Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

doi: 10.1107/S2053230X15019743

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: Details of the cloning and protein-production procedures are summarized in Table 1 . table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism J. denitrificans strain ATCC 14870 DNA source Synthetic DNA Forward primer 5-CCGTAGCAAT GGATCC ATGAAGAAGAGAAAGTTGAGAGCGTCAGC-3 Reverse primer 5-TCGTAATGCC GCGGCCGC TCATGAGACCACAACATCCATACAGTTG-3 Expression vector pUCBB-eGFP Expression host E. coli BL21 Star (DE3) Complete amino-acid sequence of the construct produced HGWVTDPPSRQALCASGETSFDCGQISYEPQSVEAPKGATTCSGGNEAFAILDDNSKPWPTTEIASTVDLTWKLTAPHNTSTWEYFVDGQLHQTFDQKGQQPPTSLTHTLTDLPTGEHTILARWNVSNTNNAFYNCMDVVVS Open in a separate window caption a8 Macromolecule-production information

Techniques: Expressing, Plasmid Preparation, Sequencing, Construct, Produced

Journal:

Article Title: Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)

doi:

Figure Lengend Snippet: Chromosomal signature of SmtB/ArsR and regulons based on predicted operator sequences.

Article Snippet: Intergenic and whole genome sequences were scanned at PIGED using scoring matrices derived from both 6-2-6 and 12-2-12 versions of these 60 predicted operator sequences to ensure a complete data set from this analysis. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Organism SmtB/ArsR synonym α3 a α5 Operator position b Predicted regulon c Bacillus anthracis strains GBAA0594 + + –28 COG0640 →(25)COG2217 BA0594 + + –28 COG0640 →(25)COG2217 BAS0563 + + –28 COG0640 →(25)COG2217 Bacillus cereus strains BCZK0507 + + –28 COG0640 →(25)COG2217 BCE0662 + + –28 COG0640 →(25)COG2217 BC0595 + + –28 COG0640 →(25)COG2217 Bacillus clausii KSM-K16 ABC3390 – + –18 COG0640 →(12)COG1230 Bacillus licheniformis BLI02201 – + –95 COG1230(BLI03452) ATCC 14580 BLI00472 + – –41 COG2217(BLi03539) Bacillus subtilis subsp. subtilis BSU19120 – + –85 COG1230(BSU26650) str.

Techniques:

Journal:

Article Title: Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)

doi:

Figure Lengend Snippet: Signature sequences for SmtB/ArsR protein-DNA interactions. WebLogo (Crooks et al. 2004) was used to generate consensus profiles for (A) sixty SmtB/ArsR operator sites identified in this study and (B) forty-three amino acid sequences comprising the winged helix-turn-helix DNA binding motif of predicted autoregulatory SmtB/ArsR proteins. Secondary structural elements of the DNA binding motif are shown beneath the respective amino acid sequences comprising the alpha helices and beta sheets. αR represents the recognition helix of the DNA binding motif.

Article Snippet: Intergenic and whole genome sequences were scanned at PIGED using scoring matrices derived from both 6-2-6 and 12-2-12 versions of these 60 predicted operator sequences to ensure a complete data set from this analysis. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Organism SmtB/ArsR synonym α3 a α5 Operator position b Predicted regulon c Bacillus anthracis strains GBAA0594 + + –28 COG0640 →(25)COG2217 BA0594 + + –28 COG0640 →(25)COG2217 BAS0563 + + –28 COG0640 →(25)COG2217 Bacillus cereus strains BCZK0507 + + –28 COG0640 →(25)COG2217 BCE0662 + + –28 COG0640 →(25)COG2217 BC0595 + + –28 COG0640 →(25)COG2217 Bacillus clausii KSM-K16 ABC3390 – + –18 COG0640 →(12)COG1230 Bacillus licheniformis BLI02201 – + –95 COG1230(BLI03452) ATCC 14580 BLI00472 + – –41 COG2217(BLi03539) Bacillus subtilis subsp. subtilis BSU19120 – + –85 COG1230(BSU26650) str.

