Journal: BMC Genomics

Article Title: MicroRNA-146 function in the innate immune transcriptome response of zebrafish embryos to Salmonella typhimurium infection

doi: 10.1186/1471-2164-14-696

Figure Lengend Snippet: Microarray analysis of miRNA expression during bacterial infections of zebrafish embryos and adult fish. The Venn diagrams show the miRBase annotated miRNAs or miRNA star sequences (*) that were up-regulated (A) or down-regulated (B) during infection of zebrafish embryos with S. typhimurium SL1027 or infection of adult zebrafish with M. marinum Mma20. S. typhimurium infection of embryos was performed by micro-injection into the caudal vein at 28 hpf and miRNA expression was analyzed at 8 hpi in comparison with control embryos mock-injected with PBS. Adult zebrafish were infected with M. marinum by intraperitoneal infection and miRNA expression at 6 dpi was compared with PBS-injected controls.

Article Snippet: Custom-designed 8×15 k microarray slides were ordered from Agilent Technologies.

Techniques: Microarray, Expressing, Infection, Injection

Journal: Nature Communications

Article Title: The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

doi: 10.1038/s41467-021-22077-4

Figure Lengend Snippet: Two independent screens were performed, one with a mutant strain in which the RSA1 gene was deleted ( rsa1 Δ ::Nat R ) and the other with a mutant used as reference strain. Two independent experiments were performed for each of these screens. The query strain and the reference strain were mated with a pool of strains containing all the viable strains from the haploid gene deletion collection. After selection of heterozygous diploids, sporulation and selection of the haploid, double mutants were grown for ~18 generations in rich liquid medium (YPD). Microarrays were used to measure the relative abundance of double mutants with query versus the reference populations. Normalized results are expressed as log2(Q/R) (see Methods section). Negative values indicate a synthetic growth defect. Positive values reveal either epistatic (buffering) or suppressive (alleviating) interactions between RSA1 and the selected genes. The genetic interactions with RSA1 are indicated by green arrows for the positive log2(Q/R) values and by red arrows for the negative values. The exact values are given in parentheses. HC heterochromatin.

Article Snippet: The relative measured fitness of the double mutants log2(Q/R) was estimated from the values of the intensity of hybridization signal on custom glass slide oligonucleotide microarrays (custom Agilent, GEO GPL18088) for the query double mutant population (Q) compared with a reference double mutant population obtained in parallel (R).

Techniques: Mutagenesis, Selection

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Weighed Venn diagrams of the number of transcripts and proteins whose concentration was significantly altered in B. megaterium growing in M9 minimal medium with 0.6, 1.2 and 1.8 M NaCl, respectively. A gene or a transcript was considered significantly regulated when its concentration was either 1.75-fold higher or lower compared to 0 M NaCl. Gene expression was determined by microarray analysis and intracellular proteins were identified and quantified by proteome analysis using LC-IMS E .

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Concentration Assay, Expressing, Microarray

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Pox route and overflow metabolism in B. megaterium DSM319 growing in M9 minimal medium supplemented with different NaCl concentrations. Purple arrows correspond to reactions of the Pox route while red arrows indicate organic acid secretions. Gene expression was determined by microarray analysis using purified RNA samples obtained from four biological replicates. Intracellular proteins were identified and quantified by proteome analysis using LC-IMS E for cells originating from three biological replicates. Values are indicated as fold change compared to expression in cells grown at 37°C in M9 minimal medium without additional NaCl supplementation. Metabolites were quantified by mass spectroscopy. Ach: acetyl-CoA hydrolase; AckA: acetate kinase; AcsA: acetyl-CoA synthetase; Ldh: lactate dehydrogenase; Pdh: pyruvate dehydrogenase; Pox: pyruvate oxidase; Pta: phosphate acetyltransferase.

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Expressing, Microarray, Purification, Mass Spectrometry

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium

doi: 10.3389/fbioe.2020.00047

Figure Lengend Snippet: Integrated view of the response of the central carbon metabolism of B. megaterium DSM319 to ionic osmotic stress. Transcriptome and proteome data are indicated as the determined fold change compared to cultivation in minimal medium without NaCl supplementation. Gene expression was determined by microarray analysis using purified RNA samples obtained from four biological replicates. Intracellular proteins were identified and quantified by proteome analysis using LC-IMS E for cells originating from three replicates. Bar plots represent intracellular metabolite concentrations in μmol g CDW –1 . Intracellular metabolite concentrations were determined by LC-MS/MS using a differential method, i.e., subtracting extracellular metabolite concentration from the global metabolite concentration.

Article Snippet: Then, samples were loaded on an Agilent microarray slide (8 × 15 K custom made) comprising 2–3 60 bp DNA probes for each gene of B. megaterium and hybridization took place for 17 h at 65°C and 10 min –1 in a hybridization oven (Agilent Technologies, Waldbronn, Germany).

Techniques: Expressing, Microarray, Purification, Liquid Chromatography with Mass Spectroscopy, Concentration Assay