Journal: Nucleic Acids Research

Article Title: Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

doi: 10.1093/nar/gkn899

Figure Lengend Snippet: Schematic of the CLADE approach. CLADE as utilized in this study starts at the top of the schematic with an initial choice of DNA sequences. These sequences may be generated entirely in silico , or optionally, as with some of the sequences here, utilizing prior knowledge generated in vitro . These sequences are synthesized on a custom microarray and bound with the chosen ligand, here the APC protein. Analysis of binding intensities gives a distribution of fitnesses; the frequency distribution of Generation 1 binding to APC protein is shown by way of example. Some of these sequences are selected in silico , based on the in vitro score distribution, here using tournament selection (see Materials and methods section). These sequences are then mutated in silico to generate a new sequence set which can then be synthesised in vitro , and so on round the cycle as often as is required. The final aptamer set offers a greatly increased binding affinity to the ligand.

Article Snippet: Image analysis used Combimatrix Microarray Imager ( https://webapps.combimatrix.com/customarray/customarrayHome.jsp ).

Techniques: Generated, In Silico, In Vitro, Synthesized, Microarray, Protein Binding, Binding Assay, Selection, Sequencing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Estrogen-induced FXR1 promotes endocrine resistance and bone metastasis in breast cancer via BCL2 and GPX4

doi: 10.3389/fcell.2025.1563353

Figure Lengend Snippet: Screening of estrogen-regulated mRBPs in ER+ breast cancer. (a) , The schematic of iTRAQ quantitative proteomics. MCF-7 cells were treated with 10 nM estrogen for 48 h after 6 days of estrogen deprivation. (b) , Heat map representation of the 302 mRBP gene ratios (Treat/Control) in the iTRAQ quantitative proteomics. Each group represents three independent experiments. (c) , The heatmap plotted the relative expression levels of 612 mRBPs in tamoxifen-resistant(R) and parental(S) MCF-7 cells. (d) , Schematic diagram of 11 potential mRBPs in breast cancer. The left circle shows 100 proteins upregulated in quantitative proteomics. The right circle shows 100 genes upregulated in tamoxifen-resistant cells. (e) , Kaplan–Meier plots of RFS in breast cancer patients with different levels of FXR1 expression. (f) , Correlation analysis of FXR1 and ESR1 in TCGA ER+ breast cancer samples by GEPIA 2. (g, h) , Kaplan–Meier plots of RFS in ER+ (g) and ER- (h) patients with different levels of FXR1 expression. (i), Expression levels of FXR1, FMR1, and FXR2 in normal tissue (n = 291) and tumor tissue (n = 1,085) were analyzed by GEPIA 2. (j) , Protein levels of FXR1 in different cancers (tumor and normal samples). (k) , IHC staining of FXR1 of the representative patients in breast cancer tissue microarray. Scale bar: 500 μm (5✕), 100 μm (20✕). (l) , IHC H-scores of FXR1 in breast normal and tumor sections. (m) , IHC H-scores of FXR1 in ER+ and ER- breast tumor sections. Results are shown as mean ± S.D. *P < 0.05; **P < 0.01; ***P < 0.001; ns not significant (Unpaired two-tailed Student’s t test).

Article Snippet: The tissue microarray (ZL-BrcSur180) was obtained from Zhuoli Biotechnology Co., Ltd. (Shanghai, China), and detailed patient information is listed in .

Techniques: Multiplex sample analysis, Quantitative Proteomics, Control, Expressing, Immunohistochemistry, Microarray, Two Tailed Test

Journal: PLoS ONE

Article Title: Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

doi: 10.1371/journal.pone.0060202

Figure Lengend Snippet: RT, ST, RI, SI, and YL represent the rhizome tip, shoot tip, rhizome internodes, shoot internodes, and young leaves, respectively. Expression levels were calculated based on the expression level of YL genes set to 1. Expression profiles obtained by real time PCR for one gene, Sb01g036550, were not consistent with data obtained from microarray analysis. Correlation coefficients (r) for the remaining 11 genes were 0.74, 0.74, 0.74, 0.74, 0.77, 0.74, 0.82, 0.76, 0.76, 0.94, and 0.76, from left to right, respectively. Bars donate standard deviation.

Article Snippet: RNA amplification, labeling, and hybridization, and microarray imaging were carried out by a specialized biotech company, CapitalBio Corporation (Beijing, China).

Techniques: Expressing, Real-time Polymerase Chain Reaction, Microarray, Standard Deviation

Journal: PLoS ONE

Article Title: Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

doi: 10.1371/journal.pone.0060202

Figure Lengend Snippet: In situ localization of transcripts corresponding to the genes (a) Sb01g047010 and (c) Sb06g028820 in S. propinquum rhizome tips are illustrated; (b) and (d) represent the sense probe for control. Corresponding microarray-based expression profiles of these two genes are also shown as bar graphs for comparison.

Article Snippet: RNA amplification, labeling, and hybridization, and microarray imaging were carried out by a specialized biotech company, CapitalBio Corporation (Beijing, China).

Techniques: In Situ, Control, Microarray, Expressing, Comparison

Journal: PLoS ONE

Article Title: Tissue-Specific Transcriptomic Profiling of Sorghum propinquum using a Rice Genome Array

doi: 10.1371/journal.pone.0060202

Figure Lengend Snippet: The heat map was produced by analyzing genes comprising rhizome related DEGs for methyl jasmonate (MJ), ethylene (C 2 H 4 ), abscisic acid (ABA), auxin (AUX), gibberellic acid (GA), zeatin, brassinosteroids (BR), and salicylic acid (SA). Subfigures a–g represent the seven gene sets analyzed: DEGs of RT vs. ST in O. longistaminata from (a) transcriptome sequencing and (c) microarray analysis, and (e) results of the present study in S. propinquum ; DEGs of underground tissues (RT and RI) vs. above-ground tissues (ST, SI, and YL) in O. longistaminata from (b) transcriptome sequencing and (d) microarray analysis, and (f) results of the present study in S. propinquum ; and (g) candidate rhizome-enriched genes in S. halepense (pSH) and S. propinquum . In the HORMONOMETER analysis, orange (1) = complete correlation, white (0) = no correlation, and blue (-1) = anti-correlation.

Article Snippet: RNA amplification, labeling, and hybridization, and microarray imaging were carried out by a specialized biotech company, CapitalBio Corporation (Beijing, China).

Techniques: Produced, Sequencing, Microarray