Biological organisation | EPFL Graph Search

Biological organisation is the organisation of complex biological structures and systems that define life using a reductionistic approach. The traditional hierarchy, as detailed below, extends from atoms to biospheres. The higher levels of this scheme are often referred to as an ecological organisation concept, or as the field, hierarchical ecology. Each level in the hierarchy represents an increase in organisational complexity, with each "object" being primarily composed of the previous level's basic unit. The basic principle behind the organisation is the concept of emergence—the properties and functions found at a hierarchical level are not present and irrelevant at the lower levels. The biological organisation of life is a fundamental premise for numerous areas of scientific research, particularly in the medical sciences. Without this necessary degree of organisation, it would be much more difficult—and likely impossible—to apply the study of the effects of various physical an

Lead Optimisation of a Novel Small Molecule Notch Inhibitor

Viktoria Reinmüller

Notch signalling represents a form of cell-to-cell communication that plays a pivotal role for cellular organisation during embryonic and postnatal development, as well as in the homeostasis of adult organs and tissues. Malfunction of this signalling pathway leads to aberrant regulation of the activities of the cells and may result in the loss of their integrity. The consequences include developmental defects, inherited disease syndromes as well as cancer. Accordingly, the discovery of Notch signalling regulating agents is highly desirable in order to extend the possibilities of clinical treatments providing benefits to patients suffering from Notch-associated diseases. In the frame of the present thesis, the initial steps in the lead optimisation of a novel small molecule Notch inhibitor were investigated. This compound, herein referred to as CB103, had been recently discovered in our laboratory by means of phenotypic high-throughput screenings of small molecule libraries for Notch regulators. CB103 turned out to exhibit an unconventional mode of action within the scope of known small molecule Notch inhibitors, due to its ability to block the NICD-mediated, thus activated form of the signalling pathway. However, the concrete cellular targets remained unknown. The aims of the present thesis comprised the structural optimisation and the concomitant retrospective identification of the cellular target molecules of CB103. This was pursued by implementing a repetitive cycle of the redesign of derivatives, their synthesis and their bioactivity assessment, leading to a comprehensive library of direct CB103 analogues. These investigations resulted not only in the identification of additional Notch inhibiting derivatives with in vivo activity, but surprisingly also in the discovery of molecules that appear to enhance Notch signalling. Moreover, the detailed knowledge about the structure-activity relationship was used to develop tagged versions of CB103 for target identification experiments entailing pull-down assays and yeast-three-hybrid (Y3H) screens. In this context, the Y3H system identified the enzyme soluble epoxide hydrolase (sEH) as a true cellular interaction partner of CB103. Additional interesting protein candidates were revealed by the diverse pull-down approaches and are currently under further investigation.

EPFL2015

Organisation and dynamics of mitochondria and their RNA.

Timo Henry René Rey

The organisation of molecules into dynamic cells, and collaboration of many of those cells over a billion years led to the evolution of human life. During the last century, biologists then began to unravel the marvels of cellular organisation with ever increasing detail. We now know, single cells not only comprise a defining DNA, but also a multitude of organelles. Mitochondria are such organelles, and produce cellular energy, at the heart of cellular metabolism. For this, they transcribe their own genome into mtRNA, and assemble respiratory chains. In recent decades, novel approaches, and technology enabled to shed new light on the spatial organisation of sub-cellular and mitochondrial processes. Thereby mtRNA was discovered to accumulate into small foci inside the mitochondrial matrix by fluorescence microscopy. Certain mitochondrial proteins also have also been found to conglomerate in these mitochondrial RNA granules (MRGs), but merely nothing is known about the structural, dynamic, and biophysical properties of MRGs, and their functional importance remains elusive. The development of superresolution microscopy has led to a revolution and revival of imaging methods for cell biology. This technology now enables investigation of sub-cellular biology at the nanometre scale, and to illuminate MRGs inside mitochondria.
In this thesis I investigate the organisational principles governing single cell and mitochondrial biology. First, I explore the application of superresolution microscopy to study the spatial organisation of nuclear DNA domains (TADs). I find high throughput STORM microscopy (htSTORM) allows to monitor effects of drug treatment on spatial rearrangement of a cancer associated TAD, together with established bulk-sample analysis. Next, I study the organisation of mitochondrial dynamics, by live-cell structured illumination microscopy (SIM). How different molecular pathways associated with mitochondrial proliferation or degradation are organised has long been a matter of debate. We discover a pattern for spatial organisation of mitochondrial fission, which distribute along the mitochondrial network in a bimodal manner. With this framework we distinguish different types of fissions, and show that distinct molecular features are associated with mitochondrial proliferation, or degradation through mitophagy. I find actin to be involved in proliferative midzone fission, whereas peripheral fission is associated with elevated reactive oxygen levels, and precedes mitophagy. By htSTORM, SIM and additional microscopy methods I then elucidate the biophysical organisation of intra-mitochondrial processes and MRGs. I show that the MRG ultrastructure consists of compacted RNA embedded within a dynamic protein cloud. Furthermore, MRGs associate with the inner mitochondrial membranes, and their distribution is governed by mitochondrial dynamics. MRGs can now be understood as nanoscopic, robust and fluid compartments, likely to influence intra-mitochondrial reaction kinetics. Finally, I also begin to unravel the spatial and biophysical organisation of mitochondrial transcription.
My results contribute to a holistic and dynamic picture of mitochondrial organisation. I highlight advantages of state-of-the-art microscopy to investigate spatial and temporal organisation of sub-cellular processes, and mark the onset of single organelle biology, in the context of other recent studies of sub-mitochondrial organisation.

EPFL2021

Robotic manipulation to investigate the physical principles of biological self-organization

Fazil Emre Uslu

Self-organization is the spontaneous formation of ordered patterns and networks from a population of comparatively simple elements or individuals with no prior information on neither the formation process nor the final organization. While the construction of tissues and organs is driven by the collective action of many eukaryotic cells, at a higher scale, social insects govern massive colonies via cooperative group behavior. In biological self-organization, unlike inanimate matter, interaction rules of elements are not constant but generally evolve in time and space in a history-dependent fashion. Recent technological advances in molecular biology, genetics, microscopy, and quantitative analysis have made it possible to follow the development of tissues, organs, and entire embryos at the single-cell level with high temporal resolution. Automated video tracking systems based on identification labels allow tracking of all members in insect colonies to identify individual interactions and patterns of social organization. These studies have shown that individuals must allocate themselves to actions or tasks in a dynamic manner following simple rules that incorporate local stimuli received directly from the environment and from interactions with other individuals. The majority of the available platforms provide observation only and do not allow manipulation of conditions for probing the self-organizing systems. Application of spatiotemporally resolved physical stimuli to individuals will reveal a more complete understanding of biological self-organization.In this thesis, I have developed robotic manipulation platforms along with computational models to investigate the principles of self-organization in biological systems. I have worked on two complementary experimental models at different scales to prove the generality of my approach. The first robotic manipulation platform explores the transmission and transduction of mechanical signals within a connected fiber network and associated cellular responses. I developed a biocompatible magnetic microactuator and a magnetic control system to apply physiologically relevant traction forces to cells cultured on fibrous matrices. Along with the experimental platform, I have developed a finite element-modeling framework that simulates stresses on a digital copy of the fiber network. The second robotic manipulation platform controls the temperature on the nest floor of ant colonies. The system is integrated with a real-time tracking system that is capable of following interactions among hundreds of individuals. The ant colony is stimulated to transport their brood by changing the temperature of the next floor in a spatially patterned way. We explored how ants processed thermal signals, coordinated the transport of brood, and interacted with one another.

EPFL2022