Journal: ACS Applied Polymer Materials

Article Title: 3D-Bioprinted Marine Bacteria for the Degradation of Polyhydroxybutyrate Bioplastics

doi: 10.1021/acsapm.5c03370

Figure Lengend Snippet: Growth and PHB degradation of marine bacteria. (A) Growth curves of Bacillus sp. NRRL B-14911 (dark green), C. testosteroni (light green), Marinobacter sp. NK-1 (light brown), and Microbulbifer sp. SOL66 (dark brown) cultured in Marine Broth at 30 °C. (B) Degradation of PHB by the marine bacteria species was determined by growing bacterial colonies on Marine Broth-agar plates containing PHB powder and measuring the radii of the clear zones of depolymerized PHB formed around the colonies after 7 days ( n = 8). **** P ≤ 0.0001 by one-way ANOVA statistical analysis.

Article Snippet: The bacteria strains used in this study are Bacillus sp. NRRL B-14911 , (Agricultural Research Service Culture Collection, United States Department of Agriculture), Comamonas testosteroni (ATCC 11996), Marinobacter sp. NK-1 (ATCC 700491), Microbulbifer sp. SOL66 (ATCC 70072), and Escherichia coli BL21 (ATCC BAA-1025).

Techniques: Bacteria, Cell Culture

Journal: Chemical Science

Article Title: Ammonia monooxygenase: a work in progress

doi: 10.1039/d6sc01048b

Figure Lengend Snippet: (A) The AMO heterotrimer in native membranes of N. europaea ATCC 19718, as resolved to 2.77 Å by cryo-EM. α 3 β 3 γ 3 arrangement of the amoA (red), amoB (blue), and amoC (green) subunits shown from the side (left) and the top (right). PDB: 9CL6. (B) The pMMO heterotrimer in native membranes of Methylocystis sp. Rockwell ATCC 49242, as resolved to 2.48 Å by cryo-EM. α 3 β 3 γ 3 arrangement of the pmoA (red), pmoB (blue), and pmoC (green) subunits shown from the side (left) and the top (right). PDB: 9CL5.

Article Snippet: Sequence comparison by Musiani, Ciurli and coworkers of pmoD from Methylocystis sp. ATCC 49242 (Rockwell) and amoD/E from N. europaea demonstrate 38% and 28% sequence identity, respectively.

Techniques: Cryo-EM Sample Prep

Journal: Chemical Science

Article Title: Ammonia monooxygenase: a work in progress

doi: 10.1039/d6sc01048b

Figure Lengend Snippet: The AMO (A) and pMMO (B) trimer, with the exogenous helix of unknown function along the face of the amoC/pmoC subunit, shown in pink. AMO from PDB: 9CL6, from N. europaea ATCC 19718, as resolved to 2.77 Å by cryo-EM. pMMO from PDB: 9CL5, from Methylocystis sp. ATCC 49242, as resolved to 2.48 Å by cryo-EM.

Article Snippet: Sequence comparison by Musiani, Ciurli and coworkers of pmoD from Methylocystis sp. ATCC 49242 (Rockwell) and amoD/E from N. europaea demonstrate 38% and 28% sequence identity, respectively.

Techniques: Cryo-EM Sample Prep

Journal: Chemical Science

Article Title: Ammonia monooxygenase: a work in progress

doi: 10.1039/d6sc01048b

Figure Lengend Snippet: (A) The His-brace motif from a lytic polysaccharide monooxygenase (LPMO) originating in species Phytophthora infestans T30-4 , as characterized by X-ray diffraction to 1.01 Å. (PDB: 6Z5Y). (B) The Cu B site in pMMO from Methylocystis sp. ATCC 49242, as resolved to 2.48 Å by cryo-EM. (PDB: 9CL5). (C) The Cu B site in AMO from N. europaea ATCC 19718, as resolved to 2.77 Å by cryo-EM. (PDB: 9CL6).

Article Snippet: Sequence comparison by Musiani, Ciurli and coworkers of pmoD from Methylocystis sp. ATCC 49242 (Rockwell) and amoD/E from N. europaea demonstrate 38% and 28% sequence identity, respectively.

Techniques: Cryo-EM Sample Prep

Journal: Chemical Science

Article Title: Ammonia monooxygenase: a work in progress

doi: 10.1039/d6sc01048b

Figure Lengend Snippet: Overlay of the cryo-EM structures containing Cu D site from pmoC ( Methylocystis sp. ATCC 49242, 2.48 Å cryo-EM) (PDB: 9CL5) and a metal-free Cu D site from amoC ( N. europaea ATCC 19718, 2.77 Å cryo-EM) (PDB: 9CL6). pmoC is shown in green, while amoC is shown in cyan. Residues from pmoC are shown in parentheses, while those from amoC are not.

Article Snippet: Sequence comparison by Musiani, Ciurli and coworkers of pmoD from Methylocystis sp. ATCC 49242 (Rockwell) and amoD/E from N. europaea demonstrate 38% and 28% sequence identity, respectively.