Techniques: Binding Assay

Journal:

Article Title: Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)

doi:

Figure Lengend Snippet: Phylogeny of SmtB/ArsR/CadC family proteins. Amino acid sequences for SmtB/ArsR proteins containing the DNA recognition signature, together with MerR from Streptomyces lividans (Brunker et al. 1996) and other characterized ArsR and CadC proteins were used to reconstruct a previous phylogenetic tree describing relationships among ArsR, SmtB, and CadC proteins (Busenlehner 2003). All amino acid sequences contain DNA recognition signatures except those listed as ARSR, MERR, or CADC. Neighboring joining analysis, bootstrapping, and tree visualization were performed using the MEGA3 software package (Kumar et al. 2004). A solid circle at a node indicates the level of bootstrap support is > 50%, while scale refers to p-distance value estimates. Synonyms for archaeal sequences are boxed. VNG7125 shares significant sequence similarity with other ArsR pro teins, but is separated from this partition because of an apparent 22 N-terminal amino acid extension that could be the result of misannotation regarding the translational start site. Unlisted synonyms have been collapsed into families based on their identical or near-identical sequences. The CZRA S. aureus str. grouping includes SACOL2137, SAR2233, SAV2145, SA1947, SAS2048, and MW2069. The Bacillus sp. grouping includes B. anthracis (GBAA0594, BA0594, BAS0563), B. cereus (BCZK0507, BCE0662, BC0595), and B. thuringiensis (BT9727-0505). The NmtR Mycobacterium sp. grouping includes (RV3744, Mb3770, MT3852). For synonym–organism relationships, consult Table 1.

Article Snippet: Intergenic and whole genome sequences were scanned at PIGED using scoring matrices derived from both 6-2-6 and 12-2-12 versions of these 60 predicted operator sequences to ensure a complete data set from this analysis. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Organism SmtB/ArsR synonym α3 a α5 Operator position b Predicted regulon c Bacillus anthracis strains GBAA0594 + + –28 COG0640 →(25)COG2217 BA0594 + + –28 COG0640 →(25)COG2217 BAS0563 + + –28 COG0640 →(25)COG2217 Bacillus cereus strains BCZK0507 + + –28 COG0640 →(25)COG2217 BCE0662 + + –28 COG0640 →(25)COG2217 BC0595 + + –28 COG0640 →(25)COG2217 Bacillus clausii KSM-K16 ABC3390 – + –18 COG0640 →(12)COG1230 Bacillus licheniformis BLI02201 – + –95 COG1230(BLI03452) ATCC 14580 BLI00472 + – –41 COG2217(BLi03539) Bacillus subtilis subsp. subtilis BSU19120 – + –85 COG1230(BSU26650) str.

Techniques: Software, Sequencing

Journal: Journal of Clinical Microbiology

Article Title: Automated Detection of Toxigenic Clostridium difficile in Clinical Samples: Isothermal tcdB Amplification Coupled to Array-Based Detection

doi: 10.1128/JCM.00621-12

Figure Lengend Snippet: bpHDA amplification rate. Various cell input amounts were amplified by bpHDA, and ln(C. difficile cell count) was plotted against Cp values. The line represents best-fit linear regression.

Article Snippet: The analyzer moves fluids through channels connecting the blister packs and control chambers, mixing and heating where needed, and finally capturing a chip image which is processed to return assay results. table ft1 table-wrap mode="anchored" t5 caption a7 Organism Strain Toxin production C. difficile ToxB result b Clostridium difficile ATCC 43255 A and B Pos ATCC 43600 A and B Pos ATCC 43599 A and B Pos ATCC 17857 A and B Pos BAA-1805 A and B Pos BAA-1382 A and B Pos CCUG 20309 B only Pos ATCC 43598 B only Pos ATCC 43593 Neg Clostridium sordellii ATCC 9714 tcsL Neg Campylobacter jejuni ATCC 33560 Neg Citrobacter freundii ATCC 8090 Neg Enterococcus faecalis ATCC 29212 Neg Escherichia coli ATCC 4157 Neg Listeria monocytogenes ATCC 6896 Neg Proteus vulgaris ATCC 6896 Neg Pseudomonas aeruginosa ATCC 10145 Neg Salmonella enterica ATCC 13311 Neg Shigella flexneri ATCC 25929 Neg Staphylococcus epidermidis ATCC 12228 Neg Open in a separate window a Organisms were cultured, spiked into a pooled negative fecal sample, and tested. b Pos, positive; Neg, negative.

