Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains

doi: 10.1107/S2053230X16014072

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: The protein was concentrated (at room temperature) using a 10 kDa molecular-weight cutoff ultrafiltration centrifugation column (Sartorius, Germany), further purified by gel filtration on a S200 16/60 size-exclusion column (GE Healthcare, Germany) in 50 m M Tris pH 7.5, 100 m M NaCl buffer and concentrated. table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism Unknown DNA source Unknown Forward primer † Gene-specific att B1 primer as designed by GeneArt for Gateway cloning Reverse primer Gene-specific att B2 primer as designed by GeneArt for Gateway cloning Cloning vector pENTR221 Expression vector pDEST17 Expression host E. coli BL21 (DE3) Complete amino-acid sequence of the construct produced MSYYHHHHHHLESTSLYKKAGF ENLYFQS AQVEPCGPVPTENQLRWQDMEMYAFIHYSLNTYTDEEWGYGNEDPQLFNPSSLDCRQWARVCKQAGMRGIIFTAKHHCGFCMWPSAYTEYSVKNSPWKNGKGDVVRELADACREEGLKFAVYLSPWDRNHPAYGQPAYVAYFRNQLRELLTNYGEIFEVWFDGANGGDGWYGGANETRKIDRTTYYQWPETYKMIRQLQPNCLIWNDGSDRGDLRWVGTEAGNVGETNWSLLNHDGEVEWHMLHYGLENGDSWVPGETNTSIRPGWFYHDTENEHVKSLSKLMDTYYKSVGRNSTLLLNFPIAPNGRIHPNDSLRGIAFKKMIGEVFRKNLAEKARTQTKGDETVIDFGKPTTFNRFLAEEDIRYGQRVKKFLLEAEINGQWQQLKDALVENGDGLTTIGHRRIICFPTVNATKLRFTVVNTKCEPFIKKLGVYLAPELTADIPDAGEKKSSNLHLFFSSPTQMMIDWETEQTITSFRYLPPQESKDGTVTHYTLWASTDWSNWTKLASGEFSNVVNNPIWQTIKFQPVRAKILKLDADRLATGNRMAYGDVEVNLKLNIEN Open in a separate window † The att B1 forward primer contained an upstream rTEV cleavage site (underlined) caption a8 Macromolecule-production information

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

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: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Crystal structure of the aromatic-amino-acid aminotransferase from Streptococcus mutans

doi: 10.1107/S2053230X18018472

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: Macromolecule-production information is summarized in Table 1 . table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism S. mutans DNA source S. mutans strain UA159 (ATCC 700610) Forward primer 5′-CGC GGATCC ATGGATTTGAGTAAACGTTTTA-3′ Reverse primer 5′-CCG CTCGAG TTAGTCTGCATATTGCTCC-3′ Cloning vector pGEX-6P-1 Expression vector pGEX-6P-1 Expression host E. coli strain BL21 (DE3) Complete amino-acid sequence of the construct produced GPMDLSKRFNKNLNKIEVSMIRQFDQSISDIPDVLKLTLGEPDFATPKHIKEAAKRAIDADESHYTGMAGLLALRQAASAFVKEKYHLTYNPDNEILVTIGATEALSASLTAILEPGDKVLLPAPAYPGYEPVVNLVGAEVVEIDTRSNDFVLTPEMLEEAILKEGEALKAVILNYPTNPTGVTYSRQQIKNLAEVLKKYPIFVISDEVYAELTYTGESHVSIAEYLPDQTILISGLSKSHAMTGWRLGLIFAPAVLTAQLIKSHQYLVTAATTSVQFAAIEALTNGKDDALPMKEEYIKRRDYIIEKMEAMKFKIIKPDGAFYIFAKIPVAQGQDSFKFLQDFAKEKAVAFIPGVAFGKYGEGYLRISYAASMETIKEAMKRLKEFMEQYAD Open in a separate window caption a8 Macromolecule-production information 2.2.

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

Journal: Molecular imaging and biology

Article Title: The Impact of Positron Range on PET Resolution, Evaluated with Phantoms and PHITS Monte Carlo Simulations for Conventional and Non-conventional Radionuclides

doi: 10.1007/s11307-019-01337-2

Figure Lengend Snippet: Simulation organ volumes, organ uptake values from Holland et al. used in simulations, and corresponding organ-level mean signal recovery in the modified Digimouse phantom, for different radionuclides

Article Snippet: Note in particular the poor quantitative accuracy provided by Ga-68 and As-72 for small structures, e.g ., tumor, spleen. table ft1 table-wrap mode="anchored" t5 Table 4. caption a7 Source tissue Source %ID/cc Volume (cc) Whole-organ mean signal recovery (%ID/cc) l RT ⊗ PSF scanner 52 Mn 18 F 89 Zr 86 y 68 Ga 72 As Tumor 42.4 0.06304 29.09 27.84 27.60 24.95 18.65 14.35 9.630 Brain 0.84 0.3651 3.111 3.118 3.124 3.169 3.116 3.103 2.767 Heart 1.79 0.1754 1.654 1.655 1.649 1.668 1.738 1.828 1.978 Kidney (L) 5.36 0.2085 4.698 4.631 4.616 4.454 4.005 3.680 3.197 Kidney (R) 5.36 0.2076 4.669 4.580 4.565 4.380 3.880 3.544 3.038 Liver 11.8 1.059 10.07 9.903 9.873 9.504 8.428 7.757 6.481 Lung (L) 0.66 0.1028 1.090 1.090 1.098 1.205 1.468 1.686 1.720 Lung (R) 0.66 0.1998 1.009 0.9931 0.9974 1.038 1.143 1.230 1.261 Pancreas 0.84 0.01359 2.747 2.948 2.993 3.389 3.661 3.912 3.417 Spleen 25.8 0.1082 15.17 14.38 14.23 12.64 9.497 7.498 5.436 Stomach 0.84 0.1832 1.536 1.640 1.661 1.904 2.477 2.891 3.067 Skeleton 13.7 0.643 7.578 7.404 7.372 6.984 6.005 5.369 4.414 Rem. body 0.84 18.46 1.382 1.382 1.383 1.398 1.407 1.416 1.189 Open in a separate window Simulation organ volumes, organ uptake values from Holland et al. used in simulations, and corresponding organ-level mean signal recovery in the modified Digimouse phantom, for different radionuclides

Techniques: Modification

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