Journal: Biotechnology & Biotechnological Equipment

Article Title: Bacillus velezensis R22 inhibits the growth of multiple fungal phytopathogens by producing surfactin and four fengycin homologues

doi: 10.1080/13102818.2024.2313072

Figure Lengend Snippet: Figure 1. Phylogenetic tree of Bacillus spp. based on 16S rRNA sequences through maximum-likelihood methods with 1000 bootstrap replications using MEGA version 6.0. Escherichia coli BL21(DE3) (AM946981.2) was used as an outgroup in the analysis. NCBI GenBank accession numbers used in the comparison reference strains are the following: B. velezensis FZB42, OR485707; B. amyloliquefaciens ATCC 23350, NR_118950; B. licheniformis ATCC 14580, NC_006270.3; B. aerius MN-1, MN252912; B. safensis ATCC BAA-1126T, AF234854; B. aryabhattai B8W22, NZ_JYOO01000023. NCBI acc. no. of the newly isolated strains are OR482395, OR482394, OR482396, OR482397, OP554433, MK461937, MK461933, MK461938, MK461934, MK461936, OR482398, OR482400, OR482399, MK461947.

Article Snippet: Escherichia coli Bl21(De3) (am946981.2) was used as an outgroup in the analysis. ncBi genBank accession numbers used in the comparison reference strains are the following: B. velezensis FZB42, oR485707; B. amyloliquefaciens atcc 23350, nR_118950; B. licheniformis atcc 14580, nc_006270.3; B. aerius mn-1, mn252912; B. safensis atcc Baa-1126t, aF234854; B. aryabhattai B8W22, nZ_Jyoo01000023. ncBi acc. no. of the newly isolated strains are oR482395, oR482394, oR482396, oR482397, op554433, mK461937, mK461933, mK461938, mK461934, mK461936, oR482398, oR482400, oR482399, mK461947.

Techniques: Comparison, Isolation

Journal: Biotechnology & Biotechnological Equipment

Article Title: Bacillus velezensis R22 inhibits the growth of multiple fungal phytopathogens by producing surfactin and four fengycin homologues

doi: 10.1080/13102818.2024.2313072

Figure Lengend Snippet: Figure 3. PCR amplification of fenA gene encoding fengycin synthetase A. Designations: M, molecular weight marker (Perfect PlusTM 1 kb DNA Ladder, EURx); 1, B. velezensis R7; 2, B. amyloliquefaciens R10; 3, B. velezensis R19; 4, B. velezensis R22; 5, B. velezensis R23; 6, negative control (E. coli DH5α).

Article Snippet: Escherichia coli Bl21(De3) (am946981.2) was used as an outgroup in the analysis. ncBi genBank accession numbers used in the comparison reference strains are the following: B. velezensis FZB42, oR485707; B. amyloliquefaciens atcc 23350, nR_118950; B. licheniformis atcc 14580, nc_006270.3; B. aerius mn-1, mn252912; B. safensis atcc Baa-1126t, aF234854; B. aryabhattai B8W22, nZ_Jyoo01000023. ncBi acc. no. of the newly isolated strains are oR482395, oR482394, oR482396, oR482397, op554433, mK461937, mK461933, mK461938, mK461934, mK461936, oR482398, oR482400, oR482399, mK461947.

Techniques: Amplification, Molecular Weight, Marker, Negative Control

Journal: Biotechnology & Biotechnological Equipment

Article Title: Bacillus velezensis R22 inhibits the growth of multiple fungal phytopathogens by producing surfactin and four fengycin homologues

doi: 10.1080/13102818.2024.2313072

Figure Lengend Snippet: Figure 4. PCR amplification of specific fragments of srfAA gene encoding surfactin synthetase A (A) and lchAA gene for lichenysin synthase (B). Lanes and samples: M, molecular weight marker (Perfect PlusTM 1 kb DNA Ladder, EURx); (A): 1, B. velezensis R7; 2, B. amyloliquefaciens R10; 3, B. velezensis R19; 4, B. velezensis R22; 5, B. velezensis R23; 6, negative control (E. coli DH5α); (B) 1, B. licheniformis 16-1; 2, B. licheniformis 13; 3, B. licheniformis 24; 4, B. licheniformis 39; 5, B. licheniformis 55-1; 6, negative control (E. coli DH5α).

