Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy

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Association between habitual snoring,middle ear disease,and speech problems in young children with non-syndromic cleft palate anomalies

The purpose of this study was to investigate the association between habitual snoring (HS), middle ear disease (MED), and speech problems in children with cleft palate. This cross-sectional study included children aged 2.0–7.9 years with non-syndromic cleft palate anomalies. Parents completed the Pediatric Sleep Questionnaire and a questionnaire about MED. Audiograms and speech assessment were also conducted. Ninety-five children were enrolled; 15.2% of families reported HS, 97.6% MED, and 17.1% speech problems. HS (37.5% vs 10.3%, P = 0.007) and early episodes of MED (92.3% vs 58.2%, P = 0.021) were more likely to be reported for children with isolated cleft palate when compared to those with cleft lip and palate. Children with cleft lip and palate had a higher frequency of MED with effusion compared to those with Robin sequence (86.4% vs 57.1%, P = 0.049). The odds ratio for HS in children with ≥1 episode of MED in the last year was 7.37 (95% confidence interval 1.55–35.15, P = 0.012). There was a trend for children with speech problems reported by parents to have HS (30.8% vs 11.5%, P= 0.076). Anatomical factors play a role in the frequency of upper airway symptoms in children with cleft palate. A recent history of at least one episode of MED was associated with an increased frequency of HS.     

The Effect of Treatment Sequence on Overall Survival for Men With Metastatic Castration-resistant Prostate Cancer: A Multicenter Retrospective Study

IntroductionWe aimed to evaluate the treatment sequence for patients with metastatic castration-resistant prostate cancer (mCRPC) in real-world practice and compare overall survival in each sequential therapy.Patients and MethodsWe retrospectively evaluated 146 patients with mCRPC who were initially treated with androgen deprivation therapy as metastatic hormone-naive prostate cancer in 14 hospitals between January 2010 and March 2019. The agents for the sequential therapy included new androgen receptor-targeted agents (ART: abiraterone acetate or enzalutamide), docetaxel, and/or cabazitaxel. We evaluated the treatment sequence for mCRPC and the effect of sequence patterns on overall survival.ResultsThe median age was 71 years. A total of 35 patients received ART-ART, 33 received ART-docetaxel, 68 received docetaxel-ART, and 10 received docetaxel-cabazitaxel sequences. The most prescribed treatment sequence was docetaxel-ART (47%), followed by ART-ART (24%). Overall survival calculated from the initial diagnosis reached 83, 57, 79, and 37 months in the ART-ART, ART-docetaxel, docetaxel-ART, and docetaxel-cabazitaxel, respectively. Multivariate Cox regression analyses showed no significant difference in overall survival between the first-line ART (n = 68) and first-line docetaxel (n = 78) therapies (hazard ratio [HR], 0.84; P = .530), between the ART-ART (n = 35) and docetaxel-mixed (n = 111) sequences (HR, 0.82; P = .650), and between the first-line abiraterone (n = 32) and first-line enzalutamide (n = 36) sequences (HR, 1.58; P = .384).ConclusionThe most prescribed treatment sequence was docetaxel followed by ART. No significant difference was observed in overall survival among the treatment sequences in real-world practice.     

Spatial and temporal expansion of intrahepatic metastasis by molecularly‐defined clonality in multiple liver cancers

Multiple hepatocellular carcinoma (HCC) is divided into two categories: intrahepatic metastasis (IM), which is a true relapse of HCC, and multicentric origin (MO), which is a second primary tumor. Clinical diagnosis of multiple HCC is usually made based on tumor location and/or time to recurrence; however, it is often difficult to distinguish the two types of multiple HCC. Using 41 matched pairs of multiple HCC specimens, we confirmed the accuracy of clinical diagnoses using exome sequence data and investigated the importance of discriminating the type of multiple HCC. Genomic analysis revealed that 18 (43.9%) patients diagnosed as having genomic IM had common mutations in a pair of HCC tumors with the main tumor of these patients being more progressive compared to those with genomic MO. The accuracy of clinical diagnosis based on lobe (Definition 1) and segment (Definition 2) were 68.3% and 78.0%, respectively. Intriguingly, recurrence ≥2 years after initial surgery for 3 patients was IM. The survival of patients with clinical IM was significantly shorter than for those with clinical MO based on both Definition 1 (P = 0.045) and Definition 2 (P = 0.043). However, mean survival was not different between the patients with genomic IM and those with MO (P = 0.364). Taken together, genomic analysis elucidated that liver cancer may spread more extensively and more slowly than previously thought. In addition, distinguishing multiple HCC as IM or MC may have provided biological information but was not of clinical importance with respect to patient prognosis.     

