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1.
Acta Histochem ; : 151509, 2020 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-31964534

RESUMO

It was well known that a critical process of oogenesis in the female mammalian was the entry of mitotic oogonia into meiosis. Early studies from model animal mice suggested that the retinoic acid (RA) response signal protein STRA8 (stimulated by retinoic acid gene 8) and the meiosis-specific chromosomal behavior marker protein SCP3 (Synaptonemal Complex Protein 3) were two crucial molecular markers during meiosis. The expression of STRA8 and SCP3 at different stages in rat ovaries was investigated by immunohistochemistry, qRT-PCR and Western Blot. Immunohistochemistry results showed that STRA8 and SCP3 were mainly expressed in embryonic stage. And STRA8 was expressed in the cytoplasm and nucleus of the ovaries after birth. qRT-PCR and Western Blot results showed that the mRNA and protein levels of STRA8 and SCP3 were expressed in embryonic stage. The expression of STRA8 and SCP3 indicated germ cells enter meiosis in rats embryo, and STRA8 and SCP3 could serve as molecular markers for the meiosis in rats. The localization of STRA8 in the nucleus increased the possibility that STRA8 might act as transcription factor or activate transcription to function after birth.

2.
Jpn J Nurs Sci ; : e12320, 2020 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-31957242

RESUMO

AIM: Disturbance of urinary function is a common complication after rectal cancer surgery, and it may affect patients' psychological well-being, consequently may develop post-traumatic stress disorder. Personal resilience might increase people's ability to manage life's challenges. However, limited study to explore their relationships. This study examined the relationships among lower urinary symptoms, resilience, and post-traumatic stress symptoms (PTSS) in post-surgery patients with rectal cancer. METHODS: A cross-sectional study design was used and included 188 patients with diagnosed rectal cancer who had undergone surgery over 24 months and were recruited from a hospital in southern Taiwan. The outcome measurements included a resilience scale, International Prostate Symptom Score (IPSS), the Chinese Davidson Trauma Scale, personal characteristics, and disease-related variables. RESULTS: There were significant relationships among age at diagnosed, self-reported physical status, perceived satisfied with recovery, urinary tract symptoms, resilience, and overall PTSS. The stepwise regression demonstrated that five factors, self-reported physical status, resilience, urinary tract symptoms, age at diagnosed and gender, and together explained 27.7% of overall PTSS variance (10.7, 6.7, 3.7, 4.8 and 1.8% of variance, respectively). CONCLUSION: The study demonstrates that patients with diagnosed rectal cancers long-term outcomes of PTSS, urinary tract symptoms, and resilience after surgery; in addition, self-reported physical status, resilience, urinary tract symptoms, age at diagnosed and gender are the major predictors of PTSS. A better understanding of the long-term outcomes of post-surgery in rectal cancer patients and its related factors may help to decreasing the PTSS after surviving cancer.

3.
Talanta ; 206: 120206, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31514889

RESUMO

Hemoglobin (Hb) plays an important role in oxygen carriage for mammals, which is also a typical biomarker for certain diseases. Although numerous methods had been developed for the detection of Hb in red blood cells, analytical technology for the monitoring of low-abundance Hb in serum or plasma is still a challenge. Herein, persistent luminescence nanoparticles (PLNPs) with strong near-infrared (NIR) emission character behaving as a label-free probe for the highly sensitive and selective detection of Hb were developed. Further studies revealed that the sensing mechanism should be attributed to the Hb-induced dynamic quenching process. Moreover, the nanoprobe showed high selectivity to Hb against the common existing substances in human serum and a linear response to Hb ranging from 1 to 50 nM with an extremely high limit of detection (LOD) of 0.13 nM. Finally, applicability of the proposed probe for the detection of Hb in human serum samples was validated.


