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A wide range of life-history tactics can be found within salmonid fish. The genetic basis for these adaptations remains largely unknown, but we have sought to investigate any large scale genetic changes associated with a non-anadromous life cycle. After the most recent ice age (approximately 9,500 years ago), some populations of Atlantic salmon Salmo salar L., were trapped in fresh water and developed into isolated landlocked populations that managed to complete a full life cycle without ever reaching the marine environment. To explore whether this transition was accompanied by gene-loss events, high-throughput sequencing of a non-migratory Namsblank (‘smablank’), an Atlantic salmon from the river Namsen in Norway, was performed. There were no indications of loss of coding regions and a phylogenetic analysis based on the mitochondrial genome revealed a close genetic relationship between anadromous Atlantic salmon and Namsblank. Lack of large-scale genomic changes suggests that fine-scale (epi)genetic alterations and population genetics processes underlie adaptation to the landlocked life-style. Key words: Landlocked, gene-loss, salmon, Illumina.

In late summer 2014, an outbreak of ocular disease occurred in the Norwegian muskox (Ovibos moschatus) population. Animals showed rings of pus around their eyes and one euthanized animal was diagnosed with acute keratoconjunctivitis. The DNA sequence analysis of eye-swab samples from this animal revealed a high abundance of Mycoplasma conjunctivae.

Master's thesis in Relational treatment Sammendrag Bakgrunn: Som behandler i poliklinikk møter jeg pasienter med ulike symptomer som skal forstås, diagnostiseres og behandles. Det er flere behandlere som vegrer seg for å stå i behandling med pasienter som har diagnosen emosjonelt ustabil personlighetsforstyrrelse. Det er relasjonelle utfordringer i å få kontakt med pasienten, forstå hva de sliter med og med å komme i posisjon til å følge pasienten i en bedringsprosess. Formål med studien: å finne svar på problemstillingen: Hvordan kan en forstå de relasjonelle utfordringene i møte med pasienten som har fått diagnosen emosjonell ustabil personlighetsforstyrrelse? -Fokus på lidelsen og den terapeutiske alliansen i lys av et kjønnsperspektiv Metode som er brukt: kvalitativ litteraturstudie 3 sentrale funn fremheves: • Symptomene forstås ikke likt av behandlere av ulikt kjønn og det lager utfordringer i relasjoner i forhold til diagnostisering og behandling. • Den gode terapeutiske alliansen er avhengig av gode holdninger, kunnskap om tilknytning, mentalisering og praktisk erfaring. • Kjønnsperspektivet er for lite presentert i forståelsen av symptombilde og det kan ha betydning for hvordan denne lidelsen blir forstått og møtt. Konklusjon: Det er viktig for behandlere å fokusere og reflektere over egne holdninger i møte med pasienter. Manglende selvforståelse, for lite kunnskap om lidelsen, manglende praktisk erfaring og veiledning kan bidra til relasjonelle utfordringer mellom behandler og pasient. Det å være bevisst sitt eget kjønn i møte med pasienten og å være undrende sammen i møte på hvilke forventninger pasienter har til seg selv med fokus på sitt eget kjønn, kan ha betydning for å forstå denne lidelsen bedre. Abstract Background: As a therapist in an out-patient clinic I personally meet numerous patients with different symptoms that got to be understood, diagnosed & treated. There are many therapists who balks at having charge of treatment with the patient group who are diagnosed with borderline personality disorder. There are relational challenges in getting contact with the patient, understanding what the patient is having difficulties with and getting into a position from where you can be with the patient in an ongoing recovery process. Purpose of the study: to find answers to the issue: How can one understand the relative challenges encountered by the patient who has been diagnosed with borderline personality disorder? Focus on the disorder and the therapeutic alliance in light of a gender perspective Method used: qualitative literature study Findings: • Symptoms are not understood in the same way by therapists of different gender and it poses relative challenges on the way to diagnosis and treatment. • The good therapeutic alliance is dependent on good attitudes, knowledge of attachment and practical experience. • The gender perspective is too little presented in understanding the symptom source and it may affect how this disorder is understood and met. Conclusion: It is important for therapists to focus and reflect on their own attitudes in dealing with patients. Lack of self-understanding, insufficient knowledge of the disorder, lack of practical experience and guidance can contribute to relative challenges between the therapist and the patient. Being aware of their own gender in meeting with the patient and being wondering together in meeting what expectations patients have for themselves with focus on their own gender may be important for understanding this suffering better.

