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1.
FEBS Lett ; 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38589226

RESUMO

Overactivation of the epidermal growth factor receptor (EGFR) is critical for the development of multiple cancers. Previous studies have shown that the cell membrane is a key regulator of EGFR kinase activity through its interaction with the EGFR juxtamembrane domain (JM). However, the lipid recognition specificity of EGFR-JM and its interaction details remain unclear. Using lipid strip and liposome pulldown assays, we showed that EGFR-JM could specifically interact with PI(4,5)P2-or phosphatidylserine-containing membranes. We further characterized the JM-membrane interaction using NMR-titration-based chemical shift perturbation and paramagnetic relaxation enhancement analyses, and found that residues I649 - L659 comprised the membrane-binding site. Furthermore, the membrane-binding region contains the predicted dimerization motif of JM, 655LRRLL659, suggesting that membrane binding may affect JM dimerization and, therefore, regulate kinase activation.

2.
Arch Biochem Biophys ; 756: 109997, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38621443

RESUMO

The preservation of the native conformation and functionality of membrane proteins has posed considerable challenges. While detergents and liposome reconstitution have been traditional approaches, nanodiscs (NDs) offer a promising solution by embedding membrane proteins in phospholipids encircled by an amphipathic helical protein MSP belt. Nevertheless, a drawback of commonly used NDs is their limited homogeneity and stability. In this study, we present a novel approach to construct covalent annular nanodiscs (cNDs) by leveraging microbial transglutaminase (MTGase) to catalyze isopeptide bond formation between the side chains of terminal amino acids, specifically Lysine (K) and Glutamine (Q). This methodology significantly enhances the homogeneity and stability of NDs. Characterization of cNDs and the assembly of membrane proteins within them validate the successful reconstitution of membrane proteins with improved homogeneity and stability. Our findings suggest that cNDs represent a more suitable tool for investigating interactions between membrane proteins and lipids, as well as for analyzing membrane protein structures.

3.
J Phys Chem Lett ; 15(10): 2708-2714, 2024 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-38427973

RESUMO

CPEB3 ribozyme is a self-cleaving RNA that occurs naturally in mammals and requires divalent metal ions for efficient activity. Ribozymes exhibit preferences for specific metal ions, but the exact differences in the catalytic mechanisms of various metal ions on the CPEB3 ribozyme remain unclear. Our findings reveal that Mn2+ functions as a more effective cofactor for CPEB3 ribozyme catalysis compared to Mg2+, as confirmed by its stronger binding affinity to CPEB3 by EPR. Cleavage assays of CPEB3 mutants and molecular docking analyses further showed that excessive Mn2+ ions can bind to a second binding site near the catalytic site, hindering CPEB3 catalytic efficiency and contributing to the Mn2+ bell-shaped curve. These results implicate a pivotal role for the local nucleobase-Mn2+ interactions in facilitating RNA folding and modulating the directed attack of nucleophilic reagents. Our study provides new insights and experimental evidence for exploring the divalent cation dependent cleavage mechanism of the CPEB3 ribozyme.


Assuntos
RNA Catalítico , Animais , RNA Catalítico/química , Magnésio/química , Simulação de Acoplamento Molecular , Conformação de Ácido Nucleico , Cátions Bivalentes/metabolismo , Catálise , Mamíferos/genética , Mamíferos/metabolismo
4.
Medicine (Baltimore) ; 103(13): e37470, 2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38552099

