Global Innovation Policy Index

Ranks fifty-five nations' strategies to boost innovation capacity: policies on trade, scientific research, information and communications technologies, tax, intellectual property, domestic competition, government procurement, and high-skill immigration

A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes)

The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6–D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae.Fil: Fromm, Amir. Tel Aviv University George S. Wise Faculty Of Life Sciences; IsraelFil: Atkinson, Stephen D.. State University of Oregon; Estados UnidosFil: Alama Bermejo, Gema. Universidad Nacional del Comahue. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". - Provincia de Río Negro. Ministerio de Agricultura, Ganadería y Pesca. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Centro Nacional Patagónico. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni"; ArgentinaFil: Cartwright, Paulyn. University of Kansas; Estados UnidosFil: Bartholomew, Jerri. State University of Oregon; Estados UnidosFil: Huchon, Dorothée. Tel Aviv University George S. Wise Faculty Of Life Sciences; Israe

NRP2 as an Emerging Angiogenic Player; Promoting Endothelial Cell Adhesion and Migration by Regulating Recycling of α5 Integrin.

Angiogenesis relies on the ability of endothelial cells (ECs) to migrate over the extracellular matrix via integrin receptors to respond to an angiogenic stimulus. Of the two neuropilin (NRP) orthologs to be identified, both have been reported to be expressed on normal blood and lymphatic ECs, and to play roles in the formation of blood and lymphatic vascular networks during angiogenesis. Whilst the role of NRP1 and its interactions with integrins during angiogenesis has been widely studied, the role of NRP2 in ECs is poorly understood. Here we demonstrate that NRP2 promotes Rac-1 mediated EC adhesion and migration over fibronectin (FN) matrices in a mechanistically distinct fashion to NRP1, showing no dependence on β3 integrin (ITGB3) expression, or VEGF stimulation. Furthermore, we highlight evidence of a regulatory crosstalk between NRP2 and α5 integrin (ITGA5) in ECs, with NRP2 depletion eliciting an upregulation of ITGA5 expression and disruptions in ITGA5 cellular organization. Finally, we propose a mechanism whereby NRP2 promotes ITGA5 recycling in ECs; NRP2 depleted ECs were found to exhibit reduced levels of total ITGA5 subunit recycling compared to wild-type (WT) ECs. Our findings expose NRP2 as a novel angiogenic player by promoting ITGA5-mediated EC adhesion and migration on FN

Transcriptome-Wide Comparisons and Virulence Gene Polymorphisms of Host-Associated Genotypes of the Cnidarian Parasite Ceratonova shasta in Salmonids

Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. Ceratonova shasta exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from C. shasta genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for C. shasta genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the data sets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed single-nucleotide polymorphism-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of C. shasta in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.Fil: Alama Bermejo, Gema. Universidad Nacional del Comahue. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". - Provincia de Río Negro. Ministerio de Agricultura, Ganadería y Pesca. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni". Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet Centro Nacional Patagónico. Centro de Investigación Aplicada y Transferencia Tecnológica en Recursos Marinos "Almirante Storni"; Argentina. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República Checa. State University of Oregon; Estados UnidosFil: Meyer, Eli. Oregon State University; Estados UnidosFil: Atkinson, Stephen D.. Oregon State University; Estados UnidosFil: Holzer, Astrid S.. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Wiśniewska, Monika M.. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República ChecaFil: Kolísko, Martin. Academy of Sciences of the Czech Republic. Biology Centre. Institute of Parasitology; República Checa. University of South Bohemia; República ChecaFil: Bartholomew, Jerri. Oregon State University; Estados Unido

