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1.
Proc Natl Acad Sci U S A ; 120(22): e2220148120, 2023 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-37216506

RESUMO

Exploring the potential lead compounds for Alzheimer's disease (AD) remains one of the challenging tasks. Here, we report that the plant extract conophylline (CNP) impeded amyloidogenesis by preferentially inhibiting BACE1 translation via the 5' untranslated region (5'UTR) and rescued cognitive decline in an animal model of APP/PS1 mice. ADP-ribosylation factor-like protein 6-interacting protein 1 (ARL6IP1) was then found to mediate the effect of CNP on BACE1 translation, amyloidogenesis, glial activation, and cognitive function. Through analysis of the 5'UTR-targetd RNA-binding proteins by RNA pulldown combined with LC-MS/MS, we found that FMR1 autosomal homolog 1 (FXR1) interacted with ARL6IP1 and mediated CNP-induced reduction of BACE1 by regulating the 5'UTR activity. Without altering the protein levels of ARL6IP1 and FXR1, CNP treatment promoted ARL6IP1 interaction with FXR1 and inhibited FXR1 binding to the 5'UTR both in vitro and in vivo. Collectively, CNP exhibited a therapeutic potential for AD via ARL6IP1. Through pharmacological manipulation, we uncovered a dynamic interaction between FXR1 and the 5'UTR in translational control of BACE1, adding to the understanding of the pathophysiology of AD.


Assuntos
Doença de Alzheimer , Animais , Camundongos , Regiões 5' não Traduzidas , Doença de Alzheimer/tratamento farmacológico , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Secretases da Proteína Precursora do Amiloide/genética , Secretases da Proteína Precursora do Amiloide/metabolismo , Ácido Aspártico Endopeptidases/genética , Ácido Aspártico Endopeptidases/metabolismo , Cromatografia Líquida , Proteína do X Frágil da Deficiência Intelectual/genética , Biossíntese de Proteínas , Espectrometria de Massas em Tandem
2.
Molecules ; 29(7)2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38611768

RESUMO

In industrial manufacturing, pyrrhotite(Fe1-xS), once depressed, is commonly activated for flotation. However, the replacement of CuSO4 is necessary due to the need for exact control over the dosage during the activation of pyrrhotite, which can pose challenges in industrial settings. This research introduces the use of FeSO4 for the first time to efficiently activate pyrrhotite. The impact of two different activators on pyrrhotite was examined through microflotation experiments and density functional theory (DFT) calculations. Microflotation experiments confirmed that as the CuSO4 dosage increased from 0 to 8 × 10-4 mol/L, the recovery of pyrrhotite initially increased slightly from 71.27% to 87.65% but then sharply decreased to 16.47%. Conversely, when the FeSO4 dosage was increased from 0 to 8 × 10-4 mol/L, pyrrhotite's recovery rose from 71.27% to 82.37%. These results indicate a higher sensitivity of CuSO4 to dosage variations, suggesting that minor alterations in dosage can significantly impact its efficacy under certain experimental conditions. In contrast, FeSO4 might demonstrate reduced sensitivity to changes in dosage, leading to more consistent performance. Fe ions can chemically adsorb onto the surface of pyrrhotite (001), creating a stable chemical bond, thereby markedly activating pyrrhotite. The addition of butyl xanthate (BX), coupled with the action of Fe2+ on activated pyrrhotite, results in the formation of four Fe-S bonds on Fe2+. The proximity of their atomic distances contributes to the development of a stable double-chelate structure. The S 3p orbital on BX hybridizes with the Fe 3d orbital on pyrrhotite, but the hybrid effect of Fe2+ activation is stronger than that of nonactivation. In addition, the Fe-S bond formed by the addition of activated Fe2+ has a higher Mulliken population, more charge overlap, and stronger covalent bonds. Therefore, Fe2+ is an excellent, efficient, and stable pyrrhotite activator.