RESUMO

BACKGROUND: Long-term physical exercise has been shown to benefit patients with Parkinson disease (PD), but there is a lack of evidence regarding the underlying mechanism. A better understanding of how such benefits are induced by exercise might contribute to the development of therapeutic targets for improving the motor function in individuals with PD. The purpose of this study was therefore to investigate the possible association between exercise-induced motor improvements and the changes in serum microRNA (miRNA) levels of PD patients through small RNA sequencing for the first time. METHODS: Thirteen PD patients completed our 3-month home-and-community-based exercise program, while 6 patients were assigned to the control group. Motor functions were measured, and small RNA sequencing with data analysis was performed on serum miRNAs both before and after the program. The results were further validated by quantitative real-time polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were then conducted to determine the role of differentially expressed miRNAs. RESULTS: The 3-month home-and-community-based exercise program induced significant motor improvements in PD patients in terms of Unified Parkinson's Disease Rating Scale activities of daily living and Motor Subscale (P < .05), comfortable walking speed (P = .003), fast walking speed (P = .028), Six-Minute Walk Test (P = .004), Berg Balance Scale (P = .039), and Timed Up and Go (P = .002). A total of 11 miRNAs (10 upregulated and one downregulated) were identified to be remarkably differentially expressed after intervention in the exercise group, but not in the control group. The results of miRNA sequencing were further validated by quantitative real-time polymerase chain reaction. It was found that the targets of altered miRNAs were mostly enriched in the mitogen-activated protein kinase, Wnt, and Hippo signaling pathways and the GO annotations mainly included binding, catalytic activity, and transcription regulator activity. CONCLUSION: The exercise-induced motor improvements were possibly associated with changes in circulating miRNA levels in PD patients. These miRNAs, as well as the most enriched pathways and GO terms, may play a critical role in the mechanism of exercise-induced benefits in PD and serve as novel treatment targets for the disease, although further investigations are needed.


Assuntos
MicroRNAs , Doença de Parkinson , Humanos , MicroRNAs/metabolismo , Doença de Parkinson/genética , Doença de Parkinson/terapia , Atividades Cotidianas , Caminhada , Modalidades de Fisioterapia
5.
Infect Genet Evol ; 119: 105570, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38382768

RESUMO

INTRODUCTION: Balamuthia amoebic encephalitis (BAE), caused by Balamuthia mandrillaris, is a rare and life-threatening infectious disease with no specific and effective treatments available. The diagnosis of BAE at an early stage is difficult because of the non-specific clinical manifestations and neuroimaging. CASE DESCRIPTION: A 52-year-old male patient, who had no previous history of skin lesions, presented to the emergency department with an acute headache, walking difficulties, and disturbance of consciousness. The patient underwent a series of examinations, including regular cerebrospinal fluid (CSF) studies and magnetic resonance imaging, and tuberculous meningoencephalitis was suspected. Despite being treated with anti-TB drugs, no clinical improvement was observed in the patient. Following corticosteroid therapy, the patient developed a rapid deterioration in consciousness with dilated pupils. Metagenomic next-generation sequencing (mNGS) revealed an unexpected central nervous system (CNS) amoebic infection, and the patient died soon after the confirmed diagnosis. CONCLUSION: This study highlights the application of mNGS for the diagnosis of patients with suspected encephalitis or meningitis, especially those caused by rare opportunistic infections.


Assuntos
Amebíase , Balamuthia mandrillaris , Infecções Protozoárias do Sistema Nervoso Central , Encefalite , Encefalite Infecciosa , Masculino , Humanos , Pessoa de Meia-Idade , Encefalite Infecciosa/diagnóstico , Encefalite/diagnóstico , Encefalite/patologia , Balamuthia mandrillaris/genética , Infecções Protozoárias do Sistema Nervoso Central/diagnóstico , Amebíase/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala
6.
Artif Life ; 30(1): 106-135, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38393968

RESUMO

Nowadays, interdisciplinary fields between Artificial Life, artificial intelligence, computational biology, and synthetic biology are increasingly emerging into public view. It is necessary to reconsider the relations between the material body, identity, the natural world, and the concept of life. Art is known to pave the way to exploring and conveying new possibilities. This survey provides a literature review on recent works of Artificial Life in visual art during the past 40 years, specifically in the computational and software domain. Having proposed a set of criteria and a taxonomy, we briefly analyze representative artworks of different categories. We aim to provide a systematic overview of how artists are understanding nature and creating new life with modern technology.


