The construction of a new mobile recombineering system of pYM-Red

Recombineering is a new developed genetic engineering technology in the past few years. A new recombineering system named pYM-Red was constructed by gap-repair, that is a technology called in vivo cloning. Linear PCR fragments that amplified from low copy plasmid pACYC184 were used as gene targeting vector. The length of subcloned DNA sequence including Red gene and a series regulatory sequences are about 6.7 kb. The biology function of Red gene in pYM-Red was tested by gene replacement (galkkan) of W3110 chromosome. Factors that effect recombination efficiency were precisely confirmed. When induced 10 min at 42 degrees C and using 300 ng linear DNA fragment as targeting molecules, the efficiency of pYM-Red mediated recombination can reach one positive recombination clone per four thousands electroporation survived cells, it is 5 similar to 6 folds higher than pBR322-Red and pKD46 recombination system

Methonotrophic Biomass Quant BUP

Raw LC-MS/MS data and MaxQuant output files (txt folder) from quantitative bottom-up proteomics analysis of the fermeted biomass from methanotrophic bacteria described in the manuscript "Emulsifier peptides derived from seaweed, methanotrophic bacteria, and potato proteins identified by quantitative proteomics and bioinformatics". The biomass was pre-fractionated by SDS-PAGE and subsequently in-gel digested as described in M&M. The remaining two raw data files can be found in "Gregersen, Simon (2021), “Methonotrophic Biomass Quant BUP part2”, Mendeley Data, V1", doi: 10.17632/76v7mnmyr3.

CodfishHydrolysatesMS

MS raw data, MaxQuant output files, and Table S4 for the manuscript "Biofunctionality of enzymatically derived peptides from codfish (Gadus morhua) frame; Bulk in vitro properties, quantitative proteomics, and bioinformatic prediction

Methonotrophic Biomass Quant BUP part2

Raw LC-MS/MS data and MaxQuant output files (txt folder) from quantitative bottom-up proteomics analysis of the fermeted biomass from methanotrophic bacteria described in the manuscript "Emulsifier peptides derived from seaweed, methanotrophic bacteria, and potato proteins identified by quantitative proteomics and bioinformatics". The biomass was pre-fractionated by SDS-PAGE and subsequently in-gel digested as described in M&M. This is the second part of the dataset for the manuscript. The former set can be found in "Gregersen, Simon (2021), “Methonotrophic Biomass Quant BUP”, Mendeley Data, V1", doi: 10.17632/g45gbw5r7n.

E.denticulatum quant BUP

MaxQuant output files (txt folder) from quantitative bottom-up proteomics analysis of two pilot-scale hot-water extracts from E. denticulatum, described in the manuscript "Proteomic characterization of pilot scale hot-water extracts from the industrial carrageenan red seaweed Eucheuma denticulatum" Extract A is labelled "A-013-05e" and Extract B "A-022-05e". Data is organized as exploratory phase (unspecific analysis with 1%, 5%, and 10% FDR as well as semi-specific analysis with 1% and 5% FDR) and as final phase (for tryptic and semi-specific analysis with optimized search parameters). Raw MS data are available upon request. Repository also contains the reference protein database (in .fasta format) as well as qRNAseq data

Norovirus recombination in ORF1/ORF2 overlap

Norovirus (NoV) genogroups I and II (GI and GII) are now recognized as the predominant worldwide cause of outbreaks of acute gastroenteritis in humans. Three recombinant NoV GII isolates were identified and characterized, 2 of which are unrelated to any previously published recombinant NoV. Using data from the current study, published sequences, database searches, and molecular techniques, we identified 23 recombinant NoV GII and 1 recombinant NoV GI isolates. Analysis of the genetic relationships among the recombinant NoV GII isolates identified 9 independent recombinant sequences; the other 14 strains were close relatives. Two of the 9 independent recombinant NoV were closely related to other recombinants only in the polymerase region, and in a similar fashion 1 recombinant NoV was closely related to another only in the capsid region. Breakpoint analysis of recombinant NoV showed that recombination occurred in the open reading frame (ORF)1/ORF2 overlap. We provide evidence to support the theory of the role of subgenomic RNA promoters as recombination hotspots and describe a simple mechanism of how recombination might occur in NoV

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