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  • We characterized single-cell transcriptional profiles of the cardiac non-myocyte cell pool in C57BL/6J mice. The cell preparation we sequenced consisted of metabolically active, nucleated non-myocyte cells from heart ventricles of female and male mice which were depleted of endothelial cells. The goals of this experiment included examining cellular diversity, identifying markers of understudied cell populations, exploring functional roles of different cell types, and characterizing sexual dimorphism in cardiac gene expression.
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  • We aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and intracellular metabolome during steady state in low- and high-producers of p-coumaric acid in two strain backgrounds, S288c or CEN.PK. For analysis of the differential gene expression, we did pairwise comparisons between the optimized and non-optimized strains for p-CA production: CEN.PK strains (ST4288 and ST4408) and the S288c strains (ST4353 and ST4397). Transcriptome analysis showed that the CEN.PK strain was less affected by engineering towards higher p-CA production than the S288c strain, as the number of significantly up-/down-regulated genes was correspondingly 652 and 1927 amongst others, strain S288c had downregulations in gene sets involved in amino acid and protein biosynthesis. This suggests that CEN.PK may be a better platform strain for production of aromatic compounds than the S288c strain.
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  • RNA-sequencing of twelve treatments: two cultivars (Embrapa 45 and BR 4), two oxygen conditions [fully aerobic state (normoxy) and hypoxic], and three treatment sampling times (0.5h, 4h, and 28h). For each of twelve treatments, equimolar quantities of purified total RNA from roots of twelve plants [three biological replicates (four plantlets per replicate)] were pooled to result one library. After processing the twelve libraries (poly-A purification, fractionation, cDNA synthesis using random primers, and ligation to bar-coded adapters), fragments of 150250 pb were isolated and multiplexed, resulting one sequencing library (a pooled of equimolar quantities from twelve initial libraries; each library with a specific barcode for further bioinformatic discrimination). Sequencing library was used to produce clusters for a 1 x 100 bp single end-sequencing run into one lane on a flow cell for sequencing in a Hi-Seq 2000 (Illumina).
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  • This experiment was designed to compare transcription profile between healthy controls and patients of rheumatoid arthritis.
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  • We have discovered that neutrophils that infiltrate the spinal cord of mice with EAE, a model of multiple sclerosis, but not intravascular neutrophils that crawl on the luminal endothelial surface, bear on their surface the adhesion molecule Icam1. The goal of this experiment was to use Icam1 to isolate these two neutrophil subpopulations in order to compare their transcriptomes and gain insights into their properties. To this end, EAE was induced in C57BL/6J mice by immunization with myelin oligodendrocyte glycoprotein (MOG) peptide (a.a. 35-55) and adjuvants (i.e. complete Freund’s adjuvant and pertussis toxin). On day 15 post-immunization, intravascular neutrophils (CD45hiCD11b+CD11c−Ly6g+Icam1−) and extravasated neutrophils (CD45hiCD11b+CD11c−Ly6g+Icam1+) were isolated from spinal cords by FACS. For comparison, we simultaneously isolated two other populations of myeloid cells: macrophages (CD45hiCD11b+CD11c−Ly6g−) and dendritic cells (CD45hiCD11b+CD11c+Ly6g−). RNA was analyzed in biological duplicate using Affymetrix GeneChip Mouse Gene 2.0 ST arrays.
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  • Here, we profiled transcription across the cell cycle in single human myxoid liposarcoma cells, without prior synchronization. Flourescence-activated cell sorting was used to infer G1, S or G2/M cell cycle stages after staining cells for DNA content. Single-cell RNA-sequencing was performed according to the Smart-seq2 protocol.
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  • Alveolar macrophages (AMs) are lung resident phagocytes. They derive from fetal liver monocytes, which colonize the lung during embryonic development and give rise to fully mature AMs perinatally. We have identified TGF- signaling as an indispensible regulator during this process. To analyze the impact of TGF- on the entire transcriptome of AMs, we performed RNA-seq on AMs deficient of Tgfbr2 in CD11cCre/+ Tgfbr2fl/fl mice at P3 with Tgfbr2fl/fl littermates as a control.
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  • While the toxicity of the main constituents of electronic cigarette (ECIG) liquids, nicotine, propylene glycol (PG), and vegetable glycerin (VG), has been assessed individually in separate studies, limited data on the inhalation toxicity of them is available when in mixtures. In this 90-day subchronic inhalation study, Sprague-Dawley rats were nose-only exposed to filtered air, nebulized vehicle (saline), or three concentrations of PG/VG mixtures, with and without nicotine. Standard toxicological endpoints were complemented by molecular analyses using transcriptomics, proteomics, and lipidomics. Compared with vehicle exposure, the PG/VG aerosols showed only very limited biological effects with no signs of toxicity. Addition of nicotine to the PG/VG aerosols resulted in effects in line with nicotine effects observed in previous studies, including up-regulation of xenobiotic enzymes (Cyp1a1/Fmo3) in the lung and metabolic effects, such as reduced serum lipid concentrations and expression changes of hepatic metabolic enzymes. No toxicologically relevant effects of PG/VG aerosols (up to 1.520mg PG/L + 1.890mg VG/L) were observed, and no adverse effects for PG/VG/nicotine were observed up to 438/544/6.7mg/kg/day. This study demonstrates how complementary systems toxicology analyses can reveal, even in the absence of observable adverse effects, subtoxic and adaptive responses to pharmacologically active compounds such as nicotine.