Assuntos
Hemoglobinas/análise , Substâncias Luminescentes/química , Nanopartículas Metálicas/química , Cromo/química , Gálio/química , Humanos , Limite de Detecção , Luminescência , Medições Luminescentes/métodos , Tamanho da Partícula , Zinco/química
4.
Front Genet ; 10: 1012, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31681435

RESUMO

The whole-genome sequencing (WGS) data can potentially discover all genetic variants. Studies have shown the power of WGS for genome-wide association study (GWAS) lies in the ability to identify quantitative trait loci and nucleotides (QTNs). However, the resequencing of thousands of target individuals is expensive. Genotype imputation is a powerful approach for WGS and to identify causal mutations. This study aimed to evaluate the imputation accuracy from genotyping-by-sequencing (GBS) to WGS in two pig breeds using a resequencing reference population and to detect single-nucleotide polymorphisms (SNPs) and candidate genes for farrowing interval (FI) of different parities using the data before and after imputation for GWAS. Six hundred target pigs, 300 Landrace and 300 Large White pigs, were genotyped by GBS, and 60 reference pigs, 20 Landrace and 40 Large White pigs, were sequenced by whole-genome resequencing. Imputation for pigs was conducted using Beagle software. The average imputation accuracy (allelic R 2) from GBS to WGS was 0.42 for Landrace pigs and 0.45 for Large White pigs. For Landrace pigs (Large White pigs), 4,514,934 (5,533,290) SNPs had an accuracy >0.3, resulting an average accuracy of 0.73 (0.72), and 2,093,778 (2,468,645) SNPs had an accuracy >0.8, resulting an average accuracy of 0.94 (0.93). Association studies with data before and after imputation were performed for FI of different parities in two populations. Before imputation, 18 and 128 significant SNPs were detected for FI in Landrace and Large White pigs, respectively. After imputation, 125 and 27 significant SNPs were identified for dataset with an accuracy >0.3 and 0.8 in Large White pigs, and 113 and 18 SNPs were found among imputed sequence variants. Among these significant SNPs, six top SNPs were detected in both GBS data and imputed WGS data, namely, SSC2: 136127645, SSC5: 103426443, SSC6: 27811226, SSC10: 3609429, SSC14: 15199253, and SSC15: 150297519. Overall, many candidate genes could be involved in FI of different parities in pigs. Although imputation from GBS to WGS data resulted in a low imputation accuracy, association analyses with imputed WGS data were optimized to detect QTNs for complex trait. The obtained results provide new insight into genotype imputation, genetic architecture, and candidate genes for FI of different parities in Landrace and Large White pigs.

5.
Molecules ; 24(18)2019 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-31533306

RESUMO

Adipogenesis is a complex biological process and the main cause of obesity. Recently, microRNAs (miRNAs), a class of small endogenous non-coding RNAs, have been proven to play an important role in adipogenesis by the post-transcriptional regulation of target genes. In this current study, we observed an increment of miR-152 expression during the process of 3T3-L1 cell audiogenic differentiation. A functional analysis indicated that the overexpression of miR-152 inhibited pre-adipocyte proliferation and suppressed the expression of some cell cycle-related genes. Moreover, the overexpression of miR-152 promoted lipid accumulation in 3T3-L1 preadipocytes accompanied by increase of the expression of some pro-audiogenic genes. Additionally, a dual-luciferase reporter assay demonstrated lipoprotein lipase (LPL) was a direct target gene of miR-152 during preadipocyte differentiation. Further analysis showed that miR-152 was positively correlated with adipogenesis and intramuscular fat formation in vivo. Taken together, our findings suggest that miR-152 could suppress 3T3-L1 preadipocyte proliferation, whereas it could promote 3T3-L1 preadipocyte differentiation by negatively regulating LPL. The findings indicate that miR-152 might have a therapeutic significance for obesity and obesity-related metabolic syndrome.