Techniques: Cryo-EM Sample Prep

Journal: Chemical Science

Article Title: Ammonia monooxygenase: a work in progress

doi: 10.1039/d6sc01048b

Figure Lengend Snippet: The structure of monomeric pmoD from Methylocystis sp. ATCC 49242, as observed by X-ray diffraction to 1.90 Å resolution (PDB: 6CPD). On the left is the structure of the homodimer, as purified. On the right, the ligands binding to the Cu ion are shown with corresponding distances. Note that this is the monomeric form of the protein, which does not contain the Cu A site formed by the homodimeric species.

Article Snippet: Sequence comparison by Musiani, Ciurli and coworkers of pmoD from Methylocystis sp. ATCC 49242 (Rockwell) and amoD/E from N. europaea demonstrate 38% and 28% sequence identity, respectively.

Techniques: Purification, Binding Assay

Journal: Frontiers in Nutrition

Article Title: Raspberry aqueous extract ameliorates MAFLD in mice by regulating gut microbiota and purine metabolism

doi: 10.3389/fnut.2026.1818086

Figure Lengend Snippet: Ileibacterium is closely correlated with MAFLD phenotypes. (A) Linear discriminant analysis (LDA ≥ 2.0) scores derived from LEfSe Analysis. (B) The correlation between the changed genera responding to MAFLD-related index. (C) Statistical analysis of the top 10 bacterial species with different bacterial abundance between HFD and RE group. * p < 0.05, ** p < 0.01, *** p < 0.001. Data are expressed as mean ± SD ( n = 5).

Article Snippet: Ileibacterium valens (ATCC No. TSD-63, purchased from Ningbo, China, catalog No. B260897) was revived and inoculated into culture medium (Ningbo, China, catalog No. KDM150) at a 4% (V/V) inoculum size, followed by incubation at 37 °C for 24 h. After cultivation, the bacterial suspension was centrifuged at 3,000 rpm for 10 min, and the resulting cell pellet was washed three times with pre-chilled sterile PBS at 4 °C.

Techniques: Derivative Assay

Journal: PeerJ

Article Title: Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum : Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov

doi: 10.7717/peerj.9151

Figure Lengend Snippet: Summary table of comparisons for all species, including a subset of carbon usage types. We show the specific strain names for the three Paraburkholderia sp. nov. and the reference Paraburkholderia strains, the number of Paraburkholderia sp. nov. isolates in each group with the type strain in bold, whether or not the isolates are associated with D. discoideum (positive association indicated by a + sign), average bacterial length, optimal growth temperature, and metabolic tests. Next, a subset of about one-fourth of the relevant carbon types follows. P. agricolaris and P. bonniea are able to utilize some carbons that their close Paraburkholderia relatives cannot. A plus (+) symbol indicates all isolates were able to use a specific carbon and a minus (−) symbol indicates that they could not use that carbon. A number value indicates the percentage of strains in a specific group that can utilize that particular carbon. Specifics for each individual strain can be found in the supplemental information (raw data files).

Article Snippet: The ability to reduce nitrate to nitrite is present in all three of the Paraburkholderia sp. nov. type strains and P. fungorum ATCC BAA-364 and P. phymatum STM815.

Techniques: Activity Assay

Journal: PeerJ

Article Title: Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum : Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov

doi: 10.7717/peerj.9151

Figure Lengend Snippet: We measured the length of about one hundred bacteria for each Paraburkholderia sp. nov. and for the nonsymbionts (see ). We used seven strains for P. agricolaris , seven strains for P. hayleyella , two strains for P. bonniea , and three strains for non-symbionts. On average, we found all three symbiont bacteria species are significantly shorter than non-symbiont bacteria species. Significant differences in length found between bacteria are indicated by different letters which reflect results of a Benjamini-Hochberg correction for multiple comparisons.

Article Snippet: The ability to reduce nitrate to nitrite is present in all three of the Paraburkholderia sp. nov. type strains and P. fungorum ATCC BAA-364 and P. phymatum STM815.

Techniques: Bacteria

Journal: PeerJ

Article Title: Endosymbiotic adaptations in three new bacterial species associated with Dictyostelium discoideum : Paraburkholderia agricolaris sp. nov., Paraburkholderia hayleyella sp. nov., and Paraburkholderia bonniea sp. nov

doi: 10.7717/peerj.9151

Figure Lengend Snippet: We tested a range of temperatures to determine growth range and optimal temperature. P. hayleyella and P. bonniea have reduced range of growth and grow less densely compared to P. agricolaris and the non-symbionts. P. agricolaris has the same range as the three nonsymbiont Paraburkholderia but grows less densely at 37 °C and best at 30 °C compared to the non-symbionts.

Article Snippet: The ability to reduce nitrate to nitrite is present in all three of the Paraburkholderia sp. nov. type strains and P. fungorum ATCC BAA-364 and P. phymatum STM815.

Techniques: