Exploration of the pathological mechanism of endometriosis in rats using high-throughput sequencing

2019 ◽  
Author(s):  
Furui Miao ◽  
Zhenjuan Li ◽  
Muyue Li ◽  
Yushan Fan
Keyword(s):  
Treatment Group ◽  
Drug Treatment ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Receptor Interaction ◽  
Sham Operation ◽  
Sequencing Data ◽  
Sham Operation Group ◽  
Operation Group ◽  
Drug Treatment Group

Abstract Background : This study aimed to explore the pathological mechanism of endometriosis (EMs) in rats by high-throughput sequencing. Methods : Rat EMs model, sham operation group and drug treatment group were established. Uterine tissue was collected for construction of sequencing library and high-throughput sequencing. Data quality was examined. KEGG pathway enrichment analysis was carried out. Results : Percentages of both high-quality sequence Reads and high-quality sequence bases accounted for more than 98%, suggesting that the data quality was acceptable. Total sequences mapped to reference genome (Total Mapped) accounted for more than 90% of total sequences used for mapping (Clean Reads), suggesting that the mapping results of the sequencing data were acceptable. There were 440 differentially expressed genes (DEGs) in the drug treatment group compared with the sham operation group, 382 DEGs in the drug treatment group compared with the model group, and 503 DEGs in the sham operation group compared with the model group. We screened genes ENSRNOG00000023079 and ENSRNOG00000012175 related to vascular endothelial growth factor pathway. The DEGs were mainly enriched in the signaling pathways such as phagosome, natural killer cell mediated cytotoxicity, Janus kinase-signal transducers and activators of transcription signaling pathway, hematopoietic cell lineage, cytokine-cytokine receptor interaction, regulation of actin cytoskeleton and extracellular matrix-receptor interaction. Conclusions : EMs might begin with the inflammatory response of the ectopic endometrium. Phagocytes played a key role in this process. The ectopic endometrium adhered to the abdominal wall with the help of the inflammation reaction, generated blood vessels, and finally transformed into growing lesions.

A long-term survival rat model of spinal cord ischemia injury: Thoracic aortic occlusion combined with aortic bypass circulation

Vascular ◽  
2021 ◽  
pp. 170853812110601
Author(s):  
Cheng-yong Yin ◽  
Jun-jie Fei ◽  
Yu-yin Duan ◽  
Ke Yang ◽  
Xin Li ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Treatment Group ◽  
Thoracic Aorta ◽  
Aortic Occlusion ◽  
Control Group ◽  
Sham Operation ◽  
Term Survival ◽  
Sham Operation Group ◽  
Aortic Bypass ◽  
Operation Group

Objective This study aims to investigate the methods for rat spinal cord ischemia injury models with a high long-term survival rate. Methods The rats were divided into three groups: the treatment group, the control group, and the sham operation group. The treatment group had a blocked thoracic aorta (landing zone 3 by Ishimaru – T11) + aortic bypass circulation for 20 min. In the control group, the thoracic aorta at the landing zone 3 was blocked for 20 min. In the sham operation group, only thoracotomy without thoracic aortic occlusion was performed. The mean arterial blood pressure (MABP) of the thoracic aorta and caudal artery before and after thoracic aortic occlusion was monitored intraoperatively. Spinal cord function was monitored by a transcranial motor evoked potential (Tc-MEP) during the operation. Spinal cord function was evaluated by the BBB scale (Basso, Beattie, & Bresnahan locomotor rating scale) scores at multiple postoperative time points. The spinal cord sections of the rats were observed for 7 days after surgery, and the survival curves were analyzed for 28 days after surgery. Results After aortic occlusion, the MABP of thoracic aorta decreased to 6% of that before occlusion, and the MABP of caudal artery decreased to 63% of that before occlusion in the treatment group. In the control group, the MABP of both thoracic aorta and caudal artery decreased to 19% of that before occlusion. The Tc-MEP waveform of the treatment group disappeared after 6 min, and that of the control group disappeared after 8 min until the end of surgery. There was no change in the Tc-MEP waveform in the sham operation group. The BBB score of the treatment group decreased more obviously than the control group, and there was a significant difference. There was no decrease in the sham group. Spinal cord sections showed a large number of degeneration and necrosis of neurons, infiltration of inflammatory cells, and proliferation of surrounding glial cells in the treatment group. In the control group, multiple neurons were necrotic. The histology of the sham operation group was normal. The 28-day survival rate of the treatment group was 73.3%, which was higher than the control group (40.0%), and there was a significant difference ( p < 0.05). Conclusion Thoracic aortic occlusion combined with aortic bypass is an effective modeling method for rats with accurate modeling effects and high long-term survival rates.

scholarly journals In Vivo Analysis of the Biocompatibility and Bone Healing Capacity of a Novel Bone Grafting Material Combined with Hyaluronic Acid

2021 ◽  
Vol 22 (9) ◽  
pp. 4818
Author(s):  
Annica Pröhl ◽  
Milijana Batinic ◽  
Said Alkildani ◽  
Michael Hahn ◽  
Milena Radenkovic ◽  
...  
Keyword(s):  
Bone Substitute ◽  
Sham Operation ◽  
Bone Substitute Material ◽  
Water Binding ◽  
Sham Operation Group ◽  
Operation Group ◽  
Substitute Material ◽  
Tissue Reactions ◽  
Inflammatory Tissue

The present in vivo study analyses both the inflammatory tissue reactions and the bone healing capacity of a newly developed bone substitute material (BSM) based on xenogeneic bone substitute granules combined with hyaluronate (HY) as a water-binding molecule. The results of the hyaluronate containing bone substitute material (BSM) were compared to a control xenogeneic BSM of the same chemical composition and a sham operation group up to 16 weeks post implantationem. A major focus of the study was to analyze the residual hyaluronate and its effects on the material-dependent healing behavior and the inflammatory tissue responses. The study included 63 male Wistar rats using the calvaria implantation model for 2, 8, and 16 weeks post implantationem. Established and Good Laboratory Practice (GLP)-conforming histological, histopathological, and histomorphometrical analysis methods were conducted. The results showed that the new hyaluronate containing BSM was gradually integrated within newly formed bone up to the end of the study that ended in a condition of complete bone defect healing. Thereby, no differences to the healing capacity of the control BSM were found. However, the bone formation in both groups was continuously significantly higher compared to the sham operation group. Additionally, no differences in the (inflammatory) tissue response that was analyzed via qualitative and (semi-) quantitative methods were found. Interestingly, no differences were found between the numbers of pro- and anti-inflammatory macrophages between the three study groups over the entire course of the study. No signs of the HY as a water-binding part of the BSM were histologically detectable at any of the study time points, altogether the results of the present study show that HY allows for an optimal material-associated bone tissue healing comparable to the control xenogeneic BSM. The added HY seems to be degraded within a very short time period of less than 2 weeks so that the remaining BSM granules allow for a gradual osteoconductive bone regeneration. Additionally, no differences between the inflammatory tissue reactions in both material groups and the sham operation group were found. Thus, the new hyaluronate containing xenogeneic BSM and also the control BSM have been shown to be fully biocompatible without any differences regarding bone regeneration.

Changes in adiponectin expression in acute myocardial infarction rats and the significance of bisoprolol intervention

2011 ◽  
Vol 89 (2) ◽  
pp. 109-115 ◽  
Author(s):  
Song Zhang ◽  
Ben He ◽  
Steven Goldstein ◽  
Junbo Ge ◽  
Zuyue Wang ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Acute Myocardial Infarction ◽  
Protein Expression ◽  
Reverse Transcriptase ◽  
Rat Model ◽  
Protective Factor ◽  
Sham Operation ◽  
Rt Pcr ◽  
Sham Operation Group ◽  
Operation Group

The aims of this study were to explore the changes in expression of myocardial adiponectin (APN), changes in serum APN, and the significance of bisoprolol intervention in acute myocardial infarction (AMI) rats. An AMI rat model was established for the purposes of this study and was used for analysis of serum APN as determined by ELISA. Changes in expression of myocardial APN mRNA and APN protein in AMI rats were determined via reverse transcriptase (RT)–PCR and immunohistochemistry. Serum APN concentration and APN protein expression of the myocardium decreased significantly in the AMI groups compared with the sham operation group, with the lowest serum APN and APN protein expression on day 7 after AMI. On days 7 and 10 after AMI, the expression of myocardial APN mRNA in the AMI groups decreased significantly compared with the sham operation group. However, the APN mRNA increased on day 10 compared with that on day 7. Notably, there was an increase in levels of serum APN and myocardial APN expression after bisoprolol intervention. The expression of myocardial APN and serum APN decreased in AMI rats. APN may be an important protective factor against AMI. Bisoprolol can also protect against AMI because it increases APN expression.