This article outlines a design procedure for variable speed Francis turbines using optimization software. A fully parameterized turbine design procedure is implemented in MATLAB. ANSYS CFX is used to create hill diagrams for each turbine design. An operation mode of no incidence losses is chosen, and the mean efficiency in the range of the best efficiency point is used as optimization criterion. This characteristic is extracted for each design, and optiSLang is used for system coupling and optimization. In the global optimization loop, the downhill simplex method is used to maximize the turbine performance. For this article, the bounding geometry of the runner is kept as in the original configuration. This way, the performance of the different variable speed turbines can be compared directly. Two optimization parameters describing the blade leading-edge geometry have been used in the optimization procedure. The resulting design was an almost circular leading edge, and shows an increase in mean efficiency of 0.25% compared to the reference case. There was a significant change in the turbine performance, with close to no change at the best efficiency point, and an increase in efficiency of almost 1% at low rotational speed. The outlined procedure is parallelizable and can be performed within an industrial timeframe. © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

In this study, we have investigated whether the Chinese informal economic sanctions against Norwegian salmon had a negative effect on Norwegian salmon exporting firms’ financial performance. According to theory on international trade, economic sanctions distorts trade flows between countries and reduce the potential benefits and welfare gains from trade. Since trade takes place through firms, it is expected that firms will be negatively affected by economic sanctions. However, a firm’s opportunity to circumvent such market distortions could lead to a different conclusion. We performed a fixed effects estimation to examine whether Norwegian salmon exporters were financially affected by the Chinese sanctions. Our results indicate that the Chinese sanctions had a negative financial impact on Norwegian salmon exporting firms, and that this negative effect was larger in the first three years of the sanction period. This can be explained by the different costs an exporting firm may face when economic sanctions are imposed. However, the observed long-run effect is close to zero, supporting the empirical literature stating that sanctions-busting activities are always likely. The normative implications of our study stress the importance of countries developing and evaluating their exporting industries’ normative standards to prevent the potential criminalizing side effects of economic sanctions. However, firms are also responsible in these manners. Bribery and smuggling are criminalized because of their harmful consequences and informal economic sanctions are no legitimate excuse for criminal practices. nhhmas

Poxviruses are large DNA viruses of vertebrates and insects causing disease in many animal species, including reptiles, birds, and mammals. Although poxvirus-like particles were detected in diseased farmed koi carp, ayu, and Atlantic salmon, their genetic relationships to poxviruses were not established. Here, we provide the first genome sequence of a fish poxvirus, which was isolated from farmed Atlantic salmon. In the present study, we used quantitative PCR and immunohistochemistry to determine aspects of salmon gill poxvirus disease, which are described here. The gill was the main target organ where immature and mature poxvirus particles were detected. The particles were detected in detaching, apoptotic respiratory epithelial cells preceding clinical disease in the form of lethargy, respiratory distress, and mortality. In moribund salmon, blocking of gas exchange would likely be caused by the adherence of respiratory lamellae and epithelial proliferation obstructing respiratory surfaces. The virus was not found in healthy salmon or in control fish with gill disease without apoptotic cells, although transmission remains to be demonstrated. PCR of archival tissue confirmed virus infection in 14 cases with gill apoptosis in Norway starting from 1995. Phylogenomic analyses showed that the fish poxvirus is the deepest available branch of chordopoxviruses. The virus genome encompasses most key chordopoxvirus genes that are required for genome replication and expression, although the gene order is substantially different from that in other chordopoxviruses. Nevertheless, many highly conserved chordopoxvirus genes involved in viral membrane biogenesis or virus-host interactions are missing. Instead, the salmon poxvirus carries numerous genes encoding unknown proteins, many of which have low sequence complexity and contain simple repeats suggestive of intrinsic disorder or distinct protein structures. IMPORTANCE Aquaculture is an increasingly important global source of high-quality food. To sustain the growth in aquaculture, disease control in fish farming is essential. Moreover, the spread of disease from farmed fish to wildlife is a concern. Serious poxviral diseases are emerging in aquaculture, but very little is known about the viruses and the diseases that they cause. There is a possibility that viruses with enhanced virulence may spread to new species, as has occurred with the myxoma poxvirus in rabbits. Provision of the first fish poxvirus genome sequence and specific diagnostics for the salmon gill poxvirus in Atlantic salmon may help curb this disease and provide comparative knowledge. Furthermore, because salmon gill poxvirus represents the deepest branch of chordopoxvirus so far discovered, the genome analysis provided substantial insight into the evolution of different functional modules in this important group of viruses.

