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1.
Immunity ; 54(2): 308-323.e6, 2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33421362

RESUMO

Th17 cells are known to exert pathogenic and non-pathogenic functions. Although the cytokine transforming growth factor ß1 (TGF-ß1) is instrumental for Th17 cell differentiation, it is dispensable for generation of pathogenic Th17 cells. Here, we examined the T cell-intrinsic role of Activin-A, a TGF-ß superfamily member closely related to TGF-ß1, in pathogenic Th17 cell differentiation. Activin-A expression was increased in individuals with relapsing-remitting multiple sclerosis and in mice with experimental autoimmune encephalomyelitis. Stimulation with interleukin-6 and Activin-A induced a molecular program that mirrored that of pathogenic Th17 cells and was inhibited by blocking Activin-A signaling. Genetic disruption of Activin-A and its receptor ALK4 in T cells impaired pathogenic Th17 cell differentiation in vitro and in vivo. Mechanistically, extracellular-signal-regulated kinase (ERK) phosphorylation, which was essential for pathogenic Th17 cell differentiation, was suppressed by TGF-ß1-ALK5 but not Activin-A-ALK4 signaling. Thus, Activin-A drives pathogenic Th17 cell differentiation, implicating the Activin-A-ALK4-ERK axis as a therapeutic target for Th17 cell-related diseases.


Assuntos
Ativinas/metabolismo , Encefalomielite Autoimune Experimental/imunologia , Esclerose Múltipla/imunologia , Inflamação Neurogênica/imunologia , Células Th17/imunologia , Fator de Crescimento Transformador beta/metabolismo , Receptores de Ativinas Tipo I/genética , Receptores de Ativinas Tipo I/metabolismo , Ativinas/genética , Animais , Diferenciação Celular , Células Cultivadas , Humanos , Camundongos , Camundongos Knockout , Terapia de Alvo Molecular , Transdução de Sinais
2.
Development ; 151(13)2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38953252

RESUMO

Spermatogonial stem cell (SSC) self-renewal and differentiation provide foundational support for long-term, steady-state spermatogenesis in mammals. Here, we have investigated the essential role of RNA exosome associated DIS3 ribonuclease in maintaining spermatogonial homeostasis and facilitating germ cell differentiation. We have established male germ-cell Dis3 conditional knockout (cKO) mice in which the first and subsequent waves of spermatogenesis are disrupted. This leads to a Sertoli cell-only phenotype and sterility in adult male mice. Bulk RNA-seq documents that Dis3 deficiency partially abolishes RNA degradation and causes significant increases in the abundance of transcripts. This also includes pervasively transcribed PROMoter uPstream Transcripts (PROMPTs), which accumulate robustly in Dis3 cKO testes. In addition, scRNA-seq analysis indicates that Dis3 deficiency in spermatogonia significantly disrupts RNA metabolism and gene expression, and impairs early germline cell development. Overall, we document that exosome-associated DIS3 ribonuclease plays crucial roles in maintaining early male germ cell lineage in mice.


Assuntos
Fertilidade , Espermatogônias , Testículo , Animais , Masculino , Camundongos , Diferenciação Celular , Complexo Multienzimático de Ribonucleases do Exossomo/metabolismo , Complexo Multienzimático de Ribonucleases do Exossomo/genética , Exossomos/metabolismo , Fertilidade/genética , Infertilidade Masculina/genética , Camundongos Knockout , Estabilidade de RNA/genética , Células de Sertoli/metabolismo , Espermatogênese , Espermatogônias/metabolismo , Espermatogônias/citologia , Testículo/metabolismo
3.
Nat Methods ; 21(7): 1349-1363, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38849569

RESUMO

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.