3.
Neurobiol Dis ; 181: 106103, 2023 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-36997128

RESUMO

Epilepsy is considered to result from an imbalance between excitation and inhibition of the central nervous system. Pathogenic mutations in the methyl-CpG binding domain protein 5 gene (MBD5) are known to cause epilepsy. However, the function and mechanism of MBD5 in epilepsy remain elusive. Here, we found that MBD5 was mainly localized in the pyramidal cells and granular cells of mouse hippocampus, and its expression was increased in the brain tissues of mouse models of epilepsy. Exogenous overexpression of MBD5 inhibited the transcription of the signal transducer and activator of transcription 1 gene (Stat1), resulting in increased expression of N-methyl-d-aspartate receptor (NMDAR) subunit 1 (GluN1), 2A (GluN2A) and 2B (GluN2B), leading to aggravation of the epileptic behaviour phenotype in mice. The epileptic behavioural phenotype was alleviated by overexpression of STAT1 which reduced the expression of NMDARs, and by the NMDAR antagonist memantine. These results indicate that MBD5 accumulation affects seizures through STAT1-mediated inhibition of NMDAR expression in mice. Collectively, our findings suggest that the MBD5-STAT1-NMDAR pathway may be a new pathway that regulates the epileptic behavioural phenotype and may represent a new treatment target.


Assuntos
Epilepsia , Receptores de N-Metil-D-Aspartato , Animais , Camundongos , Memantina/farmacologia , Receptores de N-Metil-D-Aspartato/metabolismo , Convulsões/genética , Transdução de Sinais , Fator de Transcrição STAT1/metabolismo
4.
Reprod Biomed Online ; 47(4): 103254, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37524030

RESUMO

RESEARCH QUESTION: Does blastocyst storage time have an impact on pregnancy and neonatal outcomes following the first single vitrified/warmed high-quality blastocyst transfer cycle for young women? DESIGN: Retrospective cohort study in a university-affiliated reproductive medical centre. RESULTS: A total of 2938 patients undergoing their first frozen embryo transfer (FET) cycle with a single high-quality blastocyst (Day 5: 3BB and above; Day 6: 4BB and above) transferred were divided into five groups: Group A with storage time ≤3 months (n = 1621), Group B with storage time of 4-6 months (n = 657), Group C with storage time of 7-12 months (n = 225), Group D with storage time of 13-24 months (n = 104), and Group E with storage time of 25-98 months (n = 331). After adjusting for confounding factors by multivariate logistic regression, there were no significant differences in live birth rate [Group A as reference; Group B: adjusted odds ratio (aOR) 0.954 (95% CI 0.791- 1.151); Group C: aOR 0.905 (95% CI 0.674-1.214); Group D: aOR 0.727 (95% CI 0.474-1.114); Group E: aOR 1.185 (955 CI 0.873-1.608)], ß-human-chorionic-gonadotropin-positive rate, clinical pregnancy rate and miscarriage rate between Group A and the other groups. Among all singletons born after FET, there were no significant differences with regards to gestational age, preterm birth, birthweight, low birthweight, high birthweight and macrosomia. CONCLUSION: Long-term cryostorage of human vitrified high-quality blastocysts does not affect pregnancy or neonatal outcomes.


Assuntos
Criopreservação , Nascimento Prematuro , Gravidez , Recém-Nascido , Humanos , Feminino , Peso ao Nascer , Vitrificação , Estudos Retrospectivos , Transferência Embrionária , Taxa de Gravidez , Blastocisto
5.
J Theor Biol ; 573: 111610, 2023 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-37604411

RESUMO

In this paper, a single species model with Allee effect driven by correlated colored noises is proposed and investigated. The stationary probability density of the model is obtained using the approximative Fokker-Planck equation, and its shape is discussed in detail. P-bifurcation and noise-induced bistability are explored, followed by the observation of noise-enhanced stability through mean first passage time analysis. Our findings demonstrate that: (i) noise can induce P-bifurcation, causing the structure of a stationary probability distribution to shift from unimodal to monotonic under positive correlation and switch from unimodal to bimodal under negative correlation; (ii) correlation time promotes population growth, leading to a higher probability of large population size and delaying the extinction process; (iii) noise-enhanced stability induced by multiplicative noise depends on both additive noise and correlation time, while it always exists for additive noise.


Assuntos
Crescimento Demográfico , Densidade Demográfica , Probabilidade
6.
Bioinformatics ; 37(6): 750-758, 2021 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-33063094

RESUMO

MOTIVATION: Infection with strains of different subtypes and the subsequent crossover reading between the two strands of genomic RNAs by host cells' reverse transcriptase are the main causes of the vast HIV-1 sequence diversity. Such inter-subtype genomic recombinants can become circulating recombinant forms (CRFs) after widespread transmissions in a population. Complete prediction of all the subtype sources of a CRF strain is a complicated machine learning problem. It is also difficult to understand whether a strain is an emerging new subtype and if so, how to accurately identify the new components of the genetic source. RESULTS: We introduce a multi-label learning algorithm for the complete prediction of multiple sources of a CRF sequence as well as the prediction of its chronological number. The prediction is strengthened by a voting of various multi-label learning methods to avoid biased decisions. In our steps, frequency and position features of the sequences are both extracted to capture signature patterns of pure subtypes and CRFs. The method was applied to 7185 HIV-1 sequences, comprising 5530 pure subtype sequences and 1655 CRF sequences. Results have demonstrated that the method can achieve very high accuracy (reaching 99%) in the prediction of the complete set of labels of HIV-1 recombinant forms. A few wrong predictions are actually incomplete predictions, very close to the complete set of genuine labels. AVAILABILITY AND IMPLEMENTATION: https://github.com/Runbin-tang/The-source-of-HIV-CRFs-prediction. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Infecções por HIV , HIV-1 , Variação Genética , Infecções por HIV/genética , HIV-1/genética , Humanos , Epidemiologia Molecular , Filogenia
7.
FASEB J ; 35(5): e21445, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33774866

RESUMO

Mitochondrial Tu translation elongation factor (TUFM or EF-Tu) is part of the mitochondrial translation machinery. It is reported that TUFM expression is reduced in the brain of Alzheimer's disease (AD), suggesting that TUFM might play a role in the pathophysiology. In this study, we found that TUFM protein level was decreased in the hippocampus and cortex especially in the aged APP/PS1 mice, an animal model of AD. In HEK cells that stably express full-length human amyloid-ß precursor protein (HEK-APP), TUFM knockdown or overexpression increased or reduced the protein levels of ß-amyloid protein (Aß) and ß-amyloid converting enzyme 1 (BACE1), respectively. TUFM-mediated reduction of BACE1 was attenuated by translation inhibitor cycloheximide (CHX) or α-[2-[4-(3,4-Dichlorophenyl)-2-thiazolyl]hydrazinylidene]-2-nitro-benzenepropanoic acid (4EGI1), and in cells overexpressing BACE1 constructs deleting the 5' untranslated region (5'UTR). TUFM silencing increased the half-life of BACE1 mRNA, suggesting that RNA stability was affected by TUFM. In support, transcription inhibitor Actinomycin D (ActD) and silencing of nuclear factor κB (NFκB) failed to abolish TUFM-mediated regulation of BACE1 protein and mRNA. We further found that the mitochondria-targeted antioxidant TEMPO diminished the effects of TUFM on BACE1, suggesting that reactive oxygen species (ROS) played an important role. Indeed, cellular ROS levels were affected by TUFM knockdown or overexpression, and TUFM-mediated regulation of apoptosis and Tau phosphorylation at selective sites was attenuated by TEMPO. Collectively, TUFM protein levels were decreased in APP/PS1 mice. TUFM is involved in AD pathology by regulating BACE1 translation, apoptosis, and Tau phosphorylation, in which ROS plays an important role.


Assuntos
Doença de Alzheimer/patologia , Secretases da Proteína Precursora do Amiloide/metabolismo , Modelos Animais de Doenças , Mitocôndrias/patologia , Fator Tu de Elongação de Peptídeos/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Secretases da Proteína Precursora do Amiloide/genética , Precursor de Proteína beta-Amiloide/fisiologia , Animais , Humanos , Camundongos , Camundongos Transgênicos , Mitocôndrias/metabolismo , Fator Tu de Elongação de Peptídeos/genética , Fosforilação , Presenilina-1/fisiologia
8.
BMC Pregnancy Childbirth ; 22(1): 305, 2022 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-35399086

