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Α-Helical Segment 190 Α-Ketobutyrate 613 Α-Proteobacteria 780, 791 Α/Β

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Index A acyltransferase 123 adduct formation 815, 822 α-helical segment 190 adenosine-5´-phosphosulfate (APS) 610, 613 α-ketobutyrate 613 adenosine-5´-phosphosulfate reductase 610, 611 α-Proteobacteria 780, 791 adenosyl-GDP-cobinamide 91 α/β heterodimer 137–139 adenosyl cobalamin 72, 73, 82, 91 α helix 511 adenosylcobinamide phosphate 91 α polypeptide 175, 188, 204 adenosylcobyric acid 90 αβ LH1 subunit 513 adenylylsulfate 610, 613 A-branch 301 adenylysulfate:phosphate adenylyltransferase (APAT) 610 A-side electron transfer 346 Adiantum capillus-veneris 814 aa3-type cytochrome c oxidase 407, 408, 541, 636, 788 AdoMet:diacylglycerol 3-amino-3-carboxypropyl transferase AAA+ 69, 748 128 AAA+ ATPases 749 ADP-inhibition 477 AAA proteins 69 ADP sulfurylase 610 AAA+ proteins 70 Aequoria victoria 845 AAnP. See aerobic anoxygenic phototrophs aerobic anoxygenic phototrophs 19, 31, 32–52, 599 AAP. See aerobic anoxygenic phototrophs carbon metabolism 40–41 ABC. See ATP-binding cassette (ABC) deep ocean absorbance spectra vertical distribution 50 in vivo 39 ecological roles 47–51 absorption maxima 431 environment 32 carotenoid 926 evolution 38–40 absorption transitions 200 marine 48–49 accA 122 morphology 35 accB 122 nutritional status 43 accC 122 phylogeny 33, 37 accD 122 taxonomy 37 acceptor pool 530 aerobic bacteria 112 acceptor quinone 379, 380–399 aerobic cobalamin biosynthetic pathway 84 reactions 382 aerobic conditions 58, 72, 112, 417 acceptor quinone complex 383 aerobic cyclization system 72 accessory phototrophy 50 aerobic pathway 84 Acetobacteraceae 603, 614 aerobic photosynthetic bacteria 98, 99, 112 3-acetoxychlorophyllide a 68 aerobic phototoxicity 38 acetyl carbonyl 204 aerobic phototrophic bacteria 19 Acidiphilium 34, 112, 113, 599, 608 aerobic purple bacteria 19–20 Acidiphilium acidophilum 599 aerobic repression Acidiphilium cryptum 603, 614 CrtJ 716–721 Acidiphilium cryptum JF-5 790, 791, 792 aerobic repressor 784, 785 Acidiphilium rubrum 112, 113 aerobic respiration 149 Acidisphaera 34 aerotaxis 651 Acidithiobacillus 459, 608 AerR 785, 791 Acidithiobacillus ferrooxidans 459, 666 aerR 785, 786, 789 acidophilic purple bacteria 11 affi nity chromatography 849 acid pocket 715 AFFM. See atomic force fl uorescence microscopy (AFFM) acpP 122 AFM. See atomic force microscopy (AFM) acpS 122 AFM topographs 164 ACP synthase 122 Agrobacteria 694 acrylic acid 546 Agrobacterium 702 AcsF 42, 72 Agrobacterium tumefaciens 805 acsF 44, 47, 51, 72, 794 ALA. See δ-aminolevulinate; See 5-aminolevulinic acid (ALA) actin fi lament 486 ALAD. See δ-aminolevulinic acid dehydratase action spectrum 871 ALA dehydratase 60 + – active P QB state 957, 961, 963 ALA synthase 778, 780, 782, 783, 786, 788, 791 acyl carrier protein (ACP) 122 Alcaligenes eutrophus 744 976 Index Alcaligenes faecalis 635 hexagonally packed 945 alcohols 40 LH2 size heterogeneity 948 Alexandrium 48 packing density 946 algae 103 ring size 151 algal blooms 48 antenna absorption transition 203–205 Alkalilimnicola 600 antenna