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Figure 4 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 4 Results of gyrB gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–26: positive samples of size 222 bp; Well 27: negative control; Well 28: positive control of Pseudomonas aeruginosa PTCC 17589.

Figure 6 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 6 Results of exoT gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–36: positive samples of size 471 bp; Well 37: negative control; Well 38: positive control of Pseudomonas aeruginosa PTCC 17589.

Figure 5 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 5 Results of rhlR gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 50 bp; Well 2–26: positive samples of size 133 bp; Well 27: negative control; Well 28: positive control of Pseudomonas aeruginosa PTCC 17589.

Figure 18 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 18 The expression rates of MexB gene in the gold nanoparticles-treated samples and non-treated samples; a significant decrease in gene expression was observed between treated and non-treated samples in comparison with the control group. The G74 gene was used as an internal control.

Figure 15 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 15 Melting curve analysis to ensure the specificity of the amplified fragments of the MexB gene that the measured curves of the gene in all samples are consistent and single-peaked.

Figure 17 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 17 The expression rates of MexA gene in the gold nanoparticles-treated samples and non-treated samples; a significant decrease in gene expression was observed between treated and non-treated samples in comparison with the control group. The G74 gene was used as an internal control.

Figure 14 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 14 Melting curve analysis to ensure the specificity of the amplified fragments of the MexA gene; the measured curves of the gene in all samples are consistent and in the form of single-peak.

Figure 10 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 10 Percentage of Pseudomonas aeruginosa isolates carrying gyrB, rhlR, exoT, lasR, Pela, and toxA.

Figure 16 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 16 Melting curve analysis to ensure the specificity of the amplified fragments of the MexB gene; the measured curves of the gene in all samples are consistent and in the form of single-peak.

Figure 11 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 11 Results of MexA gene replication in clinical isolates of Pseudomonas aeruginosa. Well 1: marker size 1 kb; Well 2–8: positive samples of size 316 bp; Well 9: positive control of Pseudomonas aeruginosa PTCC 17589.

Figure 12 from: Dorri K, Modaresi F, Shakibaie MR, Moazamian E (2022) Effect of gold nanoparticles on the expression of efflux pump mexA and mexB genes of Pseudomonas aeruginosa strains by Quantitative real-time PCR. Pharmacia 69(1): 125-133. https://doi.org/10.3897/pharmacia.69.e77608

Figure 12 Results of MexB gene replication in clinical isolates of Pseudomonas aeruginosa. Well 6: marker size 1 kb; Well 1–5 and 8–12: positive samples of size 244 bp; Well 7: positive control of Pseudomonas aeruginosa PTCC 17589.

opencc-zeroFeb 2022View details →

Elevated expression of TUBA1C in breast cancer predicts poor prognosis

α1C-tubulin (TUBA1C) is a member of the α-tubulin family and has served as a potential biomarker in a variety of cancers in many studies. In this study, the gene expression profile of TUBA1C in The Cancer Genome Atlas (TCGA) was extracted for analysis, and the prognostic value of TUBA1C in breast cancer was comprehensively evaluated. The Wilcoxon signed-rank test, Kruskal-Wallis test, and logistic regression analysis were performed to confirm the correlations between TUBA1C expression and the clinical characteristics of breast cancer patients. The effect of TUBA1C expression on the survival of breast cancer patients was assessed by Kaplan-Meier curve, Cox regression analysis, and the Kaplan-Meier plotter (an online database). The TCGA data set was used for the Gene Set Enrichment Analysis (GSEA). The results confirmed that high TUBA1C expression in breast cancer was closely correlated with survival time, survival status, and tumor size. In addition, elevated TUBA1C expression can predict poor overall survival (OS), recurrence-free survival (RFS), and distant metastasis-free survival (DMFS). Univariate and multivariate analyses (Cox regression analyses) confirmed that TUBA1C was an independent prognostic factor for the OS of breast cancer patients. The GSEA identified that the high TUBA1C expression phenotype was differentially enriched in cell cycle, basal transcription factor, P53 signaling pathway, pathways in cancer, TOLL-like receptor signaling pathway, and NOD-like receptor signaling pathway. In summary, high messenger RNA (mRNA) expression of TUBA1C is an independent risk factor for poor prognosis of breast cancer.