RESUMO

BACKGROUND: The impact of Chlamydia trachomatis infection (CT) on the outcomes of In-Vitro Fertilization / Intracytoplasmic sperm injection (IVF/ICSI) has been controversial. METHODS: A total of 431 infertility women aged 20-38 years with or without Chlamydia trachomatis infection before fresh/ frozen embryo transfer were included to investigate the effect of cured CT infection. The infected group was divided into two subgroups for ≤3 months and > 3 months according to the different intervals between Chlamydia trachomatis positive testing and embryo transfer. The effect of chlamydia infection and the intervals between infection and embryo transfer on pregnancy outcomes was analyzed with correction for potential confounders within a multivariable model. RESULTS: Our results revealed that implantation rate was significantly lower and the premature rupture of membranes (PROM) was higher in women with CT infection than non-infection. The multivariate logistic regression analysis adjusting for baseline characteristics showed no significant difference in live birth rate between neither two groups nor two subgroups. CONCLUSIONS: The study suggests that previous Chlamydia trachomatis infection would lead to high risk of PROM. The intervals between infection and embryo transfer would not impact the pregnancy outcomes of IVF/ICSI.


Assuntos
Infecções por Chlamydia , Injeções de Esperma Intracitoplásmicas , Infecções por Chlamydia/epidemiologia , Chlamydia trachomatis , Feminino , Fertilização in vitro/métodos , Humanos , Gravidez , Taxa de Gravidez , Estudos Retrospectivos , Injeções de Esperma Intracitoplásmicas/métodos
9.
Arch Gynecol Obstet ; 306(6): 1901-1911, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-35306582

RESUMO

PURPOSE: Chromosomal mosaicism becomes a common phenomenon in Preimplantaion genetic testing (PGT). This meta-analysis was conducted to study which feature of chromosomal mosaicism was compatible for embryo transfer. METHODS: After searching the database PubMed, Embase, CCTR and related reviews up until May 2021. Two reviewers extracted relevant information and assessed study quality by the Newcastle-Ottawa scale independently. Summary Odd Radios (OR) were calculated using fixed- or random-effects models for clinical outcomes. A network meta-analysis compared the clinical outcomes of different chromosomes. RESULTS: A total of six studies with 1,106 cycles of single mosaic embryo transferred were included. Significant results of implantation rate (IR), miscarriage rate (MR), and ongoing pregnancy/live birth rate (OP/LBR) were observed when comparing embryos with mosaicism level < 50% and ≥ 50% [OR 1.42, 95% CI (1.06, 1.89); OR 0.45, 95% CI (0.27, 0.75); OR 1.74, 95% CI (1.28, 2.37)], and embryos with mosaicism with only affecting segmental chromosome(s) and only involving whole chromosome(s) [OR 1.31, 95% CI (1.01, 1.71); OR 0.57, 95% CI (0.36, 0.93); OR 1.51, 95% CI (1.15, 2.00)]. Embryos with only mosaic gains or losses had significant higher IR and OP/LBR than complex mosaicism [Gains vs complex: OR 1.75, 95% CI (1.20, 2.54); OR 1.73, 95% CI (1.16, 2.58). Losses vs complex: OR 1.90, 95% CI (1.34, 2.71); OR 2.10, 95% CI (1.44, 3.07)]. Mosaic embryos with only one chromosome involved had significant favorable outcomes of IR and OP/LBR than with three or more chromosomes involved [OR 1.76, 95% CI (1.23, 2.52); OR 1.86, 95% CI (1.25,2.78)]. Chr. 7, Chr. 2, Chr. 1, Chr. 18, Chr. 11, Chr. X, Chr. 13, Chr. 14, Chr. 12, and Chr. 9 were considered as prioritized chromosomes of mosaic embryos for transfer. CONCLUSIONS: This analysis support the embryos with mosaicism level ≥ 50%, whole chromosome(s) involved, multiple mosaic abnormalities were associated with worse pregnancy outcomes. Mosaicism level of 50% could be used as a threshold to assess the mosaic embryos.


Assuntos
Diagnóstico Pré-Implantação , Gravidez , Feminino , Humanos , Diagnóstico Pré-Implantação/métodos , Mosaicismo , Aneuploidia , Blastocisto , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Transferência Embrionária , Testes Genéticos/métodos , Fertilização in vitro
10.
J Neurochem ; 157(4): 1351-1365, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-32920833

RESUMO

Thioredoxin-2 (TXN2) is a mitochondrial protein and represents one of the intrinsic antioxidant enzymes. It has long been recognized that mitochondrial dysfunction and oxidative stress contribute to the pathogenesis of Alzheimer's disease (AD). We hypothesized that mitochondrial TXN2 might play a role in AD-like pathology. In this study, we found that in SH-SY5Y and HEK cells stably express full-length human amyloid-ß precursor protein (HEK-APP), TXN2 silencing or over-expression selectively increased or decreased the transcription of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1), respectively, without altering the protein levels of others enzymes involved in the catalytic processing of APP. As a result, ß-amyloid protein (Aß) levels were significantly decreased by TXN2. In addition, in cells treated with 3-nitropropionic acid (3-NP) that is known to increase reactive oxygen species (ROS) and promote mitochondrial dysfunction, TXN2 silencing resulted in further enhancement of BACE1 protein levels, suggesting a role of TXN2 in ROS removal. The downstream signaling might involve NFκB, as TXN2 reduced the phosphorylation of p65 and IκBα; and p65 knockdown significantly attenuated TXN2-mediated regulation of BACE1. Concomitantly, the levels of cellular ROS, apoptosis-related proteins and cell viability were altered by TXN2 silencing or over-expression. In APPswe/PS1E9 mice, an animal model of AD, the cortical and hippocampal TXN2 protein levels were decreased at 12 months but not at 6 months, suggesting an age-dependent decline. Collectively, TXN2 regulated BACE1 expression and amyloidogenesis via cellular ROS and NFκB signaling. TXN2 might serve as a potential target especially for early intervention of AD.


Assuntos
Secretases da Proteína Precursora do Amiloide/metabolismo , Precursor de Proteína beta-Amiloide/metabolismo , Ácido Aspártico Endopeptidases/metabolismo , Proteínas Mitocondriais/metabolismo , Tiorredoxinas/metabolismo , Doença de Alzheimer/metabolismo , Animais , Encéfalo/metabolismo , Regulação da Expressão Gênica , Humanos , Camundongos , Mitocôndrias/metabolismo , Transdução de Sinais/fisiologia
11.
Biochem Biophys Res Commun ; 582: 8-15, 2021 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-34678594

RESUMO

Gap junction beta 1 (GJB1) is the pathogenic gene of X-linked Charcot-Marie-Tooth type 1 (CMTX1), a rare hereditary sensorimotor neuropathy. However, different mutations of GJB1 result in heterogeneous clinical manifestations with only some mutations leading to central nervous system involvement. We previously reported two GJB1 missense mutations: one novel mutation (c.212T > G) found in a CMTX1 family that only manifested as peripheral neuropathy, and another previously reported mutation GJB1(c.311A > C) leading to involvement of the peripheral nerves and cerebral white matter. However, the mechanism by which GJB1 mutations lead to CMTX1 has not been fully characterized. Here, we generated Schwann cells and primary cultured oligodendrocytes with these two mutations, resulting in the Cx32I71S (GJB1 c.212T > G) and Cx32K104T (GJB1 c.311A > C) mutants, to analyze the pathogenic mechanism using cytology, molecular biology, and electrophysiological methods. Both mutants showed abnormal endoplasmic reticulum aggregation, especially the Cx32K104T mutant, leading to an increase in endoplasmic reticulum stress, resulting in apoptosis. Furthermore, whole-cell patch clamp experiments in oligodendrocytes revealed that the Cx32K104T mutant reduced the cell membrane potential and inwardly rectifying potassium currents, which may be a vital element for central involvement. Therefore, our results may provide a new perspective for understanding the pathogenesis of CMTX1.


Assuntos
Doença de Charcot-Marie-Tooth/genética , Conexinas/genética , Mutação de Sentido Incorreto , Oligodendroglia/metabolismo , Potássio/metabolismo , Células de Schwann/metabolismo , Animais , Apoptose/genética , Linhagem Celular , Doença de Charcot-Marie-Tooth/metabolismo , Doença de Charcot-Marie-Tooth/patologia , Conexinas/deficiência , Retículo Endoplasmático/genética , Retículo Endoplasmático/metabolismo , Estresse do Retículo Endoplasmático/genética , Expressão Gênica , Humanos , Ativação do Canal Iônico , Potenciais da Membrana/fisiologia , Modelos Biológicos , Oligodendroglia/patologia , Técnicas de Patch-Clamp , Cultura Primária de Células , Agregados Proteicos/genética , Ratos , Ratos Sprague-Dawley , Células de Schwann/patologia , Proteína beta-1 de Junções Comunicantes
12.
Prenat Diagn ; 41(6): 681-689, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-33411373