Viral diseases pose a significant threat to the productivity in aquaculture. Heart- and skeletal muscle inflammation (HSMI) is an emerging disease in Atlantic salmon (Salmo salar) farming. HSMI is associated with Piscine orthoreovirus (PRV) infection, but PRV is ubiquitous in farmed Atlantic salmon and thus present also in apparently healthy individuals. This has brought speculations if additional etiological factors are required, and experiments focusing on the causal relationship between PRV and HSMI are highly warranted. A major bottleneck in PRV research has been the lack of cell lines that allow propagation of the virus. To bypass this, we propagated PRV in salmon, bled the fish at the peak of the infection, and purified virus particles from blood cells. Electron microscopy, western blot and high-throughput sequencing all verified the purity of the viral particles. Purified PRV particles were inoculated into naive Atlantic salmon. The purified virus replicated in inoculated fish, spread to naive cohabitants, and induced histopathological changes consistent with HSMI. PRV specific staining was demonstrated in the pathological lesions. A dose-dependent response was observed; a high dose of virus gave earlier peak of the viral load and development of histopathological changes compared to a lower dose, but no difference in the severity of the disease. The experiment demonstrated that PRV can be purified from blood cells, and that PRV is the etiological agent of HSMI in Atlantic salmon.

A resonance phenomenon is observed experimentally in the runner channels of the Francis-99 model turbine runner. An incompressible CFD simulation is unable to simulate this. Two different coupled physics schemes are therefore presented to investigate if such effects can be replicated through simulations. The first procedure is a fully coupled acoustic-structural simulation, where the surrounding fluid is modelled using acoustic theory. This includes added mass effects and pressure propagation, but not advective and viscous effects. The second procedure is a quasi two-way coupled Fluid-Structure approach based on modal decomposition of the structural domain. In this procedure, the incompressible Navier-Stokes equations are solved along with the structural deformation. The fully coupled acoustic-structural approach does successfully exhibit a magnification of the pressure through the runner channels, indicating a resonance effect. The exact values of the acoustic pressure amplitudes are highly sensitive to the damping, the blade connection to the shroud close to the trailing edge, and more. The second procedure manages to simulate the structural deformation with the correct nodal diameters excited by the Rotor Stator Interaction, all inside the fluid solver. The pressure amplitudes however, does not exhibit the desired resonance effect, likely due to the assumption of incompressible fluid. Content from this work may be used under the terms of theCreative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Published under licence by IOP Publishing Ltd

As Francis turbines are chasing a higher efficiency, while trying to accommodate a wider load region, turbine blade fatigue is becoming a more pronounced problem. Details of the Fluid-Structure Interaction (FSI) between the turbine blades and the passing water is necessary to accurately predict the dynamic behavior of a runner in the design phase. The dynamic behavior of the turbine blades is characterized by three properties: The added mass of the surrounding water, the increased stiffness due to passing water, and the hydrodynamic damping provided by the surrounding water. Of the aforementioned properties, the hydrodynamic damping is not yet fully understood. When the turbine blades are excited close to resonance, the damping of the vibrating system determines the vibrational amplitude, and is therefore important in order to estimate the lifetime of a runner. The hydrodynamic damping of passing water has been investigated in a simplified setup, where the turbine blades are represented by a 2D hydrofoil. Two separate hydrofoil geometries have been tested. The hydrofoils were mounted in a "fixed-beam" configuration, meaning that both the deflection and the angle at the fastening point is zero. This setup was chosen, since it is the way that turbine blades are fastened in a Francis runner, and should therefore give applicable results when performing modal testing. The hydrofoils were mounted without any angle of attack, and exposed to water velocities up to 28 m/s. Modal tests in the entire velocity regime indicates that the damping factor increases linearly with water velocity, but at different rates below an above lock-in. The damping factor is rapidly increasing when the velocity goes beyond that of lock-in. This behavior is observed for both hydrofoils, even if the magnitude of the vortex shedding is of different magnitude for the two. A slight increase in natural frequency was also observed with increasing velocity, due to a combination of a stiffening effect of the water passing over the deflected blade, and a reduced added mass effect, in that the amount of water that vibrates with the hydrofoil is diminished when the water velocity is sufficiently high, i.e. it is blown away. The measurements have been compared with CFD simulations, indicating that the observed trend does indeed continue up to at least 45 m/s, indicating that the results are applicable to the velocity regimes occurring in a prototype Francis runner Content from this work may be used under the terms of theCreative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Published under licence by IOP Publishing Ltd