Assuntos
Arte , Inteligência Artificial , Vida Artificial , Biologia Computacional , Biologia Sintética
7.
Front Public Health ; 12: 1148705, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38327578

RESUMO

Objectives: The present study analyzed the impact of the COVID-19 pandemic on the prevalence and incidence of new leprosy cases, as well as the diversity, distribution, and temporal transmission of Mycobacterium leprae strains at the county level in leprae-endemic provinces in Southwest China. Methods: A total of 219 new leprosy cases during two periods, 2018-2019 and 2020-2021, were compared. We genetically characterized 83 clinical isolates of M. leprae in Guizhou using variable number tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs). The obtained genetic profiles and cluster consequences of M. leprae were compared between the two periods. Results: There was an 18.97% decrease in the number of counties and districts reporting cases. Considering the initial months (January-March) of virus emergence, the number of new cases in 2021 increased by 167% compared to 2020. The number of patients with a delay of >12 months before COVID-19 (63.56%) was significantly higher than that during COVID-19 (48.51%). Eighty-one clinical isolates (97.60%) were positive for all 17 VNTR types, whereas two (2.40%) clinical isolates were positive for 16 VNTR types. The (GTA)9, (TA)18, (TTC)21 and (TA)10 loci showed higher polymorphism than the other loci. The VNTR profile of these clinical isolates generated five clusters, among which the counties where the patients were located were adjacent or relatively close to each other. SNP typing revealed that all clinical isolates possessed the single SNP3K. Conclusion: COVID-19 may have a negative/imbalanced impact on the prevention and control measures of leprosy, which could be a considerable fact for official health departments. Isolates formed clusters among counties in Guizhou, indicating that the transmission chain remained during the epidemic and was less influenced by COVID-19 preventative policies.


Assuntos
COVID-19 , Hanseníase , Humanos , Mycobacterium leprae/genética , Pandemias , DNA Bacteriano/genética , COVID-19/epidemiologia , Hanseníase/epidemiologia , Hanseníase/microbiologia , China/epidemiologia
8.
Chem Asian J ; 19(5): e202301069, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38234110

RESUMO

A metal-free heterogeneous protocol is established herein for the synthesis of value-added γ-amino acid scaffolds via carbocarboxylation of alkenes with CO2 and alkylamines under visible light irradiation. The protocol shows broad substrate scope under mild reaction conditions and good stability of the catalyst for recycle tests. Moreover, the methodology could be feasible to the late-stage derivatization of several natural products, enriching the chemical arsenal for practical application.

9.
Theriogenology ; 215: 31-42, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38000127

RESUMO

The branched-chain amino acids (BCAAs: leucine, isoleucine and valine) are essential for animal growth and metabolic health. However, the effect of valine on male reproduction and its underlying molecular mechanism remain largely unknown. Here, we showed that l-valine supplementation (0.30% or 0.45%, water drinking for 3 weeks) did not change body and testis weights, but significantly altered morphology of sertoli cells and germ cells within seminiferous tubule, and enlarged the space between seminiferous tubules within mouse testis. l-valine treatment (0.45%) increased significantly the Caspase3/9 mRNA levels and CASPASE9 protein levels, therefore induced apoptosis of mouse testis. Moreover, gene expression levels related to autophagy (Atg5 and Lamb3), DNA 5 mC methylation (Dnmt1, Dnmt3a, Tet2 and Tet3), RNA m6A methylation (Mettl14, Alkbh5 and Fto), and m6A methylation binding proteins (Ythdf1/2/3 and Igf2bp1/2) were significantly reduced. Protein abundances of ALKBH5, FTO and YTHDF3 were also significantly reduced, but not for ATG5 and TET2. Testis transcriptome sequencing detected 537 differentially expressed genes (DEGs, 26 up-regulated and 511 down-regulated), involved in multiple important signaling pathways. RT-qPCR validated 8 of 9 DEGs (Cd36, Scd1, Insl3, Anxa5, Lcn2, Hsd17b3, Cyp11a1, Cyp17a1 and Agt) to be decreased significantly, consistent with RNA-seq results. Taken together, l-valine treatment could disturb multiple signaling pathways (autophagy and RNA methylation etc.), and induce apoptosis to destroy the tissue structure of mouse testis.


Assuntos
Testículo , Valina , Camundongos , Masculino , Animais , Valina/farmacologia , Valina/metabolismo , Células de Sertoli/metabolismo , Apoptose , Suplementos Nutricionais
10.
Plants (Basel) ; 12(23)2023 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-38068668

RESUMO

In this study, we analyzed the components of Mentha spp. essential oils (EOs) and evaluated their major constituents and binary combinations against Reticulitermes dabieshanensis. We also determined the activities of esterases (ESTs), glutathione S-transferases (GSTs), and acetylcholinesterase activity (AChE) in treated insects. According to our findings, the most effective oils were those obtained from M. citrata (with the major constituent linalool constituting 45.1%), M. piperita (menthol, 49.1%), and M. spicata (carvone, 69.0%), with LC50 values of 0.176, 0.366, and 0.146 µL/L, respectively. The LC50 values were recorded for linalool (0.303 µL/L), followed by menthol (0.272 µL/L), and carvone (0.147 µL/L). The insecticidal potency increased with binary mixtures of major active constituents, with carvone strongly synergizing the toxicity of linalool and menthol against R. dabieshanensis. Compared to the control, except for M. citrata treated with no difference in α-NA or GST activity, the activities of ESTs and GST in other treatment groups were significantly increased. Additionally, our results found that Mentha spp. EOs and their major constituents inhibited the activity of AChE in vivo and in vitro. Finally, we performed a structure-based virtual screening of linalool, menthol, and carvone to identify that linalool had the greatest potential to bind to the active site of AChE. The present study suggests that Mentha spp. EOs could provide an additional approach for the management of termites over synthetic insecticides.

12.
Curr Allergy Asthma Rep ; 23(11): 635-645, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37804376

RESUMO

PURPOSE OF REVIEW: As a sulfone antibacterial agent, dapsone has been widely used to treat leprosy. Moreover, dapsone is also used in many immune diseases such as herpetic dermatitis because of its anti-inflammatory and immunomodulatory effects. However, dapsone can cause several adverse effects, the most serious being dapsone hypersensitivity syndrome. Dapsone hypersensitivity syndrome is characterized by a triad of eruptions, fever, and organ involvement, which limits the application of dapsone to some extent. RECENT FINDINGS: In this article, we review current research about the interaction model between HLA-B*13:01, dapsone, and specific TCR in dapsone-induced drug hypersensitivity. In addition to the proposed mechanisms, we also discussed clinical features, treatment progress, prevalence, and prevention of dapsone hypersensitivity syndrome. These studies reveal the pathogenesis, clinical features, and prevalence from the perspectives of genetic susceptibility and innate and adaptive immunity in dapsone hypersensitivity syndrome, thereby guiding clinicians on how to diagnose, prevent, and treat dapsone hypersensitivity syndrome.


Assuntos
Hipersensibilidade a Drogas , Hipersensibilidade , Hanseníase , Humanos , Dapsona/efeitos adversos , Hipersensibilidade a Drogas/diagnóstico , Hipersensibilidade a Drogas/genética , Hipersensibilidade a Drogas/terapia , Hipersensibilidade/complicações , Síndrome , Hanseníase/induzido quimicamente , Hanseníase/complicações , Hanseníase/tratamento farmacológico
13.
Plants (Basel) ; 12(10)2023 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-37653948

RESUMO

Cytochrome P450 (CYP74) family members participate in the generation of oxylipins and play essential roles in plant adaptation. However, the metabolic reprogramming mediated by CYP74s under cold stress remains largely unexplored. Herein, we report how cold-triggered OsHPL1, a member of the CYP74 family, modulates rice metabolism. Cold stress significantly induced the expression of OsHPL1 and the accumulation of OPDA (12-oxo-phytodienoic acid) and jasmonates in the wild-type (WT) plants. The absence of OsHPL1 attenuates OPDA accumulation to a low temperature. Then, we performed a widely targeted metabolomics study covering 597 structurally annotated compounds. In the WT and hpl1 plants, cold stress remodeled the metabolism of lipids and amino acids. Although the WT and hpl1 mutants shared over one hundred cold-affected differentially accumulated metabolites (DAMs), some displayed distinct cold-responding patterns. Furthermore, we identified 114 and 56 cold-responding DAMs, specifically in the WT and hpl1 mutants. In conclusion, our work characterized cold-triggered metabolic rewiring and the metabolic role of OsHPL1 in rice.

14.
Mol Med ; 29(1): 96, 2023 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-37438701

RESUMO

BACKGROUND: Spinocerebellar ataxia type 3 (SCA3) is the most common autosomal dominant hereditary ataxia worldwide, which is however in a lack of effective treatment. In view of that engineered exosomes are a promising non-invasive gene therapy transporter that can overcome the traditional problem of poor drug delivery, the aim of this study was to evaluate, for the first time, the value of exosome-based microRNA therapy in SCA3 and the therapeutic effects of intravenously administrated ATXN3 targeting microRNAs in transgenic SCA3 mouse models. METHODS: The rabies virus glycoprotein (RVG) peptide-modified exosomes loaded with miR-25 or miR-181a were peripherally injected to enable targeted delivery of miRNAs to the brain of SCA3 mice. The behaviors, ATXN3 level, purkinje cell and other neuronal loss, and neuroinflammation were evaluated 4 weeks after initial treatment. RESULTS: The targeted and efficient delivery of miR-25 and miR-181a by modified exosomes substantially inhibited the mutant ATXN3 expression, reduced neuron apoptosis and induced motor improvements in SCA3 mouse models without increasing the neuroinflammatory response. CONCLUSIONS: Our study confirmed the therapeutic potential of engineered exosome-based miR-25 and miR-181a treatment in substantially reducing ATXN3 aggregation and cytotoxicity by relying on its targeted and efficient drug delivery performance in SCA3 mice. This treatment method shows a promising prospect for future clinical applications in SCA3.


Assuntos
Exossomos , Doença de Machado-Joseph , MicroRNAs , Camundongos , Animais , Doença de Machado-Joseph/genética , Doença de Machado-Joseph/terapia , Camundongos Transgênicos , Apoptose , MicroRNAs/genética
15.
Cancer Med ; 12(12): 13279-13289, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37162297

RESUMO

BACKGROUND: To evaluate the impact of radiosensitivity on outcomes of spinal metastases treated with stereotactic body radiotherapy (SBRT) and identify the correlated prognostic factors. METHODS: The authors retrospectively reviewed the records of all patients who underwent SBRT with no prior radiation for spinal metastases between October 2015 and October 2020 at Sun Yat-sen University Cancer Center. On the basis of radiosensitivity, patients were divided into two groups-radiosensitive and radioresistant. The endpoints included local control (LC), overall survival (OS), pain relief, and time to pain relief. RESULTS: A total of 259 (82.5%) patients with 451 lesions were assessable with a median follow-up time of 10.53 months. The 1-, 2-, and 3-year OS rates were 59%, 52%, and 44%, respectively. The median survival was 33.17 months. Higher Karnofsky Performance Scale score and shorter time to diagnosis of spinal metastases from primary cancer at consult predicted for better OS (p = 0.02 and p < 0.001, respectively). The presence of other metastases (p = 0.04) and pain at enrollment assessed by the Brief Pain Inventory predicted for worse OS (p = 0.01). The 6-, 12-, and 24-month LC rates were 88%, 86%, and 82%, respectively. Younger age was identified for better LC and pain relief (p < 0.001 and p = 0.04, respectively). There was no variable independently associated with time to pain relief. As for toxicity, no Grade ≥3 toxicity was observed. CONCLUSIONS: Regardless of radiosensitivity, SBRT is feasible and appears to be an effective treatment paradigm for patients with spinal metastases, with limited accepted toxicities.


Assuntos
Radiocirurgia , Neoplasias da Coluna Vertebral , Humanos , Radiocirurgia/efeitos adversos , Estudos Retrospectivos , Resultado do Tratamento , Tolerância a Radiação , Dor/etiologia
16.
Angew Chem Int Ed Engl ; 62(27): e202304861, 2023 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-37102784

RESUMO

Light-driven fixation of CO2 in organics has emerged as an appealing alternative for the synthesis of value-added fine chemicals. Challenges remain in the transformation of CO2 as well as product selectivity due to its thermodynamic stability and kinetic inertness. Here we develop a boron carbonitride (BCN) with the abundant terminal B/N defects around the mesoporous walls, which essentially enhances surface active sites as well as charge transfer kinetics, boosting the overall rate of CO2 adsorption and activation. In this protocol, anti-Markovnikov hydrocarboxylation of alkenes with CO2 to an extended carbon chain is achieved with good functional group tolerance and specific regioselectivity under visible-light irradiation. The mechanistic studies demonstrate the formation of CO2 radical anion intermediate on defective boron carbonitride, leading to the anti-Markovnikov carboxylation. Gram-scale reaction, late-stage carboxylation of natural products and synthesis of anti-diabetic GPR40 agonists reveal the utility of this method. This study sheds new insight on the design and application of metal-free semiconductors for the conversion of CO2 in an atom-economic and sustainable manner.

