Cellular & Molecular Imaging

TrypTag genome-wide protein localisation project data. Widefield epifluorescence microscope images of protein subcellular localisation in the unicellular eukaryotic pathogen Trypanosoma brucei by endogenous tagging with mNeonGreen (mNG). This deposition includes the localisations, ontology and microscopy data used to build the TrypTag database. Data can also be browsed at TrypTag.org. If you use this data resource please cite Billington et al. 2023 Nature Microbiology (doi:10.1038/s41564-022-01295-6). We recommend including this citation in the results or methods if TrypTag was used as part of a discovery process. If directly using TrypTag images, please also indicate in the figure legend or similar which images are from TrypTag. If carrying out a large-scale data analysis, please also cite this BioStudies deposition. Data can be mined via the cellular localization imaging or cellular component GO term searches at the genome database TriTrypDB.org (part of VEuPathDB). If you do, please also cite the genome database. You may also find the following papers informative: Dean et al. 2016 Trends in Parasitology (doi:10.1016/j.pt.2016.10.009), which describes the original project aims and workflow. Halliday et al. 2019 Molecular and Biochemical Parasitology (doi:10.1016/j.molbiopara.2018.12.003), which describes the localisation ontology with example images and comparison to Leishmania.

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).

Large reference dataset of lightfield microscopic imaging data for diversity research of bryophytes (bryology)

A reference dataset containing macroscopic and bright-field microscopic images of 16 specimens of thallose liverworts of biological soil crusts collected in Southern Sweden and Germany

Protein synthesis is a core cellular process, necessary throughout the complex lifecycle of Plasmodium parasites, thus specific translation inhibitors would be a valuable class of antimalarial drugs, capable of both treating symptomatic infections in the blood and providing chemoprotection by targeting the initial parasite population in the liver, preventing both human disease and parasite transmission back to the mosquito host. As increasing numbers of antiplasmodial compounds are identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of molecular target or mechanism, it would be useful to gain deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential. Here, we probed that relationship using the P. berghei-HepG2 liver stage infection model. Using o-propargyl puromycin-based labeling of the nascent proteome in P. berghei-infected HepG2 monolayers coupled with automated confocal feedback microscopy to generate unbiased, single parasite image sets of P. berghei liver stage translation, we determined translation inhibition EC50s for five compounds, encompassing parasite-specific aminoacyl tRNA synthetase inhibitors, compounds targeting the ribosome in both host and parasite, as well as DDD107498, which targets Plasmodium eEF2, and is a leading antimalarial candidate compound being clinically developed as cabamiquine. Compounds were then tested at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony.

In Arabidopsis thaliana the root stem cell niche (SCN) is maintained by a complex regulatory network crucial for growth and developmental plasticity. However, many aspects of this network, particularly concerning stem cell quiescence and replenishment, remain unclear. Here, we investigate the interactions of key transcription factors (TFs) BRASSINOSTEROID AT VASCULAR AND ORGANIZING CENTRE (BRAVO), PLETHORA 3 (PLT3) and WUSCHEL-RELATED HOMEOBOX 5 (WOX5) in SCN maintenance. Analysis of mutants reveals their combinatorial regulation of cell fates and divisions in the SCN. Additionally, studies using Fluorescence Resonance Energy Transfer Fluorescence Lifetime Imaging Microscopy (FRET-FLIM) in combination with novel analysis methods enable us to quantify protein-protein interaction (PPI) affinities and higher-order complex formation among these TFs. Our finding were integrated into a computational model, indicating that cell type specific protein complex profiles and formations, influenced by prion-like domains in PLT3, play an important role in regulating the SCN. We propose that these unique protein complex signatures may serve as indicators of cell specificity, enriching the regulatory network that governs stem cell maintenance and replenishment in the Arabidopsis root.

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.

Manuscript abstract: Malaria transmission relies on sporozoite formation in the mosquito midgut and subsequent salivary gland invasion. Despite their importance, the cell biology of these processes remains poorly understood. We apply Mosquito Tissue Ultrastructure Expansion Microscopy (MoTissU-ExM), which physically expands infected mosquito tissues while preserving host and parasite ultrastructure. MoTissU-ExM reveals parasite structures and organelles, including features previously seen only by electron microscopy and novel structures not observed before. We use MoTissU-ExM to investigate sporozoite formation and salivary gland invasion, focusing on rhoptries - secretory organelles critical for host cell invasion. We establish a timeline for rhoptry biogenesis, show that two rhoptries are consumed during salivary gland invasion, and provide the first evidence that rhoptry pairs are specialized for different invasion events. We further characterize RON11 as the first protein involved in sporozoite rhoptry biogenesis; its disruption produces sporozoites that specifically fail to invade salivary gland epithelial cells, blocking parasite transmission. Dataset description: This dataset contains all microscopy data associated with the linked publication "Unlocking new understanding of Plasmodium sporozoite biology with expansion microscopy". All samples were prepared by ultrastructure-expansion microscopy (U-ExM). All samples were imaged on either a Zeiss LSM900 or LSM980 microscope, using either Airyscan-SR or Airyscan-MPLX modes. File names will include the magnification of the objective lens used as follows: 5x = EC Plan-Neofluar 5x/0.16NA Air 10x = Ziess Plan-Apochromat 10x/0.45NA air 20x = Ziess Plan-Apochromat 20x/0.8NA air 40x = Zeiss C-Apochromat 40x/1.2NA water-immersion autocorr M27 63x = Zeiss Plan-Apochromat 63x/1.4NA oil-immersion M27 Images are of mosquito tissues, or isolated parasites, from three Plasmodium species - berghei (Pb), falciparum (Pf), and yoelii (Py). Images are sorted and named as follows (folder name, file name) Plasmodium species > Tissue type/site of isolation > Parasite strain > Species abbreviation, MG/SG, Harvest day(dpi), Dye/Fluorophores (405nm -> 647nm), Objective, Image number (1->X), as (airyscan) For example, the third image taken of a P. berghei oocyst with the RON11iKD parasite line, that was harvested on Day 14 post infection, stained with NHS Ester AF405, BODIPY-FL, anti-Tubulin AF555, and Sytox Red, and imaged on the 40x-objective would be listed as follows: Plasmodium berghei > Infected midguts > RON11iKD > RON11KD MG 14dpi NHSBFlTub-SytR 40x 1 as The majority of images in this dataset are z-stacked images, but for many oocysts a single-slice image of the whole oocyst was taken. When this is the case, the single-slice image will be indicated with "SNAP". A list of the acronyms and abbreviations used in file names are as follows MG = Midgut SG = Salivary gland Spz = Sporozoite HC = Haemocoel dpi = Days post infection NHS = NHS Ester Alexa Fluor 405 BFl = Bodipy-FL-Ceramide BTRc = Bodipy-TR-Ceramide SytR = Sytox Deep Red Tub = anti-tubulin antibody CSP = anti-circumsporozoite protein antibody RAP1 = anti-rhoptry associated protein 1 antibody iKD = Inducible knockdown Ctrl = Control KD = Knockdown RON4 = anti-rhoptry neck protein 4 antibody GFP = anti-green fluorescent protein antibody WGA = Wheat germ aglutinnin BIP = anti-BiP antibody ERD2 = anti-ERD2 antibody

This is source data for both: 1) EED IF Confocal Image data during 3 different synchronization time points; 2) RPB1-Dendra2 STORM raw data for 2 time points.

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).