Context-Aware Technology Mapping in Genetic Design Automation

Genetic design automation (GDA) tools hold promise to speed-up circuit design in synthetic biology. Their widespread adoption is hampered by their limited predictive power, resulting in frequent deviations between the in silico and in vivo performance of a genetic circuit. Context effects, i.e., the change in overall circuit functioning, due to the intracellular environment of the host and due to cross-talk among circuits components are believed to be a major source for the aforementioned deviations. Incorporating these effects in computational models of GDA tools is challenging but is expected to boost their predictive power and hence their deployment. Using fine-grained thermodynamic models of promoter activity, we show in this work how to account for two major components of cellular context effects: (i) crosstalk due to limited specificity of used regulators and (ii) titration of circuit regulators to off-target binding sites on the host genome. We show how we can compensate the incurred increase in computational complexity through dedicated branch-and-bound techniques during the technology mapping process. Using the synthesis of several combinational logic circuits based on Cello’s device library as a case study, we analyze the effect of different intensities and distributions of crosstalk on circuit performance and on the usability of a given device library

Creating sustainable meals supported by the NAHGAST online tool : approach and effects on GHG emissions and use of natural resources

Every diet has an impact on an individual’s health status, the environment, as well as on social concerns. A growing number of meals are consumed in the out-of-home catering sector, in which a systematic sustainability assessment is not part of common practice. In order to close this gap, an instrument was developed as part of the NAHGAST project. After more than one year of using the NAHGAST online tool, it needs to be assessed what positive environmental influences can be realized by using the tool. For this reason, this article deals with the question of whether an online tool can enable stakeholders from the out-of-home consumption sector to revise their meals with regard to aspects of a sustainable diet. In addition, it will be answered how precise recipe revisions of the most popular lunchtime meals influence the material footprint as well as the carbon footprint. In conclusion, an online tool can illustrate individual sustainability paths for stakeholders in the out-of-home consumption sector and enables an independent recipe revision for already existing meals. The results show that even slight changes in recipes could lead to savings of up to a third in carbon footprint as well as in material footprint. In relation to the out-of-home consumption sector, this results in the potential for substantial multiplication effects that will pave the way for the dissemination of sustainable nutrition

Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach

Mobile phone technology makes use of radio frequency (RF) electromagnetic fields transmitted through a dense network of base stations in Europe. Possible harmful effects of RF fields on humans and animals are discussed, but their effect on plants has received little attention. In search for physiological processes of plant cells sensitive to RF fields, cell suspension cultures of Arabidopsis thaliana were exposed for 24 h to a RF field protocol representing typical microwave exposition in an urban environment. mRNA of exposed cultures and controls was used to hybridize Affymetrix-ATH1 whole genome microarrays. Differential expression analysis revealed significant changes in transcription of 10 genes, but they did not exceed a fold change of 2.5. Besides that 3 of them are dark-inducible, their functions do not point to any known responses of plants to environmental stimuli. The changes in transcription of these genes were compared with published microarray datasets and revealed a weak similarity of the microwave to light treatment experiments. Considering the large changes described in published experiments, it is questionable if the small alterations caused by a 24 h continuous microwave exposure would have any impact on the growth and reproduction of whole plants

Unsupervised Meta-Analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation

Over the past years, microarray databases have increased rapidly in size. While they offer a wealth of data, it remains challenging to integrate data arising from different studies. Here we propose an unsupervised approach of a large-scale meta-analysis on Arabidopsis thaliana whole genome expression datasets to gain additional insights into the function and regulation of genes. Applying kernel principal component analysis and hierarchical clustering, we found three major groups of experimental contrasts sharing a common biological trait. Genes associated to two of these clusters are known to play an important role in indole-3-acetic acid (IAA) mediated plant growth and development or pathogen defense. Novel functions could be assigned to genes including a cluster of serine/threonine kinases that carry two uncharacterized domains (DUF26) in their receptor part implicated in host defense. With the approach shown here, hidden interrelations between genes regulated under different conditions can be unraveled