Assuntos
Perfilação da Expressão Gênica , RNA-Seq , Humanos , Animais , Camundongos , RNA-Seq/métodos , Perfilação da Expressão Gênica/métodos , Transcriptoma , Análise de Sequência de RNA/métodos , Anotação de Sequência Molecular/métodos
4.
PLoS Genet ; 18(10): e1010433, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36301831

RESUMO

Circular RNAs (circRNAs) are a new group of noncoding/regulatory RNAs that are particularly abundant in the nervous system, however, their physiological functions are underexplored. Here we report that the brain-enriched circular RNA Edis (Ect4-derived immune suppressor) plays an essential role in neuronal development in Drosophila. We show that depletion of Edis in vivo causes defects in axonal projection patterns of mushroom body (MB) neurons in the brain, as well as impaired locomotor activity and shortened lifespan of adult flies. In addition, we find that the castor gene, which encodes a transcription factor involved in neurodevelopment, is upregulated in Edis knockdown neurons. Notably, castor overexpression phenocopies Edis knockdown, and reducing castor levels suppresses the neurodevelopmental phenotypes in Edis-depleted neurons. Furthermore, chromatin immunoprecipitation analysis reveals that the transcription factor Relish, which plays a key role in regulating innate immunity signaling, occupies a pair of sites at the castor promoter, and that both sites are required for optimal castor gene activation by either immune challenge or Edis depletion. Lastly, Relish mutation and/or depletion can rescue both the castor gene hyperactivation phenotype and neuronal defects in Edis knockdown animals. We conclude that the circular RNA Edis acts through Relish and castor to regulate neuronal development.


Assuntos
Proteínas de Drosophila , Drosophila , Animais , Drosophila/genética , RNA Circular/genética , Proteínas de Drosophila/genética , Fatores de Transcrição/genética , Corpos Pedunculados , Drosophila melanogaster/fisiologia
5.
PLoS Genet ; 18(10): e1010429, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36301822

RESUMO

Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset has been functionally characterized. We identify and validate a collection of circRNAs in Drosophila, and show that depletion of the brain-enriched circRNA Edis (circ_Ect4) causes hyperactivation of antibacterial innate immunity both in cultured cells and in vivo. Notably, Edis depleted flies display heightened resistance to bacterial infection and enhanced pathogen clearance. Conversely, ectopic Edis expression blocks innate immunity signaling. In addition, inactivation of Edis in vivo leads to impaired locomotor activity and shortened lifespan. Remarkably, these phenotypes can be recapitulated with neuron-specific depletion of Edis, accompanied by defective neurodevelopment. Furthermore, inactivation of Relish suppresses the innate immunity hyperactivation phenotype in the fly brain. Moreover, we provide evidence that Edis encodes a functional protein that associates with and compromises the processing and activation of the immune transcription factor Relish. Importantly, restoring Edis expression or ectopic expression of Edis-encoded protein suppresses both innate immunity and neurodevelopment phenotypes elicited by Edis depletion. Thus, our study establishes Edis as a key regulator of neurodevelopment and innate immunity.


Assuntos
Imunidade Inata , RNA Circular , Animais , RNA Circular/genética , Imunidade Inata/genética , Fatores de Transcrição/genética , Drosophila/genética , Drosophila/metabolismo , Transdução de Sinais , RNA/genética
6.
Brief Bioinform ; 23(2)2022 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-35192692

RESUMO

A major topic of debate in developmental biology centers on whether development is continuous, discontinuous, or a mixture of both. Pseudo-time trajectory models, optimal for visualizing cellular progression, model cell transitions as continuous state manifolds and do not explicitly model real-time, complex, heterogeneous systems and are challenging for benchmarking with temporal models. We present a data-driven framework that addresses these limitations with temporal single-cell data collected at discrete time points as inputs and a mixture of dependent minimum spanning trees (MSTs) as outputs, denoted as dynamic spanning forest mixtures (DSFMix). DSFMix uses decision-tree models to select genes that account for variations in multimodality, skewness and time. The genes are subsequently used to build the forest using tree agglomerative hierarchical clustering and dynamic branch cutting. We first motivate the use of forest-based algorithms compared to single-tree approaches for visualizing and characterizing developmental processes. We next benchmark DSFMix to pseudo-time and temporal approaches in terms of feature selection, time correlation, and network similarity. Finally, we demonstrate how DSFMix can be used to visualize, compare and characterize complex relationships during biological processes such as epithelial-mesenchymal transition, spermatogenesis, stem cell pluripotency, early transcriptional response from hormones and immune response to coronavirus disease. Our results indicate that the expression of genes during normal development exhibits a high proportion of non-uniformly distributed profiles that are mostly right-skewed and multimodal; the latter being a characteristic of major steady states during development. Our study also identifies and validates gene signatures driving complex dynamic processes during somatic or germline differentiation.


