Supporting Information for. Initial Biochemical and Functional Evaluation of Murine Calprotectin Reveals Ca(II)-
|
|
- Anthony Johnson
- 5 years ago
- Views:
Transcription
1 Supporting Information for Initial Biochemical and Functional Evaluation of Murine Calprotectin Reveals Ca(II)- Dependence and Its Ability to Chelate Multiple Nutrient Transition Metal Ions Rose C. Hadley, Yu Gu, and Elizabeth M. Nolan* Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA *Corresponding author: Phone: This Supporting Information includes: Design of the Synthetic Genes S2 Supporting Tables... S4 Table S1. Mass spectrometry of mcp subunits..... S4 Table S2. Metal content of representative protein preparations S4 Table S3. Analytical SEC elution volumes... S5 Table S4. Metal content of Tris:TSB from metal-depletion studies.. S6 Table S5. Bacterial strains used in this work S7 Supporting Figures S7 Figure S1. SDS-PAGE of purified proteins... S7 Figure S2. Circular dichroism spectra of.... S8 Figure S3. Thermal denaturation of mcp and.... S8 Figure S4. Antimicrobial activity of mcp, 20-h time point S9 S1
2 Design of the Synthetic Genes All synthetic genes were optimized for E. coli codon usage and ordered from DNA 2.0 in the pet41a vector. An NdeI restriction site was placed at the 5 end and a stop codon and an XhoI restriction site was placed at the 3 end. 1. Synthetic Gene for ms100a8 E. coli optimized nucleotide sequence for NdeI-mS100A8-Stop-XhoI: CAT ATG CCG AGC GAA CTG GAG AAA GCA CTG AGC AAC CTG ATC GAC GTC TAC CAC AAC TAC AGC AAT ATT CAA GGT AAT CAT CAC GCT CTG TAC AAA AAT GAT TTC AAG AAG ATG GTT ACC ACG GAG TGC CCG CAG TTC GTG CAG AAT ATC AAC ATT GAA AAC CTG TTC CGT GAG CTG GAC ATC AAC TCC GAT AAT GCC ATT AAC TTT GAA GAG TTT TTG GCG ATG GTT ATC AAA GTG GGC GTC GCG AGC CAC AAG GAC TCT CAT AAA GAG TAA CTC GAG Translated sequence for NdeI-mS100A8-Stop-XhoI: M P S E L E K A L S N L I D V Y H N Y S N I Q G N H H A L Y K N D F K K M V T T E C P Q F V Q N I N I E N L F R E L D I N S D N A I N F E E F L A M V I K V G V A S H K D S H K E Stop L E 2. Synthetic Gene for ms100a9 E. coli optimized nucleotide sequence for NdeI-mS100A9-Stop-XhoI: CAT ATG GCG AAC AAA GCA CCT AGC CAA ATG GAA CGC AGC ATC ACT ACT ATC ATC GAC ACT TTT CAT CAA TAC TCT CGT AAA GAG GGC CAC CCG GAT ACG CTG TCC AAG AAA GAG TTC CGC CAG ATG GTT GAG GCC CAG CTG GCG ACC TTT ATG AAG AAA GAA AAA CGT AAC GAG GCA CTG ATT AAC GAC ATT ATG GAA GAT CTG GAC ACC AAT CAA GAT AAT CAG CTG AGC TTC GAA GAG TGC ATG ATG CTG ATG GCG AAG TTG ATT TTC GCT TGC CAC GAG AAG CTG CAT GAA AAC AAT CCG CGT GGT CAT GGT CAC AGC CAC GGT AAG GGT TGT GGC AAA TAA CTC GAG Translated sequence for NdeI-mS100A9-Stop-XhoI: M A N K A P S Q M E R S I T T I I D T F H Q Y S R K E G H P D T L S K K E F R Q M V E A Q L A T F M K K E K R N E A L I N D I M E D L D T N Q D N Q L S F E E C M M L M A K L I F A C H E K L H E N N P R G H G H S H G K G C G K Stop L E S2
3 3. Synthetic Gene for ms100a9(c80s)(c91s)(c111s) E. coli optimized nucleotide sequence for NdeI-mS100A9(C80S)(C91S)(C111S)-Stop-XhoI: CAT ATG GCG AAC AAA GCA CCT AGC CAA ATG GAA CGC AGC ATC ACT ACT ATC ATC GAC ACT TTT CAT CAA TAC TCT CGT AAA GAG GGC CAC CCG GAT ACG CTG TCC AAG AAA GAG TTC CGC CAG ATG GTT GAG GCC CAG CTG GCG ACC TTT ATG AAG AAA GAA AAA CGT AAC GAG GCA CTG ATT AAC GAC ATT ATG GAA GAT CTG GAC ACC AAT CAA GAT AAT CAG CTG AGC TTC GAA GAG AGC ATG ATG CTG ATG GCG AAG TTG ATT TTC GCT AGC CAC GAG AAG CTG CAT GAA AAC AAT CCG CGT GGT CAT GGT CAC AGC CAC GGT AAG GGT AGT GGC AAA TAA CTC GAG Translated sequence for NdeI-mS100A9(C80S)(C91S)(C111S)-Stop-XhoI: M A N K A P S Q M E R S I T T I I D T F H Q Y S R K E G H P D T L S K K E F R Q M V E A Q L A T F M K K E K R N E A L I N D I M E D L D T N Q D N Q L S F E E S M M L M A K L I F A S H E K L H E N N P R G H G H S H G K G S G K Stop L E Mutations are highlighted in yellow. S3
