Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet:

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques:

Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet: Quantitative analysis using the bacterial cell envelope thickness tool. ( a ) Radial plots of Pantoea sp. YR343 envelope thickness in R2A, MOPS + glucose, and MOPS + succinate media. The 0° position marks pole 1, followed counterclockwise by side 1 (90°), pole 2 (180°), and side 2 (270°). ( b ) Violin plots showing global thickness distributions across media types. ( c ) Correlation between AI- and manual-based thickness measurements (n=50).

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques:

Journal: bioRxiv

Article Title: Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

doi: 10.64898/2025.12.06.692658

Figure Lengend Snippet: Quantitative analysis using the FOV tool. ( a ) Low-magnification grid-square cryoEM image of Pantoea sp. YR343 in R2A at 260 × showing bacteria (green circles/arrows) and ice crystals (yellow arrows) in vitreous ice. Scale bar: 10 µm. ( b ) Search-map montage at 3.8 k× showing higher-resolution views of bacteria and cubic/hexagonal ice. ( c ) AI-derived bacterial counts per grid square across media. ( d ) Correlation between AI- and manual-based counts across grid squares (R²=0.97).

Article Snippet: Single colonies were used to inoculate liquid cultures in either rich R2A broth (R2A Broth Premix, TEKnova, Inc.), minimal MOPS medium supplemented with 0.4% glucose (MOPS + glucose) or minimal MOPS medium supplemented with 0.4 succinate (MOPS + succinate).

Techniques: Bacteria, Derivative Assay

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Changes of extracellular NH 4 + concentration and biomass (OD 600 ) during the anaerobic cultivation of three Clostridium strains, such as OS1-26, KCTC 1674 T , and KCTC 1790 T , by incubation time in R2A medium.

Article Snippet: Various temperature (10, 25, 30, 35, and 40 °C), pH (4, 5, 6, 7, 8, 9, and 10), and NaCl (0, 0.5, 1, 1.5, and 2%) conditions were tested for growth in R2A broth contained in Hungate anaerobic culture tubes (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 during 6 days of incubation at 200 rpm in an orbital shaker.

Techniques: Concentration Assay, Incubation

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Transcription levels of nifH gene of Clostridium sp. OS1-26 during the anaerobic cultivation in R2A medium. Transcription levels were normalized by the number of 16S rRNA copies. Statistical significance was determined by one-way ANOVA followed by Tukey’s post hoc test. p > 0.05 (ns), p < 0.01 (**), p < 0.001 (***).

Article Snippet: Various temperature (10, 25, 30, 35, and 40 °C), pH (4, 5, 6, 7, 8, 9, and 10), and NaCl (0, 0.5, 1, 1.5, and 2%) conditions were tested for growth in R2A broth contained in Hungate anaerobic culture tubes (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 during 6 days of incubation at 200 rpm in an orbital shaker.

Techniques:

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Changes of extracellular NH 4 + concentration and biomass (OD 600 ) during the anaerobic cultivation of three Clostridium strains, such as OS1-26, KCTC 1674 T , and KCTC 1790 T , by incubation time in R2A medium.

Article Snippet: The colonies of strains OS1-26, KCTC 1674 T , and KCTC 1790 T were inoculated into R2A broth contained in a Hungate anaerobic culture tube (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 and then incubated at 30 °C for 96 h. The optical density at 600 nm wavelength (OD 600 ) of the bacterial culture was measured at 0, 12, 24, 48, 72, and 96 h by using the GENESYS 30 Visible Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), followed by a collection of the culture supernatant for NH 4 + measurement, as well as cells of the strain OS1-26 for nifH transcript analysis.

Techniques: Concentration Assay, Incubation

Journal: Microorganisms

Article Title: Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain

doi: 10.3390/microorganisms12122634

Figure Lengend Snippet: Transcription levels of nifH gene of Clostridium sp. OS1-26 during the anaerobic cultivation in R2A medium. Transcription levels were normalized by the number of 16S rRNA copies. Statistical significance was determined by one-way ANOVA followed by Tukey’s post hoc test. p > 0.05 (ns), p < 0.01 (**), p < 0.001 (***).

Article Snippet: The colonies of strains OS1-26, KCTC 1674 T , and KCTC 1790 T were inoculated into R2A broth contained in a Hungate anaerobic culture tube (Chemglass, Vineland, NJ, USA) flushed and filled with N 2 and then incubated at 30 °C for 96 h. The optical density at 600 nm wavelength (OD 600 ) of the bacterial culture was measured at 0, 12, 24, 48, 72, and 96 h by using the GENESYS 30 Visible Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA), followed by a collection of the culture supernatant for NH 4 + measurement, as well as cells of the strain OS1-26 for nifH transcript analysis.

Techniques: