Cellular & Molecular Imaging

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. This is a collection of the samples included in the study, provided by COPO at Earlham Institute.

The Darwin Tree of Life project has the goal to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland. This is a collection of photographs of the samples included in the study, provided by the National History Museum (NHM).

Advances in biological imaging have transformed our understanding of living systems, yet access to state-of-the-art microscopy remains out of reach for many researchers. This is specially true for those without direct access to specialized optics laboratories or those working with non-model organisms. To overcome these barriers, we developed Flamingo: an adaptable, modular, and portable light sheet microscope designed for diverse research environments. Flamingo enables dynamic reconfiguration to suit a wide range of imaging needs and facilitates high-quality data acquisition directly in biological labs or field stations. We utilized Flamingo to image a range of intact, living, and cleared samples, demonstrating its versatility across various sample types and experimental conditions. Our fully assembled, ready-to-use Flamingo empowers biologists to pursue novel research questions and democratizes access to advanced microscopy.

Chronic Graft-Versus-Host disease (cGVHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic transplantation. CGVHD pathophysiology involves cooperation between Tfollicular helper cells (TFH) and germinal center B-cells (GCB), allo- and auto-antibody depositions in cGVHD tissues, and fibrosis. We evaluated human CD19-directed chimeric antigen receptor (CAR19) T-cell therapy in a clinically relevant murine cGVHD model with bronchiolitis obliterans syndrome (BOS). Although CD8 CAR19 T-cells effectively reduced peripheral B-cell and GCB frequencies, pulmonary function was unimproved. In contrast, a single CAR19 CD4 regulatory T-cells (Treg) infusion mitigated ongoing pulmonary disease and modulated germinal centers (GC) associated with reduced TFH frequencies compared to control Tregs but without measurable B-cell depletion. Compared to EGFR Treg infusion, mice receiving CAR19 Tregs exhibited enhanced suppression of B-cell activation, preserved splenic architecture, and provided greater opportunities for interaction with CD19+ B-cells at the B-cell follicle boundary zones. Taken together with the absence of detectable B-cell cytolysis, these findings are most consistent with GC suppression rather than B-cell depletion as the dominant mechanism. Overall, our findings suggest that CAR19 Tregs represent a promising and safe cGVHD/BOS therapeutic strategy, offering immunosuppressive benefits and improved disease outcomes that may be more limited with CD8 CAR19 T-cell treatment.

Transcription factors (TFs) efficiently locate their target DNA sequences by combining three-dimensional diffusion and one-dimensional sliding on nonspecific DNA. To balance rapid sliding with strong specific binding, TFs were proposed to switch between search and recognition conformations. For E. coli lac repressor (LacI), the folding of the hinge helices has been implicated in the conformational switch. Here, we tested how mutations in the hinge region impact the search speed and binding stability. Based on molecular dynamics simulations, we selected two LacI mutants favoring either search or recognition conformation. We measured the binding kinetics of the mutants both in vitro on DNA microarrays with 2,479 different Lac operators and in vivo via single-molecule experiments. We identified a mutation that enhances the specificity but reduces binding strength globally, and another mutation that makes the operator binding stronger but also reduces the specificity. However, the altered specificity impacts the search time less than expected. Instead, the major effect was impaired dissociation in response to IPTG induction for the strongly binding mutant. Together with earlier reports of affinity–inducibility trade-offs in LacI, our data support the model in which the trade-off is between binding stability and inducibility rather than between speed and binding stability. This post provides raw fluorescence imaging datasets from single-molecule live-cell experiments and Protein Binding Microarray (PBM) experiments, along with the info of all the codes necessary to replicate the analyses of our study. Code for analysis and figure generation is found in: 10.17044/scilifelab.29040599 Data: - Data Folders with prefix: 'Microscopy_Data_' are for Protein Binding Microarray experiments and Single Molecule experiments (raw fluorescence images) - Data Folders with prefix: 'MD_Data_' are for MD simulations, download it from the Scilifelab repo, see in the link section.

Raw and processed fluorescence microscopy data to accompany the paper, "Image quality metrics fail to accurately represent biological information in fluorescence microscopy".

The images and complementary information presented here are related to the article: Simiyu, B. M. & R. Kurmayer, 2022. Response of planktonic diatoms to eutrophication in Nyanza Gulf of Lake Victoria, Kenya. Limnologica 93:125958 https://doi.org/10.1016/j.limno.2022.125958. The associated data article contains data and information on the identification of common diatoms using screening electron microscopy ( Phillips XL20 SEM). Diatoms presented belong in to six genera (11 species) and include: three chain forming centrics, four single cell centrics, two araphid diatoms originally described from L. Victoria, and one small highly variable preferentially epiphytic Nitzschia species. The method used for sample cleaning and analysis is presented.

The images and complementary information presented here are related to the article: Simiyu, B. M. & R. Kurmayer, 2022. Response of planktonic diatoms to eutrophication in Nyanza Gulf of Lake Victoria, Kenya. Limnologica 93:125958 https://doi.org/10.1016/j.limno.2022.125958. The associated data article contains data and information on the identification of common diatoms using screening electron microscopy ( Phillips XL20 SEM). Diatoms presented belong in to six genera (11 species) and include: three chain forming centrics, four single cell centrics, two araphid diatoms originally described from L. Victoria, and one small highly variable preferentially epiphytic Nitzschia species. The method used for sample cleaning and analysis is presented.

The European Reference Genome Atlas (ERGA) initiative is a pan-European scientific response to current threats to biodiversity. Reference genomes provide the most complete insight into the genetic basis that forms each species and represent a powerful resource in understanding how biodiversity functions. This is a collection of the samples included in the study, provided by COPO at Earlham Institute.