Racing Multi-Objective Selection Probabilities

In the context of Noisy Multi-Objective Optimization, dealing with uncertainties requires the decision maker to define some preferences about how to handle them, through some statistics (e.g., mean, median) to be used to evaluate the qualities of the solutions, and define the corresponding Pareto set. Approximating these statistics requires repeated samplings of the population, drastically increasing the overall computational cost. To tackle this issue, this paper proposes to directly estimate the probability of each individual to be selected, using some Hoeffding races to dynamically assign the estimation budget during the selection step. The proposed racing approach is validated against static budget approaches with NSGA-II on noisy versions of the ZDT benchmark functions

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation

A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

<p>Abstract</p> <p>Background</p> <p>Non-coding RNAs (ncRNA) are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the <it>Prochlorococcus/Synechococcus </it>group of marine cyanobacteria.</p> <p>Results</p> <p>Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of <it>Prochlorococcus</it>, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'.</p> <p>Conclusion</p> <p>Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of <it>E. coli </it>and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.</p

Qualitätskriterien transdisziplinärer Forschung : ein Leitfaden für die formative Evaluation von Forschungsprojekten

Transdisziplinäre Forschung befasst sich mit lebensweltlichen Problemstellungen. Bei der Forschungsarbeit müssen Experten/innen aus verschiedenen Fächern bzw. Disziplinen und aus der Praxis zusammenwirken, um die komplexe Problematik umfassend behandeln zu können. Diese Vielfalt, die besondere Formen der Kooperation, der Differenzierung und Integration, Methoden und Theorien impliziert, bringt es mit sich, dass gängige, bei der fachbezogenen Bewertung hinreichende Verfahren der Evaluation und der Qualitätssicherung nicht unmittelbar auf solche Forschungsvorhaben übertragen werden können. Diesem Mangel an Kriterien und Methoden der Evaluation begegnet Evalunet, das Evaluationsnetzwerk für transdisziplinäre Forschung, mit dem vorgelegten Leitfaden für die Forschungspraxis, der vor allem ausführlich beschriebene Qualitätskriterien enthält und ebenso Aussagen zu methodischen und Verfahrensfragen macht. Er ist aus der empirischen Auswertung konkreter transdisziplinärer Forschungsprojekte und unter Mithilfe zahlreicher Experten und Expertinnen aus verschiedenen Fachrichtungen entstanden. Der Leitfaden dient dem Zweck der Evaluation von transdisziplinären Forschungsprojekten, wobei dieses Instrument auf den Aspekt des Lernens aus dem Evaluationsvorgang (formative Evaluation) zugeschnitten ist und bei der Aus- und Bewertung auf einen Diskurs setzt (diskursive Evaluation). Neben einer Evaluierung mittels der ausführlich beschriebenen Detailkriterien ist auch eine weniger aufwändige Evaluation mit Hilfe einer Kriterienauswahl (Basiskriterien) möglich. Die Qualitätskriterien können auch für die Konzipierung neuer transdisziplinärer Forschungsvorhaben genutzt werden.Transdisciplinary research projects investigate problems from everyday life. Experts from various disciplines and practitioners from the practical field in question have to co-operate to cope with the problem appropriately. Multiple forms of co-operation, differentiation and integration, methods and theories are significant for such projects. So conventional methods of disciplinary evaluation cannot be transferred and applied directly. In this situation, Evalunet, the Network for Transdisciplinary Evaluation, offers this guide, which provides researchers with very detailed evaluation criteria and descriptions of evaluation methods and practices. The criteria and procedures were identified in an empirical process by evaluating a number of transdisciplinary research projects. In this process, the Evalunet team was supported by numerous experts from various research areas. The main purpose of the guide is to provide guidance for the evaluation of transdisciplinary research projects. The criteria mainly support discursive evaluation processes that initiate learning processes for researchers and evaluators (formative evaluation). A set with a reduced number of criteria (Basiskriterien) offers a basic procedure for the evaluation, while the larger set with more detailed criteria (Detailkriterien) provides explanations and assistance in making a judgement. Criteria can also be used for conceiving and constructing new research projects

