Cellular & Molecular Imaging

The large variety of inflorescence architectures evolved in grasses depends on shape, longevity and determinacy of meristems directing growth of the main and lateral axes. The CLAVATA pathway is known to regulate meristem size and inflorescence architecture in grasses. However, how individual meristem activities are determined and integrated to generate specific inflorescences is not yet understood. We found that activity of distinct meristems in the barley inflorescence is controlled by a signalling pathway comprising the receptor-like kinase Hordeum vulgare CLAVATA1 (HvCLV1) and the secreted CLAVATA3/EMBRYO-SURROUNDING REGION RELATED (CLE)-family peptide FON2-LIKE CLE PROTEIN1 (HvFCP1). HvFCP1 and HvCLV1 interact to promote spikelet formation, but restrict inflorescence meristem and rachilla proliferation. Hvfcp1 or Hvclv1 mutants generate additional rows of spikelets and supernumerary florets from extended rachilla activity. HvFCP1/HvCLV1 signalling coordinates meristem activity through regulation of trehalose-6-phosphate levels. Our discoveries outline a path to engineer inflorescence architecture via specific regulation of distinct meristem activities.

Vascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flowers heads. We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. The vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature.

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

Our calendar goes into a second round! After having a first edition of the NFDI4BIOIMAGE calendar in 2024, we were eager to assemble an improved version for 2025. This time, we invited also other consortia of the National Research Data Infrastructure (NFDI) to contribute with the aim to extend our calendar to a consortium spanning edition. In this year’s calendar we present very different types of images, taken by mobile phones, cameras, drones, and microscopes, representing the work of our colleagues from the various consortia of NFDI. As you may know, biological images often include additional information in the form of technical metadata, detailing the conditions under which the image was captured. Ideally, this technical data is paired with biological metadata, which explains the specimen depicted and how it was prepared. This year, we also requested that authors submit their images with complete accompanying metadata – a "full package". In bioimaging, the use of metadata standards, specifically the Recommended Metadata for Biological Images (REMBI) guideline (https://doi.org/10.1038/s41592-021-01166-8), has become increasingly common. Many of the submissions for this calendar adhere to REMBI guidelines with comprehensive metadata annotations alongside the bioimage data, as you can observe on the right accompanying our cover image. However, for images captured with other tools, such as mobile phones or drones – images not typically classified as biological – the required metadata differs to accurately convey what is shown and why the image was created. Through this calendar, we step outside the bioimaging sphere to explore how metadata for other types of images might be structured. We hope you will find it as exciting as we do to see all the different contributions and the plethora of information that will teach you more about the respective images. NFDI4BIOMAGE – who we are and what we are aiming for The NFDI4BIOIMAGE consortium started its work in March 2023 as one of the third round applicants within the NFDI, funded by the Federal Ministry for Education and Research (BMBF) and the Länder. Our consortium is working on solutions for bioimage data management along the bioimage life cycle. Bioimaging is an indispensable tool within life and medical sciences. But bioimaging data is also a very divers type of data that is present in numerous proprietary file types, is usually of large size and covers many different imaging modalities. Due to this heterogeneity, storage and interaction with bioimaging data is not trivial and is handled very differently within the research community. Our aim is to find solutions for appropriate bioimage storage, data handling, data analysis, data publication, and to provide overarching standards and support for bioimage data management for the scientific community. Our final goal is to enable researchers to make their bioimaging data Findable, Accessible, Interoperable, and Reusable (FAIR). If you need help or advise on how to handle your bioimaging data, NFDI4BIOIMAGE Data Stewards are here to provide support. Beginning of 2024 we have set up a Help Desk to get in contact with our Data Steward team. You can use the help request form (https://nfdi4bioimage.de/help-desk/) or write an e-mail to helpdesk@nfdi4bioimage.de. For further information you can also get in contact with our project office via e-mail (office@nfdi4bioimage.de) or visit our webpage https://nfdi4bioimage.de.

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

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).

The microtubule cytoskeleton consists of dynamic intracellular filaments and is involved in numerous processes, ranging from nuclear division to intracellular transport. Some of these microtubule-mediated processes are conserved in all eukaryotic lineages while others are specific for certain groups of organisms. Here, we focus on the microtubule cytoskeleton of oomycetes in the genus Phytophthora, a group of harmful plant pathogens. In Phytophthora palmivora lines expressing GFP-tagged α-tubulin we observed a conserved microtubule localization in the mitotic spindle and dynamic cytoplasmic microtubules between adjacent nuclei. These microtubules originated from the mitotic spindle and rapidly increased in length after mitosis. Since microtubule minus-ends are likely associated with MTOCs on the nuclear surface, the plus-ends of microtubules originating from adjacent nuclei likely maintain an antiparallel connection which may play a role in nuclear spacing. This idea was strengthened by erratic nuclear motility and positioning after microtubule depolymerization. Besides aberrant nuclear positioning we also observed less sustained tip growth in the absence of microtubules. This suggests that microtubules radiating into the hyphal tip from the apical nucleus function in sustaining tip growth. Altogether, this study provides novel insights in the localization, dynamics and functions of the microtubule cytoskeleton in the coenocytic Phytophthora hyphae.

In multicellular organisms, tissue architecture reflects not only dedicated patterning genes but the integrated state of core cellular physiology. Whether the same holds for the communities that bacteria build has been difficult to test at scale. To this end, we developed µPULLI, a high-throughput platform that pairs low-magnification, label-free brightfield timelapse microscopy with computer vision. Using µPULLI, we screened a genome-wide Vibrio cholerae transposon library. Our screen revealed that community architecture is governed as much by core physiology as by dedicated biofilm genes: perturbations to central metabolism, cofactor biosynthesis, and cell-envelope architecture each leave distinctive, pathway-specific fingerprints on how a community develops. These fingerprints arise through both transcriptional and non-transcriptional mechanisms, including cell-surface changes invisible to RNA sequencing. Small molecules drive communities predictably through this phenotype space, and the principle holds across taxonomically diverse pathogens. Emergent community architecture thus encodes the integrated physiological state of its constituent cells, revealing a rich, largely untapped layer of biological information that can be read from simple, low-magnification brightfield videos of growing cultures.

The ratio of tumour mass to lactate or LDH values in blood are informative indicator of the tumour histological peculiarities .