Impact of substrate moisture content on growth and performance of black soldier fly larvae

Experimental data and data analyses growth, respiration and performance of black soldier fly larvae grown at different substrate moisture content

Kirkegaard2017 - 16S rRNA gene amplicon survey of anaerobic digesters

RData file with OTUtables and metadata for a comprehensive survey of anaerobic digester

Calmodulin mutant - F141L apo-form Unstructured C-domain

Assembly members: entity_1, polymer, 148 residues, 16687.334 Da. Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens Experimental source: Production method: recombinant technology Host organism: Escherichia coli Entity Sequences (FASTA): entity_1: ADQLTEEQIAEFKEAFSLFD KDGDGTITTKELGTVMRSLG QNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEE LVQMMTA

Calcium bound form of human calmodulin mutant F141L

Assembly members: entity_1, polymer, 148 residues, 16687.334 Da. entity_CA, non-polymer, 40.078 Da. Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens Experimental source: Production method: recombinant technology Host organism: Escherichia coli Entity Sequences (FASTA): entity_1: ADQLTEEQIAEFKEAFSLFD KDGDGTITTKELGTVMRSLG QNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEE LVQMMTA

2MJS : Anoplin R5K T8W in DPC micelles

Experimental Technique/Method:SOLUTION NMR Resolution: Classification:ANTIMICROBIAL PROTEIN Release Date:2014-12-03 Deposition Date:2014-01-16 Revision Date:2015-01-14#2015-01-28 Molecular Weight:24057.64 Macromolecule Type:Protein Residue Count:11 Atom Site Count:1582 DOI:10.2210/pdb2mjs/pdb Abstract: Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure-activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL-NH2 ) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or-most efficiently-a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α-helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide

2MJT : Anoplin R5F T8W in DPC micelles

Experimental Technique/Method:SOLUTION NMR Resolution: Classification:ANTIMICROBIAL PROTEIN Release Date:2014-12-03 Deposition Date:2014-01-16 Revision Date:2015-01-14#2015-01-28 Molecular Weight:24075.64 Macromolecule Type:Protein Residue Count:11 Atom Site Count:1584 DOI:10.2210/pdb2mjt/pdb Abstract: Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure-activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL-NH2 ) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or-most efficiently-a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α-helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide

Influence of biofilm growth age, media, antibiotic concentration and exposure time on Staphylococcus aureus and Pseudomonas aeruginosa biofilm removal in vitro

Abstract Background Biofilm is known to be tolerant towards antibiotics and difficult to eradicate. Numerous studies have reported minimum biofilm eradication concentration (MBEC) values of antibiotics for many known biofilm pathogens. However, the experimental parameters applied in these studies differ considerably, and often the rationale behind the experimental design are not well described. This makes it difficult to compare the findings. To demonstrate the importance of experimental parameters, we investigated the influence of biofilm growth age, antibiotic concentration and treatment duration, and growth media on biofilm eradication. Additionally, OSTEOmycin™, a clinically used antibiotic containing allograft bone product, was tested for antibiofilm efficacy. Results The commonly used Calgary biofilm device was used to grow 24 h and 72 h biofilms of Staphylococcus aureus and Pseudomonas aeruginosa, which were treated with time-dependent vancomycin (up to 3000 mg L− 1) and concentration-dependent tobramycin (up to 80 mg L− 1), respectively. Two common bacteriological growth media, tryptic soy broth (TSB) and cation-adjusted Mueller Hinton broth (CaMHB), were tested. We found for both species that biofilms were more difficult to kill in TSB than in CaMHB. Furthermore, young biofilms (24 h) were easier to eradicate than old biofilms (72 h). In agreement with vancomycin being time-dependent, extension of the vancomycin exposure increased killing of S. aureus biofilms. Tobramycin treatment of 24 h P. aeruginosa biofilms was found concentration-dependent and time-independent, however, increasing killing was indicated for 72 h P. aeruginosa biofilms. Treatment with tobramycin containing OSTEOmycin T™ removed 72 h and 168 h P. aeruginosa biofilms after 1 day treatment, while few 72 h S. aureus biofilms survived after 2 days treatment with vancomycin containing OSTEOmycin V™. Conclusions This study demonstrated biofilm removal efficacy was influenced by media, biofilm age and antibiotic concentration and treatment duration. It is therefore necessary to taking these parameters into consideration when designing experiments. The results of OSTEOmycin™ products indicated that simple in vitro biofilm test could be used for initial screening of antibiofilm products. For clinical application, a more clinically relevant biofilm model for the specific biofilm infection in question should be developed to guide the amount of antibiotics used for local antibiofilm treatment