Article Snippet: Escherichia coli Bl21(De3) (am946981.2) was used as an outgroup in the analysis. ncBi genBank accession numbers used in the comparison reference strains are the following: B. velezensis FZB42, oR485707; B. amyloliquefaciens atcc 23350, nR_118950; B. licheniformis atcc 14580, nc_006270.3; B. aerius mn-1, mn252912; B. safensis atcc Baa-1126t, aF234854; B. aryabhattai B8W22, nZ_Jyoo01000023. ncBi acc. no. of the newly isolated strains are oR482395, oR482394, oR482396, oR482397, op554433, mK461937, mK461933, mK461938, mK461934, mK461936, oR482398, oR482400, oR482399, mK461947.

Techniques: Amplification, Molecular Weight, Marker, Negative Control

Journal: Microorganisms

Article Title: Identification of Phage RNA Polymerases That Minimize Double-Stranded RNA By-Product Formation and Their Characterization via In Vitro Transcription

doi: 10.3390/microorganisms14030564

Figure Lengend Snippet: Expression analysis of 44 RNA polymerase (RNAP) variants. All RNAP variants were expressed in E. coli BL21(DE3), and crude lysate samples were analyzed via SDS-PAGE. An empty vector control (IPTG-induced cells harboring an empty pET28a vector) was used for the gels to determine host-derived background protein bands. The gel images show sections of gels at sizes relevant for the respective protein. The samples were collected after four hours of induction with 0.5 mM IPTG. The size of all proteins is given in kilodaltons (kDa) and indicated below each SDS gel.

Article Snippet: BL21(DE3) Competent E. coli , C2527H , NEB Inc..

Techniques: Expressing, SDS Page, Plasmid Preparation, Control, Derivative Assay, SDS-Gel

Journal: Cell

Article Title: Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis

doi: 10.1016/j.cell.2019.09.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains T3 From Ian Molineux (University of Texas, Austin) N/A E. coli NEB5α New England Biolabs cat no. C2987I E. coli BL21 ATCC ATCC PTA-5073 E. coli BL21 ΔwaaC This paper E. coli BL21–369 E. coli BL21 ΔwaaG This paper E. coli BL21–372 E. coli BL21 PRM01 This paper E. coli BL21 PRM01 E. coli BL21 PRM02 This paper E. coli BL21 PRM02 E. coli BL21 PRM03 This paper E. coli BL21 PRM03 E. coli BL21 PRM04 This paper E. coli BL21 PRM04 E. coli BL21 PRM05 This paper E. coli BL21 PRM05 E. coli BL21 PRM06 This paper E. coli BL21 PRM06 E. coli BL21 PRM07 This paper E. coli BL21 PRM07 E. coli BL21 PRM08 This paper E. coli BL21 PRM08 E. coli MG1655 ATCC ATCC 700926 Yersinia pseudotuberculosis YPIII ATCC ATCC 29833 Chemicals, Peptides, and Recombinant Proteins Lysogeny Broth (LB medium) LabExpress cat no. 3001 LB Agar LabExpress cat no. 3002 Critical Commercial Assays KAPA Biosystems HiFi KAPA Biosystems Kapa/Roche kit code: KK2602 KAPA Biosystems Robust 2G KAPA Biosystems Kapa/Roche kit code: KK5516 KAPA SYBR®FAST qPCR Kit KAPA Biosystems Kapa/Roche kit code: KK4618 TURBO DNase Thermo Fisher cat no. AM2239 Deposited Data NGS data characterizing library diversity This paper Available upon request Spreadsheet summarizing EOP Data in This paper N/A Variable domain of an antibody Protein Data Bank; Harris et al., 1997 PDB ID: 1IGT T7 gp17 crystal structure Protein Data Bank; Garcia-Doval and van Raaij, 2012 PDB ID: 4A0T Experimental Models: Organisms/Strains Mouse: Crl:CD1(ICR) Charles River Strain Code: 022 Oligonucleotides See Table S5 for list of all oligonucleotides used in this study This paper N/A Recombinant DNA pSLM49 This paper (Encodes T3 gene 17) N/A pSLD18 This paper (Recombineering plasmid for making LPS mutants) N/A Software and Algorithms SWISS-MODEL Arnold et al., 2006 https://swissmodel.expasy.org/ seqtk Heng Li, MIT https://github.com/lh3/seqtk FASTAptamer Alam et al., 2015 https://burkelab.missouri.edu/fastaptamer.html Open in a separate window KEY RESOURCES TABLE list-behavior=unordered prefix-word= mark-type=disc max-label-size=0 Vastly diverse phagebody libraries containing 10 7 different members were created Structure-informed engineering of viral tail fibers generated host-range alterations Bacterial resistance to phagebodies was not observed across long timescales Select phagebodies limit bacterial growth in a mouse wound infection model