RESUMO

OBJECTIVES: To study the feasibility of using unbalanced embryos as a reference in distinguishing euploid carrier and noncarrier embryos by single nucleotide polymorphism (SNP) array-based preimplantation genetic testing (PGT) for reciprocal translocations. METHODS: After comprehensive chromosome screening (CCS), euploid embryos were identified as normal or carriers using a family member as a reference. Next, unbalanced embryos were used as a reference, and the results were compared with the previous ones. Karyotypes of transferred embryos were validated by prenatal diagnosis. RESULTS: Of 995 embryos from 110 couples, 288 were found to be euploid. Using a family member as a reference, 142 and 144 embryos were tested to be euploid noncarrier and carrier respectively, and the remaining 2 embryos were undetermined. When unbalanced embryos were selected as references, all the results were consistent with the previous ones. A total of 107 embryos were transferred, resulting in 66 clinical pregnancies. Karyotypes of prenatal diagnosis were all in accordance with the results of tested embryos. CONCLUSIONS: SNP array-based haplotyping is a rapid and effective way to distinguish between euploid carrier and noncarrier embryos. In case no family member is available as a reference, unbalanced embryos can be used for identification of euploid carrier and noncarrier embryos.


Assuntos
Heterozigoto , Polimorfismo de Nucleotídeo Único/genética , Translocação Genética/genética , Adulto , Transferência Embrionária/métodos , Estudos de Viabilidade , Feminino , Testes Genéticos/métodos , Humanos , Masculino
13.
Entropy (Basel) ; 22(3)2020 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-33286103

RESUMO

Genome-wide association study (GWAS) has turned out to be an essential technology for exploring the genetic mechanism of complex traits. To reduce the complexity of computation, it is well accepted to remove unrelated single nucleotide polymorphisms (SNPs) before GWAS, e.g., by using iterative sure independence screening expectation-maximization Bayesian Lasso (ISIS EM-BLASSO) method. In this work, a modified version of ISIS EM-BLASSO is proposed, which reduces the number of SNPs by a screening methodology based on Pearson correlation and mutual information, then estimates the effects via EM-Bayesian Lasso (EM-BLASSO), and finally detects the true quantitative trait nucleotides (QTNs) through likelihood ratio test. We call our method a two-stage mutual information based Bayesian Lasso (MBLASSO). Under three simulation scenarios, MBLASSO improves the statistical power and retains the higher effect estimation accuracy when comparing with three other algorithms. Moreover, MBLASSO performs best on model fitting, the accuracy of detected associations is the highest, and 21 genes can only be detected by MBLASSO in Arabidopsis thaliana datasets.

14.
Entropy (Basel) ; 22(2)2020 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-33286029

RESUMO

HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time. In this study, we propose a new and effective alignment-free method for the phylogenetic analysis of HIV-1 viruses using complete genome sequences. Our method combines the position distribution information and the counts of the k-mers together. We also propose a metric to determine the optimal k value. We name our method the Position-Weighted k-mers (PWkmer) method. Validation and comparison with the Robinson-Foulds distance method and the modified bootstrap method on a benchmark dataset show that our method is reliable for the phylogenetic analysis of HIV-1 viruses. PWkmer can resolve within-group variations for different known subtypes of Group M of HIV-1 viruses. This method is simple and computationally fast for whole genome phylogenetic analysis.