complex 146–151; See also light-harvesting 1 Alkalilimnicola ehrlichei 604, 615 complex; See also light-harvesting 2 complex alkaliphilic purple bacteria 10–11 artifi cial 861 Alkalispirillum 600 synthesis 147 Allochromation vinosum 612, 745 antenna connectivity 170 Allochromatium 8 antenna domain formation 944 Allochromatium minutissimum 607 antenna domains 257, 945, 946, 949 Allochromatium vinosum 3, 4, 6, 103, 384, 515, 596, 601, 604, antenna heterogeneity 944 606, 609, 610, 613, 615, 853 antenna proteins 200–201 Allochromatium warmingii 601 anthraquinone 304, 382, 391 allosteric 791 antibiotic resistance markers 842 alphaproteobacteria 5, 18–19, 59, 98, 99, 111, 112, 581, 597 antimycin 519 phototrophic 597 antimycin A 435, 455, 526 alternative nitrogenase 769 antioxidative 41 amidase 90 anti sigma factor FlgM 645 amino acid APAT 611 distribution 918, 920 APB. See aerobic phototrophic bacteria model sequence 920 apoCyt c 409 motifs 918, 920 apoCyt c heme binding 413 sequence contexts 922 apocytochrome c 407 amino acid sequence 921 apoptosis 527 model 916 AppA 652, 718, 719, 732, 785, 818, 831 5-aminolevulinic acid (ALA) 778, 780, 782, 783, 786, 788, light-responding antirepressor 718 791 regulatory role 718 aminopropanol 82 appA 785 aminopropyltriethoxysilane 862 apparent equilibrium constant 520, 524 ammonium transporter 769–770 apr 603 AmtB 769–770 APS kinase 613, 615 amphiphile 146 APS reductase 615 amphiphilic protein maquettes 905–907 APS reductase pathway 610 AmtB 769–770 Aquifex aeolicus 749 ammonium transporter 769–770 Arabidopsis thaliana 72, 612, 847 anaerobic ammonia oxidation 624 ArcB/ArcA 753 anaerobic aromatic compound ArcB sensor kinase 754 degradation 589–590 Archaea 609, 746 anaerobic benzoate degradation 580–589 Arhodomonas aquaeolei 600 anaerobic benzoate photometabolism 580 aromatic compounds 577–591 anaerobic conditions 72, 523 degradation 577–591 anaerobic respiration 149 aromatic residues 916, 918, 920, 922, 924 anaerobiosis 848 arrA 549 analogs 184 arrB 549 anaplerotic CO2 fi xation 40 ars determinants 662 anaplerotic CO2 incorporation 48 arsABC 673, 675 AnfA 769 arsC gene family 676 anfA 765 arsenate 549, 663 anfHDGK 769 arsenate reductase 676 anfHDK 761 arsenate respiration 549 anhydrorhodovibrin 929, 931 arsenic 548–550 anisotropy decay 243 arsenite 550 annihilation experiments 148 arsenite oxidase 459, 549, 552 Antarctica 4 arsenite oxidation 549, 664 antenna ars operon 663 clustering 945 Arsukibacterium ikkense 601 complex assembly 946 artifi cial antenna complex 861 domain formation 944 artifi cial LH1-type complex 873 heterogeneity 944 Aspergillus nidulans 847 Index 977 assembly 195 B core complexes 172 assembly factor β-barrel 416 LhaA 174 β-carotene 98, 113 assembly factor for LH2 174 β-carotene ketolase 113 assembly pathways 407 β-dodecyl maltoside 260 assembly protein β-galactosidase 780, 789 Surf1 545 β-hydroxydecanoyl-ACP dehydratase 122 assimilatory nitrate reductase (Nas) 548, 637 β-hydroxyl-ACP dehydratase 122 assimilatory sulfate reduction 610, 612–615, 613, 616 β-ketoacyl-ACP reductase 122 asymmetrical ζ-carotene 104 β-ketoacyl-ACP synthase I 122 AT-rich codons 850 β-ketoacyl-ACP synthase II 