A Cambrian–Ordovician boundary section in the Rafnes–Herøya submarine tunnel, Skien–Langesund District, southern Norway

Rock specimens and contained fossils collected in 1976 from a submarine tunnel driven between Herøya and Rafnes in the Skien–Langesund area of southern Norway, have been restudied. The contained fossils include olenid and agnostoid trilobites, graptolites and brachiopods, groups described in detail for the first time from the area and documenting a Cambrian–Ordovician boundary section unique in the district where the upper Cambrian Alum Shale Formation is elsewhere overlain by the Middle Ordovician Rognstranda Member of the Huk Formation (Kundan in terms of Baltoscandian chronostratigraphy). The hiatus at the base of the Huk Formation is thus smaller in the section described herein, beginning at a level within rather than below the Tremadocian. Estimated thickness of the Alum Shale includes 10–12 m of Miaolingian and 20–22 m of Furongian strata with trilobite zones identified, and a Tremadocian section of 8.1 m identified by species of the dendroid graptolite Rhabdinopora in the basal 2.6 m and Bryograptus ramosus at the top. The Tremadocian section is preserved in a postulated zone of synsedimentary subsidence along the Porsgrunn–Kristiansand Fault Zone, while at the same time there was extensive erosion across an emergent, level platform elsewhere in the Skien–Langesund District and the southern part of the Eiker–Sandsvær District to the north. Aspects of stratigraphy and tectonics are highlighted together with a discussion on the Cambrian– Ordovician boundary locally and worldwide

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions. Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. Availability and implementation: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics onlin

Potential of multi-species livestock farming to improve the sustainability of livestock farms: A review.

Diversified farming systems are proposed as a major mechanism to address the many sustainability issues of today's agriculture. Multi-species livestock farming, i.e. keeping two or more animal species simultaneously on the same farm, is an option that has received little attention to date. Moreover, most studies of multi-species livestock farming are limited, usually focusing on selected dimensions of farm sustainability and addressing lower organizational levels (i.e. within the farm) and rather limited time horizons (e.g. a few weeks in a grazing season). Thus, a comprehensive assessment of multi-species livestock farming in terms of farm sustainability is lacking. In this context, we outline and discuss potential benefits and limitations of multi-species livestock farming for livestock farm sustainability from existing literature and list issues on multi-species livestock farming requiring further research. We show that multi-species livestock farming has the potential to improve the three dimensions of sustainability reviewed - economic viability for farmers, environmental soundness and social acceptability by being respectful of animals and humans - as long as locally relevant farming practices are implemented, especially an appropriate stocking rate during grazing. If relevant practices are not observed, multi-species livestock farming may produce undesirable effects, such as competition for resource acquisition during grazing, parasitic cross-infection and more intense work peaks. Therefore, we identify four focal research areas for multi-species livestock farming. First, characterizing the management of multi-species livestock farms. To do this, we suggest considering the integration of production enterprises (e.g. cattle and sheep enterprises) within the farm from three perspectives: farming practices (e.g. grazing management), work organization and sales. Second, exploring the complementarity of livestock species on multi-species livestock farms. This is especially true for species combinations that have been largely ignored (e.g. ruminants and monogastrics), even though they may have potential due to complementary diet compositions and resource-acquisition strategies. Third, assessing the sustainability of multi-species livestock farm scenarios (current or alternative) according to the management practices and production conditions, which requires adapting existing methods/models or developing new ones. Fourth, characterizing conditions for success and obstacles for multi-species livestock farming along the value chain from production to consumption, considering stakeholders' objectives, work habits and constraints. Increasing understanding should help prioritize actions and organize them to scale up multi-species livestock farming

The active metabolite of leflunomide, A77 1726, increases the production of IL-1 receptor antagonist in human synovial fibroblasts and articular chondrocytes