7.
Sci Rep ; 9(1): 9667, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31273229

RESUMO

Socially affected traits are affected by direct genetic effects (DGE) and social genetic effects (SGE). DGE and SGE of an individual directly quantify the genetic influence of its own phenotypes and the phenotypes of other individuals, respectively. In the current study, a total of 3,276 Large White pigs from different pens were used, and each pen contained 10 piglets. DGE and SGE were estimated for six socially affected traits, and then a GWAS was conducted to identify SNPs associated with DGE and SGE. Based on the whole-genome re-sequencing, 40 Large White pigs were genotyped and 10,501,384 high quality SNPs were retained for single-locus and multi-locus GWAS. For single-locus GWAS, a total of 54 SNPs associated with DGE and 33 SNPs with SGE exceeded the threshold (P < 5.00E-07) were detected for six growth traits. Of these, 22 SNPs with pleiotropic effects were shared by DGE and SGE. For multi-locus GWAS, a total of 72 and 110 putative QTNs were detected for DGE and SGE, respectively. Of these, 5 SNPs with pleiotropic effects were shared by DGE and SGE. It is noteworthy that 2 SNPs (SSC8: 16438396 for DGE and SSC17: 9697454 for SGE) were detected in single-locus and multi-locus GWAS. Furthermore, 15 positional candidate genes shared by SGE and DGE were identified because of their roles in behaviour, health and disease. Identification of genetic variants and candidate genes for DGE and SGE for socially affected traits will provide a new insight to understand the genetic architecture of socially affected traits in pigs.

8.
Acta Histochem ; 121(6): 718-723, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31253359

RESUMO

Body temperature could lead to interruption of spermatogenesis, but the molecular mechanism was still unclear. Cryptorchidism was defined as the failure of testes to enter the scrotum, which exposed the testes to body temperature. Meiosis was a unique feature of germ cell development. Whether cryptorchidism damage the initiation of meiosis in boars had not been reported. The aim of this study was to determine whether spermatogonia in the cryptorchid testes entered into meiosis by detecting meiosis-related markers stimulated by retinoic acid gene 8 (STRA8) and synaptonemal complex protein 3 (SCP3). Three boars with spontaneous unilateral abdominal cryptorchidism were used. The testis located in the abdomen was cryptorchidism group, the scrotal testis of the same animal was used as control. HE results showed that only Sertoli cells, and a few spermatogonia remained in the seminiferous tubules, and no spermatids were seen compared with the control. Immunohistochemistry results showed that in both control and cryptorchidism group, STRA8 was mainly expressed in the nucleus of spermatogonia and spermatocytes. In control group, SCP3 was expressed in the nucleus of spermatocytes. In cryptorchidism group, SCP3 immunopositive cells were also observed. qRT-PCR and Western Blot results showed that the mRNA and protein levels of STRA8 and SCP3 were significantly decreased in cryptorchid boars. The expression of STRA8 and SCP3 in cryptorchidism suggested that spermatogonia could still enter meiosis in cryptorchid boars.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/biossíntese , Temperatura Corporal , Criptorquidismo/metabolismo , Regulação da Expressão Gênica , Proteínas Nucleares/biossíntese , Testículo/metabolismo , Animais , Criptorquidismo/patologia , Masculino , Suínos , Testículo/patologia
9.
Eur Neurol ; 81(1-2): 87-93, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31117107

RESUMO

BACKGROUND: Primary lateral sclerosis (PLS) is considered a rare variant of motor neuron disease (MND) characterized by selective upper motor neuron dysfunction leading to limb weakness, spasticity, and even bulbar symptoms. Previous studies have demonstrated that mutations in ALSIN, spastic paraplegia 7 (SPG7), TBK1, ALS2, ERLIN2, and FIG4 are responsible for PLS. Most of them occurred in childhood to young-adult onset patients. The aim of this study was to identify the genetic lesion of patients with adult-onset PLS. METHODS: We applied whole-exome sequencing (WES) and MND and ataxia-related genes filtering strategies to discover the genetic factors in a Chinese adult-onset PLS family. Sanger sequencing was used in the cosegregation analysis in the affected family members. RESULTS: A mutation (c.2219A>G/p.Y740C) in exon 17 of SPG7 was identified in an adult-onset PLS patient and cosegregated with the affected members in this family. Meanwhile, the mutation was predicted to be deleterious by 3 bioinformatics programs (Polymorphism phenotyping-2, sorting intolerant from tolerant and MutationTaster). This variant may cause the structure changes of paraplegin protein. CONCLUSIONS: We employed WES to detect a missense mutation of SPG7 gene in a PLS family. This finding expands the spectrum of known SPG7 mutations, and it may contribute to novel approaches to genetic diagnosis and counseling of families with PLS.