Techniques: Amplification, Cell Counting

Journal: Journal of Clinical Microbiology

Article Title: Automated Detection of Toxigenic Clostridium difficile in Clinical Samples: Isothermal tcdB Amplification Coupled to Array-Based Detection

doi: 10.1128/JCM.00621-12

Figure Lengend Snippet: Internal control. Cells were spiked into a pooled negative fecal sample. (A) Amplification curves, in triplicate, of 4,000 CFU of the internal control cells (IC; dotted lines) or 4,000 CFU of the internal control cells plus 1 (solid) or 10 (dashed) CFU of C. difficile. (B) Melting analysis of the nine reactions shown in panel A. Amplified material from representative reaction mixtures containing the internal control cells only or the internal control cells plus C. difficile was detected on chips as indicated. The chip legend is shown in Fig. 1C.

Article Snippet: The analyzer moves fluids through channels connecting the blister packs and control chambers, mixing and heating where needed, and finally capturing a chip image which is processed to return assay results. table ft1 table-wrap mode="anchored" t5 caption a7 Organism Strain Toxin production C. difficile ToxB result b Clostridium difficile ATCC 43255 A and B Pos ATCC 43600 A and B Pos ATCC 43599 A and B Pos ATCC 17857 A and B Pos BAA-1805 A and B Pos BAA-1382 A and B Pos CCUG 20309 B only Pos ATCC 43598 B only Pos ATCC 43593 Neg Clostridium sordellii ATCC 9714 tcsL Neg Campylobacter jejuni ATCC 33560 Neg Citrobacter freundii ATCC 8090 Neg Enterococcus faecalis ATCC 29212 Neg Escherichia coli ATCC 4157 Neg Listeria monocytogenes ATCC 6896 Neg Proteus vulgaris ATCC 6896 Neg Pseudomonas aeruginosa ATCC 10145 Neg Salmonella enterica ATCC 13311 Neg Shigella flexneri ATCC 25929 Neg Staphylococcus epidermidis ATCC 12228 Neg Open in a separate window a Organisms were cultured, spiked into a pooled negative fecal sample, and tested. b Pos, positive; Neg, negative.

Techniques: Control, Amplification

Journal: Journal of Clinical Microbiology

Article Title: Automated Detection of Toxigenic Clostridium difficile in Clinical Samples: Isothermal tcdB Amplification Coupled to Array-Based Detection

doi: 10.1128/JCM.00621-12

Figure Lengend Snippet: Assay specificity a

Article Snippet: The analyzer moves fluids through channels connecting the blister packs and control chambers, mixing and heating where needed, and finally capturing a chip image which is processed to return assay results. table ft1 table-wrap mode="anchored" t5 caption a7 Organism Strain Toxin production C. difficile ToxB result b Clostridium difficile ATCC 43255 A and B Pos ATCC 43600 A and B Pos ATCC 43599 A and B Pos ATCC 17857 A and B Pos BAA-1805 A and B Pos BAA-1382 A and B Pos CCUG 20309 B only Pos ATCC 43598 B only Pos ATCC 43593 Neg Clostridium sordellii ATCC 9714 tcsL Neg Campylobacter jejuni ATCC 33560 Neg Citrobacter freundii ATCC 8090 Neg Enterococcus faecalis ATCC 29212 Neg Escherichia coli ATCC 4157 Neg Listeria monocytogenes ATCC 6896 Neg Proteus vulgaris ATCC 6896 Neg Pseudomonas aeruginosa ATCC 10145 Neg Salmonella enterica ATCC 13311 Neg Shigella flexneri ATCC 25929 Neg Staphylococcus epidermidis ATCC 12228 Neg Open in a separate window a Organisms were cultured, spiked into a pooled negative fecal sample, and tested. b Pos, positive; Neg, negative.

Techniques: