Biology subjects

Warren, C. R.

Publications and source records attributed to Warren, C. R..

4 recordsLinked to original sources

bioRxiv2026

HiFiTaxa: a reproducible analysis pipeline for full length 16S rRNA gene and ITS amplicon sequencing from PacBio reads

Long-read amplicon sequencing profiles communities at high resolution, but taxonomic accuracy depends on the reference, classifier and the parameters used. Here, we present HiFiTaxa, a reproducible, single command Nextflow pipeline for PacBio HiFi 16S rRNA gene and fungal ITS amplicons. It builds versioned references from current GTDB and UNITE releases and supports Bayesian lowest common ancestor (BLCA) and naive Bayes (NB) classifiers and the read level profilers Emu (16S rRNA gene) and EMITS (ITS). We benchmarked them on mock communities and on holdouts with 10% of GTDB or UNITE databases sequences withheld. On the 16S rRNA gene mock of 20 species, BLCA detected all 20 species and reported two false positives, NB detected 17 and reported none, and Emu detected all 20 and reported eight. In the GTDB holdout, for taxa represented in the reference, BLCA reached 80.0% species level accuracy against 48.1% for the exact matching species step of NB. However, NB produced fewer incorrect assignments for taxa absent from the reference. On fungal ITS, BLCA had slightly higher holdout accuracy at species level(54.7%) against 52.2% for NB. NB was more conservative for novel taxa, and EMITS detected the most mock species. HiFiTaxa therefore offers a single reproducible workflow that uses current GTDB and UNITE releases and enables users to choose between different classifier algorithms depending on their needs.

bioinformatics↗

bioRxiv2026

Polarization-engineered aberration-resilient light sheet microscopy

Light sheet fluorescence microscopy enables volumetric imaging with high imaging speed, optical sectioning capability, and reduced photobleaching and phototoxicity, and has become a workhorse in bioimaging. However, widely adopted Gaussian light sheets face an inherent trade-off between axial resolution and field-of-view due to diffraction. State-of-the-art nondiffracting light sheets--including Bessel beam, Airy beam, and lattice light sheet--alleviate this trade-off but suffer from optical aberrations that compromise performance with increasing imaging depth. While the integration of adaptive optics offers a promising solution, such integrated systems are typically complex, expensive, and slow due to the need for serial mapping and correction of spatially varying aberrations across the specimen. Here, we present polarization-engineered aberration-resilient light sheet (PEARLS), a new class of monochromatic nondiffracting light sheet with temporally invariant profile and robustness to optical aberrations. In comparison with existing light sheets, PEARLS showed significantly reduced photobleaching and enhanced aberration-resilience, permitting imaging of three-dimensional subcellular dynamics in optically complex environments. We applied PEARLS for noninvasive observations of biological dynamics in various living systems, revealing phenotypic diversity across spatial and temporal scales--from rapid membrane dynamics and organelle interactions in cultured cells to coordinated mitosis and cell migrations in developing embryos.

cell biology↗

bioRxiv2025

The CryoEM Structure of Human GPR75: Insights into ECL2-Mediated Activation

GPR75 is one of the most promising emerging targets for the treatment of obesity and related co-morbidities, as its loss of function directly correlates with a decreased body mass index (BMI) in humans. To date, little is known about the structure and underlying biology of GPR75, which is classified as an orphan GPCR and has low homology to other GPCRs. Here, we describe the cryoEM structure of ICL3-BRIL-fused, unliganded human GPR75, together with functional data on G-protein coupling and effects of its putative ligands. GPR75 is present in an active-like state probably induced by the structure of its extracellular loop 2 (ECL2) which folds back deeply into the orthosteric pocket. This feature is important for both receptor integrity and signaling, as shown by mutagenesis studies. This structural finding is consistent with moderate constitutive activity for Gi1, while Gq does not seem to be recruited. Furthermore, functional data indicate that the putative ligands 20-HETE and CCL5 have no measurable effect on GPR75. Significance StatementObesity is a major global health crisis which will affect a quarter of the worlds population by 2035. Many existing therapies have significant shortcomings, including emetic effects and the need for frequent injections. GPR75 is an understudied orphan GPCR which has recently emerged as one of the most promising novel obesity targets based on large-scale human genetic studies. However, the sparse knowledge we currently have about this receptor presents a major roadblock for the development of effective GPR75-based therapies. This study investigates the basic biology of GPR75 on a molecular level, including its structure and downstream signaling. These findings provide the groundwork for future efforts targeting GPR75 to fight the obesity pandemic.

biochemistry↗

bioRxiv2019

The contribution of PIP2-type aquaporins to photosynthesis in response to increased vapour pressure deficit

Roles of three different plasma membrane aquaporins (PIPs) in leaf-level gas exchange of Arabidopsis thaliana were examined using single, double and triple knockout mutants and compared to the Columbia-0 wild type (WT) plants. Since multiple Arabidopsis PIPs are implicated in conducting carbon dioxide across membranes, we focused on identifying whether the examined isoforms affect photosynthesis, either mediated through the control of stomatal conductance to water vapour (gs) or mesophyll conductance of CO2 (gm) or a combination of both. In two separate studies, we grew Arabidopsis plants in a low humidity environment and under high humidity conditions. We found that the contribution of functional PIPs to gs was larger under conditions of low air humidity when the evaporative demand was high, whereas any effect of lacking PIP function was minimal under higher humidity conditions. The pip2;4 knockout mutants had 44% higher gs than the WT under low humidity conditions, which in turn resulted in an increased photosynthetic rate (Anet). AtPIP2;4 is thus likely to be involved in maintaining a positive water balance and high water use efficiency through mediation of transmembrane water flow. The lack of functional AtPIP2;5 on the other hand did not affect gs, but reduced gm indicating a possible role in regulating CO2 membrane permeability. This potential regulatory function was indeed confirmed by subsequent stopped flow measurements of yeast expressing AtPIP2;5.

plant biology↗