Biology subjects

Boddicker, A.

Publications and source records attributed to Boddicker, A..

3 recordsLinked to original sources

bioRxiv2026

CytosMPS: an automated multimodal pooled screening platform for protein, morphology and transcriptomics

Cytos Multimodal Pooled Screening (CytosMPS) measures CRISPR guide identity, morphology, native 3' transcriptome, and protein abundance and localization in the same fixed cells. Following IL-1{beta} stimulation, cells with higher nuclear NF-{kappa}B show lower phospho-p38/HSP27 and higher NFKBIA/DUSP1 in the same cell, a measurement neither imaging nor transcriptomics alone provides. TGFBR2 and CTNNB1 perturbations produce distinct multimodal phenotypes. Guide representation and perturbation transcriptional responses agree with an orthogonal single-cell transcriptomic platform.

cell biology↗

bioRxiv2025

A simplified hybrid capture approach retains high specificity and enables PCR-free workflow

Hybrid capture is a critical technology for selective enrichment of genomic regions of interest, enabling cost-effective focused sequencing in both clinical and research applications. We present a simplified hybrid capture approach that eliminates complexities typically associated with hybridization-based selection methods by directly loading the hybridization product onto the sequencing flow cell. The workflow removes bead-based steps, washes, and post-hybridization PCR, while retaining high capture specificity and library complexity. The approach is enabled by the development of a streptavidin flow cell surface, a method to circularize and amplify captured targets on the flow cell, and a fast hybridization protocol. We demonstrate application across targeted panel sizes and improvements to library complexity and variant calling. We also show how the approach can be used to create an entirely PCR-free targeted sequencing workflow that further improves variant calling and enables the detection of repeat expansions.

genomics↗

bioRxiv2018

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution from freshwater systems by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies revealed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using enrichment methods and genomic sequencing, we identified four novel Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome assembly revealed highly conserved 16S rRNA gene sequences, but a surprisingly broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggest that Nitrotoga can metabolize in low oxygen or anaerobic conditions, which may support a previously unrecognized environmental niche. An array of antibiotic and metal resistance genes likely allows Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses reveal a deeply divergent nitrite oxidoreductase alpha subunit (NxrA) not represented in any other NOB, suggesting a novel evolutionary trajectory for Nitrotoga. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments. This work considerably expands our knowledge of the Nitrotoga genus and improves our understanding of their role in the global nitrogen cycle.

microbiology↗