Techniques: Virus, Recombinant, Plasmid Preparation, Software

Journal: The Journal of Biological Chemistry

Article Title: Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii

doi: 10.1016/j.jbc.2022.102195

Figure Lengend Snippet: Identification and purification of cysteate acyl-ACP transferase. A , TLC separation of 3-keto[ 14 C]capnine (3[ 14 C]KC) arising from SulA activity using cellular lysates from Escherichia coli cells expressing nothing (empty vector control), alfi_1224 (SulA), or alfi_1465 . The thin-layer plate is representative of four independent experiments. B , purified SulA migrates as a single 85 kDa species ( V e = 76.6 ml) based on a calibrated HiLoad 16/600 Superdex 200 column (98.1 kDa theoretical homodimer mass). Left inset , molecular weight calculation using calibration standards described under . Right inset , SDS gel electrophoresis shows SulA purity (∼48 kDa) along with molecular weight standards. C , the sedimentation velocity profile (fringe displacement) was fit to a continuous sedimentation coefficient distribution model c(S). SulA sedimented as a 98.9 kDa homodimer with a sedimentation coefficient of 5.11 S. ACP, acyl carrier protein; SulA, cysteate acyl-ACP transferase.

Article Snippet: E. coli strain BL21(DE3) cells harboring the pET-SulA or pET-SulA(K281A) expression plasmids were grown in 2 l LB medium with 50 μg/ml kanamycin (Gold Biotechnology) at 37 °C and 200 rpm shaking to A 600 = 0.6.

Techniques: Purification, Activity Assay, Expressing, Plasmid Preparation, Molecular Weight, SDS-Gel, Electrophoresis, Sedimentation

Journal: Nature chemical biology

Article Title: Monitoring methionine sulfoxide with stereospecific mechanism-based fluorescent sensors

doi: 10.1038/nchembio.1787

Figure Lengend Snippet: E. coli cells expressing MetSOx ( a ) or MetROx ( b ) were incubated with MetO for ~30 min, and then rinsed to remove the oxidant. Arrows indicate the addition (↓) of MetO and rinsing (↑) the cells for two representative experiments (Assay 1 and Assay 2). MetSOx ( c ) and MetROx ( d ) oxidized fractions calculated from (n = 3), using and , respectively, described in the “ online methods ” section.

Article Snippet: SoluBL21 TM E. coli (Gelantis, San Diego, CA) cells were transformed with an indicated expression vector and grown in Luria-Bertani containing ampicillin (50 μg.ml −1 ) at 37°C.

Techniques: Expressing, Incubation