17.
Molecules ; 28(5)2023 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-36903258

RESUMO

The volatile metabolites of Salvia sclarea, Rosmarinus officinalis, Thymus serpyllum, Mentha spicata, Melissa officinalis, Origanum majorana, Mentha piperita, Ocimum basilicum and Lavandula angustifolia were determined by gas chromatography-mass spectrometry. The vapor insecticidal properties of the analyzed essential oils and their compounds were screened using Reticulitermes dabieshanensis workers. The most effective oils were S. sclarea (major constituent linalyl acetate, 65.93%), R. officinalis (1,8-cineole, 45.56%), T. serpyllum (thymol, 33.59%), M. spicata (carvone, 58.68%), M. officinalis (citronellal, 36.99%), O. majorana (1,8-cineole, 62.29%), M. piperita (menthol, 46.04%), O. basilicum (eugenol, 71.08%) and L. angustifolia (linalool, 39.58%), which exhibited LC50 values ranging from 0.036 to 1.670 µL/L. The lowest LC50 values were recorded for eugenol (0.060 µL/L), followed by thymol (0.062 µL/L), carvone (0.074 µL/L), menthol (0.242 µL/L), linalool (0.250 µL/L), citronellal (0.330 µL/L), linalyl acetate (0.712 µL/L) and 1,8-cineole (1.478 µL/L). The increased activity of esterases (ESTs) and glutathione S-transferase (GST) were observed but only alongside the decreased activity of acetylcholinesterase (AChE) in eight main components. Our results indicate that S. sclarea, R. officinalis, T. serpyllum, M. spicata, M. officinalis, O. marjorana, M. piperita, O. basilicum and L. angustifolia essential oils (EOs) and their compounds, linalyl acetate, 1,8-cineole, thymol, carvone, citronellal, menthol, eugenol and linalool could be developed as control agents against termites.


Assuntos
Lamiaceae , Óleos Voláteis , Óleos Voláteis/química , Lamiaceae/química , Timol/química , Mentol/farmacologia , Eucaliptol , Eugenol , Acetilcolinesterase , Óleos de Plantas/química
18.
Mol Biol Rep ; 50(4): 3379-3387, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36729208

RESUMO

BACKGROUND: Normalization of the expression profiling of target genes, in a tissue-specific manner and under different experimental conditions, requires stably expressed gene(s) to be used as internal reference(s). However, to study the molecular regulation of oocyte meiosis initiation during ovary development in chicken embryos, stable reference gene(s) still need to be compared and confirmed. METHODS AND RESULTS: Six candidate genes previously used as internal references for the chicken embryo (Actb, Cvh, Dazl, Eef1a, Gapdh and Rpl15) were chosen, and their expression profiles in left ovaries dissected at five chicken embryonic days (E12.5, E15.5, E17.5, E18.5 and E20.5) were evaluated, respectively. Separately, GeNorm, NormFinder, BestKeeper and Comparative ΔCt methods were used to assess the stability of candidate reference genes, and all results were combined to give the final rank by RefFinder. All methods identified that Eef1a and Rpl15 were the two most stable internal reference genes, whereas Cvh is the most unstable one. Moreover, expression levels of three marker genes for chicken oocyte meiosis entry (Stra8, Scp3 and Dmc1) were normalized, based on Eef1a, Rpl15, or their combinations, respectively. CONCLUSION: Our findings provide the most suitable internal reference genes (Eef1a and Rpl15), to investigate further molecular regulation of ovary development and oocyte meiosis initiation in chicken embryos.