Assuntos
Benchmarking , Modelos Teóricos , Análise de Célula Única/métodos , Algoritmos , Animais , Microambiente Celular , Análise de Dados , Árvores de Decisões , Perfilação da Expressão Gênica/métodos , Humanos , Espermatogênese
7.
Allergy ; 79(3): 643-655, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-38263798

RESUMO

BACKGROUND: Adult asthma is complex and incompletely understood. Plasma proteomics is an evolving technique that can both generate biomarkers and provide insights into disease mechanisms. We aimed to identify plasma proteomic signatures of adult asthma. METHODS: Protein abundance in plasma was measured in individuals from the Agricultural Lung Health Study (ALHS) (761 asthma, 1095 non-case) and the Atherosclerosis Risk in Communities study (470 asthma, 10,669 non-case) using the SOMAScan 5K array. Associations with asthma were estimated using covariate adjusted logistic regression and meta-analyzed using inverse-variance weighting. Additionally, in ALHS, we examined phenotypes based on both asthma and seroatopy (asthma with atopy (n = 207), asthma without atopy (n = 554), atopy without asthma (n = 147), compared to neither (n = 948)). RESULTS: Meta-analysis of 4860 proteins identified 115 significantly (FDR<0.05) associated with asthma. Multiple signaling pathways related to airway inflammation and pulmonary injury were enriched (FDR<0.05) among these proteins. A proteomic score generated using machine learning provided predictive value for asthma (AUC = 0.77, 95% CI = 0.75-0.79 in training set; AUC = 0.72, 95% CI = 0.69-0.75 in validation set). Twenty proteins are targeted by approved or investigational drugs for asthma or other conditions, suggesting potential drug repurposing. The combined asthma-atopy phenotype showed significant associations with 20 proteins, including five not identified in the overall asthma analysis. CONCLUSION: This first large-scale proteomics study identified over 100 plasma proteins associated with current asthma in adults. In addition to validating previous associations, we identified many novel proteins that could inform development of diagnostic biomarkers and therapeutic targets in asthma management.


Assuntos
Asma , Hipersensibilidade Imediata , Adulto , Humanos , Proteômica/métodos , Asma/metabolismo , Biomarcadores , Fenótipo , Proteínas Sanguíneas/genética
8.
Chemistry ; : e202402636, 2024 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-39109460

RESUMO

In this work, we report the syntheses of three Pt(II) emitters, namely, Pt4N1, Pt4N2, and Pt4N3, to which their tetradentate chelates were assembled by linking two pyrazolate chelates with a single xylenylamino entity. Functionalization of Pt4N1 was achieved upon addition of electronegative CF3 substituent on pyridinyl groups and switching to more electron deficient pyrazinyl groups in giving Pt4N2 and Pt4N3, respectively. The vertical arranged xylenylamino entity has effectively suppressed the inter-molecular π-π stacking and Pt···Pt interaction, as shown by the single crystal X-ray structural analyses. Upon fabrication of OLED devices, Pt4N2 and Pt4N3 based devices delivered efficient cyan and green emission, with an EQEmax of 15.2% and 11.2%, respectively, affirming the successfulness of the tetradentate chelating strategy.

