Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N⁶-methyladenosine (m⁶A) and N⁵-methylcytosine (m⁵C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m⁶A and m⁵C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m⁶A modifications tended to be modified by m⁵C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m⁶A- and m⁵C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.
RNA ; Oryza/genetics* ; RNA, Messenger ; Gene Expression Profiling ; Transcriptome ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods* ; RNA Processing, Post-Transcriptional

To investigate the correlation between the number of peripheral blood circulating tumor cells (CTCs) and clinicopathological features of early breast cancer. 
 Methods: The clinical and pathological data from 100 patients with early breast cancer treated by a breast cancer treatment team in the Department of Breast Surgery, Second Xiangya Hospital, Central South University, were collected from January 2017 to December 2018. For these patients, their peripheral blood CTCs were detected, enumerated and typed by CanpatrolTM CTC assay.
 Results: The positive rate of CTCs was 90% in peripheral blood of patients with early breast cancer, and the majority of molecular phenotypes was hybrid CTCs (55.6%). The positive rate of CTCs was only related to the pathological type of tumor (P<0.05), but not to other clinicopathological features. No correlation between clinicopathological features and the total number of CTCs, the number of epithelial CTCs or the number of hybrid CTCs was found. However, the number of mesenchymal CTCs was significantly correlated with the expression of hormone receptors and Ki-67 (r=0.200, P<0.05), and there was a significant correlation between the proportion of mesenchymal CTCs and the expression level of Ki-67 (r=0.213, P<0.05).
 Conclusion: The number of CTCs is not correlated with all clinicopathological features, but patients with negative hormone receptor and high expression of Ki-67 probably have more hybrid CTCs.
Biomarkers, Tumor ; Breast Neoplasms ; Epithelial-Mesenchymal Transition ; Humans ; Neoplastic Cells, Circulating

Objective To establish a molecular typing system of Staphylococcus aureus by using resolution melting for food-poi-soning fast tracing.Methods Primers were designed and synthesized according to the literature of VNTR in Staphylococcus au-reus ,and were used to perform molecular typing on the strains which had detected by PFGE,then 4 types of VNTRs were with higher discriminatory power were selected.On this basis,we established a molecular typing system for the detection of 59 Staphy-lococcus aureus isolated from food poisoning.Results The molecular typing system has good precision for detection.The standard deviation(s)of within-batch repetitive experiments were 0.03 -0.05 ℃,between-batch repetitive experiments were 0.04 -0.06℃,between-day repetitive experiments were 0.04-0.06 ℃.At the same time,the 59 strains of Staphylococcus aureus were divided into 19 types which were 11 epidemic clones and 8 sporadic clones.The correlation coefficient of Simpson was 0.916 4.Conclusion The molecular typing system for Staphylococcus aureus based on resolution melting was simple,fast and repeatable.It can be ap-plied to fast tracing and screen of Staphylococcus aureus in food poisoning.

The rice Rim2/Hipa is a stress-induced transposon superfamily recently identified in Oryza genomes. Genomic variation was found in the Rim2 core region among rice genetic resources/genomes, indicative of high genomic divergence accumulated during the Rim2 evolution. Based on the divergence and quiescent state of the Rim2 elements, a Rim2 paralog display-based fingerprinting approach was developed to effectively identify rice genetic resources and explore their genetic relationships within a set of rice germplasm including 45 accessions ofO. sativa and 8 accessions of its wild relatives O. rufipogon. A dendrogram showed not only clear genetic diversity of rice germplasm, but also considerable genetic differentiation among wild rice resources. The wild rice relatives were either clustered as an independent group, or among the japonica varieties. This Rim2-based fingerprinting approach could also serve as a sensitive tool to identify rice hybrids from their parents, and variety stability, demonstrating its great potential in evolution study ofrice genomes and in rice breeding and seed production.