09091 Abstracts Collection -- Formal Methods in Molecular Biology

From 23. February to 27. February 2009, the Dagstuhl Seminar 09091 ``Formal Methods in Molecular Biology \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Linking intraspecific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off

Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in interspecific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species' traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterised a trait-dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r 2 of 34% to 57% and confirmed theoretical expectations of density-dependent population growth and species interactions in the system. Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics. A plain language summary is available for this article

Influence Networks compared with Reaction Networks: Semantics, Expressivity and Attractors

International audienceBiochemical reaction networks are one of the most widely used formalism in systems biology to describe the molecular mechanisms of high-level cell processes. However modellers also reason with influence diagrams to represent the positive and negative influences between molecular species and may find an influence network useful in the process of building a reaction network. In this paper, we introduce a formalism of influence networks with forces, and equip it with a hierarchy of Boolean, Petri net, stochastic and differential semantics, similarly to reaction networks with rates. We show that the expressive power of influence networks is the same as that of reaction networks under the differential semantics, but weaker under the discrete semantics. Furthermore, the hierarchy of semantics leads us to consider a (positive) Boolean semantics without test for absence, that we compare with the (negative) Boolean semantics with test for absence of gene regulatory networks à la Thomas. We study the monotonicity properties of the positive semantics and derive from them an algorithm to compute attractors in both the positive and negative Boolean semantics. We illustrate our results on models of the literature about the p53/Mdm2 DNA damage repair system, the circadian clock, and the influence of MAPK signaling on cell-fate decision in urinary bladder cancer

Marine Mammals

This highly-readable Open Access textbook provides basic background information about marine mammals and anthropogenic impacts on them. The book includes inspiring exercises for education school programs in natural sciences. The book also provides advice on career paths using case studies of marine scientists and veterinarians describing their journeys from student to profession. By sharing real-life career paths, readers find answers to questions such as “What needs to be considered when choosing a career in science?” and “What kind of tasks do scientists undertake on a daily basis?” Marine mammals are amongst some of the most celebrated creatures on Earth, with their high intelligence, social and communicating skills, and capacity for deep diving. Alongside general information about marine mammals, the book aims at generating awareness of the impact of litter and noise pollution on the marine environment using marine mammals as an example. Huge numbers of marine animals, including marine mammals, die every year from entanglement in fishing gear, by ingestion of litter or because of chemical pollution. In the last decade many technological and scientific tools have been developed to aid research, for instance miniaturised sound recorders which can be attached to cetaceans and seals and record noise levels around them, their vocal production as well as their diving behaviour. This Open Access textbook can be used by undergraduate students interested in the fundamentals of marine mammal biology and medicine, and in pursuing the profession of a marine scientist

The effect of cryopreservation on the genome of fish reproductive cells

A thesis submitted for the degree of Doctor of Philosophy of the University of LutonCryopreservation has been extensively used in human reproductive medicine, aquaculture and conservation programs for endangered species. Many studies have been devoted to the mechanisms of cryodamage. However, in spite of growing successes of cryopreservation, post-thaw recovery of reproductive and embryonic cells often remains poor. It is known that cryopreservation causes extensive damage to membrane, results in decreased metabolism of cells, and disturbs the bioenergetical processes of cells by damage to mitochondria. Nonetheless, it has not yet been identified clearly if cryopreservation causes some disruption in the genetic integrity of reproductive cells and the safety of this approach still needs to be confirmed. The present study was undertaken on the spermatozoa of weather loach (Misgurnus tassilis) and blastomeres cells of zebrafish (Danio rerio). It was shown that survival was decreased for embryos derived from sperm after cryoprotectant treatment or cryopreservation. Some evidence has emerged that this decrease is more likely to reflect some genetic instability caused by cryopreservation of sperm. The present study showed for the first time that the DNA repair system of oocytes was activated after fertilisation with cryopreserved sperm. The effect of DNA repair system was also studied. It was found that incubation of fertilised eggs in caffeine could reverse the detrimental effects of cryopreservation of loach sperm on subsequent embryo development. On the other hand incubation of fertilised eggs with 3-aminobenzamide - inhibitor of the poly (ADP-ribose) polymerase (PARP)- brought further decrease in the survival of embryos derived from cryopreserved sperm. The effect of individual donors of sperm and eggs on overall embryo survival was also studied and these investigations revealed significant differences between different donors. Effect of cryopreservation on zebrafish blastomeres was studied at the DNA molecular level. Mitochondrial DNA was sequenced after cryopreservation and increased level of frequency of the mutation was observed. This finding showed that cryopreservation might potentially increase the instability of mtDNA genome. The significance of these changes on the subsequent function of the cells is to be elucidated. Meanwhile this study suggests that it is important to be cautious in making judgements on the safety of cryopreservation techniques in reproduction

Geometry linking the art of building and the Universe: Geometric patterns on shells and grid shells

Geometry links the art of building and the physics of space-time. Mathematical breakthroughs in geometry have led to new ways of designing our structures and our ability to visualise and describe the world, phenomena in nature and the universe. However, in contemporary architecture and structural engineering, a more profound understanding of geometry has been forgotten. This thesis aims to resurrect geometry in architecture and engineering in connection with the rapid development of new digital tools for design and production—particularly the connection between the structural action related to the design of the geometrical patterns on shells structures are treated. A brief historical overview of geometry is conducted, and with an emphasis on its applications in architecture in terms of structural design and economic production. Furthermore, the connection to a sustainable building culture from the standpoint of the Davos declaration 2018, calling for a high-quality Baukultur is investigated. The concept of Baukultur (building culture in English) defined in the Davos declaration is related to architectural quality but has a broader meaning as it concerns the final product and the associated processes and its effect in society. Moreover, the concept of craftsmanship and workshop culture is examined, and how it is already present in computer code development and contemporary innovative research cultures combining architectural design and technology. Taking departure from the 18th-century experimental scientist Joseph Plateau and the contemporary artist Andy Goldsworthy, the connection between scientific and artistic research is investigated.Four articles are included; all connected to various ways of architectural applications of geometry in the design process. The first article describes a way to interpret empirically derived brick patterns, specifically the bed joints, using differential geometry. Two methods to apply this in the design processes of new brick vaults are presented. The first is purely geometrical and can be applied on an arbitrary shape with the possibility to apply several patterns; the second is an iterative method of generating a funicular shape and its pattern simultaneously. The second and third paper describes the design and construction process of two different wooden structures built of straight planar laths. Both studies examine the possibilities of using geometry as a link between various parameters in a design process using digital tools to achieve complex forms using simple elements and production methods. The fourth paper examines an appropriate form for a shell, that can balance aesthetics, structural performance and build-ability, with a proposal for the use of surfaces with constant solid angle. In this paper, the surface was generated with a Delaunay triangulation. Thus, future studies would include incorporation of other types of patterns facilitating buildability