Journal: Biotechnology for Biofuels and Bioproducts

Article Title: Evaluating isoprenol production using the IPP-bypass pathway in the oleaginous yeast Rhodosporidium toruloides

doi: 10.1186/s13068-026-02750-w

Figure Lengend Snippet: Isoprenol titers from the IPP-bypass pathways. A Individual titers from 15 distinct colonies of the IPP-bypass pathway transformed into wild-type R. toruloides and individual titers from 5 wild-type colonies. The line represents the median of each dataset. B Individual titers from 15 colonies of each transformation and 5 parent colonies of the IPP-bypass pathway transformed into wild type, dCK, MVA002, and MVA003. The lines in both parts represent the median of each dataset.

Article Snippet: Full genome sequencing on MVA003 (Plasmidsaurus, Louisville, KY, USA) showed that only ERG13 and HMGR were successfully integrated into the genome (Additional File 3) highlighting the random nature of ATMT.

Techniques: Transformation Assay

Journal: Biotechnology for Biofuels and Bioproducts

Article Title: Evaluating isoprenol production using the IPP-bypass pathway in the oleaginous yeast Rhodosporidium toruloides

doi: 10.1186/s13068-026-02750-w

Figure Lengend Snippet: Isoprenol titers from the IPPb pathway with A alterations to the PhoA or AphA constructs or B alternative terminal phosphatases. Each point represents individual titers from 15 distinct colonies screened from each transformation. The horizontal lines represent the median of each dataset. Black points represent transformations in the MVA002 background, whereas blue represents transformations into the MVA003 background

Article Snippet: Full genome sequencing on MVA003 (Plasmidsaurus, Louisville, KY, USA) showed that only ERG13 and HMGR were successfully integrated into the genome (Additional File 3) highlighting the random nature of ATMT.

Techniques: Construct, Transformation Assay

Journal: bioRxiv

Article Title: Mucinolysome in gut microbiomes of farm animals and humans

doi: 10.1101/2025.10.14.682383

Figure Lengend Snippet: Dockerin and cohesin domain sequence pairs were used as input to AlphaFold3 for 3D structure and interaction predictions. The resulting PDB files were input to FoldDock to calculate the pDockQ scores. Scores larger than 0.3 are shown. ( A ) Protein-protein interactions (PPIs) are predicted between cohesins (rows) and dockerins (columns) in GHs of C. perfringens ATCC 13124. “+” and “-“ indicate the presence and absence of experimentally characterized PPIs . ( B ) PPIs are predicted between cohesins in scaffoldins (rows) and dockerins in GHs (columns) of ET540. ( C ) A conceptual model is proposed illustrating the protein organization in the mucinolysome of ET540. ( D ) Predicted PPI interface between cSca1-Doc and cSca5-Coh. Hydrogen-bond contacts are shown as red dashed lines with corresponding distance < 3.5 Å between atoms. Sequences of cSca1-Doc and cSca5-Coh are shown beside the PPI interface structure with residues highlighted corresponding to residues in the hydrogen-bond contact interface. ( E ) Sequence alignment of cSca1-Doc against dockerin sequences in four ATCC 13124 proteins. Key residues involved in hydrogen-bonding (#) and van der Waals (*) contacts are indicated. Residues for cSca1-Doc are predicted, while residues for ATCC 13124 proteins were published previously . The two EF hand motifs are indicated. ( F ) Sequence alignment of cSca5-Coh against cohesin sequences in five published ATCC 13124 proteins .

Article Snippet: Full genome sequencing was performed by Plasmidsaurus using a combination of long-read sequencing with Oxford Nanopore and short-read Illumina sequencing.

Techniques: Sequencing, Protein-Protein interactions