Assuntos
Galinhas , Perfilação da Expressão Gênica , Animais , Feminino , Embrião de Galinha , Galinhas/genética , Perfilação da Expressão Gênica/métodos , Ovário , Reação em Cadeia da Polimerase em Tempo Real/métodos , Padrões de Referência
19.
Reprod Domest Anim ; 58(5): 605-613, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36755113

RESUMO

Alternative polyadenylation (APA) generates different 3'-untranslated regions (3'UTRs) to regulate gene expression and localization, and affects a variety of biological processes. Here, we characterized the 3'UTR dynamics during the oocyte-to-zygote transition by analysing our previously reported porcine single-cell RNA-seq (scRNA-seq) datasets (in vitro matured metaphase II (MII) oocytes, in vitro fertilized zygotes (IVF1) and parthenogenetically activated 1-cell embryos (PA1)). After IVF1 versus MII comparison, dynamic analyses of APA from RNA-seq (DaPars) method identified 139 mRNAs with significantly different 3'UTRs (padj . ≤ .05), mainly enriched in cell cycle, regulation of cyclin-dependent protein kinase activity, histone modification, mRNA surveillance, and regulation of actin cytoskeleton. For PA1 versus MII comparison, 105 mRNAs with significantly different 3'UTRs (padj . ≤ .05) were identified to be mainly enriched in intracellular transport, mitotic spindle organization, cell cycle, pyruvate metabolism and glycolysis/gluconeogenesis. Furthermore, there were 7 mRNAs with more significant 3'UTR differences (|△PDUI| ≥ 0.45 and |log2 [PDUI ratio]| ≥ 0.59) respectively in IVF1 versus MII (Lrp2bp, Mtfr2, Nhlrc2, Psip1, Smu1, Ssr1 and Wtap) and PA1 versus MII (Asf1b, Dimt1, Nap1l1, Ncoa4, Nudt21, Pnn and Rpl15) comparisons. Integrative genomics viewer analysis further identified that 3'UTRs of Psip1, Smu1, Ssr1 and Wtap had more than 140 nt average length changes, whereas those of Dimt1, Nap1l1 and Rpl15 were shortened with more than 460 nt. Regulatory elements (PAS, CPE, microRNA binding sites and m6 A sites) in 3'UTRs of different lengths were predicted. Our findings provide useful information to further investigate the molecular mechanism of 3'UTR in regulating the oocyte-to-zygote transition of pig embryos.


Assuntos
Poliadenilação , Zigoto , Animais , Suínos , Zigoto/metabolismo , Regiões 3' não Traduzidas , Oócitos/metabolismo
20.
Theriogenology ; 196: 79-87, 2023 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-36401935

RESUMO

Alternative polyadenylation (APA) affects the composition of cis-elements in 3'-untranslated region (3'-UTR), to regulate gene expression and localization, and subsequently the downstream biological processes. Acute heat stress could change rapidly the cellular transcriptome, however the underlying molecular changes are less explored. Here, we systematically catalogued the global 3'-UTRome dynamics, by analyzing our previously reported transcriptome sequencing data of porcine immature Sertoli (iST) cells before (Control group), acute heat stress treatment at 43 °C for 0.5h (HS0.5 group), and 36h recovery culture (HS0.5-R36h group) after acute heat stress treatment. After three group comparisons (HS0.5 vs. Control, HS0.5-R36 vs. HS0.5, and HS0.5-R36 vs. Control), DaPars (dynamic analysis of alternative polyadenylation) identified 639, 464 and 290 mRNAs, and APAtrap (a tool to identify APA sites and detect changes of APA site usage) identified 713, 518 and 321 mRNAs, with significantly different 3'-UTRs (Padj.≤0.05), respectively. These genes with different 3'-UTR patterns were mainly enriched in P53, glycolysis/gluconeogenesis, HIF-1, apoptosis, PI3K-Akt and AMPK signaling pathways. Further analysis identified that average 3'-UTR lengths of Acss2, Inpp1 and Nr1h4 were more than 140 nt longer (HS0.5-R36 vs. HS0.5), and contained different cis-elements (PAS, CPE and microRNA binding sites). Moreover, Hsp70.2, Inhbb and Dhrs were identified to have extremely different 3'-UTR abundances. Further 3'RACE assays validated several 3'-UTRs of Nr1h4, and RT-qPCR confirmed the abundance changes of different 3'-UTR isoforms for Nr1h4 and Hsp70.2. Our findings provide useful information and resources to further uncover the molecular role of 3'-UTR, in regulating the response of porcine iST cells to acute heat stress.


Assuntos
Fosfatidilinositol 3-Quinases , Células de Sertoli , Suínos , Animais , Masculino , Histona-Lisina N-Metiltransferase , Resposta ao Choque Térmico/genética
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