brucella infections are extremely difficult to treat, there is an urgent need for more effective therapeutics. As a facultative intracellular bacterium, Brucella is strictly parasitic in the host cell. Here, we performed proteomic and transcriptomic and metabolomic analyses on Brucella infected patients, mice and cells that provided an extensive "map" of physiological changes in brucellosis patients and characterized the metabolic pathways essential to the response to infection, as well as the associated cellular response and molecular mechanisms. This is the first report utilizing multi-omics analysis to investigate the global response of proteins and metabolites associated with Brucella infection, and the data can provide a comprehensive insight to understand the mechanism of Brucella infection. We demonstrated that Brucella increased nucleotide synthesis in the host, consistent with increased biomass requirement. We also identified IMPDH2, a key regulatory complex that controls nucleotide synthesis during Brucella infection. Pharmacological targeting of IMPDH2, the rate-limiting enzyme in guanine nucleotide biosynthesis, efficiently inhibits B. abortus growth both in vitro and in vivo. Through screening a library of natural products, we identified oxymatrine, an alkaloid obtained primarily from Sophora roots, is a novel and selective IMPDH2 inhibitor. In further in vitro bacterial inhibition assays, oxymatrine effectively inhibited the growth of B. abortus, which was impaired by exogenous supplementation of guanosine, a salvage pathway of purine nucleotides. This moderately potent, structurally novel compound may provide clues for further design and development of efficient IMPDH2 inhibitors and also demonstrates the potential of natural compounds from plants against Brucella.
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Brucella abortus , Brucelosis , Humanos , Animales , Ratones , Brucella abortus/metabolismo , Proteómica , Multiómica , Brucelosis/microbiología , Brucelosis/prevención & control , Nucleótidos/metabolismoRESUMEN
Biomimetic structures to fabricate bioelectronic interfaces that allow sensors to electrically communicate with electrodes have potential applications in the development of biosensors. Herein, inspired by the structure feature of nitric oxide (NO) sensory protein, we constructed a biomimetically catalytic center, the histamine coordinated iron phthalocyanine (FePc), for efficient and sensitive detection of NO. In specific, NO is recognized by axial tethered FePc, and the oxidative signal of NO on FePc is converted into output signal through electrocatalytic oxidation. Based on the fabricated catalytic structure on the carbon fiber electrode, on one hand, the macrocyclic π system of FePc enabled a rapid redox process, which facilitates electron transfer, thereby greatly improving sensitivity. On the other hand, by coordination with histamine on the electrode surface, FePc can enhance the electrochemical oxidation activity toward NO and promote catalytic detection, which have been revealed by electrochemical characterizations and density functional theory theoretical calculations. The designed electrochemical microsensor exhibits a low limit of detection (0.03 nM) and shows a wide detection range (0.1 nM-2 µM). In addition, the electrochemical microsensor has been successfully used for real-time monitoring of NO release by live cells. So, this work shows a new strategy for the design of bio-inspired electrochemical microsensors that may provide a potential analytical tool for tracing biological signal molecules with enzyme-free biomimetically catalytic centers.
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Histamina , Óxido Nítrico , Microelectrodos , Compuestos Ferrosos/química , Electrodos , Técnicas ElectroquímicasRESUMEN
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.
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Plancton , Virus ARN , Agua de Mar , Viroma , Ciclo del Carbono , Ecosistema , Océanos y Mares , Plancton/clasificación , Plancton/metabolismo , Plancton/virología , Virus ARN/clasificación , Virus ARN/genética , Virus ARN/aislamiento & purificación , Agua de Mar/virología , Viroma/genéticaRESUMEN
The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.
