Cellular & Molecular Imaging

A library of 1024 pesticides was screened at sublethal doses for effects on the behaviour of Drosophila third instar larvae.

Tara Expeditions are global scientific voyages that probe morphological and molecular diversity, evolution and ecology of marine plankton to explore how they are impacted by changes in the Earth's climate. The first expeditions collected samples of marine plankton containing viruses, bacteria, archaea, protists and planktonic metazoans living in the photic layer of the world's oceans. These expeditions, the first taking place between 2009 and 2013, include Tara Oceans: a global view, and Tara Oceans Polar Circle, both of which followed the same sampling protocol. This dataset includes 1074 pictures of 284 planktonic taxa (mainly microalgae and other Ciliate and Radiolarian protists) collected from the vicinity of the Marquesas Islands in the Southern Pacific Ocean during the Tara Oceans expedition. Multiple samples particularly of the size fractions 5-20 and 20 180 um from four sites and two depths were processed with different methods and studied in detail using scanning electron microscopy.

Tara Expeditions are global scientific voyages that probe morphological and molecular diversity, evolution and ecology of marine plankton to explore how they are impacted by changes in the Earth's climate. The first expeditions collected samples of marine plankton containing viruses, bacteria, archaea, protists and planktonic metazoans living in the photic layer of the world's oceans. These expeditions, the first taking place between 2009 and 2013, include Tara Oceans: a global view, and Tara Oceans Polar Circle, both of which followed the same sampling protocol. This dataset includes 1074 pictures of 284 planktonic taxa (mainly microalgae and other Ciliate and Radiolarian protists) collected from the vicinity of the Marquesas Islands in the Southern Pacific Ocean during the Tara Oceans expedition. Multiple samples particularly of the size fractions 5-20 and 20 180 um from four sites and two depths were processed with different methods and studied in detail using scanning electron microscopy.

Light microscopy and scanning electron microscopy images of snow algae field samples containing Rosetta gen. nov., including type material.

Drosophila notum containing SOP cells (labelled with RFP-Pon). Stained for total tubulin and poly-glutamylated tubulin.

Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We introduce a wildtype strain (Pantoea sp. YR343, n=3) or an EPS-defective strain (Pantoea sp. YR343 ΔUDP, n=3) to the porous media platform and then simulate a rainfall event using gravity-driven flow of bacterial growth media.

Fetal hematopoiesis takes place in the liver before colonizing the bone marrow where it will persist for life. This colonization is thought to be mediated by specification of a microenvironment that selectively recruits hematopoietic cells to the nascent bone marrow. The identity and mechanisms regulating the specification of this “colonization niche” are unclear. Here we identify a VCAM1+ sinusoidal colonization niche in the diaphysis that regulates neutrophil and hematopoietic stem cell colonization of the bone marrow. Using confocal microscopymicroscopy, we found that colonizing hematopoietic stem and progenitor cells (HSPC) and myeloid cells selectively localize to a subset of VCAM1+ sinusoids in the center of the diaphysis. Vcam1 deletion in endothelial cells impaired hematopoietic colonization while depletion of yolk-sac-derived osteoclasts abrogateddisrupted VCAM1+ expression, resulting in impaired and neutrophil and HSPC colonization ofto the bone marrow. Unexpectedly, depletion of yolk-sac-derived myeloid cells also increased fetal liver hematopoietic stem cell numbers, function and erythropoiesis in an osteoclast-independent mannerof osteoclast activity. Thus, the yolk sac produces two different types of myeloid cells in different organs that have oppositedistinct roles in regulating fetal hematopoiesis: while yolk-sac derived myeloid cells in the bone marrow promote hematopoietic colonization by specifying a VCAM1+ colonization niche, a different subset of yolk-sac-derived myeloid cells inhibitsregulates HSC in the fetal liverfetal liver hematopoiesis.

The cyanoHAB forming cyanobacteria Microcystis and Planktothrix frequently produce high intracellular amounts of microcystins (MCs) or anabaenopeptins (APs). In this study, chemically modified MCs and APs have been localized on a subcellular level in Microcystis and Planktothrix applying copper-catalyzed alkyne-azide cycloaddition (CuACC). For this purpose, three different non-natural amino acids carrying alkyne or azide moieties were fed to individual P. agardhii strains No371/1 and CYA126/8 as well as to M. aeruginosa strain Hofbauer showing promiscuous incorporation of various amino acid substrates during non-ribosomal peptide synthesis (NRPS). Moreover, CYA126/8 peptide knock-out mutants and non-toxic strain Synechocystis PCC6803 were processed under identical conditions. Simultaneous labelling of modified peptides with ALEXA405 and ALEXA488 and lipid staining with BODIPY 505/515 were performed to investigate the intracellular location of the modified peptides. Pearson correlation coefficients (PCC) obtained from confocal images were calculated between the different fluorophores and the natural autofluorescence (AF), and between labelled modified peptides and dyed lipids to investigate the spatial overlap between peptides and the photosynthetic complex, and between peptides and lipids. Overall, labelling of modified MCs (M. aeruginosa) and APs (P. agardhii) using both fluorophores revealed in-creased intensity in MC/AP producing strains. For Synechocystis lacking NRPS, no labelling using either ALEXA405 or ALEXA488 was observed. Lipid staining in M. aeruginosa and Synechocystis was intense while in Planktothrix it was more variable. When compared with AF, both modified peptides and lipids showed a heterologous distribution. In comparison, the correlation between stained lipids and labelled peptides was not increased suggesting a reduced spatial overlap.

The following data includes raw images, metadata, measurements and processed images as well as classifiers for image segmentations and masks created with the ImageJ/Fiji plugin Labkit to measure the leaf area. This dataset provides all acquired information for my Bachelor's thesis about leaf traits of Bryophyta related moss species.

Quantitative gene regulation can be achieved in two ways: “digital” or “analog”. “Digital” refers to binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state. “Analog” refers to graded expression levels at each gene copy. In response to cold, the Arabidopsis floral repressor FLOWERING LOCUS C (FLC) exhibits digital Polycomb silencing, facilitating quantitative epigenetic memory. However, whether analog or digital regulation is involved before cold is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find both analog and digital modes of FLC regulation and demonstrate temporal separation between the two, with analog preceding digital. Intermediate analog FLC expression levels subsequently allow slow population-level digital silencing, where individual gene copies switch OFF stochastically and heritably without cold. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways are integrated.