As part of an ongoing investigation into the mitigation of vortex induced vibrations of hydrofoils, a combined experimental and numerical study of the fluid-structure interactions and wake of a hydrofoil at lock-in has been conducted at the Waterpower laboratory of the Norwegian University of Science and Technology. The hydrofoil has a blunt trailing edge and Von Karman vortex shedding induces a lock-in effect at a chord based Reynolds number of about 2,7106. The present paper presents the initial measurements of vortex shedding frequencies going through lock-in, along with CFD simulations at lock-off conditions as well as some empirical estimates of vortex shedding. Experimentally the hydrofoil wake was studied in detail using particle image velocimetry (PIV). Hydrofoil vibration frequencies were measured by both a strain gauge positioned near the trailing edge of the foil as well as by a laser doppler vibrometer (LD-V). Numerically the phenomena was simulated using ANSYS CFX. Several different turbulence models was tested, from the two-equation standard k − model to the scale adaptive SST-SAS model, with considerably different results. It is observed that the vibrations induced at lock-in considerably shifts and reduces the hydrofoil wake velocity deficit. Further, the CFD results suggest that the driving parameter influencing the shedding frequency is the cross flow separation distance at the trailing edge.

Gill diseases cause considerable losses in Norwegian salmon farming. In 2015, we characterized salmon gill poxvirus (SGPV) and associated gill disease. Using newly developed diagnostic tools, we show here that SGPV infection is more widely distributed than previously assumed. We present seven cases of complex gill disease in Atlantic salmon farmed in seawater and freshwater from different parts of Norway. Apoptosis, the hallmark of acute SGPV infection, was not easily observed in these cases, and qPCR analysis was critical for identification of the presence of SGPV. Several other agents including Costia-like parasites, gill amoebas, Saprolegnia spp. and bacteria were observed. The studied populations experienced significant mortalities, which increased to extreme levels when severe SGPV infections coincided with smoltification. SGPV infection appears to affect the smoltification process directly by affecting the gills and chloride cells in particular. SGPV may be considered a primary pathogen as it was often found prior to identification of complex gill disease. It is hypothesized that SGPV-induced gill damage may impair innate immunity and allow invasion of secondary invaders. The distinct possibility that SGPV has been widely overlooked as a primary pathogen calls for extended use of SGPV qPCR in Atlantic salmon gill health management.

The mobile genetic element s2m has been described in several families of single-stranded RNA viruses. The function remains elusive, but an increasing number of s2m-containing sequences are being deposited in publicly available databases. Currently, more than 700 coronavirus sequences containing s2m can be found in GenBank, including the severe acute respiratory syndrome (SARS) coronavirus genome. This is an updated review of the pattern of s2m in coronaviruses, the possible functional implications and the evolutionary history.