4 Supporting Tables Table S1. Mass spectrometry of mcp subunits. Protein ms100a8 Calculated Mass ± N Met (g/mol) b ms100a8 Observed Mass (g/mol) c ms100a9 Calculated Mass ± N Met (g/mol) d ms100a9 Observed Mass (g/mol) mcp Table S2. Metal content of representative purified murine proteins. a Metal mcp (24 µm) b (7.7 µm) b [Mn] (µm) equivalents [Fe] (µm) equivalents [Co] (µm) equivalents [Ni] (µm) equivalents [Cu] (µm) equivalents [Zn] (µm) 0 64 equivalents a Metal content was determined by ICP-MS. b Concentration of protein in the sample. S4
5 Table S3. Analytical SEC elution volume and calculated molecular weight of proteins. Protein a [Ca(II)] (mm) V e (ml) b MW (kda) mcp a The protein concentration was 100 µm. The running buffer was 75 mm HEPES, 100 mm NaCl, ph 7.0. The elution volume (V e) corresponds to the maximum peak absorbance at 280 nm. S5
6 Table S4. Metal content (µm) of Tris:TSB medium with or without treatment with 250 µg/ml mcp,, or hcp-ser. a Metal Protein n.s. b SEM Ca(II) SEM BME SEM Ca(II), SEM BME Mn untreated mcp hcp-ser Fe untreated mcp hcp-ser Co untreated mcp hcp-ser Ni untreated mcp hcp-ser Cu untreated mcp hcp-ser Zn untreated mcp hcp-ser a Metal content was determined by ICP-MS (mean ± SEM, n ³ 4). b No supplement was added to the Tris:TSB medium. S6
7 Table S5. Bacterial strains used in this work. Strain Growth Mediuma Source Escherichia coli CFT073 TSB ATCC Acinetobacter baumannii TSB ATCC Staphylococcus aureus USA 300 JE2 TSB NARSA repository Staphylococcus epidermidis NRS101 BHI NARSA repository Listeria monocytogenes BHI ATCC Lactobacillus plantarum WCFS1 MRS ATCC a The medium used for culturing and diluted with AMA buffer for the AMA assays. Supporting Figures kda kda hcp-ser mcp Figure S1. Purity of recombinant proteins by SDS-PAGE (15% Tris-glycine). The leftmost lane in each gel is a P7712S molecular weight ladder (New England Biolabs). S7
8 [Θ] λ (deg cm 2 dmol -1 ) Wavelength (nm) Figure S2. CD spectra of in the absence (black) and presence (red) of 2 mm Ca(II) (1 mm Tris-HCl, ph 7.5, 25 o C). Figure 2 of the main text presents the CD spectra of mcp. A mcp mcp +Ca(II) B +Ca(II) Fraction Unfolded 0.8 Fraction Unfolded T ( C) T ( C) Figure S3. Representative thermal denaturation plots for 10 µm of (A) mcp or (B) in the absence (black) and presence (red) of 3 mm Ca(II) (1 mm Tris-HCl, 1 mm DTT, ph 7.5). Each trace was normalized to the CD signal at 222 nm at 95 C to obtain the fraction of unfolded protein. S8
9 A mcp B E. coli CFT073 E. coli CFT A. 600 baumannii S. aureus USA300 JE S. epidermidis NRS L. monocytogenes A. baumannii S. aureus USA300 JE S. epidermidis NRS L. monocytogenes L. 600 plantarum 800 WCFS L. 600 plantarum 800 WCFS [mcp] µg/ml [] µg/ml Ca(II) +Ca(II) Figure S4. mcp inhibits growth of various bacterial species. (A) Growth inhibitory activity of mcp. (B) Growth inhibitory activity of. Both proteins were assayed in the absence (black) and presence (red) of a 2-mM Ca(II) supplement in the AMA medium (Tris:TSB, T = 37 o C, 20 h) (mean ± SDM, n ³ 3).Figure 5 of the main text contains data from the same assay at the 8-h timepoint. S9
Practical Bioinformatics
5/2/2017 Dictionaries d i c t i o n a r y = { A : T, T : A, G : C, C : G } d i c t i o n a r y [ G ] d i c t i o n a r y [ N ] = N d i c t i o n a r y. h a s k e y ( C ) Dictionaries g e n e t i c C o
More informationSUPPORTING INFORMATION FOR. SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA
SUPPORTING INFORMATION FOR SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA Aik T. Ooi, Cliff I. Stains, Indraneel Ghosh *, David J. Segal
More informationHigh throughput near infrared screening discovers DNA-templated silver clusters with peak fluorescence beyond 950 nm
Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2018 High throughput near infrared screening discovers DNA-templated silver clusters with peak fluorescence
More informationClay Carter. Department of Biology. QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.
QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture. Clay Carter Department of Biology QuickTime and a TIFF (LZW) decompressor are needed to see this picture. Ornamental tobacco
More informationSupplementary Information
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 Directed self-assembly of genomic sequences into monomeric and polymeric branched DNA structures
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Zn 2+ -binding sites in USP18. (a) The two molecules of USP18 present in the asymmetric unit are shown. Chain A is shown in blue, chain B in green. Bound Zn 2+ ions are shown as
More informationSUPPLEMENTARY DATA - 1 -
- 1 - SUPPLEMENTARY DATA Construction of B. subtilis rnpb complementation plasmids For complementation, the B. subtilis rnpb wild-type gene (rnpbwt) under control of its native rnpb promoter and terminator
More informationSEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS. Prokaryotes and Eukaryotes. DNA and RNA
SEQUENCE ALIGNMENT BACKGROUND: BIOINFORMATICS 1 Prokaryotes and Eukaryotes 2 DNA and RNA 3 4 Double helix structure Codons Codons are triplets of bases from the RNA sequence. Each triplet defines an amino-acid.
More informationCrick s early Hypothesis Revisited
Crick s early Hypothesis Revisited Or The Existence of a Universal Coding Frame Ryan Rossi, Jean-Louis Lassez and Axel Bernal UPenn Center for Bioinformatics BIOINFORMATICS The application of computer
More informationNumber-controlled spatial arrangement of gold nanoparticles with
Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2016 Number-controlled spatial arrangement of gold nanoparticles with DNA dendrimers Ping Chen,*
More informationCharacterization of Pathogenic Genes through Condensed Matrix Method, Case Study through Bacterial Zeta Toxin
International Journal of Genetic Engineering and Biotechnology. ISSN 0974-3073 Volume 2, Number 1 (2011), pp. 109-114 International Research Publication House http://www.irphouse.com Characterization of
More informationSupplementary Information for
Supplementary Information for Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding Sebastian Pechmann & Judith Frydman Department of Biology and BioX, Stanford
More informationSupplemental data. Pommerrenig et al. (2011). Plant Cell /tpc
Supplemental Figure 1. Prediction of phloem-specific MTK1 expression in Arabidopsis shoots and roots. The images and the corresponding numbers showing absolute (A) or relative expression levels (B) of
More informationAdvanced topics in bioinformatics
Feinberg Graduate School of the Weizmann Institute of Science Advanced topics in bioinformatics Shmuel Pietrokovski & Eitan Rubin Spring 2003 Course WWW site: http://bioinformatics.weizmann.ac.il/courses/atib
More informationSupplemental Figure 1.
A wt spoiiiaδ spoiiiahδ bofaδ B C D E spoiiiaδ, bofaδ Supplemental Figure 1. GFP-SpoIVFA is more mislocalized in the absence of both BofA and SpoIIIAH. Sporulation was induced by resuspension in wild-type
More informationSSR ( ) Vol. 48 No ( Microsatellite marker) ( Simple sequence repeat,ssr),
48 3 () Vol. 48 No. 3 2009 5 Journal of Xiamen University (Nat ural Science) May 2009 SSR,,,, 3 (, 361005) : SSR. 21 516,410. 60 %96. 7 %. (),(Between2groups linkage method),.,, 11 (),. 12,. (, ), : 0.
