Which Elements to Build Co-localization Workflows? From Metrology to Analysis

Spatial and quantitative gene expression analysis of SREB receptors in the gonads of green-spotted pufferfish (Dichotomyctere nigroviridis)

Super-conserved Receptors Expressed in Brain (SREB) are a highly conserved family of orphan G protein-coupled receptors that consist of three members in most vertebrates: SREB1 (GPR27), SREB2 (GPR85), and SREB3 (GPR173). Each receptor is associated with diverse physiological processes and expressed in both ovaries and testes, but reproductive functions are only beginning to be understood. In addition, some fishes gained a novel fourth gene, SREB3B, which may have unique functions. The purpose of this study was to conduct a spatial and quantitative analysis of SREBs in the gonads of pufferfish (Dichotomyctere nigroviridis), which expresses all four genes. Multiplex RNAscope and absolute qPCR were used to assess gene expression patterns in both ovaries and testes. Expression was detected in early ovaries and dominated by sreb1 (approximately 2500 copies/ng RNA vs. 300 or less for others), with notable expression of all receptors in primary oocytes, granulosa cells, and small numbers of extra-follicular cells. Within primary oocytes, sreb1 and sreb3b exhibited diffuse patterns that may indicate early functions, while sreb2 and sreb3a were granular and may reflect stored mRNA. Early testicular development was dominated by sreb1 and sreb2 (∼5000 copies/ng RNA) in spermatogonia. These patterns were somewhat reduced in late testes (∼1000-2600 copies/ng RNA), but sreb3b exhibited a novel spatial pattern (∼380 copies/ng RNA) within spermatogenic cysts. These results highlight diverse roles for the SREB family, and sreb3b is hypothesized to have unique roles in fish reproduction.

Quality assessment in light microscopy for routine use through simple tools and robust metrics

Although there is a need to demonstrate reproducibility in light microscopy acquisitions, the lack of standardized guidelines monitoring microscope health status over time has so far impaired the widespread use of quality control (QC) measurements. As scientists from 10 imaging core facilities who encounter various types of projects, we provide affordable hardware and open source software tools, rigorous protocols, and define reference values to assess QC metrics for the most common fluorescence light microscopy modalities. Seven protocols specify metrics on the microscope resolution, field illumination flatness, chromatic aberrations, illumination power stability, stage drift, positioning repeatability, and spatial-temporal noise of camera sensors. We designed the MetroloJ_QC ImageJ/Fiji Java plugin to incorporate the metrics and automate analysis. Measurements allow us to propose an extensive characterization of the QC procedures that can be used by any seasoned microscope user, from research biologists with a specialized interest in fluorescence light microscopy through to core facility staff, to ensure reproducible and quantifiable microscopy results.

Analysis of conditional colocalization relationships and hierarchies in three-color microscopy images

Colocalization analysis of multicolor microscopy images is a cornerstone approach in cell biology. It provides information on the localization of molecules within subcellular compartments and allows the interrogation of known molecular interactions in their cellular context. However, almost all colocalization analyses are designed for two-color images, limiting the type of information that they reveal. Here, we describe an approach, termed "conditional colocalization analysis," for analyzing the colocalization relationships between three molecular entities in three-color microscopy images. Going beyond the question of whether colocalization is present or not, it addresses the question of whether the colocalization between two entities is influenced, positively or negatively, by their colocalization with a third entity. We benchmark the approach and showcase its application to investigate receptor-downstream adaptor colocalization relationships in the context of functionally relevant plasma membrane locations. The software for conditional colocalization analysis is available at https://github.com/kjaqaman/conditionalColoc.

3D positioning of tagged DNA loci by widefield and super-resolution fluorescence imaging of fixed yeast nuclei

This protocol describes how to culture, image, and determine the nuclear position of a fluorescently tagged DNA locus in the 3D nucleoplasm of fixed Saccharomyces cerevisiae cells. Here, we propose a manual scoring method based on widefield images and an automated method based on 3D-SIM images. Yeast culture conditions have to be followed meticulously to get the best biological response in a given environment. For complete details on the use and execution of this protocol, please refer to Forey et al. (2020).

In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead

Complexity of DNA damage is considered currently one if not the primary instigator of biological responses and determinant of short and long-term effects in organisms and their offspring. In this review, we focus on the detection of complex (clustered) DNA damage (CDD) induced for example by ionizing radiation (IR) and in some cases by high oxidative stress. We perform a short historical perspective in the field, emphasizing the microscopy-based techniques and methodologies for the detection of CDD at the cellular level. We extend this analysis on the pertaining methodology of surrogate protein markers of CDD (foci) colocalization and provide a unique synthesis of imaging parameters, software, and different types of microscopy used. Last but not least, we critically discuss the main advances and necessary future direction for the better detection of CDD, with important outcomes in biological and clinical setups.