Biological warfare | EPFL Graph Search

Biological warfare, also known as germ warfare, is the use of biological toxins or infectious agents such as bacteria, viruses, insects, and fungi with the intent to kill, harm or incapacitate humans, animals or plants as an act of war. Biological weapons (often termed "bio-weapons", "biological threat agents", or "bio-agents") are living organisms or replicating entities (i.e. viruses, which are not universally considered "alive"). Entomological (insect) warfare is a subtype of biological warfare. Offensive biological warfare is prohibited under customary international humanitarian law and several international treaties. In particular, the 1972 Biological Weapons Convention (BWC) bans the development, production, acquisition, transfer, stockpiling and use of biological weapons. Therefore, the use of biological agents in armed conflict is a war crime. In contrast, defensive biological research for prophylactic, protective or other peaceful purposes is not prohibited by the BWC. Biolo

Analytic performance modeling and analysis of detailed neuron simulations

Francesco Cremonesi, Gerhard Wellein

Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel computer performance has been supporting these developments, and at the same time maintainers of neuroscientific simulation code have strived to optimally and efficiently exploit new hardware features. Current state-of-the-art software for the simulation of biological networks has so far been developed using performance engineering practices, but a thorough analysis and modeling of the computational and performance characteristics, especially in the case of morphologically detailed neuron simulations, is lacking. Other computational sciences have successfully used analytic performance engineering, which is based on "white-box," that is, first-principles performance models, to gain insight on the computational properties of simulation kernels, aid developers in performance optimizations and eventually drive codesign efforts, but to our knowledge a model-based performance analysis of neuron simulations has not yet been conducted. We present a detailed study of the shared-memory performance of morphologically detailed neuron simulations based on the Execution-Cache-Memory performance model. We demonstrate that this model can deliver accurate predictions of the runtime of almost all the kernels that constitute the neuron models under investigation. The gained insight is used to identify the main governing mechanisms underlying performance bottlenecks in the simulation. The implications of this analysis on the optimization of neural simulation software and eventually codesign of future hardware architectures are discussed. In this sense, our work represents a valuable conceptual and quantitative contribution to understanding the performance properties of biological networks simulations.

2020

Design and validation of bioorthogonal probes for cellular disease models

Well-validated chemical probes enable testing of biological hypotheses, investigation of target tractability and translatability to the clinical phase. Consequently, these important tool compounds play a key role in the drug discovery process. Moreover, their use for target validation may ultimately help to decrease the attrition rate encountered by new molecular entities in clinical trials. Despite the number of publications describing well-validated chemical probes, for several reasons, it remains a difficult challenge to identify and select the appropriate high quality molecule enabling the desired biological and pharmacological studies in the relevant disease model. Various reports describe sets of principles to be fulfilled by high quality chemical probes, which mainly rely on verifying that chemical probes are potent, engage their intended targets in the relevant cellular model, have sufficient exposure at the desired site of action and express functional pharmacological activities by a selective modulation of their targets. Classical chemical probes include LMW ligands, which inform on the functional consequences of interacting with a particular bio-logical target in a model system. To get information on other parameters (such as sub-cellular distribution of target or compound) different tools may need to be used, often requiring specific chemical functionalization in order to observe the molecule using the currently available technologies. Compared to classical chemical probes, bioorthogonal probes can also be small molecules that elicit a functional response but with the additional advantage of being able to undergo reaction with a variety of chemical reporters (e.g. fluorophores) in situ, in bio-logical model systems such as cells and animals. Therefore, this increases their versatility; for example their visualization using imaging technologies (bioluminescence and fluorescence imaging) can provide important insights on compound permeability, in-tracellular distribution, and potentially co-localization with its protein target in relevant cellular disease models. Hence, the use of a bespoke bioorthogonal probe may answer key biological questions, which are usually only addressed by using multiple classical probes. Herein, we describe the design and the synthesis of bioorthogonal probes to study the inhibition of the p53-Mdm2 protein-protein interaction. Furthermore, we report the development of a set of assays based on fluorescence and bioluminescence techniques enabling the validation of these molecules in a cellular osteosarcoma model. Our approach for chemical probe design and validation in cellular disease models may be applied in principle to a wide range of novel drug discovery projects to provide early mechanistic understanding.

EPFL2019

Chemical and Biological Gradients along the Damma Glacier Soil Chronosequence, Switzerland

Tobias Jonas, Edward Mitchell

Soils are the product of a complex suite of chemical, biological, and physical processes. In spite of the importance of soils for society and for sustaining life on earth, our knowledge of soil formation rates and of the influence of biological activity on mineral weathering and geochemical cycles is still limited. In this paper we provide a description of the Damma Glacier Critical Zone Observatory and present a first synthesis of our multi disciplinary studies of the 150-yr soil chronosequence. The aim of our research was to improve our understanding of ecosystem development on a barren substrate and the early evolution of soils and to evaluate the influence of biological activity on weathering rates. Soil pH, cation exchange capacity, biomass, bacterial and fungal populations, and soil organic matt er show clear gradients related to soil age, in spite of the extreme heterogeneity of the ecosystem. The bulk mineralogy and inorganic geochemistry of the soils, in contrast, are independent of soil age and only in older soils (>100 yr) is incipient weathering observed, mainly as a decreasing content in albite and biotite by coincidental formation of secondary chlorites in the clay fraction. Further, we document the rapid evolution of microbial and plant communities along the chronosequence.

2011

Analytic performance modeling and analysis of detailed neuron simulations

Francesco Cremonesi, Gerhard Wellein

2020

Design and validation of bioorthogonal probes for cellular disease models

EPFL2019