11.
BMJ Open ; 9(3): e023918, 2019 03 12.
Artigo em Inglês | MEDLINE | ID: mdl-30862632

RESUMO

INTRODUCTION: The global burden of type 2 diabetes (T2DM) is steadily increasing. Experimental studies have demonstrated that a novel hormone secreted by bone cells, osteocalcin (OC), can stimulate beta-cell proliferation and improve insulin sensitivity in mice. Observational studies in humans have investigated the relationship between OC and metabolic parameters, and T2DM. Importantly, few studies have reported on the undercarboxylated form of OC (ucOC), which is the putative active form of OC suggested to affect glucose metabolism. OBJECTIVES: We will conduct a systematic review and meta-analysis to: (1) compare the levels of serum OC and ucOC between T2DM and normal glucose-tolerant controls (NGC); (2) investigate the risk ratios between serum OC and ucOC, and T2DM; (3) determine the correlation coefficient between OC and ucOC and fasting insulin levels, homeostatic model assessment-insulin resistance, haemoglobin A1c and fasting glucose levels and (4) explore potential sources of between-study heterogeneity. The secondary objective is to compare the serum OC and ucOC between pre-diabetes (PD) and NGC and between T2DM and PD. HODS AND ANALYSIS: This study will report items in line with the guidelines outlined in preferred reporting items for systematic reviews and meta-analysis of observational studies in epidemiology. We will include observational studies (cohort, case-control and cross-sectional studies) and intervention studies with baseline data. Three databases (MEDLINE, EMBASE and SCOPUS) will be searched from inception until July 2018 without language restrictions. Two reviewers will independently screen the titles and abstracts and conduct a full-text assessment to identify eligible studies. Discrepancies will be resolved by consensus with a third reviewer. The risk of bias assessment will be conducted by two reviewers independently based on the Newcastle-Ottawa Scale. Potential sources of between-study heterogeneity will be tested using meta-regression/subgroup analyses. Contour-enhanced funnel plots and Egger's test will be used to identify potential publication bias. ETHICS AND DISSEMINATION: Formal ethical approval is not required. We will disseminate the results to a peer-reviewed publication and conference presentation. PROSPERO REGISTRATION NUMBER: CRD42017073127.

12.
Acta Histochem ; 121(3): 297-302, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30723046

RESUMO

Heat stress damaged spermatogenesis and semen quality, however, the exact molecular mechanism is not clear. The objective of this study was to determine the effects of elevated ambient temperature and local testicular heating on the expressions of heat shock protein 70 and androgen receptor in boar testes. A growing body of evidence demonstrated that germ cell apoptosis can be aggravated by heat stress and androgen deprivation, and at normal temperature, withdrawal of androgen led to germ cell apoptosis. There were no reports that heat stress damaged spermatogenesis has relationship with androgen. In this study, adult boars (Landrace, n = 9) were used and randomly divided into: control group (CON), 20-27 °C; environmental hyperthermia group (EH), 37-40 °C, 3 h/d 42 d; and local testicular heating group (LTH), 42 °C 1 h. After heat treatments, all boars were castrated and the testes were harvested. qRT-PCR and Western Blot results showed that the mRNA and protein levels of heat shock protein 70 and androgen receptor were significantly increased after heat treatments. Immunohistochemistry results showed that heat stress caused a redistribution of heat shock protein 70 from the cytoplasm to the nucleus, and androgen receptor was mainly expressed in Sertoli cells. These results indicated that heat stress promoted the inhibition of heat shock protein 70 on the androgen receptor, suggesting that the possible mechanism of heat stress damaged spermatogenesis and semen quality was that heat stress reduced the sensitivity of testicular cells to androgen by up-regulating heat shock proteins.


