Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.

Additional file 6. The collected transcriptome analysis data.

Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

Epidermal growth factor receptor (EGFR) is a promising target for the treatment of different types of malignant tumors. Therefore, a combined molecular modeling study was performed on a series of quinazoline derivatives as EGFR inhibitors. The optimum ligand-based CoMFA and CoMSIA models showed reliable and satisfactory predictability (with R2cv=0.681, R2ncv=0.844, R2pred=0.8702 and R2cv=0.643, R2ncv=0.874, R2pred=0.6423). The derived contour maps provide structural features to improve inhibitory activity. Furthermore, the contour maps, molecular docking, and molecular dynamics...

Prenatal stress is a pressing issue. However, there is a lack of robust evidence for psychosocial interventions to manage this problem. This study aimed to examine the effectiveness of a mindfulness-based intervention on reducing prenatal stress compared to participation in health education groups. A randomized controlled trial was conducted in a prenatal clinic of comprehensive tertiary care from April to October 2017. A total of 108 pregnant women were randomly assigned to an intervention or...

Metformin, a common clinical drug used to treat diabetes mellitus, is found with potential antiobese actions as reported in increasing evidences. However, the detailed mechanisms of metformin-antiobesity-related hypertension remain unrevealed. We have utilized the bioinformatics strategy, including network pharmacology and molecular docking analyses, to uncover pharmacological targets and molecular pathways of bioactive compounds against clinical disorders, such as cancers, coronavirus disease 2019. In this report, the in-silico approaches using network pharmacology and molecular docking was...

Environmentally, bisphenol A (BPA) is a well-known pollutant caused human health risk, including osteosarcoma (OS). OS, a deadly bone neoplasia, may occur in children and adults. However, the anti-OS pharmacotherapy prescribes limitedly in clinical practice. Interestingly, previous experimental evidences indicate calycosin-exerting potential anti-OS actions. Thus, in this report, we aimed to further characterize and detail the therapeutic targets and molecular mechanisms of calycosin-anti-BPA-related OS by using network pharmacology and molecular docking analyses. In results, the...

Cells of the tumor microenvironment exert a vital influence on sarcoma prognosis. This study aimed to analyze and identify differentially expressed genes (DEGs) related to immunity and their significance as immune biomarkers for the accurate prediction of overall survival of patients with sarcoma. The Cancer Genome Atlas was adopted for obtaining sarcoma gene microarray and corresponding clinical information. ESTIMATE algorithm was used to calculate tumor immune microenvironment indices. Immune-associated DEGs were identified using the limma...

Warburg phenomenon refers to the development of unique metabolic patterns during the growth of tumor cells. This study stratified gastric cancer into prognostic metabolic subgroups according to changes in gene expressions related to glycolysis and cholesterol synthesis. The RNA-seq expression data, single nucleotide variants (SNV), short insertions and deletions (InDel) mutation data, copy number variation (CNV) data and clinical follow-up information data of gastric cancer tissues were downloaded from The Cancer Genome Atlas (TCGA) database....

Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.

Additional file 3. GO annotations of 196 conserved lncRNAs.

Additional file 6. The collected transcriptome analysis data.

Bacterial persistence is one of the major causes of antibiotic treatment failure and the step stone for antibiotic resistance. However, the mechanism by which persisters arise has not been well understood. Maintaining a dormant state to prevent antibiotics from taking effect is believed to be the fundamental mechanistic basis, and persisters normally maintain an intact cellular structure. Here we examined the morphologies of persisters in Acinetobacter baumannii survived from the treatment by three major classes...

Additional file 3. GO annotations of 196 conserved lncRNAs.

Aldosterone exerts an enormous function on proximal tubular cells (PTC) senescence, which is a common pathomechanism contributing to renal dysfunction. Numerous studies have shown that oxidative stress is deeply involved in the pathophysiologic processes of chronic kidney diseases. The study aims to investigate whether autophagy could regulate the process of senescence through oxidative stress in PTC both in vivo and ex vivo. Our results suggested that aldosterone treatment increased the senescence and oxidative stress as...

The current study aimed to investigate the effects of sodium butyrate on the level of colonic protein IRAK1 (interleukin-1 receptor-associated kinase 1) in irritable bowel syndrome (IBS) models as well as revealing the relationship between IRAKI level and visceral sensitivity during the progression of IBS. IBS symptoms were induced using TNBS (2,4,6-trinitrobenzene sulfonic acid) in mice and using IL-33 in HT-29 cells, which were then hanlded with sodium butyrate (100 mM for each mice and...

Previous studies have explored the association between protein-coding genes and microRNAs (miRNAs) in lung adenocarcinoma (LUAD). However, the influence of the miR-199a-3p/anterior gradient 2 (AGR2) axis in LUAD has not yet been fully explored. Therefore, this study aimed to examine the underlying roles of AGR2 and miR-199a-3p in the development of LUAD. The expression levels of miR-199a-3p and AGR2 in LUAD tissues and cells were detected via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A luciferase...

Additional file 2. Conserved lncRNAs ratios for each species.

Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

Abstract Background Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of lncRNAs. Therefore, the integration of large volumes of plant lncRNA data is required to deeply investigate the evolution of lncRNAs. Results We present a...

Abstract Background Long non-coding RNAs (lncRNAs) play vital roles in many important biological processes in plants. Currently, a large fraction of plant lncRNA studies center at lncRNA identification and functional analysis. Only a few plant lncRNA studies focus on understanding their evolutionary history, which is crucial for an in-depth understanding of lncRNAs. Therefore, the integration of large volumes of plant lncRNA data is required to deeply investigate the evolution of lncRNAs. Results We present a...

Cancer immunotherapy is a strategy that is moving to the frontier of cancer treatment in the current decade. In this study, we show evidence that 3-(2-nitrophenyl) propionic acid-paclitaxel nanoparticles (NPPA-PTX NPs), act as immunogenic cell death (ICD) inducers, stimulating an antitumor response which results in synergistic antitumor activity by combining anti-PD-L1 antibody (aPD-L1) in vivo. To investigate the antitumor immunity induced by NPPA-PTX NPs, the expression of both ICD marker calreticulin (CRT) and high mobility...

Aberrant chaperone-mediated autophagy (CMA) activation has been suggested as a tumorigenesis-promoting event in various cancers, although its roles in prostate cancer (PCa) remain elusive. Emerging evidence indicates that TPD52 isoform 1, a prostate-specific and androgen-responsive gene, contributes to the malignant progression of PCa. Here, we demonstrate that TPD52 enhances CMA activation by interacting with HSPA8/HSC70 and enhancing substrate degradation in PCa. Elevation of TPD52 is essential for CMA-induced PCa cell proliferation and stress resistance in...