Discrete Particle Swarm Optimization for the minimum labelling Steiner tree problem

Particle Swarm Optimization is an evolutionary method inspired by the social behaviour of individuals inside swarms in nature. Solutions of the problem are modelled as members of the swarm which fly in the solution space. The evolution is obtained from the continuous movement of the particles that constitute the swarm submitted to the effect of the inertia and the attraction of the members who lead the swarm. This work focuses on a recent Discrete Particle Swarm Optimization for combinatorial optimization, called Jumping Particle Swarm Optimization. Its effectiveness is illustrated on the minimum labelling Steiner tree problem: given an undirected labelled connected graph, the aim is to find a spanning tree covering a given subset of nodes, whose edges have the smallest number of distinct labels

Biomarkers as Proxies to Analyse Land-Use History in Northern Jordan

In the semi-arid 'Decapolis region' in northern Jordan, due severe land degradation in the past, 'barren' and 'impoverished' landscapes can be found today. It is widely believed that land degradation in these regions was caused by ancient land use, e.g. overgrazing due to ‘Arab mismanagement'. However, the connection of degradation with land use is far from certain. The 'Decapolis region' is located in an approximately 100 km wide transition zone from Mediterranean to steppe and desert climate. Therefore, the landscape in this region is highly sensitive to climate variations. A major sedimentation phase in the late 6th century AD appears to represent a significant climate change towards more aridity, and might be connected with a cluster of heavy rainfall events in northern Jordan. In fact, more recent studies have found that periods of predominantly pastoral land use in northern Jordan were connected with natural reforestation. Since a dating of sedimentation alone does not deliver clues about the precise reason of deposition, a multidisciplinary team is analyzing the land-use history in the ‘Decapolis’ region. This presentation focusses on ongoing biomarker analyses. Samples were selected considering geoarchaeological data, including phosphorus concentrations, archaeological data, including distribution of potsherds and other fragments on ancient fields and data of further disciplines. Vegetation changes are investigated by analyses of n-alkanes and terpenoids. Manuring with faeces is analysed by specific steroids that are indicative for faeces deposition. Preliminary results showed a high input of omnivorous (pigs, humans) faeces in some areas. Manuring with faeces of herbivores seemed to be less important

Auxin fluxes through plasmodesmata modify root-tip auxin distribution

© 2020. Published by The Company of Biologists Ltd. Auxin is a key signal regulating plant growth and development. It is well established that auxin dynamics depend on the spatial distribution of efflux and influx carriers on the cell membranes. In this study, we employ a systems approach to characterise an alternative symplastic pathway for auxin mobilisation via plasmodesmata, which function as intercellular pores linking the cytoplasm of adjacent cells. To investigate the role of plasmodesmata in auxin patterning, we developed a multicellular model of the Arabidopsis root tip. We tested the model predictions using the DII-VENUS auxin response reporter, comparing the predicted and observed DII-VENUS distributions using genetic and chemical perturbations designed to affect both carrier-mediated and plasmodesmatal auxin fluxes. The model revealed that carrier-mediated transport alone cannot explain the experimentally determined auxin distribution in the root tip. In contrast, a composite model that incorporates both carrier-mediated and plasmodesmatal auxin fluxes re-capitulates the root-tip auxin distribution. We found that auxin fluxes through plasmodesmata enable auxin reflux and increase total root-tip auxin. We conclude that auxin fluxes through plasmodesmata modify the auxin distribution created by efflux and influx carriers

Pseudomonas putida KT2440 is naturally endowed to withstand industrial-scale stress conditions

Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and β-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short- and long-term responses that increase the cellular maintenance by about 17% under the industrial-like conditions tested.publishersversionpublishe