122 ATB binding β-ketoacyl-ACP synthase III 122 Walker A and B motifs 411 β-octyl-glucoside 185 ATCC17023 critical micelle concentration 185 wild-type strain 849 micelle 185 ATCC17025 780, 782, 791 β-octylglucoside (β-OG) 140, 146, 864 ATCC17029 780, 782 β-oxidation 580, 581, 584, 585, 586, 587 atomic force fl uorescence microscopy (AFFM) 270 β helix 511 atomic force microscopy (AFM) 137, 146, 150, 163, 165, 201, β mutant 338 254, 255, 257, 258, 262, 270, 286, 478, 513, 520, 528, β mutation 347 861, 862, 864–865, 941–951 β polypeptide 175, 188, 205 fast scanning 950 ‘b’ position 454, 456 scan range 950 B-branch 301, 306 tip as nano-dissector 950 electron transfer 348, 958 atomic level structural model B-branch electron transfer 348, 958 photosynthetic unit 287 B-side electron transfer 346–348 atomic models 950 b-type heme 452, 752 atovaquone analog 445 B1020 150 ATP 90, 613 B780 934 ATP-binding cassette (ABC) 410 B798-832 35, 46 ATP-binding cassette transporter complex 410 B800 142, 150, 203, 214, 225–226, 878, 882–885 ATP-synthase 475–493, 942 B800-814 46 ATP:sulfate adenylyltransferase 610 B800-820 46, 150 ATP analog 806 B800-830 148, 150 ATPase 419, 748 B800-850 46, 150 CPx-type 661 B800-B850 920 P-type 661 fl uorescence up-conversion 225 ATPase domain 69 B800 molecule 203 ATP binding site 69 B806 46 ATP dependent oligomers 70 B820 182, 188, 932, 934 ATP hydrolysis 66, 70 dimeric structure 186 ATP production 425 hydrophobic surface area 183 ATP regenerating system 67 NMR experiments 186 ATP regeneration system 74 oligomerization 187 ATP sulfurylase 610, 611, 613, 615, 616 reversible dissociation 183 ATP synthase 254, 262, 264, 279, 476–488, 510, 538 B820-type complex 188 proton translocation 476–488 minimal requirements 190 ATP synthesis 510 B820 complex 157, 175, 183 ATP synthesis/hydrolysis 478–486 chemically synthesized polypeptides 189 auto-induce 844 heterodimeric B820 189 auto-oxidization 438 homodimeric B820 189 autophosphorylation 800, 802, 806 membrane-spanning middle segment 189 RegB 713 N-terminus 189 Avena sativa 815 protein interactions 189 average excitation lifetime 280 proteolysis 189 avoided level crossings 283 shorter synthetic polypeptides 189 Azoarcus 581, 588 B850 142, 214, 878, 885–889 Azotobacter vinelandii 637 B850 ring azoxystobin 442 elliptical deformation 207 B870 934 978 Index B875 150, 927 Mg coordination 184–188 B880 926, 932, 935 binding energy 185 B880 formation 931 modifi ed pigments 915 B890 150 molecule 204, 205 Bacillus 457, 669 distorted conformation 205 Bacillus PS3 479 monomer 338, 341 Bacillus selenitireducens 549, 664 π-π interactions 190 Bacillus subtilis 413, 813, 852 Qy-band 897 back-reaction 148 replacement 305 bacterial artifi cial chromosome (BAC) 45 spectra 897 bacterial plasma membrane 264 stereochemical aspects 915 bacteriochlorin 58, 897 surface area 897 bacteriochlorin exclusion 301 tetrapyrrole ring 42 bacteriochlorin replacement 302 transition dipoles 168 bacteriochlorin ring 141 water ligand 344 (bacterio)chlorophyll 916 bacteriochlorophyll-B850/protein interface 922 (bacterio)chlorophyll binding pocket 916 bacteriochlorophyll-binding proteins statistical analysis 916 synthetic 895, 896–907 binding 916 bacteriochlorophyll/protein interface 915, 916, 922 binding-motifs 916 packing interactions 923 binding pockets 919 bacteriochlorophyll/transmembrane helix interface 923 binding