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  • The main constituents of electronic cigarette liquids are nicotine, propylene glycol (PG), and vegetable glycerin (VG), together with distilled water and flavors. To assess the toxicity of PG/VG mixtures with and without nicotine as basic components of liquids used in e-cigarettes, a 90-day rat inhalation study according to the Organization for Economic Co-operation and Development test guideline 413 was conducted. Sprague-Dawley (SD) rats were nose-only exposed, 6?h/day, 5 days/week to filtered air, or nebulized vehicle (saline), or three concentrations of PG/VG (0.174 mg PG/l + 0.210 mg VG/l; 0.520 mg PG/l + 0.630 mg VG/l; 1.520 mg PG/l + 1.890 mg VG/l) � with (test item) and without (reference item) 23 �g nicotine/L. Standard toxicological endpoints were complemented by molecular analyses using transcriptomics, proteomics, and lipidomics. Compared to vehicle exposure, the tested PG/VG aerosols showed only very limited biological effects with no signs of toxicity, both for the standard toxicological endpoints (e.g., histopathology, clinical chemistry) and the systems toxicological analyses (transcriptomics, proteomics, and lipidomics). The addition of nicotine to the PG/VG aerosols (23 �g/l) resulted in effects in line with nicotine effects in previous studies. These included up-regulation of xenobiotic enzymes (Cyp1a1 and Fmo3) in the lung and metabolic effects, e.g., reduction in serum lipid concentrations and changes in the expression of metabolic enzymes in the liver. Signs of a generalized stress response to nicotine exposure such as decreased thymus weights were observed; and likely, a subset of the observed metabolic alterations was interlinked with this generalized stress response. Under the conditions of this 90-day SD rat inhalation study, no toxicologically relevant effects of PG/VG aerosols (up to 1.520 mg PG/l + 1.890 mg VG/l) were observed, and the no observed adverse effect level (NOAEL) for PG/VG/nicotine was determined to be 438/544/6.7 mg/kg/day. Further the study demonstrated how complementary systems toxicology analyses can reveal, also in the absence of observable adverse effects, subtoxic and adaptive responses to pharmacologically active compounds such as nicotine.
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  • The main constituents of electronic cigarette liquids are nicotine, propylene glycol (PG), and vegetable glycerin (VG), together with distilled water and flavors. To assess the toxicity of PG/VG mixtures with and without nicotine as basic components of liquids used in e-cigarettes, a 90-day rat inhalation study according to the Organization for Economic Co-operation and Development test guideline 413 was conducted. Sprague-Dawley (SD) rats were nose-only exposed, 6?h/day, 5 days/week to filtered air, or nebulized vehicle (saline), or three concentrations of PG/VG (0.174 mg PG/l + 0.210 mg VG/l; 0.520 mg PG/l + 0.630 mg VG/l; 1.520 mg PG/l + 1.890 mg VG/l) � with (test item) and without (reference item) 23 �g nicotine/L. Standard toxicological endpoints were complemented by molecular analyses using transcriptomics, proteomics, and lipidomics. Compared to vehicle exposure, the tested PG/VG aerosols showed only very limited biological effects with no signs of toxicity, both for the standard toxicological endpoints (e.g., histopathology, clinical chemistry) and the systems toxicological analyses (transcriptomics, proteomics, and lipidomics). The addition of nicotine to the PG/VG aerosols (23 �g/l) resulted in effects in line with nicotine effects in previous studies. These included up-regulation of xenobiotic enzymes (Cyp1a1 and Fmo3) in the lung and metabolic effects, e.g., reduction in serum lipid concentrations and changes in the expression of metabolic enzymes in the liver. Signs of a generalized stress response to nicotine exposure such as decreased thymus weights were observed; and likely, a subset of the observed metabolic alterations was interlinked with this generalized stress response. Under the conditions of this 90-day SD rat inhalation study, no toxicologically relevant effects of PG/VG aerosols (up to 1.520 mg PG/l + 1.890 mg VG/l) were observed, and the no observed adverse effect level (NOAEL) for PG/VG/nicotine was determined to be 438/544/6.7 mg/kg/day. Further the study demonstrated how complementary systems toxicology analyses can reveal, also in the absence of observable adverse effects, subtoxic and adaptive responses to pharmacologically active compounds such as nicotine.
    Data Types:
    • Tabular Data
    • Text
    • File Set
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