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COVID-19 , Virus no Clasificados , Virus , Biología Computacional , Virus ADN , Humanos , SARS-CoV-2RESUMEN
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Genoma Viral , Virus ARN , Virus , Evolución Biológica , Ecosistema , Océanos y Mares , Filogenia , ARN , Virus ARN/genética , Viroma/genética , Virus/genéticaRESUMEN
BACKGROUND: China has a high burden of tuberculosis and latent tuberculosis infection (LTBI). The aim of this study was to estimate the prevalence of LTBI among healthy young children and adolescents and test a 2-step approach to explore the threshold for the diagnosis of tuberculosis infection in Chengdu, China. METHODS: Healthy preschool children and school-going children in Chengdu, Sichuan Province, were screened for LTBI using the tuberculin skin test (TST). Preschool children with TST ≥ 5 mm also underwent interferon-γ release assay (IGRA) to explore the threshold of this 2-step approach. RESULTS: In total, 5667 healthy young children and adolescents completed TST test between July 2020 and January 2021 and were included in the present analysis. The age of the participants ranged from 2.4 to 18 years (median 7.25 ± 4.514 years), of which 2093 (36.9%) were younger than 5 years. The overall prevalence of LTBI was 6.37% and 6.64% in children younger than 5 years old. Fourteen of the 341 preschool children with TST ≥5 mm were interferon-γ release assay positive, of which 4 showed a TST result of 5-10 mm, and 6 preschool children received preventive treatment for LTBI. CONCLUSIONS: Healthy young children and adolescents should also be considered as important target populations for LTBI screening. TST can be recommended for first-line screening as part of a 2-step approach for LTBI screening using a positive threshold of 5 mm.
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Técnicas de Laboratorio Clínico/métodos , Ensayos de Liberación de Interferón gamma/estadística & datos numéricos , Tuberculosis Latente/diagnóstico , Tuberculosis Latente/epidemiología , Prueba de Tuberculina/estadística & datos numéricos , Adolescente , Niño , Preescolar , China/epidemiología , Técnicas de Laboratorio Clínico/normas , Femenino , Voluntarios Sanos , Humanos , Ensayos de Liberación de Interferón gamma/economía , Ensayos de Liberación de Interferón gamma/métodos , Masculino , Prevalencia , Reproducibilidad de los Resultados , Prueba de Tuberculina/economía , Prueba de Tuberculina/métodosRESUMEN
Measurement of signal molecule is critically important for understanding living systems. Nitric oxide (NO) is a key redox signal molecule that shows diverse roles in virtually all life forms. However, probing into NO's activities is challenging as NO has restricted lifetime (<10 s) and limited diffusion distance (usually <200 µm). So, for the direct acupuncture of NO within the time-space resolution, an electrochemical microsensor has been designed and fabricated in this work. Fabrication of the microsensor is achieved by (1) selective assembly of an electrocatalytic transducer, (2) attaching the transducer on carbon fiber electrode, and (3) covered it with a screen layer to reduce signal interference. The fabricated microsensor exhibits high sensitivity (LOD, 13.5 pM), wide detection range (100 pM-5 µM), and good selectivity. Moreover, studies have revealed that the availability of the sensor for efficient detection of NO is due to the formation of a specific DNA/porphyrin hybrid structure that has synergetic effects on NO electrocatalysis. Therefore, NO release by cells and tissues can be directly and precisely traced, in which we have obtained the release pattern of NO by different cancer cell lines, and have known its dynamics in tumor microenvironment. The fabricated electrocatalytic microsensor may provide a unique and useful tool for the direct assay of NO with high time-space resolution, which promisingly gives a technical solution for the bioassay of NO in living systems.
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Terapia por Acupuntura , Técnicas Biosensibles , Fibra de Carbono , Electrodos , Óxido NítricoRESUMEN
Under the current situation of the rapid development of brain-like artificial intelligence and the increasingly complex electromagnetic environment, the most bionic and anti-interference spiking neural network has shown great potential in computing speed, real-time information processing, and spatiotemporal data processing. Spiking neural network is the core part of brain-like artificial intelligence, which realizes brain-like computing by simulating the structure of biological neural network and the way of information transmission. This article first summarizes the advantages and disadvantages of the five models, and analyzes the characteristics of several network topologies. Then, it summarizes the spiking neural network algorithms. The unsupervised learning based on spike timing dependent plasticity (STDP) rules and four types of supervised learning algorithms are analyzed. Finally, the research on brain-like neuromorphic chips at home and abroad are reviewed. This paper aims to provide learning ideas and research directions for new colleagues in the field of spiking neural network.