15.
BMC Bioinformatics ; 19(Suppl 19): 521, 2018 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-30598066

RESUMO

BACKGROUND: Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been widely applied to deal with this challenging problem. However, most of them mainly focus on secondary structure information of pre-microRNAs, while ignoring sequence-order information and sequence evolution information. RESULTS: We use new features for the machine learning algorithms to improve the classification performance by characterizing both sequence order evolution information and secondary structure graphs. We developed three steps to extract these features of pre-microRNAs. We first extract features from PSI-BLAST profiles and Hilbert-Huang transforms, which contain rich sequence evolution information and sequence-order information respectively. We then obtain properties of small molecular networks of pre-microRNAs, which contain refined secondary structure information. These structural features are carefully generated so that they can depict both global and local characteristics of pre-microRNAs. In total, our feature space covers 591 features. The maximum relevance and minimum redundancy (mRMR) feature selection method is adopted before support vector machine (SVM) is applied as our classifier. The constructed classification model is named MicroRNA -NHPred. The performance of MicroRNA -NHPred is high and stable, which is better than that of those state-of-the-art methods, achieving an accuracy of up to 94.83% on same benchmark datasets. CONCLUSIONS: The high prediction accuracy achieved by our proposed method is attributed to the design of a comprehensive feature set on the sequences and secondary structures, which are capable of characterizing the sequence evolution information and sequence-order information, and global and local information of pre-microRNAs secondary structures. MicroRNA -NHPred is a valuable method for pre-microRNAs identification. The source codes of our method can be downloaded from https://github.com/myl446/MicroRNA-NHPred .


Assuntos
Algoritmos , Biologia Computacional/métodos , Genoma Humano , Aprendizado de Máquina , MicroRNAs/química , MicroRNAs/genética , Humanos , Máquina de Vetores de Suporte
17.
Cell Physiol Biochem ; 46(1): 160-177, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29587280

RESUMO

BACKGROUND/AIMS: The imbalance between excitation and inhibition is a defining feature of epilepsy. GluA1 is an AMPA receptor subunit that can strengthen excitatory synaptic transmission when upregulated in the postsynaptic membrane, which has been implicated in the pathogenesis of epilepsy. cGKII, a cGMP-dependent protein kinase, regulates the GluA1 levels at the plasma membrane. METHODS: To explore the role of cGKII in epilepsy, we investigated the expression of cGKII in patients with temporal lobe epilepsy (TLE) and in a pilocarpine-induced rat model and then performed behavioral, histological, and electrophysiological analyses by applying either a cGKII agonist or inhibitor in the hippocampus of the animal model. RESULTS: cGKII expression was upregulated in the epileptogenic brain tissues of both humans and rats. Pharmacological activation or inhibition of cGKII induced changes in epileptic behaviors in vivo and epileptic discharges in vitro. Further studies indicated that cGKII activation disrupted the balance of excitation and inhibition due to strengthened AMPAR-mediated excitatory synaptic transmission. Moreover, cGKII regulated epileptic seizures by phosphorylating GluA1 at Ser845 to modulate the expression and function of GluA1 in the postsynaptic membrane. CONCLUSION: These results suggest that cGKII plays a key role in seizure activity and could be a potential therapeutic target for epilepsy.


Assuntos
Proteína Quinase Dependente de GMP Cíclico Tipo II/metabolismo , Epilepsia/patologia , Hipocampo/metabolismo , Receptores de AMPA/metabolismo , 4-Aminopiridina/farmacologia , Adolescente , Adulto , Animais , Encéfalo/metabolismo , Encéfalo/patologia , Carbazóis/farmacologia , Carbazóis/uso terapêutico , Criança , GMP Cíclico/análogos & derivados , GMP Cíclico/farmacologia , Proteína Quinase Dependente de GMP Cíclico Tipo II/antagonistas & inibidores , Modelos Animais de Doenças , Epilepsia/induzido quimicamente , Epilepsia/tratamento farmacológico , Potenciais Evocados/efeitos dos fármacos , Feminino , Hipocampo/efeitos dos fármacos , Humanos , Masculino , Pilocarpina , Ratos , Ratos Sprague-Dawley , Receptores de AMPA/genética , Transmissão Sináptica/efeitos dos fármacos , Tionucleotídeos/farmacologia , Regulação para Cima , Adulto Jovem
18.
Proc Natl Acad Sci U S A ; 112(50): E6964-72, 2015 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-26621702

RESUMO

Autism spectrum disorders (ASDs) are a group of highly inheritable mental disorders associated with synaptic dysfunction, but the underlying cellular and molecular mechanisms remain to be clarified. Here we report that autism in Chinese Han population is associated with genetic variations and copy number deletion of P-Rex1 (phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1). Genetic deletion or knockdown of P-Rex1 in the CA1 region of the hippocampus in mice resulted in autism-like social behavior that was specifically linked to the defect of long-term depression (LTD) in the CA1 region through alteration of AMPA receptor endocytosis mediated by the postsynaptic PP1α (protein phosphase 1α)-P-Rex1-Rac1 (Ras-related C3 botulinum toxin substrate 1) signaling pathway. Rescue of the LTD in the CA1 region markedly alleviated autism-like social behavior. Together, our findings suggest a vital role of P-Rex1 signaling in CA1 LTD that is critical for social behavior and cognitive function and offer new insight into the etiology of ASDs.