More informationSupporting Information
Supporting Information T. Pellegrino 1,2,3,#, R. A. Sperling 1,#, A. P. Alivisatos 2, W. J. Parak 1,2,* 1 Center for Nanoscience, Ludwig Maximilians Universität München, München, Germany 2 Department of
More informationBuilding a Multifunctional Aptamer-Based DNA Nanoassembly for Targeted Cancer Therapy
Supporting Information Building a Multifunctional Aptamer-Based DNA Nanoassembly for Targeted Cancer Therapy Cuichen Wu,, Da Han,, Tao Chen,, Lu Peng, Guizhi Zhu,, Mingxu You,, Liping Qiu,, Kwame Sefah,
More informationSupplemental Table 1. Primers used for cloning and PCR amplification in this study
Supplemental Table 1. Primers used for cloning and PCR amplification in this study Target Gene Primer sequence NATA1 (At2g393) forward GGG GAC AAG TTT GTA CAA AAA AGC AGG CTT CAT GGC GCC TCC AAC CGC AGC
More informationNSCI Basic Properties of Life and The Biochemistry of Life on Earth
NSCI 314 LIFE IN THE COSMOS 4 Basic Properties of Life and The Biochemistry of Life on Earth Dr. Karen Kolehmainen Department of Physics CSUSB http://physics.csusb.edu/~karen/ WHAT IS LIFE? HARD TO DEFINE,
More informationElectronic supplementary material
Applied Microbiology and Biotechnology Electronic supplementary material A family of AA9 lytic polysaccharide monooxygenases in Aspergillus nidulans is differentially regulated by multiple substrates and
More informationTM1 TM2 TM3 TM4 TM5 TM6 TM bp
a 467 bp 1 482 2 93 3 321 4 7 281 6 21 7 66 8 176 19 12 13 212 113 16 8 b ATG TCA GGA CAT GTA ATG GAG GAA TGT GTA GTT CAC GGT ACG TTA GCG GCA GTA TTG CGT TTA ATG GGC GTA GTG M S G H V M E E C V V H G T
More informationTable S1. Primers and PCR conditions used in this paper Primers Sequence (5 3 ) Thermal conditions Reference Rhizobacteria 27F 1492R
Table S1. Primers and PCR conditions used in this paper Primers Sequence (5 3 ) Thermal conditions Reference Rhizobacteria 27F 1492R AAC MGG ATT AGA TAC CCK G GGY TAC CTT GTT ACG ACT T Detection of Candidatus
More informationModelling and Analysis in Bioinformatics. Lecture 1: Genomic k-mer Statistics
582746 Modelling and Analysis in Bioinformatics Lecture 1: Genomic k-mer Statistics Juha Kärkkäinen 06.09.2016 Outline Course introduction Genomic k-mers 1-Mers 2-Mers 3-Mers k-mers for Larger k Outline
More information6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008
MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.
More informationSUPPLEMENTARY INFORMATION
DOI:.8/NCHEM. Conditionally Fluorescent Molecular Probes for Detecting Single Base Changes in Double-stranded DNA Sherry Xi Chen, David Yu Zhang, Georg Seelig. Analytic framework and probe design.. Design
More information3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies. 3. Evolution makes sense of homologies
Richard Owen (1848) introduced the term Homology to refer to structural similarities among organisms. To Owen, these similarities indicated that organisms were created following a common plan or archetype.
More informationThe role of the FliD C-terminal domain in pentamer formation and
The role of the FliD C-terminal domain in pentamer formation and interaction with FliT Hee Jung Kim 1,2,*, Woongjae Yoo 3,*, Kyeong Sik Jin 4, Sangryeol Ryu 3,5 & Hyung Ho Lee 1, 1 Department of Chemistry,
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION DOI:.38/NCHEM.246 Optimizing the specificity of nucleic acid hyridization David Yu Zhang, Sherry Xi Chen, and Peng Yin. Analytic framework and proe design 3.. Concentration-adjusted
More informationevoglow - express N kit Cat. No.: product information broad host range vectors - gram negative bacteria
evoglow - express N kit broad host range vectors - gram negative bacteria product information Cat. No.: 2.1.020 evocatal GmbH 2 Content: Product Overview... 4 evoglow express N kit... 4 The evoglow Fluorescent
More informationEvolvable Neural Networks for Time Series Prediction with Adaptive Learning Interval
Evolvable Neural Networs for Time Series Prediction with Adaptive Learning Interval Dong-Woo Lee *, Seong G. Kong *, and Kwee-Bo Sim ** *Department of Electrical and Computer Engineering, The University
More informationevoglow - express N kit distributed by Cat.#: FP product information broad host range vectors - gram negative bacteria
evoglow - express N kit broad host range vectors - gram negative bacteria product information distributed by Cat.#: FP-21020 Content: Product Overview... 3 evoglow express N -kit... 3 The evoglow -Fluorescent
More informationpart 3: analysis of natural selection pressure
part 3: analysis of natural selection pressure markov models are good phenomenological codon models do have many benefits: o principled framework for statistical inference o avoiding ad hoc corrections
More informationThe Trigram and other Fundamental Philosophies
The Trigram and other Fundamental Philosophies by Weimin Kwauk July 2012 The following offers a minimal introduction to the trigram and other Chinese fundamental philosophies. A trigram consists of three
More informationydci GTC TGT TTG AAC GCG GGC GAC TGG GCG CGC AAT TAA CGG TGT GTA GGC TGG AGC TGC TTC
Table S1. DNA primers used in this study. Name ydci P1ydcIkd3 Sequence GTC TGT TTG AAC GCG GGC GAC TGG GCG CGC AAT TAA CGG TGT GTA GGC TGG AGC TGC TTC Kd3ydcIp2 lacz fusion YdcIendP1 YdcItrgP2 GAC AGC
More informationCodon Distribution in Error-Detecting Circular Codes
life Article Codon Distribution in Error-Detecting Circular Codes Elena Fimmel, * and Lutz Strüngmann Institute for Mathematical Biology, Faculty of Computer Science, Mannheim University of Applied Sciences,
More informationChemiScreen CaS Calcium Sensor Receptor Stable Cell Line
PRODUCT DATASHEET ChemiScreen CaS Calcium Sensor Receptor Stable Cell Line CATALOG NUMBER: HTS137C CONTENTS: 2 vials of mycoplasma-free cells, 1 ml per vial. STORAGE: Vials are to be stored in liquid N
More informationProtein Threading. Combinatorial optimization approach. Stefan Balev.