opencc-zeroMar 2022View details →

mRNA expression analysis of the hippocampus in a Vervet monkey model of FASD

The vervet monkey (Chlorocebus aethiops) has proven to be an invaluable tool for researching voluntary alcohol ingestion and the sequelae that can arise from such behaviour. In this study, a vervet monkey model for fetal alcohol spectrum disorder was generated by providing a cohort of alcohol preferring, pregnant dams the option to ingest alcohol between gestational days 90-165 with a corresponding sucrose matched control group. Subsequently, gene expression analysis of the hippocampus was contrasted at 5 months and 2 years using the GeneChip Rhesus Macaque Genome Array in a 2x2 study design which interrogated two independent variables, Age and Alcohol consumption. The analysis identified a global downregulation of expression when interrogating Alcohol as a main effect with a relative balance of upregulation and downregulation using Age as a main effect. Functional annotation of both independent variables was performed with Alcohol generating broad functional annotation clusters which could implicate an epigenetic role in downregulation, while Age reliably produced functional annotation clusters predominantly related to development. Furthermore, our data reveal a novel connection between EFNB1 and FASD which is highly plausible given its role in development as well as its central role in craniofrontal nasal syndrome (CFNS).

Paired blood-brain gene expression data from GTEx (v8)

Transcriptomic dataset from the GTEx Project used for training BrainGENIE models

opencc-zeroMar 2022View details →

Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii)

Understanding wildlife diseases' effects on populations requires insight into local environmental conditions, host defence mechanisms, host life-history trade-offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils' capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils' immune system. By using RT-qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex eco-evolutionary interactions of not only conventional host-parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.

openMar 2022View details →

Characterization of molecular toolkits for the control of gene expression in E. coli and E. coli-based cell-free expression system

This dataset shows the characterization of 4 genetic elements designed to control gene expression in prokaryotic systems. DNA sequences carrying inducible promoters were rationally designed based on existing regulatory elements. Through fluorescent reporters, gene expression in the presence and absence of small regulatory molecules was followed over a time frame of 20 hours. The kinetics were followed in two settings: in vivo within E. coli cells and in vitro using cell-free systems derived from E. coli cell extracts. Finally, possible interferences among regulatory elements were evaluated following the expression of paired transcription and translation units carrying two different reporter genes under the control of different regulatory elements.

opencc-by-4.0Apr 2022View details →

Avian auditory hair cell regeneration is accompanied by JAK/STAT-dependent expression of immune-related genes in supporting cells

Normalized log count matrix and single cell experiment container

opencc-zeroDec 2012View details →

Data from: Extracellular matrix-associated gene expression in adult sensory neurons cultured on laminin substrates

Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.

opencc-zeroJul 2022View details →

RNA-seq based expression of DEGs in roots and leaves of bread wheat

RNA from roots and leaves of twenty eight bread wheat genotypes was extracted, purified, quantified and sent to Beijing Genomics Institute (BGI) for sequencing. Briefly, mRNAs were isolated and fragmented from total RNA using the oligo (dT) method for cDNA synthesis. The 75-bp single-end sequencing libraries were constructed, and sequencing was performed on HiSeq X Ten (Illumina, San Diego, USA) using standard protocols. Adapters with unknown bases (N's > 5%) and low quality were removed from raw reads to produce 'clean data' as FastQ data files using a quality control software, SOAPnuke version 2.1.6. High quality single-end reads were mapped to the bread wheat reference genome (IWGSC, INSDC Assembly <a href="http://www.ebi.ac.uk/ena/data/view/GCA_900519105.1" rel="noopener">GCA_900519105.1</a>) using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software version 2.2.1. Alignment of the reference sequence with reads were performed using Bowtie. Quantification of the reads was performed using featureCounts software program. Differentially expressed genes (DEGs) were identified using DeSEQ2 in R version 4.1.1. DEGs were then filtered based on their adjusted p-value. A total of 120744 DEGs were identified with varying expression in roots and leaves. The threshold value for filtering was set at 0.1.