69份苦玄参种质SSR遗传多样性及品质性状相关标记分析

目的:采用简单重复序列(SSR)分子标记技术对广西苦玄参主产区69份苦玄参种质样本进行遗传多样性及亲缘关系分析,并筛选与苦玄参苷含量相关联的优良种质基因。为苦玄参种质资源评价、遗传进化分析及分子标记辅助育种等提供依据。方法:基于转录组测序技术,开发20对引物进行批量扩增。利用各标记位点的遗传多态信息,分析69份苦玄参种质的遗传多样性及亲缘关系,并通过一元线性和多元逐步回归分析,筛选与苦玄参苷含量相关联的分子标记。结果:20对SSR引物共扩增出76个等位基因,平均每个位点观测等位基因3.8个,高于有效等位基因数(1.9692个),稀有等位基因率为38.2%,等位基因分布不均匀。等位基因多态率范围为0~59%,平均38.24%,各位点多态率差异较大。各位点多态信息含量(PIC)变化范围为0~0.6211,平均0.3780;Shannon多态性信息指数变化范围为0~1.2401,平均0.7590;Nei’s基因多样性指数(Nei)变化范围为0~0.6823,平均0.4409;以上3个指标最高的为P21,最低为P7,各位点遗传多样性存在较大差异。各位点平均观测杂合度为0.3824,低于平均期望杂合度(0.4425),表现为杂合子缺失;平均遗传分化系数Fst为0.3659;基因流Nm平均值为0.4332,种质遗传分化较大,基因流较小。一元线性回归分析和多元逐步回归分析结果表明,与苦玄参苷IA和IB相关的位点各有5个,其中仅有1个位点与2个成分的含量均相关。结论:20个SSR标记位点遗传多样性存在较大的差异,供试69份种质遗传分化大,基因流较小;从供试20个SSR标记中筛选出9个与苦玄参苷含量相关联的标记位点,试验结果可为苦玄参遗传进化分析及良种选育和繁育等提供依据。     

江西省锐尖山香圆亲缘关系与群体结构的ISSR分析

目的:利用简单序列重复区间扩增多态性(ISSR)分子标记技术对江西省锐尖山香圆进行亲缘关系和遗传结构分析,为该药材资源的保护和利用提供理论依据。方法:采集江西省4个县6个采样地的22份锐尖山香圆叶片样本,利用试剂盒法提取基因组DNA。利用64条通用ISSR分子标记引物进行聚合酶链式反应(PCR)扩增,运用聚丙烯酰胺凝胶电泳(PAGE)方法检测条带。选择NTsys 2. 10e软件,采用非加权配对算术平均法(UPGMA)计算遗传相似系数并聚类分析。利用Structure 2. 1软件分析群体遗传结构。结果:有48条ISSR引物扩增后获得了产物,多态性条带百分率处于45. 45%～100%。UPGMA聚类分析表明4个县的锐尖山香圆资源不能按照行政区域划分分别聚为一类,群体遗传结构分析表明22份锐尖山香圆群体可以划分为3个类群。结论:江西省锐尖山香圆群体间存在着基因交流,会影响该药材不同地理来源种质资源的遗传结构组成。     

基于高通量测序技术的三叉苦幼苗转录组数据分析

目的获得三叉苦Melicope pteleifolia转录组信息特征。方法以三叉苦幼苗根、茎、叶混合样品为对象,采用二代高通量测序平台Illumina HiSeq~(TM) 2000进行转录组测序并进行系统的生物信息学分析。结果转录组测序分析共获得47 045 040条高质量序列(clean reads),Trinity de novo组装获得67 956条unigenes,平均长度787 nt。BLAST分析显示分别有42 749(61.92%)、31 152(45.84%)、26 563(39.0 9%)、17 481(25.72%)条unigenes在NR、Swiss-port、KOG、KEGG数据库得到注释信息,参与生物过程、细胞组分和分子功能3个GO类别的47个小组,共9807条unigenes注释到130个KEGG代谢通路中,筛选到19条次生代谢通路,KOG功能分类分析获得25个不同的KOG功能类群。预测共有高等植物转录因子56个家族;借助MISA软件发现7 748个SSRs,三碱基重复SSRs数量最丰富,有4 117个,出现频率为53.1%,五碱基重复SSRs相对较少,占2.2%。结论利用高通量测序技术和生物信息分析获得三叉苦转录组信息特征,为后续三叉苦功能基因的挖掘、次生代谢途径解析及其调控机制研究奠定基础。     

地黄毛蕊花糖苷合酶基因的克隆、亚细胞定位与表达特性分析

目的克隆地黄Rehmanniaglutinosa毛蕊花糖苷合酶基因(Rg Ac S1),分析其亚细胞定位和表达模式。方法在地黄的转录组数据库中通过注释和比对,获得地黄Rg Ac S1的c DNA序列,利用聚合酶链式反应(PCR)方法进行分子克隆。构建绿色荧光蛋白(GFP)融合表达载体,以农杆菌瞬时表达法观测Rg Ac S1的亚细胞定位。利用实时荧光定量PCR(q RT-PCR)检测Rg Ac S1基因在地黄块根不同部位的表达模式。结果获得地黄1个莽草酸-O-羟基肉桂酰基转移酶的全长编码序列,c DNA长度为1 659 bp,包含1个1 296 bp的开放阅读框,编码431个氨基酸残基,蛋白质相对分子质量为475 900,具有莽草酸-O-羟基肉桂酰基转移酶的典型结构域,命名为Rg Ac S1。亚细胞定位结果显示Rg Ac S1主要分布在细胞质中,在细胞核中也有分布。q RT-PCR分析表明,Rg Ac S1在地黄的周皮和根毛中表达量较高,在木质部和韧皮部表达量较低。Rg Ac S1基因在地黄品种北京1号、QH1和85-5中非菊花心中表达量均高于菊花心中的表达量,且差异达极显著水平。结论获得地黄Rg Ac S1的c DNA序列,明确了Rg Ac S1的亚细胞定位和时空表达模式,为进一步研究Rg Ac S1基因在毛蕊花糖苷合成过程中的作用奠定基础。