The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection

Background Cnidarians are the most ancient venomous organisms. They store a cocktail of venom proteins inside unique stinging organelles called nematocysts. When a cnidarian encounters chemical and physical cues from a potential threat or prey animal, the nematocyst is triggered and fires a harpoon-like tubule to penetrate and inject venom into the prey. Nematocysts are present in all Cnidaria, including the morphologically simple Myxozoa, which are a speciose group of microscopic, spore-forming, obligate parasites of fish and invertebrates. Rather than predation or defense, myxozoans use nematocysts for adhesion to hosts, but the involvement of venom in this process is poorly understood. Recent work shows some myxozoans have a reduced repertoire of venom-like compounds (VLCs) relative to free-living cnidarians, however the function of these proteins is not known. Methods We searched for VLCs in the nematocyst proteome and a time-series infection transcriptome of Ceratonova shasta, a myxozoan parasite of salmonid fish. We used four parallel approaches to detect VLCs: BLAST and HMMER searches to preexisting cnidarian venom datasets, the machine learning tool ToxClassifier, and structural modeling of nematocyst proteomes. Sequences that scored positive by at least three methods were considered VLCs. We then mapped their time-series expressions in the fish host and analyzed their phylogenetic relatedness to sequences from other venomous animals. Results We identified eight VLCs, all of which have closely related sequences in other myxozoan datasets, suggesting a conserved venom profile across Myxozoa, and an overall reduction in venom diversity relative to free-living cnidarians. Expression of the VLCs over the 3-week fish infection varied considerably: three sequences were most expressed at one day post-exposure in the fish’s gills; whereas expression of the other five VLCs peaked at 21 days post-exposure in the intestines, coinciding with the formation of mature parasite spores with nematocysts. Expression of VLC genes early in infection, prior to the development of nematocysts, suggests venoms in C. shasta have been repurposed to facilitate parasite invasion and proliferation within the host. Molecular phylogenetics suggested some VLCs were inherited from a cnidarian ancestor, whereas others were more closely related to sequences from venomous non-Cnidarian organisms and thus may have gained qualities of venom components via convergent evolution. The presence of VLCs and their differential expression during parasite infection enrich the concept of what functions a “venom” can have and represent targets for designing therapeutics against myxozoan infections

Widespread distribution of Ceratonova shasta (Cnidaria: Myxosporea) genotypes indicates evolutionary adaptation to its salmonid fish hosts

The distribution of the freshwater myxozoan parasite Ceratonova shasta in the Pacific Northwest of North America is limited to overlap in the ranges of its 2 hosts: the polychaete Manyunkia sp., and Pacific salmonids. Studies in the Klamath River (Oregon/California) and Deschutes River (Oregon), showed that the parasite population is comprised of multiple sympatric genotypes, some of which correlate with particular salmonid host species and with differences in clinical disease in those hosts. The 3 primary genotypes O, I, and II are defined by the number of a specific tri-nucleotide repeat in the internal transcribed spacer-1 region. To understand the spatial extent of host-parasite genotype patterns, we sequenced the parasite from 448 salmonid fishes from river basins in California, Oregon, Washington, Idaho, and British Columbia, Canada. We sampled intestinal tissues from 6 species of salmon and trout, both those that exist naturally with the parasite (sympatric) and those that do not naturally co-occur with the parasite and were exposed artificially in cages (allopatric). In most river basins we detected the same primary C. shasta genotypes that were described from the Klamath and Deschutes rivers, and we did not detect any novel primary genotypes. Host- parasite genotype patterns were consistent with previous data: genotype O was found in sympatric trout only; genotype I predominantly in Chinook salmon, and genotype II in all 6 fish species but dominant in coho salmon. Our findings of widespread, consistent host-parasite genotype patterns support the hypothesis that C. shasta has a long evolutionary history with salmonid fishes in the Pacific Northwest, and impels additional studies to determine if these parasite genotypes should be considered different species

Climate reconstruction from paired oxygen-isotope analyses of chironomid larval head capsules and endogenic carbonate (Hawes Water, UK) - Potential and problems