Protein Threading Combinatorial optimization approach Stefan Balev Stefan.Balev@univ-lehavre.fr Laboratoire d informatique du Havre Université du Havre Stefan Balev Cours DEA 30/01/2004 p.1/42 Outline
More informationWhy do more divergent sequences produce smaller nonsynonymous/synonymous
Genetics: Early Online, published on June 21, 2013 as 10.1534/genetics.113.152025 Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?
More informationEncoding of Amino Acids and Proteins from a Communications and Information Theoretic Perspective
Jacobs University Bremen Encoding of Amino Acids and Proteins from a Communications and Information Theoretic Perspective Semester Project II By: Dawit Nigatu Supervisor: Prof. Dr. Werner Henkel Transmission
More informationPathways and Controls of N 2 O Production in Nitritation Anammox Biomass
Supporting Information for Pathways and Controls of N 2 O Production in Nitritation Anammox Biomass Chun Ma, Marlene Mark Jensen, Barth F. Smets, Bo Thamdrup, Department of Biology, University of Southern
More informationSex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi
Supporting Information http://www.genetics.org/cgi/content/full/genetics.110.116228/dc1 Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi Ben
More informationRegulatory Sequence Analysis. Sequence models (Bernoulli and Markov models)
Regulatory Sequence Analysis Sequence models (Bernoulli and Markov models) 1 Why do we need random models? Any pattern discovery relies on an underlying model to estimate the random expectation. This model
More informationEvolutionary dynamics of abundant stop codon readthrough in Anopheles and Drosophila
biorxiv preprint first posted online May. 3, 2016; doi: http://dx.doi.org/10.1101/051557. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights reserved.
More informationNear-instant surface-selective fluorogenic protein quantification using sulfonated
Electronic Supplementary Material (ESI) for rganic & Biomolecular Chemistry. This journal is The Royal Society of Chemistry 2014 Supplemental nline Materials for ear-instant surface-selective fluorogenic
More informationThe 3 Genomic Numbers Discovery: How Our Genome Single-Stranded DNA Sequence Is Self-Designed as a Numerical Whole
Applied Mathematics, 2013, 4, 37-53 http://dx.doi.org/10.4236/am.2013.410a2004 Published Online October 2013 (http://www.scirp.org/journal/am) The 3 Genomic Numbers Discovery: How Our Genome Single-Stranded
More informationRe- engineering cellular physiology by rewiring high- level global regulatory genes
Re- engineering cellular physiology by rewiring high- level global regulatory genes Stephen Fitzgerald 1,2,, Shane C Dillon 1, Tzu- Chiao Chao 2, Heather L Wiencko 3, Karsten Hokamp 3, Andrew DS Cameron
More informationIdentification of a Locus Involved in the Utilization of Iron by Haemophilus influenzae
INFECrION AND IMMUNITY, OCt. 1994, p. 4515-4525 0019-9567/94/$04.00+0 Copyright 1994, American Society for Microbiology Vol. 62, No. 10 Identification of a Locus Involved in the Utilization of Iron by
More informationpart 4: phenomenological load and biological inference. phenomenological load review types of models. Gαβ = 8π Tαβ. Newton.