Assuntos
Proteínas de Choque Térmico HSP70/metabolismo , Temperatura Alta/efeitos adversos , Receptores Androgênicos/metabolismo , Testículo/metabolismo , Animais , Apoptose/efeitos dos fármacos , Células Germinativas/metabolismo , Calefação/efeitos adversos , Masculino , Análise do Sêmen/métodos , Células de Sertoli/patologia , Espermatozoides/patologia , Suínos , Testículo/patologia , Testosterona/metabolismo
13.
Brain Res ; 1711: 23-28, 2019 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-30615887

RESUMO

The endogenous cannabinoid system is involved in the physiological inhibitory control of pain and is of particular interest for the development of therapeutic approaches for pain management. Selective activation of the peripheral CB1 cannabinoid receptor has been shown to suppress the heightened firing of primary afferents, which is the peripheral mechanism underlying neuropathic pain after nerve injury. However, the mechanism underlying this effect of CB1 receptor remains unclear. The large-conductance calcium-activated potassium (BK) channels have been reported to participate in anticonvulsant and vasorelaxant effects of cannabinoids. We asked whether BK channels participate in cannabinoids-induced analgesia and firing-suppressing effects in primary afferents after nerve injury. Here, using mice with chronic constriction injury (CCI)-induced neuropathic pain, antinociception action and firing-suppressing effect of HU210 were measured before and after BK channel blocker application. We found that local peripheral application of HU210 alleviated CCI-induced pain behavior and suppressed the heightened firing of injured fibers. Co-administration of IBTX with HU210 significantly reversed the analgesia and the firing-suppressing effect of HU210. This result indicated that the peripheral analgesic effects of cannabinoids depends on activation of BK channels.

14.
Biosci Biotechnol Biochem ; 83(2): 291-299, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30336746

RESUMO

The development of skeletal muscle is a complex process including myoblasts proliferation and differentiation. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at post-transcriptional level. Increasing evidences indicate that miRNAs are important regulators in myogenic processes. Here, we reported that the expression of miR-10b-5p steadily decreased during myoblasts proliferation, but significantly increased during myoblasts differentiation. The over-expression of miR-10b-5p promoted myoblasts proliferation and blunted myofiber formation in C2C12 cells, while miR-10b-5p down-regulation showed an opposite result. At the same time, we observed that the down-regulation of nuclear factor of activated T-cells 5 (NFAT5) repressed the differentiation of C2C12 cells, and interestingly, miR-10b-5p could suppress NFAT5 expression. Luciferase activity assays confirmed that miR-10b-5p directly target the 3'-untranslated region (3'-UTR) of NFAT5. Overall, we proposed here a novel insight that miR-10b-5p regulates the proliferation and differentiation of C2C12 myoblasts, and the impact on myogenic differentiation is partly through targeting NFAT5. Abbreviations: NFAT5: nuclear factor of activated T-cells 5; Cyclin B: cycle protein B; Cyclin D1: cycle protein D1; Cyclin E: cycle protein E; CDK4: cyclin-dependent kinase 4; MyoD: myogenic differentiation antigen; MyoG: myogenin; Myf5: myogenic factor 5; MRF4: myogenic regulatory factor 4; MyHC: myosin heavy chain; AQP5: aquaporin-5; CACNA1C: calcium voltage-gated channel subunit alpha1 C; SRF: serum response factor; Pax7: paired box 7; KLF4: Kruppel-like factor 4; 3'-UTR: 3'-untranslated region; GM: growth medium; DM: differentiation medium.


Assuntos
Diferenciação Celular/genética , Proliferação de Células/genética , MicroRNAs/fisiologia , Mioblastos/citologia , Regiões 3' não Traduzidas , Animais , Linhagem Celular , Regulação para Baixo , Humanos , Camundongos , Fatores de Transcrição/genética
15.
J Atheroscler Thromb ; 26(2): 136-144, 2019 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-29910226

RESUMO

AIM: Dyslipidemia is the most common lipid metabolism disorder in humans, and its etiology remains elusive. Hypertriglyceridemia (HTG) is a type of dyslipidemia that contributes to atherosclerosis and coronary heart disease. Previous studies have demonstrated that mutations in lipoprotein lipase (LPL), apolipoprotein CII (APOC2), apolipoprotein AV (APOA5), glycosylphosphatidylinositol anchored high-density lipoprotein-binding protein 1 (GPIHBP1), lipase maturation factor 1(LMF1), and glycerol-3 phosphate dehydrogenase 1 (GPD1) are responsible for HTG by using genomic microarrays and next-generation sequencing. The aim of this study was to identify genetic lesions in patients with HTG. METHOD: Our study included a family of seven members from Jiangsu province across three generations. The proband was diagnosed with severe HTG, with a plasma triglyceride level of 38.70 mmol/L. Polymerase chain reaction (PCR) and Sanger sequencing were performed to explore the possible causative gene mutations for this patient. Furthermore, we measured the post-heparin LPL and hepatic lipase (HL) activities using an antiserum inhibition method. RESULTS: A compound heterozygous mutation in the LMF1 gene (c.257C>T/p.P86L and c.1184C>T/p.T395I) was identified and co-segregated with the affected patient in this family. Both mutations were predicted to be deleterious by three bioinformatics programs (Polymorphism Phenotyping-2, Sorting Intolerant From Tolerant, and MutationTaster). The levels of the plasma post-heparin LPL and HL activities in the proband (57 and 177 mU/mL) were reduced to 24% and 75%, respectively, compared with those assayed in the control subject with normal plasma triglycerides. CONCLUSION: A compound heterozygous mutation of LMF1 was identified in the presenting patient with severe HTG. These findings expand on the spectrum of LMF1 mutations and contribute to the genetic diagnosis and counseling of families with HTG.


Assuntos
Biomarcadores/análise , Heterozigoto , Hipertrigliceridemia/genética , Hipertrigliceridemia/patologia , Proteínas de Membrana/genética , Mutação , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Linhagem , Prognóstico , Adulto Jovem
16.
Artigo em Inglês | MEDLINE | ID: mdl-32054230

RESUMO

Objectives: The QingYu pig is well known for its excellent meat quality attributes in Sichuan province, China. In order to improve its production efficiency, the determination of genetic factors contributing to quantifiable economic traits of livestock is important. Moreover, the cross-breeding of QingYu pigs with western breeds possessing strong growth attributes is an efficient way to improve the performance of this breed. Methods: Here, the genetic parameters of several important reproductive traits of QingYu pigs were estimated. Furthermore, the effects of crossing Berkshire with QingYu (BQ) pigs on carcass and meat quality traits, as well as the effects of slaughter weight on carcass and meat quality of BQ were characterized. Results: QingYu pigs exhibited superior reproductive traits. The total number born (TNB) available to QingYu pigs was more than 8 parity. The observed repeatability of the reproductive traits of the QingYu pigs was between 0.10 and 0.23. The significantly correlated genetic and phenotypic of reproduction traits were consistent. Interestingly, the BQ pigs exhibited improved carcass quality, with a significant increase in loin muscle area, lean percentage and reduction in sebum percentage. As a result, BQ had higher L45min, lower cooking scores, and lower drip loss. In addition, the loin muscle area, body length, and sebum percentage were significantly higher in 90 and 100kg animals. Cooking loss showed a significant increase at 80kg, and marbling increased significantly from 90kg. Conclusion: The results of this study suggest that QingYu pigs exhibit excellent reproductive properties and heritability of these traits. Crossing with Berkshire is an efficient strategy to improve the carcass and meat quality of QingYu pigs for commercial operations. Furthermore, it appears as though the optimal slaughter weight of BQ pigs is at approximately 90kg.