Assuntos
Transtorno Autístico/psicologia , Região CA1 Hipocampal/fisiopatologia , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Depressão Sináptica de Longo Prazo , Transdução de Sinais , Comportamento Social , Sinapses/metabolismo , Animais , Variações do Número de Cópias de DNA , Fatores de Troca do Nucleotídeo Guanina/genética , Humanos , Camundongos , Camundongos Knockout , Receptores de N-Metil-D-Aspartato/metabolismo
19.
Proc Natl Acad Sci U S A ; 111(39): 14271-6, 2014 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-25232037

RESUMO

Axon pathology has been widely reported in Alzheimer's disease (AD) patients and AD mouse models. Herein we report that increased miR-342-5p down-regulates the expression of ankyrin G (AnkG), a protein known to play a critical role in establishing selective filtering machinery at the axon initial segment (AIS). Diminished AnkG expression leads to defective AIS filtering in cultured hippocampal neurons from AD mouse models, as monitored by selective exclusion of large macromolecules from the axons. Furthermore, AnkG-deficiency impairs AIS localization of Nav 1.6 channels and confines NR2B to the somatodendritic compartments. The expression of exogenous AnkG improved the cognitive performance of 12-mo-old APP/PS1 mice; thus, our data suggest that AnkG and impairment of AIS filtering may play important roles in AD pathology.


Assuntos
Doença de Alzheimer/fisiopatologia , Axônios/fisiologia , Doença de Alzheimer/genética , Doença de Alzheimer/patologia , Precursor de Proteína beta-Amiloide/genética , Precursor de Proteína beta-Amiloide/fisiologia , Animais , Anquirinas/genética , Anquirinas/fisiologia , Axônios/patologia , Células Cultivadas , Modelos Animais de Doenças , Regulação para Baixo , Humanos , Masculino , Camundongos , Camundongos Transgênicos , MicroRNAs/genética , MicroRNAs/metabolismo , Proteínas Mutantes/genética , Proteínas Mutantes/fisiologia , Presenilina-1/genética , Presenilina-1/fisiologia , Receptores de N-Metil-D-Aspartato/fisiologia
20.
Sensors (Basel) ; 17(1)2016 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-28042814

RESUMO

Changes in the structure and function of the hippocampus contribute to epilepsy, schizophrenia and other neurological or mental disorders of the brain. Since the function of the hippocampus depends heavily on the glutamate (Glu) signaling pathways, in situ real-time detection of Glu neurotransmitter release and electrophysiological signals in hippocampus is of great significance. To achieve the dual-mode detection in mouse hippocampus in vivo, a 16-channel implantable microelectrode array (MEA) was fabricated by micro-electromechanical system (MEMS) technology. Twelve microelectrode sites were modified with platinum black for electrophysiological recording and four sites were modified with glutamate oxidase (GluOx) and 1,3-phenylenediamine (mPD) for selective electrochemical detection of Glu. The MEA was implanted from cortex to hippocampus in mouse brain for in situ real-time monitoring of Glu and electrophysiological signals. It was found that the Glu concentration in hippocampus was roughly 50 µM higher than that in the cortex, and the firing rate of concurrently recorded spikes declined from 6.32 ± 4.35 spikes/s in cortex to 0.09 ± 0.06 spikes/s in hippocampus. The present results demonstrated that the dual-mode MEA probe was capable in neurological detections in vivo with high spatial resolution and dynamical response, which lays the foundation for further pathology studies in the hippocampus of mouse models with nervous or mental disorders.


Assuntos
Eletrofisiologia/instrumentação , Eletrofisiologia/métodos , Ácido Glutâmico/análise , Sistemas Microeletromecânicos/instrumentação , Sistemas Microeletromecânicos/métodos , Animais , Técnicas Biossensoriais/instrumentação , Técnicas Biossensoriais/métodos , Hipocampo/metabolismo , Camundongos , Microeletrodos , Fenilenodiaminas/análise
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