2017-07-29 part 4: and biological inference review types of models phenomenological Newton F= Gm1m2 r2 mechanistic Einstein Gαβ = 8π Tαβ 1 molecular evolution is process and pattern process pattern MutSel
More informationBiosynthesis of Bacterial Glycogen: Primary Structure of Salmonella typhimurium ADPglucose Synthetase as Deduced from the
JOURNAL OF BACTERIOLOGY, Sept. 1987, p. 4355-4360 0021-9193/87/094355-06$02.00/0 Copyright X) 1987, American Society for Microbiology Vol. 169, No. 9 Biosynthesis of Bacterial Glycogen: Primary Structure
More informationSupporting Information. An Electric Single-Molecule Hybridisation Detector for short DNA Fragments
Supporting Information An Electric Single-Molecule Hybridisation Detector for short DNA Fragments A.Y.Y. Loh, 1 C.H. Burgess, 2 D.A. Tanase, 1 G. Ferrari, 3 M.A. Maclachlan, 2 A.E.G. Cass, 1 T. Albrecht*
More informationTitle: Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation
Supplementary Information Title: Robust analysis of synthetic label-free DNA junctions in solution by X-ray scattering and molecular simulation Kyuhyun Im 1,5, Daun Jeong 2,5, Jaehyun Hur 1, Sung-Jin Kim
More informationSupplementary Information
Supplementary Information Arginine-rhamnosylation as new strategy to activate translation elongation factor P Jürgen Lassak 1,2,*, Eva Keilhauer 3, Max Fürst 1,2, Kristin Wuichet 4, Julia Gödeke 5, Agata
More informationTiming molecular motion and production with a synthetic transcriptional clock
Timing molecular motion and production with a synthetic transcriptional clock Elisa Franco,1, Eike Friedrichs 2, Jongmin Kim 3, Ralf Jungmann 2, Richard Murray 1, Erik Winfree 3,4,5, and Friedrich C. Simmel
More informationChain-like assembly of gold nanoparticles on artificial DNA templates via Click Chemistry
Electronic Supporting Information: Chain-like assembly of gold nanoparticles on artificial DNA templates via Click Chemistry Monika Fischler, Alla Sologubenko, Joachim Mayer, Guido Clever, Glenn Burley,
More informationIntroduction to Molecular Phylogeny
Introduction to Molecular Phylogeny Starting point: a set of homologous, aligned DNA or protein sequences Result of the process: a tree describing evolutionary relationships between studied sequences =
More informationChemical Biology on Genomic DNA: minimizing PCR bias. Electronic Supplementary Information (ESI) for Chemical Communications
Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2014 Chemical Biology on Genomic DA: minimizing PCR bias Gordon R. McInroy, Eun-Ang Raiber, & Shankar
More informationGlucosylglycerate phosphorylase, a novel enzyme specificity involved in compatible solute metabolism
Supplementary Information for Glucosylglycerate phosphorylase, a novel enzyme specificity involved in compatible solute metabolism Jorick Franceus, Denise Pinel, Tom Desmet Corresponding author: Tom Desmet,
More information160, and 220 bases, respectively, shorter than pbr322/hag93. (data not shown). The DNA sequence of approximately 100 bases of each
JOURNAL OF BACTEROLOGY, JUlY 1988, p. 3305-3309 0021-9193/88/073305-05$02.00/0 Copyright 1988, American Society for Microbiology Vol. 170, No. 7 Construction of a Minimum-Size Functional Flagellin of Escherichia
More informationAtTIL-P91V. AtTIL-P92V. AtTIL-P95V. AtTIL-P98V YFP-HPR
Online Resource 1. Primers used to generate constructs AtTIL-P91V, AtTIL-P92V, AtTIL-P95V and AtTIL-P98V and YFP(HPR) using overlapping PCR. pentr/d- TOPO-AtTIL was used as template to generate the constructs
More informationevoglow yeast kit distributed by product information Cat.#: FP-21040
evoglow yeast kit product information distributed by Cat.#: FP-21040 Flavin-mononucleotide-based Fluorescent Protein (FbFP) evoglow basic kit Cat.# FP-21010 Quantity 20 µg each General Information Fluorescent
More informationDiversity of Chlamydia trachomatis Major Outer Membrane
JOURNAL OF ACTERIOLOGY, Sept. 1987, p. 3879-3885 Vol. 169, No. 9 0021-9193/87/093879-07$02.00/0 Copyright 1987, American Society for Microbiology Diversity of Chlamydia trachomatis Major Outer Membrane
More informationevoglow basic kit product information
evoglow basic kit product information Cat. No.: 2.1.010 Flavin-mononucleotide-based Fluorescent Protein (FbFP) evoglow basic kit Catalog No. evo-2.1.010 Quantity 20 µg each General Information Fluorescent
More informationInsects act as vectors for a number of important diseases of
pubs.acs.org/synthbio Novel Synthetic Medea Selfish Genetic Elements Drive Population Replacement in Drosophila; a Theoretical Exploration of Medea- Dependent Population Suppression Omar S. Abari,,# Chun-Hong
More informationTHE MATHEMATICAL STRUCTURE OF THE GENETIC CODE: A TOOL FOR INQUIRING ON THE ORIGIN OF LIFE
STATISTICA, anno LXIX, n. 2 3, 2009 THE MATHEMATICAL STRUCTURE OF THE GENETIC CODE: A TOOL FOR INQUIRING ON THE ORIGIN OF LIFE Diego Luis Gonzalez CNR-IMM, Bologna Section, Via Gobetti 101, I-40129, Bologna,
More informationElectronic Supporting Information for
Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2018 Electronic Supporting Information for A DNA-conjugated small molecule catalyst enzyme mimic
More informationFliZ Is a Posttranslational Activator of FlhD 4 C 2 -Dependent Flagellar Gene Expression
JOURNAL OF BACTERIOLOGY, July 2008, p. 4979 4988 Vol. 190, No. 14 0021-9193/08/$08.00 0 doi:10.1128/jb.01996-07 Copyright 2008, American Society for Microbiology. All Rights Reserved. FliZ Is a Posttranslational
More informationcodon substitution models and the analysis of natural selection pressure
2015-07-20 codon substitution models and the analysis of natural selection pressure Joseph P. Bielawski Department of Biology Department of Mathematics & Statistics Dalhousie University introduction morphological
More informationSupplementary information. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization.