17.
Genet Mol Biol ; 41(3): 624-637, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30044467

RESUMO

Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

18.
Sci Rep ; 8(1): 9856, 2018 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-29959372

RESUMO

Protein secondary structure prediction is one of the most important and challenging problems in bioinformatics. Machine learning techniques have been applied to solve the problem and have gained substantial success in this research area. However there is still room for improvement toward the theoretical limit. In this paper, we present a novel method for protein secondary structure prediction based on a data partition and semi-random subspace method (PSRSM). Data partitioning is an important strategy for our method. First, the protein training dataset was partitioned into several subsets based on the length of the protein sequence. Then we trained base classifiers on the subspace data generated by the semi-random subspace method, and combined base classifiers by majority vote rule into ensemble classifiers on each subset. Multiple classifiers were trained on different subsets. These different classifiers were used to predict the secondary structures of different proteins according to the protein sequence length. Experiments are performed on 25PDB, CB513, CASP10, CASP11, CASP12, and T100 datasets, and the good performance of 86.38%, 84.53%, 85.51%, 85.89%, 85.55%, and 85.09% is achieved respectively. Experimental results showed that our method outperforms other state-of-the-art methods.


Assuntos
Algoritmos , Biologia Computacional/métodos , Aprendizado de Máquina , Estrutura Secundária de Proteína , Proteínas/química , Bases de Dados de Proteínas , Humanos
19.
Oncotarget ; 9(2): 1524-1541, 2018 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-29416711

RESUMO

Aging significantly affects the cardiac muscle (CM) and skeletal muscles (SM). Since the aging process of CM and SM may be different, high throughput RNA sequencing was performed using CM and SM in different age conditions to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNA (lncRNA), micro RNA (miRNA), and circular (circRNA). Several mRNAs, lncRNAs, and miRNAs were highly expressed and consistently appeared in both ages in one of the two muscle tissues. Gene ontology (GO) annotation described that these genes were required for maintaining normal biological functions of CM and SM tissues. Furthermore, 26 mRNAs, 4 lncRNAs, 22 miRNAs, and 26 circRNAs were differentially expressed during cardiac muscle aging. Moreover, 81 mRNAs, 5 lncRNAs, 79 miRNAs, and 62 circRNAs were differentially expressed during aging of skeletal muscle. When comparing the expression profiles of CM and SM during aging, the senescence process in CM and SM was found to be fundamentally different. In addition, we assessed multi-group cooperative control relationships and constructed circRNA-miRNA-mRNA co-expression networks in muscular aging. In conclusion, our findings will contribute to the understanding of muscular aging and provide a foundation for future studies on the molecular mechanisms underlying muscular aging.

20.
Gene ; 642: 522-532, 2018 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-29197588

RESUMO

Efforts have been made to characterize the high-altitude adaption in Tibetan pigs and identified vast of genes or genomic regions undergone natural selection. Nonetheless, information concerning gene expression and DNA methylation changes response to low-altitude acclimation in Tibetan pigs is long overdue. To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic and DNA methylation analysis of skeletal muscle between indigenous Tibetan pigs that reside in high altitude regions (~4000m) and their counterparts that migrated to the geographically neighboring low-altitude regions (~500m) for nearly ten generations. Many genes that related to hypoxia response (EGLN3 and FLT1) and energy metabolism (TFB2M) were differentially expressed, but without significant DNA methylation changes. We also found genes embedded in differentially methylated regions were mainly involved in 'Starch and sucrose metabolism', 'glucuronosyltransferase activity' processes. Specifically, our results showed increased SIN3A mRNA expression, with hypomethylation status of its promoter, in longissimus dorsi muscle of low-altitude Tibetan pig. Another gene, CACNG6, showed decreasing expression level with an elevated methylation in its intron 3. These results indicated DNA-methylation-mediated expression alterations in low-altitude acclimation. We envision that this study will serve as a valuable resource for mammal acclimation research and agricultural food industry.


Assuntos
Aclimatação , Metilação de DNA , Perfilação da Expressão Gênica/métodos , Sus scrofa/genética , Altitude , Animais , Ilhas de CpG , Músculo Esquelético/metabolismo , Filogenia , Regiões Promotoras Genéticas , Seleção Genética , Suínos
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