Increasing tax revenue is an important aspect of development policy as it is associated with sustainable economic development. In order to increase tax compliance, it is vital to understand its determinants. According to the fiscal contract theory, people assent to pay taxes because they value what they gain from it - public services. Tax paying is a horizontal relationship between the citizens and the state. However, focusing especially on income taxation, the vertical relationship between the citizens receives more and more attention. Because paying taxes implies giving up a part of your personal income for the benefit of your co-citizens, taxation becomes a classical collective action dilemma. Thus, the relationship between the citizens becomes an important determinant for tax compliance. The main argument put forward in this thesis is that a society that aims to increase tax compliance should be a socially cohesive society, which includes providing public services, but also values such as social capital, a common national identity and social solidarity. This is of immediate relevance to Sub-Saharan Africa, where there are huge variation in both public service provision and social cohesion, and where it is vital to understand the determinants of tax compliance in order to increase the tax to GDPratio in the region. Using data from the Afrobarometer survey Round 5 (2011-2013), this thesis performs a binary logistic cross-country analysis across 28 countries in Sub-Saharan Africa. The main finding in this thesis is that the traditional approach to the fiscal contract is what matters the most. Additionally, political legitimacy is an important determinant of tax compliance. However, social cohesion does provide some explanatory power in the sense that social solidarity also increases tax compliance. There is also reason to believe that there are huge differences between the countries, which paves the way for additional research on this topic.

Dette er et masterarbeid i form av en komparativ studie av tekst produsert for hånd, og tekst produsert i et tekstbehandlingsprogram med talesyntese i den første lese- og skriveopplæringen. Det er 21 elever fra 1. trinn med i undersøkelsen. For å svare på problemstillingen har jeg gjennomført intervjuer med alle de 21 informantene, gjort observasjoner i klasserommet og analysert 84 elevtekster gjort av informantene. Denne elevgruppen har ikke metodikken «skrive seg til lesing med talesyntese (STL+) som en del av undervisningen, men undervisning både i bokstavforming/håndskrift og tastatur. Det er viktig å poengtere at denne oppgaven ikke handler om bruk av talesyntesen som en metodikk, men som et hjelpemiddel i undervisningen. Tekstbehandlingsprogrammet med talesyntese som er bruk i studien er Linglyder. Elevtekstene viser resultater fra februar og april 2016. Studien viser at flertallet av informantene ville foretrukket å skrive i Linglyder fremfor blyant. Funn fra februar viser at alle elevene mestrer å skrive tekster i Linglyder, mens noen ikke mestret å skrive tekster for hånd. Målet med skriving er å skrive for å bli forstått og det ble samtlige informanter i tekstene i Linglyder. Funnene viser også at flere av informantene prøvde seg på lengre og grammatisk vanskeligere ord når de skrev i Linglyder og hadde den auditive støtten fra talesyntesen. Det er et betydelig bedre resultat i tekstene gjort i Linglyder enn for hånd når en ser på det skrevne språket i februar, forskjellene mellom tekst skrevet for hånd og i Linglyder jevner seg mer ut i oppgaven fra april når en ser på antall skrevne feil. Dette viser at programmet er en god hjelp i den første lese- og skriveopplæringen, og effekten minsker etter som elevene får en høyere måloppnåelse i norskfaget. Funnene kan tyde på at programmet kan hindre at noen av elevene blir hengende etter i skriving. Studien viser at noen elever fikk et like godt resultat i Linglyder som med blyant i april, men at de fikk skrevet betydelig lengre tekster med blyant. Samtidig var det andre elever som klarte betydelig bedre tekster med tanke på rettskriving i Linglyder i april. Arbeidet i Linglyder egnet seg godt til samarbeidsoppgaver og førte til en språklig samtale mellom informantene. Med selvstendig arbeid blir det nok kanskje best for denne elevgruppen å tilpasse undervisningen hvor noen skriver i Linglyder og noen skriver for hånd.

Computational Fluid Dynamics is the science of solving the governing equations of fluid motion numerically. Simulating multiphase flow has traditionally been difficult, due to non-uniform fluid properties and challenges in expressing the interfacial forces. A solver developed by the "Thermal Two-Phase Flow Laboratory" at the Norwegian University of Science and Technology, has implemented a phase-field approach in order to model the interface dynamics of multiphase flow. The goal of this thesis is to simulate low energy droplet-film collisions using this solver, and test its performance. Central to the phase-field approach is the Cahn--Hilliard equation. The equation model phase separation, and in simulations without convection, the solver was proven to be very successful. One and two droplets were simulated with ease. Several guidelines have been developed regarding what numerical resolution is needed to obtain good solutions. In simulations where the coupled Navier--Stokes and Cahn--Hilliard equations were used to model droplet-film collisions, several errors were uncovered. Most notably was the global mass loss observed for some given problem setups. The solver was also seen to be highly parameter dependent, without discovering the definite underlying solution. Even though mass was not conserved globally, many promising signs were observed with respect to the dynamical behaviour of the collisions. Coalescence, one of the known possible collision outcomes, was obtained, as well as early signs of a bouncing droplet. A proper mesh refinement and parameter study is recommended as further work in order to correct the errors discovered. Some of the physical behaviour is highly encouraging, and if the issue of mass conservation is corrected, the solver is believed to be a great tool in future multiphase simulations.

Piscine orthoreovirus (PRV-1) causes heart and skeletal muscle inflammation (HSMI) in farmed Atlantic salmon (Salmo salar). Recently, a novel PRV (formerly PRV-Om, here called PRV-3), was found in rainbow trout (Oncorhynchus mykiss) with HSMI-like disease. PRV is considered to be an emerging pathogen in farmed salmonids. In this study, molecular and antigenic characterization of PRV-3 was performed. Erythrocytes are the main target cells for PRV, and blood samples that were collected from experimentally challenged fish were used as source of virus. Virus particles were purified by gradient ultracentrifugation and the complete coding sequences of PRV-3 were obtained by Illumina sequencing. When compared to PRV-1, the nucleotide identity of the coding regions was 80.1%, and the amino acid identities of the predicted PRV-3 proteins varied from 96.7% (λ1) to 79.1% (σ3). Phylogenetic analysis showed that PRV-3 belongs to a separate cluster. The region encoding σ3 were sequenced from PRV-3 isolates collected from rainbow trout in Europe. These sequences clustered together, but were distant from PRV-3 that was isolated from rainbow trout in Norway. Bioinformatic analyses of PRV-3 proteins revealed that predicted secondary structures and functional domains were conserved between PRV-3 and PRV-1. Rabbit antisera raised against purified virus or various recombinant virus proteins from PRV-1 all cross-reacted with PRV-3. Our findings indicate that despite different species preferences of the PRV subtypes, several genetic, antigenic, and structural properties are conserved between PRV-1 and-3. Molecular and antigenic characterization of piscine orthoreovirus (PRV) from rainbow trout (oncorhynchus orthoreovirumykiss)

The application of gene technology is becoming widespread much thanks to the rapid increase in technology, resource, and knowledge availability. Consequently, the diversity and number of genetically modified organisms (GMOs) that may find their way into the food chain or the environment, intended or unintended, is rapidly growing. From a safety point of view the ability to detect and characterize in detail any GMO, independent of publicly available information, is fundamental. Pre-release risk assessments of GMOs are required in most jurisdictions and are usually based on application of technologies with limited ability to detect unexpected rearrangements and insertions. We present an array-based approach to address these problems and show with three examples (GTS 40-3-2 Roundup Ready and event A5547-127 soybean as well as T25 Liberty Link Maize) that the method can detect and characterize GMOs with high accuracy while making very few prior assumptions about the actual genetic modifications or constructs in question. Based on the array results, a simple polymerase chain reaction-scheme is also described that will enable the user to characterize the inserted sequences to DNA sequence level. The method may provide the biotechnology developers and risk regulators with a useful tool to improve pre-market risk assessments as well as seed producers and other food chain and environmental stakeholders with a platform to improve their ability to detect and characterize GMOs.

The predominant approach for quantification of genetically modified organisms (GMO) is the application of quantitative real-time PCR. However, for a large number of processed food and feed products, this approach is unsuitable, because they contain low amounts (mass) of amplifiable DNA. Here we present a novel approach, “Single molecule quantification” (SIMQUANT) for GMO quantification of samples with extremely low amounts of DNA. The approach is based on statistics and application of multiple qualitative parallel PCRs. Here the qualitative PCRs were done using real-time PCR setup, but this is not a requirement. The difference is that the quantitative real-time PCR requires that the target copy number exceeds the absolute limit of quantification (LOQabs) and provides quantity estimates by extrapolation from a linear regressional relationship between an observed cycle threshold (Ct) value and copy numbers, while with SIMQUANT the template DNA typically contains very few, e.g., one target copy per PCR volume and the quantity is estimated on the basis of observed ratio between positive and negative individual PCRs. The components of this analysis are the numbers of test samples, the size of each sample and the outcome in number and relative ratio of positive and negative test results. The approach results in a statistical estimate of the relative GM concentration based on the probability that one or more amplifiable GM template copies are present in discrete volumes. Thus, the approach is based on the ratio of discrete volumes without or with one or more PCR-amplifiable GM target copies. The approach described here can be used reliably with more than a 100-fold improvement of the practical LOQ (LOQpract) compared to real-time quantitative PCR based on standard curves.

