Development of genome-wide insertion and deletion markers for maize,based on next-generation sequencing data

Background

Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.

Results

A total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39 % of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90 %. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54.

Conclusions

The maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1797-5) contains supplementary material, which is available to authorized users.     

Assay for Laccase activity by microcalorimetry: laccase was extracted from china lacquer of Rhus vernicifera

The reactions between Laccase (extracted from China lacquer of Rhus vernicifera) and various substrates (3,4-Dihydroxybenzaldehyde, Guaiacol, Pyrogallol, Gallic acid) have been studied using LKB-2107 batch microcalorimetry system. Based on calorimetry, a new method has been proposed. Laccase activity and the Michaelis constant K(m) have been determined simultaneously by this method. The method is simple, sample-saving, and valid for a wider range of substrate concentrations. Furthermore, it can be extended for assaying other enzymes catalyzing reactions using this method.     

高危型人乳头瘤病毒感染与宫颈癌中miR-218表达的关系

目的观察高危型人乳头瘤病毒(HPV)感染与宫颈癌中miR-218表达的关系。方法收集2015年6月至2018年12月我院手术切除的宫颈癌组织并检测高危型HPV感染情况和miR-218表达量。培养HPV16阳性的SiHa细胞株并进行分组,阴性对照(NC)组转染NC模拟物、miR-218组转染miR-218模拟物,检测两组细胞凋亡率、B淋巴细胞瘤-2基因(Bcl-2)、Bcl-2相关x蛋白(Bax)、Bcl-2相互作用细胞死亡介导因子(Bim)、含半胱氨酸的天冬氨酸蛋白水解酶(Caspase)-9、Caspase-3的mRNA表达量及凋亡通路分子c-Jun氨基末端激酶(JNK)、c-Jun基因(c-Jun)、磷脂酰肌醇3-激酶(PI3K)、蛋白激酶B(AKT)、哺乳动物雷帕霉素靶蛋白(mTOR)的蛋白表达量。结果高危型HPV阳性的宫颈癌组织中miR-218表达量减少。转染24 h后,miR-218组细胞凋亡率、细胞中Bax、Bim、Caspase-9、Caspase-3的mRNA表达量及JNK、c-Jun的蛋白表达量均明显高于NC组,而细胞中Bcl-2的mRNA表达量及PI3K、AKT、mTOR的蛋白表达量均低于NC组,差异均有统计学意义(均P<0.05)。结论miR-218在高危型HPV感染的宫颈癌组织中表达减少。增加miR-218的表达能够促进HPV感染宫颈癌细胞的凋亡。该调控作用与JNK/c-Jun通路的激活及PI3K/AKT/mTOR通路的抑制有关。     

Probe droplet arrays generated in the capillary for microarray analysis

Microarray technology is a useful tool for nucleic acid detection and has been widely used in biology and related research fields. However, the procedure is labor intensive and time consuming. Microfluidic chip-based microarrays save time with better performance, but the low spot density and probe number limit its applications. To develop high performance microarrays with high spot density within a microchannel, a method is reported here for preparing microarrays in a capillary by generating probe droplet arrays. The probes in droplets are immobilized onto the inner wall of the capillary to form a one-dimensional probe array, and then a sample solution is introduced to hybridize with the probe array. The effect of the capillary's inner diameter was evaluated to realize a high-density probe array. The processes of array generation and probe immobilization were studied to avoid possible cross contamination. The background from probe immobilization during the array generation and incubation was quantified to assure sensitivity. Multiple sample detection was also demonstrated within one capillary. The capillary based microarray assay had high spot density, easy fabrication, fast detection, high sensitivity and multiple sample capacity.     