Temperature and the oxygen isotopic composition (δ18O) of meteoric water are both important palaeoclimatic variables, but separating their influences on proxies such as the δ18O of lake carbonates is often problematic. The large temperature variations that are known to have occurred in the northern mid-latitudes during the Late Glacial make this interval an excellent test for a novel approach that combines oxygen-isotope analyses of chironomid larval head capsules with co-occurring endogenic carbonate. We apply this approach to a Late Glacial lake sediment sequence from Hawes Water (NW England). Oxygen-isotope values in chironomid head capsules show marked variations during the Late Glacial that are similar to the oxygen isotope record from endogenic carbonate. However, summer temperature reconstructions based on the paired isotope values and fractionation between chironomids and calcite yield values between −20 and −4 °C, which are unrealistic and far lower than reconstructions based on chironomid assemblages at the same site. The composition of a limited number of samples of fossil chironomid larval head capsules determined using Pyrolysis gas-chromatography mass spectrometry indicates the presence of aliphatic geopolymers, suggesting that diagenetic alteration of the head capsules has systematically biased the isotope-derived temperature estimates. However, a similar trend in the isotope records of the two sources suggests that a palaeoclimate signal is still preserved

Identifying all persons in Wales with type 1 diabetes mellitus using routinely collected linked data

Introduction Type 1 diabetes mellitus (T1DM) is an autoimmune condition characterised by hyperglycaemia, caused by the destruction of insulin producing β-cells in the pancreas. Previous epidemiological population level studies of T1DM and its complications have typically used recorded T1DM diagnoses to determine diabetes status and define cohorts. Objectives and Approach The objective was to identify all persons with T1DM in Wales from Primary (~70\% population coverage) and Secondary Care (100% coverage) data held in the Secure Anonymised Information Linkage (SAIL) databank. People with a coded T1DM diagnosis (using Read codes in Primary Care data and International Classification of Disease (ICD10) codes in Secondary Care data), plus either insulin prescribed shortly after diagnosis or a hospital admission for diabetic ketoacidosis were identified as having T1DM. A sub-group of this SAIL e-cohort were validated using a register of persons diagnosed with T1DM in Wales under 15 years old (Brecon cohort). Results 18,285 people had a T1DM diagnosis and 10,539 had more T1DM than type 2 diabetes mellitus (T2DM) diagnoses. 6,375 persons were identified with T1DM in Primary Care data using our criteria, with a median diagnosis age of 19.2 years (interquartile range 11.0, 35.5). 47.5\% were diagnosed under 18 years of age. 39.6% of people with a T1DM diagnosis did not have T1DM using our criteria. False positive and negative rates of 4.8% and 4.5% respectively were achieved by comparing persons in the SAIL e-cohort against the Brecon cohort. Clinician estimated false positive and negative rates were 1.4% and 3.9% respectively. The prevalence of T1DM in Wales in 2016 was 0.37% or 11,049 people. Conclusion/Implications Our criteria for identifying people with T1DM was more reliable than using diagnosis codes alone, allowing for a more accurate, efficient and reproducible means of identifying individuals with T1DM for researchers utilising the SAIL databank, and other national health repositories

A novel myxozoan parasite of terrestrial mammals: description of Soricimyxum minuti sp. n. (Myxosporea) in pygmy shrew Sorex minutus from Hungary

As part of a biodiversity study in northwestern Hungary, we conducted a parasitological survey of small mammals. In both common shrews (Sorex araneus Linnaeus) and pygmy shrews (Sorex minutus Linnaeus), we found myxospores of a species of Soricimyxum Prunescu, Prunescu, Pucek et Lom, 2007 (Myxosporea) and plasmodia in the bile ducts within the liver. Spores from both species of shrewswere morphologically and morphometrically indistinguishable, but differed in their SSU rRNA gene sequences by 3.3%. We identified spores and developmental stages from the common shrew as Soricimyxum fegati Prunescu, Prunescu, Pucek et Lom, 2007, based on morphometric data and DNA sequence similarity. Spores from the pygmy shrew were only 96.7% similar to S. fegati, hence we identified them as a novel myxosporean Soricimyxum minuti sp. n. This is only the second myxosporean parasite species described from mammals