Antifungal Activity and the Mechanism of Ozone Against Spoilage Molds, Such as Gibberella Intermedia and Aspergillus Ochraceus Isolated From Freshly-Peeled Garlic

Abstract The antibacterial effect and mechanism of ozone (O3) treatment on freshly-peeled garlic inoculated with Gibberella intermedia (G. intermedia) and Aspergillus ochraceus (A. ochraceus) in different conditions were studied in vivo. The results showed that the specific O3 concentration, treatment time, and humidity significantly affected the garlic's indexes. The optimal treatment conditions of garlic inoculated with both molds were 6 ppm, 15 min, and 90%, respectively. After treatment with those conditions, the incidence etc of garlic were significantly reduced during storage. Differential analysis was performed for the RNA-sequencing and gene expression of the molds subjected to O3 treatment, as well as the samples that were not. The results showed that O3 treatment inhibited the growth of G. intermedia and A. ochraceus. Consequently, 2754 and 2378 differentially expressed genes, 1456 and 1591 up-regulated genes, and 1298 and 787 down-regulated genes were screened, respectively, for these molds, affecting the catalytic activity and various other pathways.

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Single-cell Bottlenecks and Dead-ends During Glioma Premalignancy

10.1101/2020.03.30.017228 ◽

2020 ◽

Cited By ~ 2

Author(s):

Matthew D. Sutcliffe ◽

Rui P. Galvao ◽

Lixin Wang ◽

Jungeun Kim ◽

Shambhavi Singh ◽

...

Keyword(s):

Gene Expression ◽

Mouse Model ◽

Rna Sequencing ◽

Replication Stress ◽

Fluctuation Analysis ◽

Global Changes ◽

Differential Analysis ◽

Cell Of Origin ◽

Cell State ◽

Genetically Engineered Mouse Model

AbstractCancer evolves from premalignant clones that accumulate mutations and adopt unusual cell states to achieve transformation. Tracking a cancer cell-of-origin through the cell-state alterations of premalignancy could provide clues for early-detection and cancer-prevention strategies. Previously we pinpointed the oligodendrocyte precursor cell (OPC) as a cell-of-origin for glioma. However, the early adaptations and cell-state changes of mutant OPCs during premalignancy are unknown. Using a genetically engineered mouse model (GEMM) of inducible Nf1–Trp53 loss in OPCs, we acutely isolated labeled mutant OPCs by laser-capture microdissection and determined gene-expression changes in two ways: global changes in gene expression were measured by differential analysis of wild-type and mutant OPCs after bulk RNA sequencing; cell-to-cell state variations were identified by a fluctuation analysis, called stochastic profiling, which uses RNA-sequencing measurements from random pools of 10 mutant cells. We chose two time points for the analysis. At 12 days after Nf1–Trp53 deletion, while bulk differences were mostly limited to increases in mitotic hallmarks and decreases in ribosome biosynthesis, stochastic profiling of mutant OPCs revealed a spectrum of stem-progenitor, proneural, and mesenchymal states as potential starting points for gliomagenesis. At 90 days after Nf1–Trp53 deletion, while bulk sequencing detected very few differentially expressed transcripts, stochastic profiling revealed multiple cell states that are absent from glial tumors, suggesting that they marked dead-ends for gliomagenesis. In parallel, we identified cells without dead-end markers but abundantly expressing key effectors of nonsense-mediated decay and homology-dependent DNA repair. This suggests that resolution of replication stress may pose a considerable bottleneck for glioma initiation in premalignant mutant OPCs.Statement of significanceIn situ heterogeneity profiling of cell states in a mouse model of glioma uncovers regulatory confusion in a glioma cell-of-origin and defines a state of replication stress that precedes tumor initiation.

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Unexpected variability of allelic imbalance estimates from RNA sequencing

10.1101/2020.02.18.948323 ◽

2020 ◽

Cited By ~ 1

Author(s):

Asia Mendelevich ◽

Svetlana Vinogradova ◽

Saumya Gupta ◽

Andrey A. Mironov ◽

Shamil Sunyaev ◽

...

Keyword(s):

Gene Expression ◽

Rna Sequencing ◽

Allelic Imbalance ◽

Experimental Methods ◽

Specific Gene ◽

Differential Analysis ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific ◽

Noise Models

RNA sequencing and other experimental methods that produce large amounts of data are increasingly dominant in molecular biology. However, the noise properties of these techniques have not been fully understood. We assessed the reproducibility of allele-specific expression measurements by conducting replicate sequencing experiments from the same RNA sample. Surprisingly, variation in the estimates of allelic imbalance (AI) between technical replicates was up to 7-fold higher than expected from commonly applied noise models. We show that AI overdispersion varies substantially between replicates and between experimental series, appears to arise during the construction of sequencing libraries, and can be measured by comparing technical replicates. We demonstrate that compensation for AI overdispersion greatly reduces technical variation and enables reliable differential analysis of allele-specific expression across samples and across experiments. Conversely, not taking AI overdispersion into account can lead to a substantial number of false positives in analysis of allele-specific gene expression

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Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies

Animals ◽

10.3390/ani11010080 ◽

2021 ◽

Vol 11 (1) ◽

pp. 80

Author(s):

Xin Li ◽

Chenying Duan ◽

Ruyi Li ◽

Dong Wang

Keyword(s):

Gene Expression ◽

Semen Quality ◽

Regulation Of Gene Expression ◽

Physiological Mechanism ◽

Interaction Network ◽

Seminiferous Tubules ◽

Differential Analysis ◽

Epididymal Sperm ◽

Bioinformatics Analyses ◽

Acrosome Formation

To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment, protein–protein interaction network (PPI network), and bioinformatics analyses were performed to uncover the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, and glycosylation, and the functional ART3 gene may play important roles during spermiogenesis. Therefore, its localisation in the seminiferous tubules and epididymal sperm were investigated using immunofluorescent analysis, and its structure and function were also predicted. Our findings provide a deeper understanding of the process of spermiogenesis, which involves acrosome formation, histone replacement, and the fine regulation of gene expression.

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Integrated single‐cell RNA sequencing analyses suggest developmental paths of cancer‐associated fibroblasts with gene expression dynamics

Clinical and Translational Medicine ◽

10.1002/ctm2.487 ◽

2021 ◽

Vol 11 (7) ◽

Author(s):

Hee Chul Chung ◽

Eun Jeong Cho ◽

Hyeonjin Lee ◽

Won‐Kyung Kim ◽

Ji‐Hye Oh ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Rna Sequencing ◽

Cancer Associated Fibroblasts ◽

Single Cell Rna Sequencing ◽

Gene Expression Dynamics

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The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽

10.1186/s12885-019-6363-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Michal Marczyk ◽

Chunxiao Fu ◽

Rosanna Lau ◽

Lili Du ◽

Alexander J. Trevarton ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Rna Sequencing ◽

Rna Extraction ◽

Formalin Fixed Paraffin ◽

Ffpe Samples ◽

Formalin Fixed Paraffin Embedded ◽

The Impact ◽

Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

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SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

Genome Biology ◽

10.1186/s13059-017-1200-8 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 32

Author(s):

Yuchao Jiang ◽

Nancy R. Zhang ◽

Mingyao Li

Keyword(s):

Gene Expression ◽

Single Cell ◽

Rna Sequencing ◽

Specific Gene ◽

Specific Gene Expression ◽

Scale Modeling ◽

Single Cell Rna Sequencing ◽

Allele Specific

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Receptor-driven invasion profiles in diffuse intrinsic pontine glioma (DIPG)

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab039 ◽

2021 ◽

Author(s):

Anju Karki ◽

Noah E Berlow ◽

Jin-Ah Kim ◽

Esther Hulleman ◽

Qianqian Liu ◽

...

Keyword(s):

Gene Expression ◽

Growth Factor ◽

Protein Expression ◽

Cell Viability ◽

Rna Sequencing ◽

Cell Invasion ◽

Growth Factor Receptor ◽

Diffuse Intrinsic Pontine Glioma ◽

Sequencing Data ◽

Pontine Glioma

Abstract Background Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric cancer with unmet clinical need. DIPG is invasive in nature, where tumor cells interweave into the fiber nerve tracts of the pons making the tumor unresectable. Accordingly, novel approaches in combating the disease is of utmost importance and receptor-driven cell invasion in the context of DIPG is under-researched area. Here we investigated the impact on cell invasion mediated by PLEXINB1, PLEXINB2, platelet growth factor receptor (PDGFR)α, PDGFRβ, epithelial growth factor receptor (EGFR), activin receptor 1 (ACVR1), chemokine receptor 4 (CXCR4) and NOTCH1. Methods We used previously published RNA-sequencing data to measure gene expression of selected receptors in DIPG tumor tissue versus matched normal tissue controls (n=18). We assessed protein expression of the corresponding genes using DIPG cell culture models. Then, we performed cell viability and cell invasion assays of DIPG cells stimulated with chemoattractants/ligands. Results RNA-sequencing data showed increased gene expression of receptor genes such as PLEXINB2, PDGFRα, EGFR, ACVR1, CXCR4 and NOTCH1 in DIPG tumors compared to the control tissues. Representative DIPG cell lines demonstrated correspondingly increased protein expression levels of these genes. Cell viability assays showed minimal effects of growth factors/chemokines on tumor cell growth in most instances. Recombinant SEMA4C, SEM4D, PDGF-AA, PDGF-BB, ACVA, CXCL12 and DLL4 ligand stimulation altered invasion in DIPG cells. Conclusions We show that no single growth factor-ligand pair universally induces DIPG cell invasion. However, our results reveal a potential to create a composite of cytokines or anti-cytokines to modulate DIPG cell invasion.

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