Supplementary information Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. Benjamin Cressiot #, Sandra J. Greive #, Wei Si ^#,
More informationdead, a New Escherichia coli Gene Encoding a Presumed
JOURNAL OF BACTERIOLOGY, June 1991, p. 3291-3302 0021-9193/91/113291-12$02.00/0 Copyright 1991, American Society for Microbiology Vol. 173, No. 11 dead, a New Escherichia coli Gene Encoding a Presumed
More informationIt is the author's version of the article accepted for publication in the journal "Biosystems" on 03/10/2015.
It is the author's version of the article accepted for publication in the journal "Biosystems" on 03/10/2015. The system-resonance approach in modeling genetic structures Sergey V. Petoukhov Institute
More informationTable S1. DNA oligonucleo3des used for 3D pol mutagenesis. Fingers Domain Entry Channel. Fidelity
Table S1. DNA oligonucleo3des used for 3D pol mutagenesis. Fingers Domain Entry Channel Fidelity Charged Residues Interac9ng with Template and Product RNAs Thumb Domain 3D pol Mutations Parental codon
More informationAn internal electron reservoir enhances catalytic CO 2 reduction by a semisynthetic enzyme
Electronic Supplementary Material (ESI) for ChemComm. This journal is The Royal Society of Chemistry 2016 An internal electron reservoir enhances catalytic CO 2 reduction by a semisynthetic enzyme Camille
More informationMicroGenomics. Universal replication biases in bacteria
Molecular Microbiology (1999) 32(1), 11±16 MicroGenomics Universal replication biases in bacteria Eduardo P. C. Rocha, 1,2 Antoine Danchin 2 and Alain Viari 1,3 * 1 Atelier de BioInformatique, UniversiteÂ
More informationWorld Journal of Pharmaceutical Research SJIF Impact Factor 8.074
SJIF Impact Factor 8.074 Volume 7, Issue 5, 966-973. Research Article ISSN 2277 7105 MOLECULAR DETECTION OF ENTEROTOXIGENIC ISOLATES OF SALMONELLA TYPHIMURIUM, SHIGELLA FLEXNERI AND STAPHYLOCOCCUS AUREUS
More informationSymmetry Studies. Marlos A. G. Viana
Symmetry Studies Marlos A. G. Viana aaa aac aag aat caa cac cag cat aca acc acg act cca ccc ccg cct aga agc agg agt cga cgc cgg cgt ata atc atg att cta ctc ctg ctt gaa gac gag gat taa tac tag tat gca gcc
More informationAppendix B Protein-Signaling Networks from Single-cell Fluctuations and Information Theory Profiling B.1. Introduction
92 Appendix B Protein-Signaling Networks from Single-cell Fluctuations and Information Theory Profiling B.1. Introduction Protein-signaling pathways play important roles in tissue processes ranging from
More informationCharacterization of Multiple-Antimicrobial-Resistant Salmonella Serovars Isolated from Retail Meats
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Jan. 2004, p. 1 7 Vol. 70, No. 1 0099-2240/04/$08.00 0 DOI: 10.1128/AEM.70.1.1 7.2004 Copyright 2004, American Society for Microbiology. All Rights Reserved. Characterization
More informationDNA sequence analysis of the imp UV protection and mutation operon of the plasmid TP110: identification of a third gene
QD) 1990 Oxford University Press Nucleic Acids Research, Vol. 18, No. 17 5045 DNA sequence analysis of the imp UV protection and mutation operon of the plasmid TP110: identification of a third gene David
More informationSupplemental Figure 1. Differences in amino acid composition between the paralogous copies Os MADS17 and Os MADS6.