Over-expression of human carcinoma-associated antigen in intrahepatic cholangiocellular carcinoma

Objective: To investigate the expression status of human carcinoma antigen (HCA) in human cholangiocellular carcinomas, and to determine the relationship between HCA and clinical features. Methods: Tissues from 60 intrahepatic cholangiocellular carcinoma (ICC) patients, and normal liver tissues from 20 hepatic hemangioma patients selected randomly were assayed for the expression of HCA by immunohistochemistry, and Western blots. Areas of poorly differentiated (n = 20), moderately-well differentiated (n = 30), highly differentiated tumors (n = 10) from different cases were evaluated. Results were recorded as positive (?5% of cells staining and staining intensity 2+ or 3+) or negative (<5% of cells staining and staining intensity <2+) and analyzed using the χ² test. Results: BCE075 and BDD048 antibodies showed similar staining patterns. The positive immunostaining of BCE075 was mainly localized in the cytoplasm and cell secretions. The staining was positive in 15% of poorly differentiated ICC, 72% of moderately-well differentiated, 100% of highly differentiated tumors. But, staining was not detected in adjacent normal tissue. The differences in HCA expression among these tissues were statistically significant. Also, we found expression of HCA to be closely associated with the degree of differentiation of ICC and tumor cell morphology. There was a correlation between expression of HCA and serum CA19-9. Conclusion: The data suggest that HCA is a potential marker for the diagnosis of cholangiocellular carcinoma.     

Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif

The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs.     

Modifying L-type calcium current kinetics: consequences for cardiac excitation and arrhythmia dynamics

The L-type Ca current (I_Ca,L), essential for normal cardiac function, also regulates dynamic action potential (AP) properties that promote ventricular fibrillation. Blocking I_Ca,L can prevent ventricular fibrillation, but only at levels suppressing contractility. We speculated that, instead of blocking I_Ca,L, modifying its shape by altering kinetic features could produce equivalent anti-fibrillatory effects without depressing contractility. To test this concept experimentally, we overexpressed a mutant Ca-insensitive calmodulin (CaM₁₂₃₄) in rabbit ventricular myocytes to inhibit Ca-dependent I_Ca,L inactivation, combined with the ATP-sensitive K current agonist pinacidil or I_Ca,L blocker verapamil to maintain AP duration (APD) near control levels. Cell shortening was enhanced in pinacidil-treated myocytes, but depressed in verapamil-treated myocytes. Both combinations flattened APD restitution slope and prevented APD alternans, similar to I_Ca,L blockade. To predict the arrhythmogenic consequences, we simulated the cellular effects using a new AP model, which reproduced flattening of APD restitution slope and prevention of APD/Ca_i transient alternans but maintained a normal Ca_i transient. In simulated two-dimensional cardiac tissue, these changes prevented the arrhythmogenic spatially discordant APD/Ca_i transient alternans and spiral wave breakup. These findings provide a proof-of-concept test that I_Ca,L can be targeted to increase dynamic wave stability without depressing contractility, which may have promise as an antifibrillatory strategy.     

Construction of a robust prognostic model for adult adrenocortical carcinoma: Results from bioinformatics and real-world data

This study aims to construct a robust prognostic model for adult adrenocortical carcinoma (ACC) by large-scale multiomics analysis and real-world data. The RPPA data, gene expression profiles and clinical information of adult ACC patients were obtained from The Cancer Proteome Atlas (TCPA), Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Integrated prognosis-related proteins (IPRPs) model was constructed. Immunohistochemistry was used to validate the prognostic value of the IPRPs model in Fudan University Shanghai Cancer Center (FUSCC) cohort. 76 ACC cases from TCGA and 22 ACC cases from GSE10927 in NCBI’s GEO database with full data for clinical information and gene expression were utilized to validate the effectiveness of the IPRPs model. Higher FASN (P = .039), FIBRONECTIN (P < .001), TFRC (P < .001), TSC1 (P < .001) expression indicated significantly worse overall survival for adult ACC patients. Risk assessment suggested significantly a strong predictive capacity of IPRPs model for poor overall survival (P < .05). IPRPs model showed a little stronger ability for predicting prognosis than Ki-67 protein in FUSCC cohort (P = .003, HR = 3.947; P = .005, HR = 3.787). In external validation of IPRPs model using gene expression data, IPRPs model showed strong ability for predicting prognosis in TCGA cohort (P = .005, HR = 3.061) and it exhibited best ability for predicting prognosis in GSE10927 cohort (P = .0898, HR = 2.318). This research constructed IPRPs model for predicting adult ACC patients’ prognosis using proteomic data, gene expression data and real-world data and this prognostic model showed stronger predictive value than other biomarkers (Ki-67, Beta-catenin, etc) in multi-cohorts.