Leflunomide is an immunomodulatory agent used for the treatment of rheumatoid arthritis. In this study, we investigated the effect of A77 1726 – the active metabolite of leflunomide – on the production of IL-1 receptor antagonist (IL-1Ra) by human synovial fibroblasts and articular chondrocytes. Cells were incubated with A77 1726 alone or in combination with proinflammatory cytokines. IL-1Ra production was determined by ELISA. A77 1726 alone had no effect, but in the presence of IL-1β or tumour necrosis factor-α it markedly enhanced the secretion of IL-1Ra in synovial fibroblasts and chondrocytes. The effect of A77 1726 was greatest at 100 μmol/l. In synovial fibroblasts and de-differentiated chondrocytes, A77 1726 also increased IL-1β-induced IL-1Ra production in cell lysates. Freshly isolated chondrocytes contained no significant amounts of intracellular IL-1Ra. A77 1726 is a known inhibitor of pyrimidine synthesis and cyclo-oxygenase (COX)-2 activity. Addition of exogenous uridine did not significantly modify the effect of A77 1726 on IL-1Ra production, suggesting that it was not mediated by inhibition of pyrimidine synthesis. Indomethacin increased IL-1β-induced IL-1Ra secretion in synovial fibroblasts and de-differentiated chondrocytes, suggesting that inhibition of COX-2 may indeed enhance IL-1β-induced IL-1Ra production. However, the stimulatory effect of indomethacin was consistently less effective than that of A77 1726. A77 1726 increases IL-1Ra production by synovial fibroblasts and chondrocytes in the presence of proinflammatory cytokines, and thus it may possess chondroprotective effects. The effect of A77 1726 may be partially mediated by inhibition of COX-2, but other mechanisms likely concur to stimulate IL-1Ra production

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Interleukin-1 plays a major role in vascular inflammation and atherosclerosis in male apolipoprotein E-knockout mice

Objective: To examine the role of the balance between interleukin (IL)-1 and IL-1 receptor antagonist (IL-1Ra) in atherosclerosis and vascular inflammation. Methods: Transgenic (Tg) mice overexpressing either secreted IL-1Ra or intracellular IL-1Ra1 as well as IL-1Ra-deficient mice (IL-1Ra −/−) were crossed with apolipoprotein E-deficient mice (ApoE −/−). Results: In males fed a cholesterol-rich diet for 10 weeks, average atherosclerotic lesion area within aortic roots was significantly decreased in ApoE −/− secreted IL-1Ra Tg (−47%) and ApoE −/− intracellular IL-1Ra1 Tg (−40%) mice as compared to ApoE −/− non-Tg controls. The extent of sudanophilic lesions was reduced within the thoraco-abdominal aorta in ApoE −/− secreted IL-1Ra (−53%) and ApoE −/− intracellular IL-1Ra1 (−67%) Tg mice. In parallel experiments, we observed early mortality and illness among double deficient mice, whereas ApoE −/− IL-1Ra +/+ and ApoE +/+ IL-1Ra −/− mice were apparently healthy. After 7 weeks of diet, ApoE −/− IL-1Ra −/− mice exhibited massive aortic inflammation with destruction of the vascular architecture, but no signs of atherosclerosis. ApoE −/− IL-1Ra +/+ had atherosclerosis and a moderate inflammatory reaction, whereas ApoE +/+ IL-1Ra −/− mice were free of vascular lesions. Macrophages were present in large amounts within inflammatory lesions in the adventitia of ApoE −/− IL-1Ra −/− mice. Conclusion: Our results demonstrate that the IL-1/IL-1Ra ratio plays a critical role in the pathogenic mechanisms leading to vascular inflammation and atherosclerosis in ApoE −/− mic

Small rodent monitoring at Birkebeiner road, Norway

Background. Northern small mammal populations are renowned for their multi-annual population cycles. Population cycles are multi-faceted and have extensive impacts on the rest of the ecosystem. In 2011, we started a student-based research activity to monitor the variation of small rodent density along an elevation gradient following the Birkebeiner Road, in southeast Norway. Fieldwork was conducted by staff and students at the University campus Evenstad, Inland Norway University of Applied Sciences, which has a long history of researching cyclic population dynamics. The faculty has a strong focus on engaging students in all parts of the research activities, including data collection. Small rodents were monitored using a set of snap trap stations. Trapped animals were measured (e.g. body mass, body length, sex) and dissected to assess their reproductive status. We also characterised the vegetation at trapping sites. New information. We provide a dataset of small rodent observations that show fluctuating population dynamics across an elevation gradient (300 m to 1,100 m a.s.l) and in contrasting habitats. This dataset encompasses three peaks of the typical 3-4-year vole population cycles; the number of small rodents and shrews captured show synchrony and peaked in years 2014, 2017 and 2021. The bank vole Myodes glareolus was by far (87%) the most common species trapped, but also other species were observed (including shrews). We provide digital data collection forms and highlight the importance of long-term data collection.publishedVersio