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Inteligencia Artificial , Redes Neurales de la Computación , Algoritmos , EncéfaloRESUMEN
BACKGROUND: Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). RESULTS: The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to â¼5% for virome and â¼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from â¼95% (whole genomes) down to â¼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. CONCLUSION: Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.
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BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.
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Metagenoma , Microbiología del Suelo , Antibacterianos , Ecosistema , Genes Bacterianos , Pradera , Humanos , ARN Ribosómico 16S/genética , Suelo , Clima Tropical , TundraRESUMEN
BPDE (benzo(a)pyren-7,8-dihydrodiol-9,10-epoxide), a metabolite of environmental carcinogenic BaP, weakens the migration and invasion of human villous trophoblast cells and may further induce miscarriage. However, the underlying mechanisms remain largely unknown. In this study, we identified that in trophoblast Swan 71 and HTR-8/SVneo cells, miR-hz02 upregulates the level of lnc-HZ02, which inhibits the expression of an RNA-binding protein HuR. HuR could interact with FAK mRNA and promote its mRNA stability, thus upregulating the FAK level and the FAK/SRC/PI3K/AKT pathway, and finally maintaining the normal migration and invasion of trophoblast cells. If trophoblast cells are exposed to BPDE, both miR-hz02 and lnc-HZ02 are upregulated, which reduce the level of HuR, weaken the interactions of HuR with FAK mRNA, downregulate FAK level and the FAK/SRC/PI3K/AKT pathway, and finally inhibit cell migration and invasion. This study provides a novel scientific understanding of the dysfunctions of human trophoblast cells.
Asunto(s)
7,8-Dihidro-7,8-dihidroxibenzo(a)pireno 9,10-óxido/toxicidad , Regulación hacia Abajo/efectos de los fármacos , Quinasa 1 de Adhesión Focal/metabolismo , MicroARNs/biosíntesis , Fosfatidilinositol 3-Quinasas/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Proteínas Proto-Oncogénicas pp60(c-src)/metabolismo , ARN Largo no Codificante/biosíntesis , Trofoblastos/metabolismo , Regulación hacia Arriba/efectos de los fármacos , Línea Celular Transformada , Humanos , Trofoblastos/patologíaRESUMEN
Environmental BaP (benzo(a)pyrene) and its metabolite BPDE (benzo(a)pyrene-7,8-dihydrodiol-9,10-epoxide) inhibit proliferation of human villous trophoblast cells, which might further induce recurrent miscarriage (RM). However, the underlying mechanisms remain largely unknown. In this work, we identified a novel lncRNA HZ01 (lnc-HZ01) that is up-regulated in both RM tissues and BPDE-exposed trophoblast cells. Lnc-HZ01 inhibits trophoblast cell proliferation and induces miscarriage. Mechanistically, lnc-HZ01 promotes MXD1 mRNA transcription by up-regulating its transcription factor c-JUN and also enhances MXD1 protein stability by up-regulating its deubiquitin enzyme USP36. Reversely, MXD1 up-regulates lnc-HZ01 level by enhancing its RNA stability due to the increased level of m6A RNA methylation on lnc-HZ01, the first example that m6A modification regulates trophoblast cell functions. Thus, lnc-HZ01 and MXD1 comprise a positive self-feedback loop, which is up-regulated in both RM tissues and BPDE-exposed trophoblast cells. Once this loop is activated by BaP or BPDE exposure, both pathways in this loop would be up-regulated, promote EIF4E transcription, inhibit trophoblast cell proliferation, and further induce miscarriage. This work provides new clinical and scientific understanding in unexplained miscarriage.