Supplemental Data. Reinheimer and Kellogg (2009). Evolution of AGL6-like MADSbox genes in grasses (Poaceae): ovule expression is ancient and palea expression is new Supplemental Figure 1. Differences in
More informationANALYZING THE DIVERSITY OF A SMALL ANTIBODY MIMIC LIBRARY. Nick Empey. Chapel Hill 2010
ANALYZING THE DIVERSITY OF A SMALL ANTIBODY MIMIC LIBRARY Nick Empey A thesis submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for
More informationAn Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded by the Common Circular Code
Bulletin of Mathematical Biology (2007) 69: 677 698 DOI 10.1007/s11538-006-9147-z ORIGINAL ARTICLE An Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded
More informationEvolutionary Analysis of Viral Genomes
University of Oxford, Department of Zoology Evolutionary Biology Group Department of Zoology University of Oxford South Parks Road Oxford OX1 3PS, U.K. Fax: +44 1865 271249 Evolutionary Analysis of Viral
More informationSupplemental Figure 1. Phenotype of ProRGA:RGAd17 plants under long day
Supplemental Figure 1. Phenotype of ProRGA:RGAd17 plants under long day conditions. Photo was taken when the wild type plant started to bolt. Scale bar represents 1 cm. Supplemental Figure 2. Flowering
More informationEvidence for RNA editing in mitochondria of all major groups of
Proc. Natl. Acad. Sci. USA Vol. 91, pp. 629-633, January 1994 Plant Biology Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta RUDOLF HIESEL, BRUNO COMBETTES*,
More informationMotif Finding Algorithms. Sudarsan Padhy IIIT Bhubaneswar
Motif Finding Algorithms Sudarsan Padhy IIIT Bhubaneswar Outline Gene Regulation Regulatory Motifs The Motif Finding Problem Brute Force Motif Finding Consensus and Pattern Branching: Greedy Motif Search
More informationCodon-model based inference of selection pressure. (a very brief review prior to the PAML lab)
Codon-model based inference of selection pressure (a very brief review prior to the PAML lab) an index of selection pressure rate ratio mode example dn/ds < 1 purifying (negative) selection histones dn/ds
More informationUsing algebraic geometry for phylogenetic reconstruction
Using algebraic geometry for phylogenetic reconstruction Marta Casanellas i Rius (joint work with Jesús Fernández-Sánchez) Departament de Matemàtica Aplicada I Universitat Politècnica de Catalunya IMA
More informationHow DNA barcoding can be more effective in microalgae. identification: a case of cryptic diversity revelation in Scenedesmus
How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae) Shanmei Zou, Cong Fei, Chun Wang, Zhan Gao, Yachao Bao, Meilin
More informationNEW DNA CYCLIC CODES OVER RINGS
NEW DNA CYCLIC CODES OVER RINGS NABIL BENNENNI, KENZA GUENDA AND SIHEM MESNAGER arxiv:1505.06263v1 [cs.it] 23 May 2015 Abstract. This paper is dealing with DNA cyclic codes which play an important role
More informationSupporting Material. Protein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling
Supporting Material Protein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling Young Shik Shin, Δ F. Remacle, ǁ Δ Rong Fan, Kiwook Hwang, Wei Wei, Habib Ahmad, R. D. Levine
More informationSupplementary Materials for
www.sciencetranslationalmedicine.org/cgi/content/full/4/148/148ra116/dc1 Supplementary Materials for Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing
More informationSUPPLEMENTARY INFORMATION
DOI: 10.1038/NCHEM.1856 A protein engineered to bind uranyl selectively and with femtomolar affinity Lu Zhou, Mike Bosscher, Salih Özçubukçu, Changsheng Zhang, Liang Zhang, Wen Zhang, Charles J. Li, Jianzhao
More informationSupporting Information
Supporting Information Mixed DNA-functionalized Nanoparticle Probes for Surface Enhanced Raman Scattering-based Multiplex DNA Detection Zhiliang Zhang, a, b Yongqiang Wen,* a Ying Ma, a Jia Luo, a Lei
More informationStructure of the Mycobacterium tuberculosis Antigen 88, a Protein Related to the Escherichia coli PstA Periplasmic
NFECrlON AND MMUNTY, Mar. 1994, p. 849-854 0019-9567/94/$04.00+0 Copyright 1994, American Society for Microbiology Vol. 62, No. 3 Structure of the Mycobacterium tuberculosis Antigen 88, a Protein Related
More informationCONTEXT-FREE CODON ALIGNMENT
CONTEXT-FREE CODON ALIGNMENT CONTEXT-FREE CODON ALIGNMENT By BIN WU, B.SC. A Thesis Submitted to the School of Graduate Studies in Partial Fulfilment of the Requirements for the Degree Master of Science
More informationSupplementary Figure 1. Schematic of split-merger microfluidic device used to add transposase to template drops for fragmentation.
Supplementary Figure 1. Schematic of split-merger microfluidic device used to add transposase to template drops for fragmentation. Inlets are labelled in blue, outlets are labelled in red, and static channels
More informationThe Cell Cycle & Cell Division. Cell Function Cell Cycle. What does the cell do = cell physiology:
Cell Function 2404 What does the cell do = cell physiology: 1. Cell Cycle & Cell Division 2. Membrane Transport 3. Secretion 4. Membrane Potential 5. Metabolism 6. Cellular Interactions 7. Cellular Control:
More informationA functional homologue of goosecoid in Drosophila
Development 122, 1641-1650 (1996) Printed in Great Britain The Company of Biologists Limited 1996 DEV1069 1641 A functional homologue of goosecoid in Drosophila Anne Goriely 1, Michael Stella 1, Catherine
More informationGene manipulation in Bacillus thuringiensis : Biopesticide Development
Gene manipulation in Bacillus thuringiensis : Biopesticide Development For safer Environment, Agriculture and Food! Samir JAOUA Univ. of Qatar, CAS, Dept of Biol. & Environ. Sc / Centre of Biotechno. Sfax,
More information