OBJECTIVES: Uterine fluid RNA can be used as a test for endometrial receptivity, but there is still no noninvasive sampling method available. The polyvinyl alcohol (PVA) formaldehyde absorbent sponge, a medical bio-absorbent sponge with good water absorption and biophilic properties, can be used to develop a new noninvasive endometrial fluid sampler. This study aims to investigate the toxicity of PVA acetal absorbent sponges on endometrial epithelial cells and its effect on RNA sequencing (RNA-Seq). METHODS: The experimental group using PVA formaldehyde absorbent sponge was prepared into 0.005%, 0.01% and 0.02% (w/v) suspension, and 0.01%, 0.05% and 0.1% (v/v) extract groups. The control group was only the complete culture medium. Nothing was added to the blank group. In vitro cytotoxicity assay was used to evaluate the survival rate of cells. Eight patients underwent in vitro fertilization treatment in the Reproductive Center of Xiangya Hospital, Central South University from November 2019 to January 2020. The uterine fluid of each patient was aspirated. The experimental group was inhaled with sterile PVA formaldehyde absorbent sponge and then immersed RNA-later solution. The control group was directly injected into the same amount of RNA-later solution. RNA-seq and data analysis was performed later. RESULTS: The vitro cytotoxicity assay showed that in suspension groups, there was no significance difference in cell survival between different co-culture time in 0.005% group (P=0.255). In the 0.01% and 0.02% group, there was no difference at each incubation time within 12 h (all P>0.05), but the cell survival rate was decreased at 24 h compared with 0 h (P<0.01, P<0.05). At the same co-culture time, the cell survival of the 3 concentration gradient groups were significantly lower than that of the control group (all P<0.05). The cell viability of the 0.005% concentration group was decreased less than 30% at 24 h, the 0.01% concentration group decreased more than 30% at 12 h, and the 0.02% concentration group was decreased more than 30% at 0 h. For extract groups, there was no significant difference in the survival rate within 6 h in 0.01% concentration group (all P>0.05), and the survival rate of 12 h and 24 h was lower than that of 0 h group (both P<0.01). In 0.05% group, there was no significant difference at each incubation time within 12 h (all P>0.05), but the survival rate at 24 h was lower than that at 0 h (P<0.05). There was no significant difference in survival rate at different culture time in 0.1% concentration group (P=0.082). At the same culture time, there was no significant difference in survival rate between 0.01% group and control group at 0, 3 and 24 h (all P>0.05). Except for 3 h, the survival rate of 0.05% and 0.1% groups was lower than that of control group (all P<0.05), and the decrease was all less than 30%. Uterine fluid RNA-seq showed that there was no significance difference in exonic rate, the detected genes and transcripts of RNA between the experiment groups and the control group (all P>0.05). CONCLUSIONS The in vitro cytotoxic of PVA formaldehyde absorbent sponge on human endometrial epithelial cell meet the national standard of the cytotoxic of medical materials. Sampling the uterine fluid with this material does not affect the RNA-Seq results. PVA formaldehyde absorbent sponge is safe and feasible when appling to the noninvasive uterine fluid sampling and RNA sequencing.
Humans ; Social Group ; Sequence Analysis, RNA ; RNA

Forensic microorganism is one of the hotspots of forensic science research. Due to its conservatism and specificity, the 16S rRNA gene is found to be an ideal marker for forensic identification. With the rapid development of high throughput sequencing technology, the research on microorganisms has been gradually applied to many fields such as environment and health care. In the field of forensic science, the results of forensic microbiology research, represented by 16S rRNA gene sequencing, are also gradually applied to forensic practice, such as biological samples identification, individual identification, postmortem interval estimation, and regional inference, which not only provide clues for the investigation of cases but also complement and assist traditional methods. This paper describes the research methods and related sequencing technologies of 16S rRNA gene sequencing, summarizes its research progress, and discusses the application value and potential of 16S rRNA in forensic science.
Forensic Sciences/trends* ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA

Exercise capacity is a valuable trait in horses, and it has been used as a horse selection criterion. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully described. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively. The expressions of 6 miRNAs, including 4 known and 2 novel miRNAs, were altered by exercise. The predicted target genes of the differentially expressed miRNAs identified by NGS were matched to the exercise-induced mRNAs determined by microarray analysis. Five genes (LOC100050849, LOC100054517, KHDRBS3, LOC100053996, and LOC100062720) from the microarray analysis were matched to the predicted target genes of the 6 miRNAs. The subset of mRNAs and miRNAs affected by exercise in peripheral blood leukocytes may be useful in elucidating the molecular mechanisms of exercise-associated physiology in horses.
Homeostasis ; Horses ; Leukocytes ; Microarray Analysis ; MicroRNAs ; Physiology ; RNA ; RNA, Messenger

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina’s sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.
Benchmarking ; Colonic Neoplasms ; Humans ; Quality Control ; RNA ; Sequence Analysis, RNA

The MinION(TM) is a miniature nanopore-based analysis device in which the characteristics of an analyte, as it passes through the nanopore, cause changes in the flow of ions through the pore, which are measured, as current flow, by a low noise amplifier and analogue-to-digital converter. Potentially any molecular analyte capable of passing through the nanopore may modify the flow of ions and generate a signal which might be diagnostic. In practice the current device is focussed on DNA sequencing, directly sequencing RNA is a likely development. With the MinION Access Program making the MinION(TM) widely available a flood of applications exploiting its real time, long read capabilities have been published. We review the background to the technology and compare it to current next generation sequencing.
Ions ; Nanopores ; Noise ; RNA ; Sequence Analysis, DNA

To identify pathways associated with survival phenotypes using gene expression data, we recently proposed the hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE) method. The HisCoM-PAGE software can consider hierarchical structural relationships between genes and pathways and analyze multiple pathways simultaneously. It can be applied to various types of gene expression data, such as microarray data or RNA sequencing data. We expect that the HisCoM-PAGE software will make our method more easily accessible to researchers who want to perform pathway analysis for survival times.
Gene Expression ; Methods ; Phenotype ; Sequence Analysis, RNA

PURPOSE: A novel retentive type of implant prosthesis that does not require the use of cement or screw holes has been introduced; however, there are few reports examining the biomechanical aspects of this novel implant. This study aimed to evaluate the biomechanical features of cementless fixation (CLF) implant prostheses.MATERIALS AND METHODS: The test groups of three variations of CLF implant prostheses and a control group of conventional cement-retained (CR) prosthesis were designed three-dimensionally for finite element analysis. The test groups were divided according to the abutment shape and the relining strategy on the inner surface of the implant crown as follows; resin-air hole-full (RAF), resin-air hole (RA), and resin-no air hole (RNA). The von Mises stress and principal stress were used to evaluate the stress values and distributions of the implant components. Contact open values were calculated to analyze the gap formation of the contact surfaces at the abutment-resin and abutment-implant interfaces. The micro-strain values were evaluated for the surrounding bone.RESULTS: Values reflecting the maximum stress on the abutment were as follows (in MPa): RAF, 25.6; RA, 23.4; RNA, 20.0; and CR, 15.8. The value of gap formation was measured from 0.88 to 1.19 µm at the abutmentresin interface and 24.4 to 24.7 µm at the abutment-implant interface. The strain distribution was similar in all cases.CONCLUSION: CLF had no disadvantages in terms of the biomechanical features compared with conventional CR implant prosthesis and could be successfully applied for implant prosthesis.
Crowns ; Finite Element Analysis ; Prostheses and Implants ; RNA

With the rapid development of molecular biotechnology, transcriptomics has been widely used in the study of gene expression. In recent years, the techniques for microbial transcriptomics research have also been rapidly developing. At the gene level, the way for obtaining sequence information has been developed from complementary validation of RNA fragment through DNA microarray to direct sequencing of full-length RNA. Spatially, the traditional population transcriptomics technique has been developed into spatial, single cell and epigenetic transcriptomics studies. With the application of transcriptomics techniques in the field of microbial research, the corresponding defects were gradually revealed and constantly improved. In this paper, the traditional and new transcriptomics techniques in the field of microbial research are summarized to provide reference for microbial transcriptomics research.
Transcriptome ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis ; RNA ; Biotechnology

The acquisition of somatic mutations is the most common event in cancer. Neoantigens expressed from genes with mutations acquired during carcinogenesis can be tumor-specific. Since the immune system recognizes tumor-specific peptides, they are potential targets for personalized neoantigen-based immunotherapy. However, the discovery of druggable neoantigens remains challenging, suggesting that a deeper understanding of the mechanism of neoantigen generation and better strategies to identify them will be required to realize the promise of neoantigen-based immunotherapy. Alternative splicing and RNA editing events are emerging mechanisms leading to neoantigen production. In this review, we outline recent work involving the large-scale screening of neoantigens produced by alternative splicing and RNA editing. We also describe strategies to predict and validate neoantigens from RNA sequencing data.
Alternative Splicing ; Carcinogenesis ; Humans ; Immune System ; Immunotherapy ; Mass Screening ; Peptides ; RNA Editing ; RNA ; Sequence Analysis, RNA

The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
Arabidopsis/metabolism* ; Oryza/metabolism* ; RNA, Circular/metabolism* ; RNA, Plant/metabolism* ; Sequence Analysis, RNA/methods*