A review of the literature on benefits, costs, and policies for wildlife management

Wildlife management is a source of conflict in many countries because of the asymmetric allocation of benefits and costs among stakeholders. A review of studies on benefits, costs, and policies shows most valuation studies estimate recreational values of hunting, which can range between 13 and 545 USD/hunting day (in 2013 prices). A majority of the studies on costs calculate losses from livestock predation and crop destruction, and show that they can correspond to 40% of profits in the agricultural sector in wildlife rich regions in the US. Most of the studies are carried out for animals in developed economies, in particular in the US. This is in contrast to studies on costs of wildlife, which to a large extent are born by farmers neighboring national parks in developing and emerging economies. However, a common feature of both valuation and cost studies is the exclusion of several costs and benefits items and of indirect effects in the economies, which can be considerable for economies with high reliance on tourism and agriculture sectors. With respect to policy choice, the literature suggests economic incentives for conflict resolutions, where the winners from wildlife compensate the losses, but studies evaluating such policies in practice are lacking

Near-Wall Flow in Turbomachinery Cascades—Results of a German Collaborative Project

This article provides a summarizing account of the results obtained in the current collabora-tive work of four research institutes concerning near-wall flow in turbomachinery. Specific questions regarding the influences of boundary layer development on blades and endwalls as well as loss mech-anisms due to secondary flow are investigated. These address skewness, periodical distortion, wake interaction and heat transfer, among others. Several test rigs with modifiable configurations are used for the experimental investigations including an axial low speed compressor, an axial high-speed wind tunnel, and an axial low-speed turbine. Approved stationary and time resolving measurements techniques are applied in combination with custom hot-film sensor-arrays. The experiments are complemented by URANS simulations, and one group focusses on turbulence-resolving simulations to elucidate the specific impact of rotation. Juxtaposing and interlacing their results the four groups provide a broad picture of the underlying phenomena, ranging from compressors to turbines, from isothermal to non-adiabatic, and from incompressible to compressible flows.The investigations reported in this article were conducted within the framework of the joint research project “Near-Wall Flow in Turbomachinery Cascades” which was funded and supported by the Deutsche Forschungsgemeinschaft (DFG) under grant number PAK 948. The responsibility for the contents of this publication lies entirely by the authors.Peer ReviewedPostprint (published version

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

<p>Abstract</p> <p>Background</p> <p>Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.</p> <p>Results</p> <p>To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (<it>Milnesium tardigradum</it>, <it>Hypsibius dujardini</it>, <it>Echiniscus testudo</it>, <it>Tulinus stephaniae</it>, <it>Richtersius coronifer</it>) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer <url>http://waterbear.bioapps.biozentrum.uni-wuerzburg.de</url>. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.</p> <p>Conclusion</p> <p>Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.</p

Gesund, umweltfreundlich und sozialverträglich : wie ein Onlinetool hilft, nachhaltiger zu kochen

Jede Kostform hat Auswirkungen auf den individuellen Gesundheitsstatus, die Umwelt und soziale Aspekte. Insbesondere ökologische und soziale Belange werden im Alltag der Außer-Haus-Verpflegung in der Regel nur vage abgeschätzt, eine systematische Nachhaltigkeitsbewertung von Speisen findet zumeist nicht statt. Seit Mai 2018 unterstützt der hier vorgestellte Menü-Rechner Akteure in unterschiedlichen Verpflegungseinrichtungen bei der Nachhaltigkeitsbewertung. Das Instrument wurde im Rahmen des NAHGAST-Projektes (www.nahgast.de) in Kooperation mit fünf Praxispartnern entwickelt und durch insgesamt 120 Rezepturen getestet und validiert. Der vorliegende Artikel gibt einen Überblick über Nachhaltigkeitsbewertungen ausgewählter Rezepturen (Gerichte mit Fisch und Fleisch, sowie vegetarische und vegane Gerichte) und stellt heraus, welche Effekte sich für die ökologische, gesundheitliche und soziale Dimension zeigen

Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations

Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant