Journal:

Article Title: DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes

doi: 10.1073/pnas.171178898

Figure Lengend Snippet: Strains used in DNA:DNA microarray hybridization analysis

Article Snippet: DNA was typically prepared from 2 ml of exponentially growing culture by using a standard method for bacterial genomic DNA (gDNA) preparation and quantification ( 12 , 13 ). table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Bacterium Culture collection Strain origin SSU rRNA accession no. gyrB accession no. S. oneidensis MR-1 ATCC 700550 TS Lake Oneida, NY, sediments AF005251 AF005694 S. oneidensis DLM7 Lower Green Bay sediments, Lake Michigan, Michigan AF387347 * AF005697 S. oneidenisis MR-4 Black Sea water column AF005252 AF005695 Shewanella sp. CL 256/73 NCTC 12093 Human cerebrospinal fluid AF387346 * AF378351 * S. putrefaciens str.

Techniques: Microarray, Hybridization

Journal:

Article Title: DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes

doi: 10.1073/pnas.171178898

Figure Lengend Snippet: Phylogenetic tree showing strains of Shewanella based on (A) SSU rRNA and (B) gyrB nucleotide sequence. Relationships calculated by using maximum-likelihood analysis. Species in bold were used in this study. Numbers at nodes represent bootstrap values (of 100 replicates).

Article Snippet: DNA was typically prepared from 2 ml of exponentially growing culture by using a standard method for bacterial genomic DNA (gDNA) preparation and quantification ( 12 , 13 ). table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Bacterium Culture collection Strain origin SSU rRNA accession no. gyrB accession no. S. oneidensis MR-1 ATCC 700550 TS Lake Oneida, NY, sediments AF005251 AF005694 S. oneidensis DLM7 Lower Green Bay sediments, Lake Michigan, Michigan AF387347 * AF005697 S. oneidenisis MR-4 Black Sea water column AF005252 AF005695 Shewanella sp. CL 256/73 NCTC 12093 Human cerebrospinal fluid AF387346 * AF378351 * S. putrefaciens str.

Techniques: Sequencing

Journal:

Article Title: DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes

doi: 10.1073/pnas.171178898

Figure Lengend Snippet: Relationship between percent similarity in nucleotide sequences for the SSU rRNA (circles) and gyrB (triangles) genes (calculated as percent similarity of test strain relative to the S. oneidensis, MR-1 strain) and percent similarity (31) determined for microarray hybridization profiles between test strains and S. oneidensis, MR-1. Note that the data were not included for E. coli and for env. isolate PV-4, the two most distantly related organisms tested in this study, as the relationship falls off at greater distances.

Article Snippet: DNA was typically prepared from 2 ml of exponentially growing culture by using a standard method for bacterial genomic DNA (gDNA) preparation and quantification ( 12 , 13 ). table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Bacterium Culture collection Strain origin SSU rRNA accession no. gyrB accession no. S. oneidensis MR-1 ATCC 700550 TS Lake Oneida, NY, sediments AF005251 AF005694 S. oneidensis DLM7 Lower Green Bay sediments, Lake Michigan, Michigan AF387347 * AF005697 S. oneidenisis MR-4 Black Sea water column AF005252 AF005695 Shewanella sp. CL 256/73 NCTC 12093 Human cerebrospinal fluid AF387346 * AF378351 * S. putrefaciens str.

Techniques: Microarray, Hybridization

Journal: iScience

Article Title: Dnmt3a overexpression disrupts skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces metabolic elasticity

doi: 10.1016/j.isci.2025.112144

Figure Lengend Snippet: Dnmt3a regulates the Akt-FoxO-atrogene axis and causes loss of sensitivity to starvation (A) PPI network of differentially expressed genes (DEGs) with FDR <0.05 and fold-change value >2 upregulated in Dnmt3a-Tg muscle compared with WT muscle (1,534 nodes and 12,704 edges are shown). Node color indicates log 2 fold-change value, and circle size of nodes indicates number of direct edges (degree). (B) The top 20 putative hub genes among the network of DEGs upregulated in Dnmt3a-Tg muscle were identified by PPI network analysis. (C) Relative mRNA expression of Akt1 in gastrocnemius muscle from young (3-month-old) WT and age-matched Dnmt3a-Tg mice ( n = 8 mice/group). (D) GSEA of a gene set of muscle FoxO signaling and putative FoxO1 target in skeletal muscle from microarray data of young (3-month-old) WT and Dnmt3a-Tg muscles ( n = 4 mice/group). (E) Relative mRNA expression of FoxO signaling pathway and atrophy-related genes in gastrocnemius muscle from young (3-month-old) WT and Dnmt3a-Tg mice ( n = 8 mice/group). (F) Weights of skeletal muscles (gastrocnemius, quadriceps, TA, EDL, and soleus) from fed and 48-h-fasted WT and Dnmt3a-Tg female mice ( n = 10–11 fed and 48-h-fasted WT mice, n = 5 fed and 48-h-fasted Dnmt3a-Tg mice). (G) Starvation-induced difference in skeletal muscle mass of gastrocnemius and EDL muscles in WT and Dnmt3a-Tg female mice ( n = 11 WT mice, n = 5 Dnmt3a-Tg mice). (H–J) Representative immunoblot images (H) and densitometric analysis (I, J) of Dnmt3a, p-Akt (Ser473), AKT, p-FoxO1 (Ser256), FoxO1, C/EBPδ, Atrogin1, 4EBP1, LC3b, and ubiquitin protein in the gastrocnemius of fed and 48-h-fasted WT and Dnmt3a-Tg female mice ( n = 7 fed and 48-h-fasted WT mice, n = 5 fed and 48-h-fasted Dnmt3a-Tg mice). (K) Relative mRNA expression of atrogenes downstream of FoxO in gastrocnemius muscles from WT and Dnmt3a-Tg mice ( n = 10–11 fed and 48-h-fasted WT mice, n = 5 fed and 48-h-fasted Dnmt3a-Tg mice). All data indicate mean ± SE. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001. (C, E, G) Student’s two-tailed unpaired t test. (F, I–K) Two-way analysis of variance (ANOVA) followed by Tukey’s post hoc test. F, fed; S, starvation; WT, wild type; Tg: Dnmt3a-Tg.

Article Snippet: Rabbit anti-phospho-FoxO1 (Ser256) , Cell Signaling , Cat# 9461; RRID: AB_329831.

Techniques: Expressing, Microarray, Muscles, Western Blot, Ubiquitin Proteomics, Two Tailed Test

Journal: iScience

Article Title: Dnmt3a overexpression disrupts skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces metabolic elasticity

doi: 10.1016/j.isci.2025.112144

Figure Lengend Snippet:

Article Snippet: Rabbit anti-phospho-FoxO1 (Ser256) , Cell Signaling , Cat# 9461; RRID: AB_329831.

Techniques: Virus, Recombinant, Injection, Immunodetection, Plasmid Preparation, Fluorescence, Lysis, Bicinchoninic Acid Protein Assay, Western Blot, Membrane, Sterility, Gene Expression, Microarray, Labeling, Hybridization, Ligation, Purification, DNA Labeling, Methylation, Library Quantification, DNA Ligation, Transfection, Methylation Sequencing, Software, Functional Assay, Mass Spectrometry, Real-time Polymerase Chain Reaction, Imaging, Microscopy