SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource for Salmonella. It comprehensively contains interactions between proteins encoded in Salmonella pathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides a Salmonella resource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available at http://salmonet.org

Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae

<p>Abstract</p> <p>Background</p> <p>Two component systems (TCS) are signal transduction pathways which typically consist of a sensor histidine kinase (HK) and a response regulator (RR). In this study, we have analyzed the evolution of TCS of the OmpR/IIIA family in <it>Lactobacillaceae </it>and <it>Leuconostocaceae</it>, two families belonging to the group of lactic acid bacteria (LAB). LAB colonize nutrient-rich environments such as foodstuffs, plant materials and the gastrointestinal tract of animals thus driving the study of this group of both basic and applied interest.</p> <p>Results</p> <p>The genomes of 19 strains belonging to 16 different species have been analyzed. The number of TCS encoded by the strains considered in this study varied between 4 in <it>Lactobacillus helveticus </it>and 17 in <it>Lactobacillus casei</it>. The OmpR/IIIA family was the most prevalent in <it>Lactobacillaceae </it>accounting for 71% of the TCS present in this group. The phylogenetic analysis shows that no new TCS of this family has recently evolved in these <it>Lactobacillaceae </it>by either lineage-specific gene expansion or domain shuffling. Furthermore, no clear evidence of non-orthologous replacements of either RR or HK partners has been obtained, thus indicating that coevolution of cognate RR and HKs has been prevalent in <it>Lactobacillaceae</it>.</p> <p>Conclusions</p> <p>The results obtained suggest that vertical inheritance of TCS present in the last common ancestor and lineage-specific gene losses appear as the main evolutionary forces involved in their evolution in <it>Lactobacillaceae</it>, although some HGT events cannot be ruled out. This would agree with the genomic analyses of <it>Lactobacillales </it>which show that gene losses have been a major trend in the evolution of this group.</p

Redefining innovation processes: The digital designers at work

As design in digital innovation has become a thing, we highlight the inconclusive concepts that describe design activity in innovation processes. Proposing an alternative theoretical lens - a sociomaterial practice lens - we claim that this view can reveal the contribution of digital designers to the work of innovation. This paper draws on a research study with digital designers in the UK. At the same time as we begin to reconceptualise the ways digital design activity can be described, we also illustrate a theoretical framework based on 1) action and knowing as ordered by collectively produced objects, 2) sociomateriality and the configuration of human bodies and materials in action, 3) the co-emergence of objects and sociomaterial configurations where each is the condition of the other. This alternative way of looking at design activity may pose some challenges to the theoretical traditions in the field. We however believe that it contains immense potential too

Geomorphological and sedimentary processes of the glacially influenced northwestern Iberian continental margin and abyssal plains

The offshore region of northwestern Iberia offers an opportunity to study the impacts of along-slope processes on the morphology of a glacially influenced continental margin, which has traditionally been conceptually characterised by predominant down-slope sedimentary processes. High-resolution multibeam bathymetry, acoustic backscatter and ultrahigh-resolution seismic reflection profile data are integrated and analysed to describe the present-day and recent geomorphological features and to interpret their associated sedimentary processes. Seventeen large-scale seafloor morphologies and sixteen individual echo types, interpreted as structural features (escarpments, marginal platforms and related fluid escape structures) and depositional and erosional bedforms developed either by the influence of bottom currents (moats, abraded surfaces, sediment waves, contourite drifts and ridges) or by gravitational features (gullies, canyons, slides, channel-levee complexes and submarine fans), are identified for the first time in the study area (spanning ~90,000 km2 and water depths of 300m to 5 km). Different types of slope failures and turbidity currents are mainly observed on the upper and lower slopes and along submarine canyons and deep-sea channels. The middle slope morphologies are mostly determined by the actions of bottom currents (North Atlantic Central Water, Mediterranean Outflow Water, Labrador Sea Water and North Atlantic Deep Water), which thereby define the margin morphologies and favour the reworking and deposition of sediments. The abyssal plains (Biscay and Iberian) are characterised by pelagic deposits and channel-lobe systems (the Cantabrian and Charcot), although several contourite features are also observed at the foot of the slope due to the influence of the deepest water masses (i.e., the North Atlantic Deep Water and Lower Deep Water). Thiswork shows that the study area is the result of Mesozoic to present-day tectonics (e.g. themarginal platforms and structural highs). Therefore, tectonism constitutes a long-term controlling factor, whereas the climate, sediment supply and bottom currents play key roles in the recent short-term architecture and dynamics. Moreover, the recent predominant along-slope sedimentary processes observed in the studied northwestern Iberian Margin represent snapshots of the progressive stages and mixed deep-water system developments of the marginal platforms on passive margins and may provide information for a predictive model of the evolution of other similar margins.Departamento de Investigación y Prospectiva Geocientífica, Unidad de Tres Cantos, Instituto Geológico y Minero de España, EspañaDepartamento de Geología y Geoquímica, Universidad Autónoma de Madrid, EspañaDepartment of Earth Sciences, Royal Holloway University of London, Reino Unid

Design thinking and design doing: Describing a process of people-centred innovation

The research forms part of the author’s long-term enquiry into the challenges of implementing Design Thinking (DT) and its relationship to Inclusive Design (ID), something that has been understudied and under-researched. Both fields advocate research with users and have a history spanning decades, but they have remained largely separate in terms of academic research and practical application. The author was approached by the series editor for his expertise at the intersection of ID and DT. “State of the art” DT ideas and approaches were evaluated through study of circa 50 recent academic publications, papers and journal articles. Field research was based on personal leadership of over 70 ID projects with government, business, and the voluntary sector leading to frontline discoveries and insights. Peer-reviewed academic publication, conference presentation, and keynote delivery helped test ideas before making the link between ID and DT and delivering the publication. This 13,000 word, sole-authored chapter outlines gaps in the long-term effectiveness of DT, outlining five principles that aim to engender a more sustainable approach by aligning it to ID. These five ideas give an overview of newly-articulated frameworks, tools and methods for academic and industry application. The chapter sets a context for 16 other chapters within the publication and establishes the need for more empirical research to link between DT and ID. The ideas in the chapter have been used to direct practice-based research projects and education programmes at the RCA as well as organisations in its network. 700 Hong Kong civil servants have been trained using these ideas, alongside numerous industry organisations including Tata Consulting Services and Panasonic

Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH)

BACKGROUND: The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist. RESULTS: To test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (±0.00) and a low level of population differentiation (mtDNA Fst= 0.56, p < 0.05; nuDNA Fst = 0.33, P < 0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (±0.03) and comparatively higher levels of population differentiation (mtDNA Fst = 0.87, P < 0.05; nuDNA Fst = 0.48, P < 0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA Fst= 0.53, P < 0. 05; nuDNA Fst= 0.12, P < 0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA Fst of 0.79 (P < 0.05) while R. dilectus populations are less structured with a mtDNA Fst= 0.18 (P < 0.05). CONCLUSION: These findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species