Journal: iScience

Article Title: High-throughput screening of FRET-based proteins using a hyperspectral microcapillary array

doi: 10.1016/j.isci.2026.115302

Figure Lengend Snippet: High-throughput screening techniques A comparison of different experimental approaches—including tubes, 96-well plates, fluidics, microcapillary, and droplet platforms —is shown. The table is updated from a previous comparison, now including our microcapillary for a more thorough overview. The time required to generate 10 K data points, including sequence information and functional labels, is calculated by dividing the experimental throughput by 10 4 .

Article Snippet: The plasmids were sequence-confirmed via Oxford Nanopore whole plasmid sequencing (Quintara Biosciences).

Techniques: High Throughput Screening Assay, Comparison, Sequencing, Functional Assay

Journal: Nucleic Acids Research

Article Title: Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1

doi: 10.1093/nar/gkag264

Figure Lengend Snippet: The conserved Bcl1 interacts via its WD40 β-propeller with Rpl1. ( A ) Proximity labelling assay with C-terminally miniTurbo-tagged RPL10A (HsRPL10A-miniTurbo) in HeLa cells. The RPL10A bait r-protein and selected enriched proteins are written in bold, the red dot highlights the highly enriched WDR89. ( B ) AlphaFold3 model of the Bcl1–Rpl1 complex. The seven-bladed β-propeller domain of Bcl1 is coloured in green and the C-terminal extension in light green; the position of residue Asn322 (N322) is indicated to better visualize from where the C-terminal extension emanates. ( C ) AlphaFold3 model of the WDR89–RPL10A complex (left) and its structural superposition with the AlphaFold3 model of the Bcl1–Rpl1 complex (right). ( D ) Predicted electrostatic surface potential of Bcl1 (left) and close-up view of two of the three Rpl1 sites, indicating residues predicted to form H-bonds with Bcl1, that are in contact with the negatively charged top surface of the β-propeller (right). ( E–G ) Y2H interaction assays between the full-length Rpl1 and Bcl1 proteins ( E ), between full-length Rpl1 and the C-terminally truncated Bcl1.N366 and Bcl1.N325 variants or the C-terminal extension of Bcl1 (323C) ( F ), and between the indicated Rpl1 mutant variants and either Bcl1 or Acl1 ( G ). Single-letter abbreviations for the amino acid residues are as follows: A, Ala; E, Glu; K, Lys; R, Arg. ( H ) In vitro binding assay between Bcl1.N366 and Rpl1. Bcl1.N366-(His) 6 or Bcl1.N366 and Rpl1b were co-expressed in E. coli and purified by Ni–NTA affinity purification. Proteins were revealed by SDS–PAGE and Coomassie staining (top) or by western blotting using anti-His and anti-Rpl1 antibodies (bottom). Bands corresponding to Bcl1.N366-(His) 6 and Bcl1.N366 or to Rpl1b are indicated by blue or black arrowheads.

Article Snippet: The DNA sequence coding for the Homo sapiens RPL10A protein was PCR-amplified from plasmid pADH111-HsRPL10A (pDK10427), generated by cloning the PCR-amplified RPL10A coding sequence [template pNTI194 (Addgene plasmid #84266)] into the Nde I/ Bam HI-restricted plasmid pADH111-LTV1 (pDK3331), and cloned by Gibson assembly between the Nhe I and Pst I restriction sites of the lentiviral donor vector pSKP-32, a pCW57.1-derived plasmid bearing the MND-Blasticidin resistance cassette instead of the hPGK-puromycin resistance cassette [ ], to generate plasmid pDS79 containing the RPL10A gene under the transcriptional control of a doxycycline-inducible promoter and fused at its 3′ end to sequences encoding the V5 tag, the miniTurbo (MT) biotin ligase, and the HA tag.

Techniques: Residue, Mutagenesis, In Vitro, Binding Assay, Purification, Affinity Purification, SDS Page, Staining, Western Blot

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Plasmids were processed with rolling circle amplification (RCA) to produce linear DNA containing multiple tandem repeats of the original plasmids. The linear DNA was prepped and sequenced on an ONT P2Solo. The resulting ONT data were then processed into ONT reads by dorado and consensus reads by an updated version of C3POa. Consensus reads and subreads originating from multiple reads covering the same plasmid were then combined into one highly accurate plasmid sequence using the newly developed Chopper.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Amplification, Plasmid Preparation, Sequencing

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: For each sequencing run, the read length distributions of the raw ONT sequencing data (grey) and R2C2 consensus reads (blue) are shown as histograms. The length of sequenced plasmids (orange) included in each run is also shown.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Sequencing

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Chopper accepts R2C2 consensus reads and their subreads produced by C3POa as input. It then bins R2C2 consensus reads by length to identify different plasmids in the sequencing data. For each length bin/plasmid, Chopper then generates a highly accurate plasmid sequence using racon and medaka for polishing.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Produced, Sequencing, Plasmid Preparation

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: Chopper was run on data from the 4 sequencing runs on individual plasmids. 100 R2C2 consensus reads were polished for each plasmid sequencing run (using the --iterations argument). Each R2C2 consensus read was polished with increasing numbers of R2C2 subreads (using the --subreads argument). With the exception of pSpCas9, Chopper produced almost entirely error-free sequences once more than 20 R2C2 subreads were used for polishing.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Sequencing, Plasmid Preparation, Produced

Journal: PLOS One

Article Title: Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper

doi: 10.1371/journal.pone.0345168

Figure Lengend Snippet: R2C2 subreads, R2C2 consensus reads, and Chopper sequences are aligned to the indicated plasmid references. Mismatches and Indels and are indicated in red, alignment ends in black B) . The error-rate of R2C2 consensus reads and Chopper sequences at specific positions of the pSpCas9 plasmid. These error-rates are shown as stacked bargraphs for a region of the plasmid that contains two homopolymers which represent a source for systematic sequencing error. C) Pairwise alignment of the pSpCas9 plasmid reference and the sequence Plasmidsaurus produced for that plasmid.

Article Snippet: To determine if commercial plasmid sequencing services would struggle with these homopolymers as well, we sent all four plasmids in this study to Plasmidsaurus for sequencing and analysis.

Techniques: Plasmid Preparation, Sequencing, Produced