There is increased evidence that mechanical processes affect cell behavior. Biochemical signals play a vital role in cell division and death as well as in cellular motion. One important question is however still unanswered: Does biochemical signaling affect the dynamics of this coordinated movement of groups of cells?

Retrieved from: https://www.nbi.ku.dk/

During differentiation and developmental processes, cells are acted on by external forces. This biomechanical signaling is sensed by specific force sensors such as the YAP receptors and can influence cell fate. The biomechanical properties of cells correlate with their lineage specification. We explore how cells sense biomechanical signals, how this signal is converted to a regulatory signal, and how the viscoelastic properties and polarity of cells play a role in lineage specification and organ development.

Scientists at DanStem discovered that cells’ sense of direction (cell polarity) determines their destiny. By discovering the signals that control cell polarity in the developing organism, scientists can now mimic it in a test tube and control the fate of human stem cells. The results accelerate the efforts to generate specialized cells, e.g. insulin-producing beta cells, from stem cells to treat and maybe even cure chronic diseases.
Research shows that cell polarity in progenitor cells not only contribute to the architecture and shape of organs, e.g. tubular systems, but also governs the fate progenitor cells.

Retrieved from: https://danstem.ku.dk/news/regulation-of-cell-polarity-by-egf-signaling-controls-both-organ-architecture-and-cell-fate/

The tension in the outer layer of cells is most often mediated by cortical actin. This tension serves to maintain cell shape and also has important roles in cellular functions as motility, endo- and exocytosis, as well as for the dynamics of protrusions as filopodia or lamellipodia. The overall stiffness of a cell is a combination of its cortical stiffness and the viscoelastic properties of its cytoplasm and nucleus. In StemPhys we explore cortical tension as well as cytoplasmic viscoelasticity of relevant model systems with the goal of understanding how this relates to cell fate and organ development.

As with radio transmission, the information between cells can be transmitted  through the abundance of a signaling molecule (think of AM radio) or by frequency of pulses (e.g. spiking neurons, think of FM radio). FGF/ERK, a key signaling pathway in early embryo development, is believed to relay frequency encoded signals (as a number of other  pathways, e.g. p53, Nf-kB and Notch/Hes). It is still unknown how the FM signal is decoded. We use mathematical models and experiements  to explore regulatory networks able to frequency decode.

Gastrulation is a morphogenetic process that describes the transformation of a seemingly unstructured blastula into a highly organized gastrula-stage embryo composed of the three germ layers ectoderm, mesoderm and endoderm.
To analyze gastrulation movements, we use a multi-disciplinary approach employing a combination of genetic, cell biological, biochemical and biophysical techniques.

Retrieved from: https://danstem.ku.dk/events/carl-philipp-heisenberg/

 ’Organoids’ are miniature three-dimensional organ-like structures made in vitro from stem cells. Our capacity to make them and understand them has progressed tremendously since 2009. They enable scientists to bridge the gap between cells growing on the bottom of a petri dish and organs in animals.

DanStem has made contributions to the organoid adventure since its beginning and the Grapin-Botton lab has succeeded in producing pancreas organoids in vitro from dispersed embryonic organ stem cells (Greggio 2013).
Retrieved from: https://danstem.ku.dk/news/the-organoid-revolution-and-danstem-contributions/

Our light sheet microscope is an Aurora Light Sheet Microscope from M2. The light sheet is formed by an airy beam and the microscope is capable of visualizing up to 600 microns inside living organisms as zebrafish with sub-cellular resolution. We use the light sheet microscope to image the developing gut region in zebrafish as well as spheroids and organoids.

To follow how cells make decisions we use time-lapse microscopy to monitor fluorescently-labeled transcription factors. The changes in cell states, e.g. intensity of the labeled protein,  often happen over several cell divisions. This means we need to follow lineages (think of ancestral tree) rather than single cells.

The ability of the liver to carry out the many diverse metabolic functions essential for body homeostasis depends on its specialized cell types and their organization within the tissue. In the embryo, progenitor cells differentiate into mature organs. This includes the transition from migratory progenitor cells into functional epithelial units consisting of polarized hepatocytes and biliary ducts. This is accompanied by dramatic changes in tissue morphology, which are driven by dynamic cell rearrangements and cell- and tissue interactions coordinated with the growth of the whole organ and embryo. How individual progenitor cells assemble a functional organ in the developing embryo is a fundamental question and remains poorly understood. Whether similar morphogenetic cell behaviours are crucial for tissue regeneration after injury is another key problem.

We combine a wide range of molecular, genetic and modern imaging techniques to identify the mechanisms driving progenitor cell positioning and differentiation in liver development and regeneration with the ultimate goal to uncover the basis of human developmental disorders and directing tissue-engineering approaches for therapeutic purposes.
Retrieved from: https://danstem.ku.dk/research1/ober/

Our optical tweezers platforms are based on near infrared focused laser beams implemented in confocal microscopes. These platforms allow for simultaneous visualization and manipulation. Utilizing photodiode detection, we use the optical tweezers to perform quantitative force measurements both in vitro and deep inside living organisms as zebrafish.

We have developed systems to expand mouse pancreas progenitors from a few cells or single cells in 3D in vitro (protocol). This leads to the formation of organoids similar to a pancreas in vitro. We use these in vitro models to study how a few cells self-organize into an organ. We are currently developing human pancreas organoids.

Retrieved from: https://danstem.ku.dk/research1/grapin_laboratory/

One important question around the development of the pancreas is what role do gene regulatory networks play in combining cell signalling with lineage transcription networks in in early embryonic differentiation. 

In the pancreas, directed differentiation informed by the knowledge of development has enabled the field to progress to the production of beta cells, with the ambition of transplanting these cells to treat diabetic patients who, depending on subtype, have reduced β-cell function, or are without them entirely. Yet, in vitro-generated cells do not fully recapitulate the function of bona fide β cells, notably lacking a tight control of insulin secretion upon glucose stimulation (Johnson, 2016). Accordingly, it is very important at this point to compare the cells we produce in vitro with endogenous cell types. Moreover, comparing progenitors with intermediates in the differentiation process may help to pinpoint where the processes diverge, and how we can improve them. Some divergences may originate from previously underappreciated differences between human pancreas development and those model organ vertebrates such as mouse, which are much easier to study. 
"Understanding human fetal pancreas development using subpopulation sorting, RNA sequencing and single-cell profiling"  Ramond, C. et. al. Development 2018 145: dev165480 doi: 10.1242/dev.165480 Published 15 August 2018

Single molecule RNA fluorescent In Situ Hybridization (smRNA FISH) is a method to detect and count single RNA molecules in single cells. We use this approach to approximate the abundances of regulatory proteins and cell-to-cell differences in a population exposed to the same environment. Combined with lineage tracking, smRNA FISH allows to quantify dynamics of the cell-state transitions.

We developed STORM and PALM super-resolution microscopy. We use these imaging modalities to explore the dynamics related to regulation on a single molecule level by tracking fluorescently labeled proteins and DNA loci. Also, we are interested in visualizing the cytoskeletal elements at the single cell level with the goal of understanding their role during stem differentiation and organ development. 

The developing pancreas undergoes complex and intriguing epithelial cell rearrangements. The gross morphology of the organ changes from an epithelial sheet to an epithelial bud and finally to a branched/tubular epithelial tree. Yet, we still do not understand how apical proteins, in a previously non-polarised epithelium, are recruited to the membrane of a pancreatic epithelial cell, extend to neighboring cells to form a plexus that is ultimately refined to a tubular network. 
Retrieved from: https://danstem.ku.dk/research1/semb_laboratory/

At all scales, living systems have both elastic and viscous properties, so-called viscoelastic properties, which are specific for the system studied and are highly optimized to support biological function.  Using optical tweezers, we quantify viscoelastic properties locally within living cells, both within individual cells as, e.g., embryonic stem cells, and also within cells that are part of a large living organism as a zebrafish. Using other modalities as real-time-deformability-cytometry and other video based methods, we also explore viscoelastic properties of entire cells, where the cortical contribution is included, and of larger entities as whole organs.