Integrative Cytomics (iCyt) Support unit platform
Co-funded by iDiv Flexpool Support Unit fund and UFZ
Diversity of microscopic biological particles plays a crucial role in important ecosystem services, e.g. water quality (phytoplankton), air quality and pollination (pollen). Many human-driven activities like climate change, eutrophication or invasive species are expected to massively change the composition of pollen abundance and phytoplankton communities. Monitoring of these tiny particles is therefore an essential task in order to detect diversity changes, issue short-term warnings, generally understand and estimate consequences for ecosystems and society, to communicate these observations in a timely way and to support and derive suitable actions. The monitoring tasks for air and water quality as well as plant-pollinator monitoring are currently performed via microscopic counting which strongly limits sampling capacity and frequency and, as a consequence restricts monitoring to low spatial and temporal resolutions. The iDiv support unit called “iCyt” (“integrative Cytomics”) will measure cells in suspension independent of their origin (water, soil or air samples of plant, animal or human origin). Our unique cutting-edge high-throughput measurement abilities of individual particles in powerful combination with deep-learning algorithms represent a transformative advance for improved air and water quality monitoring, as well as the study of plant-pollinator interactions. In addition, flow cytometry allows studying the DNA quantity of isolated plant nuclei to do ploidy-analysis of plants. The ploidy status of a plant has important ecological implications with respect to trait analysis and physiological performance of plants, relevant for ongoing biodiversity research.
The iCyt-platform facilitates utilization of existing infrastructure to support different kinds of research projects within the iDiv consortium. Several instruments are available (ImageStream X Mk II, FacsAriaII, Accuri, Multisizer) to support iDiv researchers when they need to describe various structural properties of cells in suspensions. Flow cytometry allows a semi-automatic high-throughput workflow that allows orders-of magnitude increase in sample processing compared to existing highly time-consuming microscopic methods.
Support unit instruments
- 2x Multispectral imaging flow cytometer
- Special order system with patented instrument configuration especially suitable for environmental monitoring
- 2 CCD camera system
- 20x (Numeric Aperture 0.5), 40x (Numeric Aperture 0.75) and 60x magnification (Numeric Aperture 0.9)
- 3 lasers (365 nm, 488 nm, 561 nm), Side Scatter: 785 nm
- Sample volume (20-200 µL)
- Size range (1-100 µm – upper range for spherical particles, elongated or filamentous particles can be up to 300 µm)
- Up to 12 images per particle
- Imaging rate up to 5000 Objects/s
- Volumetric counting
- Analytical flow cytometer
- Special order system especially suitable for environmental monitoring
- Sorter option in microtiter plates, slides and tubes
- 3 lasers (405 nm, 488 nm, 532 nm)
- Analytical flow cytometer
- 2 laser (488 nm, 640 nm laser), light scatter detector
- Volumetric counting
- Particle sizer and cell counter via electrical zone sensing
- Size range 0.2-1600 µm
- Fluorescence microscope (10x, 20x, 40x magnification)
- Automated slide scanning of up to three slides
- Filter setup: DAPI, GFP, TexasRed
Support unit staff
Dr. Susanne Dunker (Project coordinator)
Current projects
- OrthoDiv project (Cryptic diversity and evolution in Orthoptera: A continent-wide perspective - PIs: Holger Schielzeth, Claudia Fricke, Susanne Dunker, Octavio M. Palacios Gimenez (iDiv Flexpool project)
- ProtistQuant project (Hidden key players in trophic interactions: combining metabarcoding and multispectral imaging flow cytometry for quantitification of protists) - PIs: Martina Herrmann, Susanne Dunker, Martin Schlegel, Anna Maria Fiore-Donno, Antonis Chatzinotas (iDiv Flexpool project)
PollenNet-Project
support with pollen analysis
PolDiv project
support with pollen analysis
Phenobs support of MSc Till Deilmann, MSc Annalena Lenk, PhD candidate Carolin Plos
Canopy Crane Leipzig support of Bachelor student Emily Scheil (Working group Prof. Dr. Christian Wirth, University of Leipzig)
Dr. Forest project support with pollen analysis
Biotic interaction research support of B.Sc. Ella Schadt, B.Sc. Nele Schildt (Working group of Prof. Dr. Severin Sasso, University of Leipzig)
News
High-ranking visitors in our lab during the iDiv building inauguration event 09/2021, including the Minister Presidents of Saxony, Saxony-Anhalt and Thuringia (Photo credit: Swen Reichhold)
Forschungsspaziergang UFZ 2022
Universitätsmedizin Leipzig 03/2019
Scientific investigators
Dr. Susanne Dunker (Project coordinator)