Effect of Sirtuin1 (Sirt1) on Bone Marrow Mesenchymal Stem Cells (BMSCs) Osteogenesis/Adipogenesis via β-Catenin/The Transcription Factor T Cell Factor 1 (TCF1)/Runt-Related Transcription Factor 2 (RUNX2)

2021 ◽  
Vol 11 (10) ◽  
pp. 2070-2075
Author(s):  
Wenji Shi ◽  
Mingxing Zhao ◽  
Guangxia Shi
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Adipogenic Differentiation ◽  
Sham Operation ◽  
Runx2 Expression ◽  
Sham Operation Group ◽  
Marrow Mesenchymal Stem Cells ◽  
Operation Group ◽  
Sirna Group

Bone marrow mesenchymal stem cells (BMSCs) have self-renewal potential. Sirt1 regulates cell differentiation and apoptosis. However, Sirt1’s effect on BMSCs osteogenic/adipogenic differentiation has not been fully elucidated. SD rats were randomly divided into Osteoporosis (OP) group and sham operation group. OP rat BMSCs were isolated and assigned into control group, NC group and Sirt1 siRNA group followed by analysis of Sirt1 level by Real-time PCR, cell proliferation by MTT assay, expression of OC, OPN and FABP4 level by real time PCR, and β-Catenin/TCF1/Runx2 protein expression by Western blot. In OP group, Sirt1 expression was significantly increased and BMSCs proliferation was decreased along with reduced OC and OPN mRNA expression, increased FABP4 expression and reduced β-Catenin/TCF1/Runx2 expression compared with sham operation group (P < 0.05). In Sirt1 siRNA group, Sirt1 expression was significantly reduced, BMSCs proliferation was increased, OC and OPN mRNA expression was increased, FABP4 expression was decreased, and β-Catenin/TCF1/Runx2 expression was increased compared to OP group (P < 0.05). Sirt1 is increased in osteoporosis. Down-regulating Sirt1 in osteoporotic BMSCs can regulate β-Catenin/TCF1/Runx2 signaling and promote BMSCs osteogenic differentiation and inhibit adipogenic differentiation.

scholarly journals Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 29-40 ◽  
Author(s):  
Sten Anslan ◽  
R. Henrik Nilsson ◽  
Christian Wurzbacher ◽  
Petr Baldrian ◽  
Leho Tedersoo ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Computation Time ◽  
Potential Effect ◽  
Data Sets ◽  
Sequencing Data ◽  
Operational Taxonomic Units ◽  
High Throughput Sequencing Data ◽  
Recent Developments

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

scholarly journals Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 83-90 ◽  
Author(s):  
Yan Guo ◽  
Yulin Dai ◽  
Hui Yu ◽  
Shilin Zhao ◽  
David C. Samuels ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals Accurate fetal variant calling in the presence of maternal cell contamination

2019 ◽  
Author(s):  
Elena Nabieva ◽  
Satyarth Mishra Sharma ◽  
Yermek Kapushev ◽  
Sofya K. Garushyants ◽  
Anna V. Fedotova ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Chorionic Villus ◽  
Genetic Diagnosis ◽  
Variant Calling ◽  
Data Availability ◽  
Training Data ◽  
Sequencing Data ◽  
Maternal Cell ◽  
Fetal Dna

AbstractHigh-throughput sequencing of fetal DNA is a promising and increasingly common method for the discovery of all (or all coding) genetic variants in the fetus, either as part of prenatal screening or diagnosis, or for genetic diagnosis of spontaneous abortions. In many cases, the fetal DNA (from chorionic villi, amniotic fluid, or abortive tissue) can be contaminated with maternal cells, resulting in the mixture of fetal and maternal DNA. This maternal cell contamination (MCC) undermines the assumption, made by traditional variant callers, that each allele in a heterozygous site is covered, on average, by 50% of the reads, and therefore can lead to erroneous genotype calls. We present a panel of methods for reducing the genotyping error in the presence of MCC. All methods start with the output of GATK HaplotypeCaller on the sequencing data for the (contaminated) fetal sample and both of its parents, and additionally rely on information about the MCC fraction (which itself is readily estimated from the high-throughput sequencing data). The first of these methods uses a Bayesian probabilistic model to correct the fetal genotype calls produced by MCC-unaware HaplotypeCaller. The other two methods “learn” the genotype-correction model from examples. We use simulated contaminated fetal data to train and test the models. Using the test sets, we show that all three methods lead to substantially improved accuracy when compared with the original MCC-unaware HaplotypeCaller calls. We then apply the best-performing method to three chorionic villus samples from spontaneously terminated pregnancies.Code and training data availabilityhttps://github.com/bazykinlab/ML-maternal-cell-contamination

scholarly journals HTSeq - A Python framework to work with high-throughput sequencing data

2014 ◽  
Author(s):  
Simon Anders ◽  
Paul Theodor Pyl ◽  
Wolfgang Huber
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rapid Development ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
Sequencing Data ◽  
Standard Work ◽  
Data Formats ◽  
High Throughput Sequencing Data ◽  
Python Package

Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed. Results: We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data such as genomic coordinates, sequences, sequencing reads, alignments, gene model information, variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. Availability: HTSeq is released as open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index, https://pypi.python.org/pypi/HTSeq

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