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    US 2016O1861 68A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0186168 A1 Konieczka et al. (43) Pub. Date: Jun. 30, 2016 (54) PROCESSES AND HOST CELLS FOR Related U.S. Application Data GENOME, PATHWAY. AND BIOMOLECULAR (60) Provisional application No. 61/938,933, filed on Feb. ENGINEERING 12, 2014, provisional application No. 61/935,265, - - - filed on Feb. 3, 2014, provisional application No. (71) Applicant: ENEVOLV, INC., Cambridge, MA (US) 61/883,131, filed on Sep. 26, 2013, provisional appli (72) Inventors: Jay H. Konieczka, Cambridge, MA cation No. 61/861,805, filed on Aug. 2, 2013. (US); James E. Spoonamore, Publication Classification Cambridge, MA (US); Ilan N. Wapinski, Cambridge, MA (US); (51) Int. Cl. Farren J. Isaacs, Cambridge, MA (US); CI2N 5/10 (2006.01) Gregory B. Foley, Cambridge, MA (US) CI2N 15/70 (2006.01) CI2N 5/8 (2006.01) (21) Appl. No.: 14/909, 184 (52) U.S. Cl. 1-1. CPC ............ CI2N 15/1082 (2013.01); C12N 15/81 (22) PCT Filed: Aug. 4, 2014 (2013.01); C12N 15/70 (2013.01) (86). PCT No.: PCT/US1.4/49649 (57) ABSTRACT S371 (c)(1), The present disclosure provides compositions and methods (2) Date: Feb. 1, 2016 for genomic engineering. Patent Application Publication Jun. 30, 2016 Sheet 1 of 4 US 2016/O186168 A1 Patent Application Publication Jun. 30, 2016 Sheet 2 of 4 US 2016/O186168 A1 &&&&3&&3&&**??*,º**)..,.: ××××××××××××××××××××-************************** Patent Application Publication Jun. 30, 2016 Sheet 3 of 4 US 2016/O186168 A1 No.vaegwzºkgwaewaeg Patent Application Publication Jun. 30, 2016 Sheet 4 of 4 US 2016/O186168 A1 US 2016/01 86168 A1 Jun.
  • Comparing the Mechanisms of Metal Action in Bacteria: Insight Into Novel Genes Involved in Silver, Gallium and Copper Resistance and Toxicity in Escherichia Coli

    Comparing the Mechanisms of Metal Action in Bacteria: Insight Into Novel Genes Involved in Silver, Gallium and Copper Resistance and Toxicity in Escherichia Coli

    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2019-07-25 Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli Gugala, Natalie Gugala, N. (2019). Comparing the mechanisms of metal action in bacteria: insight into novel genes involved in silver, gallium and copper resistance and toxicity in Escherichia coli (Unpublished doctoral thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/110682 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca Gene Names GO terms (biological process) Score aaeA aaeA // "yhcQ"carboxylic // "b3241" acid // transport "ECK3230" // "transmembrane transport" -0.0487841 aaeB aaeB // "yhcP"transmembrane // "b3240" // "ECK3229"transport // "carboxylic acid transport" 0.10667059 aaeR aaeR // "yhcS"positive // "qseA" regulation // "b3243" of transcription, // "ECK3232" DNA-templated // "DNA-templated0.18076241 transcription, initiation" // "regulation of transcription, DNA-templated" // "transcription, DNA-templated" aaeX aaeX // "yhcR" // "b3242" //