9.
Langmuir ; 40(27): 13773-13783, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38920266

RESUMO

Cartilage defects in large joints are a common occurrence in numerous degenerative diseases, especially in osteoarthritis. The hydrogel-on-metal composite has emerged as a potential candidate material, as hydrogels, to some extent, replicate the composition of human articular cartilage consisting of collagen fibers and proteoglycans. However, achieving tough bonding between the hydrogel and titanium alloy remains a significant challenge due to the swelling of the hydrogel in a liquid medium. This swelling results in reduced interfacial toughness between the hydrogel and titanium alloy, limiting its potential clinical applications. Herein, our approach aimed to achieve durable bonding between a hydrogel and a titanium alloy composite in a swollen state by modifying the surface texture of the titanium alloy. Various textures, including circular and triangular patterns, with dimple densities ranging from 10 to 40%, were created on the surface of the titanium alloy. Subsequently, poly(vinyl alcohol) (PVA) hydrogel was deposited onto the textured titanium alloy using a casting-drying method. Our findings revealed that PVA hydrogel on the textured titanium alloy with a 30% texture density exhibited the highest interfacial toughness in the swollen state, measuring at 1300 J m-2 after reaching equilibrium swelling in deionized water, which is a more than 2-fold increase compared to the hydrogel on a smooth substrate. Furthermore, we conducted an analysis of the morphologies of the detached hydrogel from the textured titanium alloy after various swelling durations. The results indicated that interfacial toughness could be enhanced through mechanical interlocking, facilitated by the expanded volume of the hydrogel protrusions as the swelling time increased. Collectively, our study demonstrates the feasibility of achieving tough bonding between a hydrogel and a metal substrate in a liquid environment. This research opens up promising avenues for designing soft/hard heterogeneous materials with strong adhesive properties.

10.
Lung ; 2024 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-39153120

RESUMO

PURPOSE: Over 550 loci have been associated with human pulmonary function in genome-wide association studies (GWAS); however, the causal role of most remains uncertain. Single nucleotide polymorphisms in a disintegrin and metalloprotease domain 19 (ADAM19) are consistently related to pulmonary function in GWAS. Thus, we used a mouse model to investigate the causal link between Adam19 and pulmonary function. METHODS: We created an Adam19 knockout (KO) mouse model and validated the gene targeting using RNA-Seq and RT-qPCR. Mouse body composition was assessed using dual-energy X-ray absorptiometry. Mouse lung function was measured using flexiVent. RESULTS: Contrary to prior publications, the KO was not neonatal lethal. KO mice had lower body weight and shorter tibial length than wild-type (WT) mice. Their body composition revealed lower soft weight, fat weight, and bone mineral content. Adam19 KO had decreased baseline respiratory system elastance, minute work of breathing, tissue damping, tissue elastance, and forced expiratory flow at 50% forced vital capacity but higher FEV0.1 and FVC. Adam19 KO had attenuated tissue damping and tissue elastance in response to methacholine following LPS exposure. Adam19 KO also exhibited attenuated neutrophil extravasation into the airway after LPS administration compared to WT. RNA-Seq analysis of KO and WT lungs identified several differentially expressed genes (Cd300lg, Kpna2, and Pttg1) implicated in lung biology and pathogenesis. Gene set enrichment analysis identified negative enrichment for TNF pathways. CONCLUSION: Our murine findings support a causal role of ADAM19, implicated in human GWAS, in regulating pulmonary function.

11.
PLoS Genet ; 17(1): e1009302, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33444353

RESUMO

Human skin is continuously exposed to environmental DNA damage leading to the accumulation of somatic mutations over the lifetime of an individual. Mutagenesis in human skin cells can be also caused by endogenous DNA damage and by DNA replication errors. The contributions of these processes to the somatic mutation load in the skin of healthy humans has so far not been accurately assessed because the low numbers of mutations from current sequencing methodologies preclude the distinction between sequencing errors and true somatic genome changes. In this work, we sequenced genomes of single cell-derived clonal lineages obtained from primary skin cells of a large cohort of healthy individuals across a wide range of ages. We report here the range of mutation load and a comprehensive view of the various somatic genome changes that accumulate in skin cells. We demonstrate that UV-induced base substitutions, insertions and deletions are prominent even in sun-shielded skin. In addition, we detect accumulation of mutations due to spontaneous deamination of methylated cytosines as well as insertions and deletions characteristic of DNA replication errors in these cells. The endogenously induced somatic mutations and indels also demonstrate a linear increase with age, while UV-induced mutation load is age-independent. Finally, we show that DNA replication stalling at common fragile sites are potent sources of gross chromosomal rearrangements in human cells. Thus, somatic mutations in skin of healthy individuals reflect the interplay of environmental and endogenous factors in facilitating genome instability and carcinogenesis.


Assuntos
Dano ao DNA/efeitos da radiação , Metilação de DNA/genética , Replicação do DNA/genética , Pele/efeitos da radiação , Metilação de DNA/efeitos da radiação , Reparo do DNA/efeitos da radiação , Replicação do DNA/efeitos da radiação , Fibroblastos/efeitos da radiação , Genoma Humano/genética , Genoma Humano/efeitos da radiação , Instabilidade Genômica/efeitos da radiação , Genômica/métodos , Humanos , Mutação INDEL/efeitos da radiação , Melanócitos/efeitos da radiação , Mutagênese/genética , Mutagênese/efeitos da radiação , Pele/metabolismo , Raios Ultravioleta/efeitos adversos
12.
Angew Chem Int Ed Engl ; 63(23): e202403317, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38578721

RESUMO

We demonstrate directed translocation of ClO4 - anions from cationic to neutral binding site along the synthetized BPym-OH dye molecule that exhibits coupled excited-state intramolecular proton-transfer (ESIPT) and charge-transfer (CT) reaction (PCCT). The results of steady-state and time-resolved spectroscopy together with computer simulation and modeling show that in low polar toluene the excited-state redistribution of electronic charge enhanced by ESIPT generates the driving force, which is much stronger than by CT reaction itself and provides more informative gigantic shifts of fluorescence spectra signaling on ultrafast ion motion. The associated with ion translocation red-shifted fluorescence band (at 750 nm, extending to near-IR region) appears at the time ~83 ps as a result of electrochromic modulation of PCCT reaction. It occurs at substantial delay to PCCT that displayed fluorescence band at 640 nm and risetime of <200 fs. Thus, it becomes possible to visualize the manifestations of light-triggered ion translocation and of its driving force by fluorescence techniques and to separate them in time and energy domains.

13.
J Cell Biochem ; 124(8): 1155-1172, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37357411

RESUMO

This study aimed to explore the effect of myricitrin on osteoblast differentiation in mice immortalised bone marrow mesenchymal stem cells (imBMSCs). Additionally, ovariectomy (OVX) mice were employed to examine the effect of myricitrin on bone trabecular loss in vivo. The effect of myricitrin on the proliferation of imBMSCs was evaluated using a cell counting kit-8 assay. Alizarin red staining, alkaline phosphatase staining were performed to elucidate osteogenesis. Furthermore, qRT-PCR and western blot determined the expression of osteo-specific genes and proteins. To screen for candidate targets, mRNA transcriptome genes were sequenced using bioinformatics analyses. Western blot and molecular docking analysis were used to examine target signalling markers. Moreover, rescue experiments were used to confirm the effect of myricitrin on the osteogenic differentiation of imBMSCs. OVX mice were also used to estimate the delay capability of myricitrin on bone trabecular loss in vivo using western blot, micro-CT, tartaric acid phosphatase (Trap) staining, haematoxylin and eosin staining, Masson staining and immunochemistry. In vitro, myricitrin significantly enhanced osteo-specific genes and protein expression and calcium deposition. Moreover, mRNA transcriptome gene sequencing and molecular docking analysis revealed that this enhancement was accompanied by an upregulation of the PI3K/AKT signalling pathway. Furthermore, copanlisib, a PI3K inhibitor, partially reversed the osteogenesis promotion induced by myricitrin. In vivo, western blot, micro-CT, hematoxylin and eosin staining, Masson staining, Trap staining and immunochemistry revealed that bone trabecular loss rate was significantly alleviated in the myricitrin low- and high-dose groups, with an increased expression of osteopontin, osteoprotegerin, p-PI3K and p-AKT compared to the OVX group. Myricitrin enhances imBMSC osteoblast differentiation and attenuate bone mass loss partly through the upregulation of the PI3K/AKT signalling pathway. Thus, myricitrin has therapeutic potential as an antiosteoporosis drug.