2MJQ : Structure of antimicrobial peptide anoplin in DPC micelles

Experimental Technique/Method:SOLUTION NMR Resolution: Classification:ANTIMICROBIAL PROTEIN Release Date:2014-12-03 Deposition Date:2014-01-16 Revision Date:2015-01-14#2015-01-28 Molecular Weight:24000.55 Macromolecule Type:Protein Residue Count:11 Atom Site Count:1577 DOI:10.2210/pdb2mjq/pdb Abstract: Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure-activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL-NH2 ) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or-most efficiently-a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α-helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide

2MJR : Anoplin R5W structure in DPC micelles

Experimental Technique/Method:SOLUTION NMR Resolution: Classification:ANTIMICROBIAL PROTEIN Release Date:2014-12-03 Deposition Date:2014-01-16 Revision Date:2015-01-14#2015-01-28 Molecular Weight:24029.57 Macromolecule Type:Protein Residue Count:11 Atom Site Count:1580 DOI:10.2210/pdb2mjr/pdb Abstract: Antimicrobial peptides (AMPs) are promising candidates for battling multiresistant bacteria. Despite extensive research, structure-activity relationships of AMPs are not fully understood, and there is a lack of structural data relating to AMPs in lipids. Here we present the NMR structure of anoplin (GLLKRIKTLL-NH2 ) in a micellar environment. A vast library of substitutions was designed and tested for antimicrobial and hemolytic activity, as well as for changes in structure and lipid interactions. This showed that improvement of antimicrobial activity without concomitant introduction of strong hemolytic activity can be achieved through subtle increases in the hydrophobicity of the hydrophobic face or through subtle increases in the polarity of the hydrophilic face of the helix, or-most efficiently-a combination of both. A set of guidelines based on the results is given, for assistance in how to modify cationic α-helical AMPs in order to control activity and selectivity. The guidelines are finally tested on a different peptide

2ML3 : Solution Structure of AlgE6R3 subunit from the Azotobacter vinelandii Mannuronan C5-epimerase

Experimental Technique/Method:SOLUTION NMR Resolution: Classification:ISOMERASE Release Date:2014-10-01 Deposition Date:2014-02-18 Revision Date:2014-12-24 Molecular Weight:18477.91 Macromolecule Type:Protein Residue Count:181 Atom Site Count:1292 DOI:10.2210/pdb2ml3/pdb Abstract: The bacterium Azotobacter vinelandii produces a family of seven secreted and calcium-dependent mannuronan C-5 epimerases (AlgE1-7). These epimerases are responsible for the epimerization of β-D-mannuronic acid (M) to α-L-guluronic acid (G) in alginate polymers. The epimerases display a modular structure composed of one or two catalytic A-modules and from one to seven R-modules having an activating effect on the A-module. In this study, we have determined the NMR structure of the three individual R-modules from AlgE6 (AR1R2R3) and the overall structure of both AlgE4 (AR) and AlgE6 using small angle x-ray scattering. Furthermore, the alginate binding ability of the R-modules of AlgE4 and AlgE6 has been studied with NMR and isothermal titration calorimetry. The AlgE6 R-modules fold into an elongated parallel β-roll with a shallow, positively charged groove across the module. Small angle x-ray scattering analyses of AlgE4 and AlgE6 show an overall elongated shape with some degree of flexibility between the modules for both enzymes. Titration of the R-modules with defined alginate oligomers shows strong interaction between AlgE4R and both oligo-M and MG, whereas no interaction was detected between these oligomers and the individual R-modules from AlgE6. A combination of all three R-modules from AlgE6 shows weak interaction with long M-oligomers. Exchanging the R-modules between AlgE4 and AlgE6 resulted in a novel epimerase called AlgE64 with increased G-block forming ability compared with AlgE6