Seven bacterial isolates from farmed Atlantic cod displaying chronic granulomatous disease were characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-negative, facultatively intracellular, non-motile, strictly aerobic coccobacilli which produced H2S from cysteine-supplemented media and are therefore phenotypically consistent with members of the genus Francisella. Comparison of 16S rRNA gene sequences and six partial housekeeping gene sequences (groEL, shdA, rpoB, rpoA, pgm and atpA) confirmed the organism as a member of the genus Francisella, with Francisella philomiragia as its closest relative (99.3 % 16S rRNA gene sequence similarity, 92.2–99.0 % housekeeping gene sequence similarity). Despite the close relationship with F. philomiragia, isolates from Atlantic cod could be readily distinguished phenotypically and genetically from F. philomiragia ATCC 25015T. DNA–DNA hybridization studies revealed a mean reassociation value of 68 %. Thus, on the basis of phenotypic and molecular genetic evidence, we propose that the strains isolated from Atlantic cod should be recognized as Francisella philomiragia subsp. noatunensis subsp. nov. with the type strain 2005/50/F292-6CT (=NCIMB 14265T=LMG 23800T). Francisella philomiragia ATCC 25015T (=DSM 735T) is reclassified as Francisella philomiragia subsp. philomiragia subsp. nov.

Poxviruses are large DNA viruses of vertebrates and insects causing disease in many animal species, including reptiles, birds, and mammals. Although poxvirus-like particles were detected in diseased farmed koi carp, ayu, and Atlantic salmon, their genetic relationships to poxviruses were not established. Here, we provide the first genome sequence of a fish poxvirus, which was isolated from farmed Atlantic salmon. In the present study, we used quantitative PCR and immunohistochemistry to determine aspects of salmon gill poxvirus disease, which are described here. The gill was the main target organ where immature and mature poxvirus particles were detected. The particles were detected in detaching, apoptotic respiratory epithelial cells preceding clinical disease in the form of lethargy, respiratory distress, and mortality. In moribund salmon, blocking of gas exchange would likely be caused by the adherence of respiratory lamellae and epithelial proliferation obstructing respiratory surfaces. The virus was not found in healthy salmon or in control fish with gill disease without apoptotic cells, although transmission remains to be demonstrated. PCR of archival tissue confirmed virus infection in 14 cases with gill apoptosis in Norway starting from 1995. Phylogenomic analyses showed that the fish poxvirus is the deepest available branch of chordopoxviruses. The virus genome encompasses most key chordopoxvirus genes that are required for genome replication and expression, although the gene order is substantially different from that in other chordopoxviruses. Nevertheless, many highly conserved chordopoxvirus genes involved in viral membrane biogenesis or virus-host interactions are missing. Instead, the salmon poxvirus carries numerous genes encoding unknown proteins, many of which have low sequence complexity and contain simple repeats suggestive of intrinsic disorder or distinct protein structures.Aquaculture is an increasingly important global source of high-quality food. To sustain the growth in aquaculture, disease control in fish farming is essential. Moreover, the spread of disease from farmed fish to wildlife is a concern. Serious poxviral diseases are emerging in aquaculture, but very little is known about the viruses and the diseases that they cause. There is a possibility that viruses with enhanced virulence may spread to new species, as has occurred with the myxoma poxvirus in rabbits. Provision of the first fish poxvirus genome sequence and specific diagnostics for the salmon gill poxvirus in Atlantic salmon may help curb this disease and provide comparative knowledge. Furthermore, because salmon gill poxvirus represents the deepest branch of chordopoxvirus so far discovered, the genome analysis provided substantial insight into the evolution of different functional modules in this important group of viruses.