Assuntos
Doenças Ósseas Metabólicas , Osteogênese , Animais , Feminino , Camundongos , Diferenciação Celular , Células Cultivadas , Amarelo de Eosina-(YS)/farmacologia , Simulação de Acoplamento Molecular , Osteogênese/genética , Ovariectomia , Fosfatidilinositol 3-Quinases/metabolismo , Proteínas Proto-Oncogênicas c-akt/genética , Proteínas Proto-Oncogênicas c-akt/metabolismo , RNA Mensageiro
14.
Am J Physiol Lung Cell Mol Physiol ; 324(4): L413-L432, 2023 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-36719087

RESUMO

The COVID-19 pandemic continues to impose a major impact on global health and economy since its identification in early 2020, causing significant morbidity and mortality worldwide. Caused by the SARS-CoV-2 virus, along with a growing number of variants, COVID-19 has led to 651,918,402 confirmed cases and 6,656,601 deaths worldwide (as of December 27, 2022; https://covid19.who.int/). Despite advances in our understanding of COVID-19 pathogenesis, the precise mechanism by which SARS-CoV2 causes epithelial injury is incompletely understood. In this current study, robust application of global-discovery proteomics identified highly significant induced changes by the Spike S1 protein of SARS-CoV-2 in the proteome of alveolar type II (ATII)-like rat L2 cells that lack ACE2 receptors. Systems biology analysis revealed that the S1-induced proteomics changes were associated with three significant network hubs: E2F1, CREB1/RelA, and ROCK2/RhoA. We also found that pretreatment of L2 cells with high molecular weight hyaluronan (HMW-HA) greatly attenuated the S1 effects on the proteome. Western blotting analysis and cell cycle measurements confirmed the S1 upregulation of E2F1 and ROCK2/RhoA in L2 cells and the protective effects of HMW-HA. Taken as a whole, our studies revealed profound and novel biological changes that contribute to our current understanding of both S1 and hyaluronan biology. These data show that the S1 protein may contribute to epithelial injury induced by SARS-CoV-2. In addition, our work supports the potential benefit of HMW-HA in ameliorating SARS CoV-2-induced cell injury.


Assuntos
COVID-19 , Animais , Humanos , Ratos , Ácido Hialurônico , Pandemias , Peptidil Dipeptidase A/metabolismo , Proteoma , Proteômica , RNA Viral , SARS-CoV-2/metabolismo
15.
Nucleic Acids Res ; 49(12): 6739-6755, 2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34139016

RESUMO

The INO80 chromatin remodeler is involved in many chromatin-dependent cellular functions. However, its role in pluripotency and cell fate transition is not fully defined. We examined the impact of Ino80 deletion in the naïve and primed pluripotent stem cells. We found that Ino80 deletion had minimal effect on self-renewal and gene expression in the naïve state, but led to cellular differentiation and de-repression of developmental genes in the transition toward and maintenance of the primed state. In the naïve state, INO80 pre-marked gene promoters that would adopt bivalent histone modifications by H3K4me3 and H3K27me3 upon transition into the primed state. In the primed state, in contrast to its known role in H2A.Z exchange, INO80 promoted H2A.Z occupancy at these bivalent promoters and facilitated H3K27me3 installation and maintenance as well as downstream gene repression. Together, our results identified an unexpected function of INO80 in H2A.Z deposition and gene regulation. We showed that INO80-dependent H2A.Z occupancy is a critical licensing step for the bivalent domains, and thereby uncovered an epigenetic mechanism by which chromatin remodeling, histone variant deposition and histone modification coordinately control cell fate.


Assuntos
ATPases Associadas a Diversas Atividades Celulares/fisiologia , Proteínas de Ligação a DNA/fisiologia , Código das Histonas , Histonas/metabolismo , Células-Tronco Pluripotentes/metabolismo , ATPases Associadas a Diversas Atividades Celulares/genética , ATPases Associadas a Diversas Atividades Celulares/metabolismo , Animais , Diferenciação Celular , Linhagem Celular , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Deleção de Genes , Regulação da Expressão Gênica , Camundongos , Células-Tronco Pluripotentes/citologia , Regiões Promotoras Genéticas
16.
Anal Chem ; 94(45): 15864-15872, 2022 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-36318538

RESUMO

Multianalytes and individual differences of biofluids (such as blood, urine, or sweat) pose enormous complexity and challenges to rapid, facile, high-throughput, and accurate clinical analysis or health assessment. Deep-learning (DL)-assisted image analysis has been demonstrated to be an efficient big data process which shows accurate individual identification. However, the data-driven "black boxes" of current DL algorithms are suffering from the nontransparent inner working mechanism. In this work, we designed a programmable colorimetric chip with explainable DL to approach accurate classification and quantification analysis of sweat samples. Gel (sodium alginate) capsules with different indicators were adopted to combinate as designed programmable colorimetric chips. We collected 4600 colorimetric response images as the data set and assessed two DL algorithms and seven machine learning (ML) algorithms. Glucose, pH, and lactate in human sweat could be facilely and 100% accurately classified and quantified by the convolutional neural network (CNN) DL algorithm, and the testing results of actual sweat via the DL-assisted colorimetric approach match 91.0-99.7% with the laboratory measurements. Class activation mapping (CAM) was processed to visualize the inner working mechanism of CNN operation, which could help to verify and explicate the design rationality of colorimetric chips. The explainable DL-assisted programmable colorimetric chip provided an "end-to-end" strategy to ascertain the black box of the DL algorithm, promoted software design or principium optimization, and contributed facile indicators for clinical monitoring, disease prevention, and even new scientific discoveries.


Assuntos
Aprendizado Profundo , Humanos , Suor , Colorimetria , Redes Neurais de Computação , Processamento de Imagem Assistida por Computador/métodos , Algoritmos
18.
Small ; 18(31): e2203036, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35798317

RESUMO

Heterostructures play an irreplaceable role in high-performance optoelectronic devices. However, the preparation of robust perovskite heterostructures is challenging due to spontaneous interdiffusion of halogen anions. Herein, a vapor-phase anion exchange method universally suitable for the preparation of robust 2D Ruddlesden-Popper perovskite (RPP) heterostructures is developed. A variety of heterostructures are fabricated based on exfoliated RPP microplates (MPs). Depending on the specific organic cations, the heterostructures can be either sharp and uniform, or broad and gradient, suggesting a new anion diffusion behavior different from that in 3D perovskites. Further experimental studies reveal that the lateral transport of anions follows a threshold-dominating mechanism, while the vertical transport can be partially or completely suppressed by organic cations. Subsequently, quantitative investigation of anion diffusion in 2D perovskites is conducted. The lateral diffusion coefficient of halogen anions is calculated to be 6 to 7 orders of magnitude larger than the vertical coefficient, consistent with the observed highly anisotropic anion diffusion. In addition, it is shown that the anion exchange threshold can also enhance the thermodynamic stability of the heterostructures at elevated temperature. These results provide a general method to fabricate robust lateral RPP heterostructures, and offer important insights into anion behavior in low-dimensional perovskites.

19.
Proc Natl Acad Sci U S A ; 116(24): 11776-11785, 2019 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-31123148

RESUMO

The cytoplasmic coat protein complex-II (COPII) is evolutionarily conserved machinery that is essential for efficient trafficking of protein and lipid cargos. How the COPII machinery is regulated to meet the metabolic demand in response to alterations of the nutritional state remains largely unexplored, however. Here, we show that dynamic changes of COPII vesicle trafficking parallel the activation of transcription factor X-box binding protein 1 (XBP1s), a critical transcription factor in handling cellular endoplasmic reticulum (ER) stress in both live cells and mouse livers upon physiological fluctuations of nutrient availability. Using live-cell imaging approaches, we demonstrate that XBP1s is sufficient to promote COPII-dependent trafficking, mediating the nutrient stimulatory effects. Chromatin immunoprecipitation (ChIP) coupled with high-throughput DNA sequencing (ChIP-seq) and RNA-sequencing analyses reveal that nutritional signals induce dynamic XBP1s occupancy of promoters of COPII traffic-related genes, thereby driving the COPII-mediated trafficking process. Liver-specific disruption of the inositol-requiring enzyme 1α (IRE1α)-XBP1s signaling branch results in diminished COPII vesicle trafficking. Reactivation of XBP1s in mice lacking hepatic IRE1α restores COPII-mediated lipoprotein secretion and reverses the fatty liver and hypolipidemia phenotypes. Thus, our results demonstrate a previously unappreciated mechanism in the metabolic control of liver protein and lipid trafficking: The IRE1α-XBP1s axis functions as a nutrient-sensing regulatory nexus that integrates nutritional states and the COPII vesicle trafficking.


Assuntos
Vesículas Revestidas pelo Complexo de Proteína do Envoltório/metabolismo , Endorribonucleases/metabolismo , Nutrientes/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transporte Proteico/fisiologia , Transdução de Sinais/fisiologia , Proteína 1 de Ligação a X-Box/metabolismo , Animais , Movimento Celular/fisiologia , Imunoprecipitação da Cromatina/métodos , Retículo Endoplasmático/metabolismo , Estresse do Retículo Endoplasmático/fisiologia , Lipídeos/fisiologia , Fígado/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Regiões Promotoras Genéticas/fisiologia
20.
Zhongguo Zhong Yao Za Zhi ; 47(6): 1618-1624, 2022 Mar.
Artigo em Zh | MEDLINE | ID: mdl-35347961

RESUMO

Aconiti Kusnezoffii Radix Cocta is one of the most commonly used medicinal materials in Mongolian medicine. Due to the strong toxicity of Aconiti Kusnezoffii Radix Cocta, Mongolian medicine often uses Chebulae Fructus, Glycyrrhizae Radix et Rhizoma to reduce the toxicity, so as to ensure the curative effect of Aconiti Kusnezoffii Radix Cocta while ensuring its clinical curative effect, but the mechanism is not clear. The aim of this study was to investigate the effects of Chebulae Fructus, Glycyrrhizae Radix et Rhizoma and Aconiti Kusnezoffii Radix Cocta on the mRNA transcription and protein translation of cytochrome P450(CYP450) in the liver of normal rats. Male SD rats were randomly divided into negative control(NC) group, phenobarbital(PB) group(0.08 g·kg~(-1)·d~(-1)), Chebulae Fructus group(0.254 2 g·kg~(-1)·d~(-1)), Glycyrrhizae Radix et Rhizoma group(0.254 2 g·kg~(-1)·d~(-1)), Aconiti Kusnezoffii Radix Cocta group(0.254 2 g·kg~(-1)·d~(-1))and compatibility group(0.254 2 g·kg~(-1)·d~(-1),taking Aconiti Kusnezoffii Radix Cocta as the standard). After continuous administration for 8 days, the activities of total bile acid(TBA), alkaline phosphatase(ALP), amino-transferase(ALT) and aspartate aminotransferase(AST)in serum were detected, the pathological changes of liver tissue were observed, and the mRNA and protein expression levels of CYP1 A2, CYP2 C11 and CYP3 A1 were observed. Compared with the NC group, the serum ALP, ALT and AST activities in the Aconiti Kusnezoffii Radix Cocta group were significantly increased, and the ALP, ALT and AST activities were decreased after compatibility. At the same time, compatibility could reduce the liver injury caused by Aconiti Kusnezoffii Radix Cocta. The results showed that Aconiti Kusnezoffii Radix Cocta could inhibit the expression of CYP1 A2, CYP2 C11 and CYP3 A1, and could up-regulate the expression of CYP1 A2, CYP2 C11 and CYP3 A1 when combined with Chebulae Fructus and Glycyrrhizae Radix et Rhizoma. The level of translation was consistent with that of transcription. The compatibility of Chebulae Fructus and Glycyrrhizae Radix et Rhizoma with Aconiti Kusnezoffii Radix Cocta could up-regulate the expression of CYP450 enzyme, reduce the accumulation time of aconitine in vivo, and play a role in reducing toxicity, and this effect may start from gene transcription.


Assuntos
Sistema Enzimático do Citocromo P-450 , Fígado , Animais , Sistema Enzimático do Citocromo P-450/genética , Medicamentos de Ervas Chinesas , Glycyrrhiza , Masculino , Extratos Vegetais , Ratos , Ratos Sprague-Dawley , Terminalia
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