How to define fish pathogen relatives from a 16S rRNA sequence library and Pearson correlation analysis between defined OTUs from the library: Supplementary data to the research article "Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS".

This paper provides supplementary data to the research paper ''Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS" [1]. Here, environmental samples from a marine recirculating aquaculture system (RAS) were subjected to microbiome studies. This data article adds value to the research article by providing open access to data files that increased information retrieval from the 16S rRNA sequence library. A fasta file of full-length 16S rRNA sequences from fish pathogenic microbes was deposited in the Mendeley data repository, a collection named "Fish Pathogen Database". Alignment of this database against the short sequences in the 16S rRNA library revealed the fish pathogen-relatives. Furthermore, a link to a CSV file containing Pearson correlation data was provided, an analysis based on the relative abundance information of all operational taxonomic units defined in the microbiome dataset. Included also, the methodological description of the Pearson correlation analysis, as well as a table where correlation data for the defined fish pathogen-relatives was retrieved from the large data file (Table 1).

Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents.

The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.

Microbiome dataset from a marine recirculating aquaculture system (RAS) for salmon post-smolt production in Norway.

A marine aquaculture recycling system (RAS) for the production of post-smolt was monitored for microbial community structures during the first year of operation. Sample material was obtained monthly from the biofilter biofilm carriers, the production water (tank 3), the fish skin (tank 3) and the tank 3 wall biofilm. Additional samples were taken during outbreaks of fish skin wounds, washing of the plant, UV filtration of the inlet water and from various wall biofilms. Samples for depth profiles from all fish tanks were also collected. The sampling tools were a ladle for capturing biofilter biofilm carriers, toothbrushes for wall biofilm capture, filters for capture of water microbes and scalpels for skin tissue slicing. The sampling times were indicated by the production cycle number (cycle 2-5) and the week number within the cycle (W). Prior to bacterial community analysis, the stored samples were exposed to cell lysis and extraction of environmental DNA by commercial kits. All samples were subjected for PCR amplification of 16S rDNA sequences for library formations and prepared for Ion Torrent technology, which sequences 250 bp fragments. A total of 1.1 million reads were obtained from the 100 RAS samples analysed. The process from Ion Torren analysis to library involved bioinformatics steps with sorting, filtering, adjustment and taxonomic identification, and the final output was shown in a table as operational taxonomic units (OTUs) and relative abundance at different sampling sites and sampling time points. Of a total of 450 taxonomically assigned OTUs, 45% were classified at genus level. The 16S library raw data are deposited in the Mendeley data repository and cited in this Data in Brief article co-submitted with the article "Microbial colonization and stability in a marine post-smolt RAS inoculated with a commercial starter culture." [1]. So far, the raw data are referenced in four more publications in progress. These cover microbial shifts and enrichments between sampling times, sulfur cycling, "in vivo biofilm" and identification of relatives of fish pathogens in RAS. All library sequences are available in GenBank with accession numbers MN890148-MN891672.

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge.

Rock and fluid samples were collected from three hydrothermal chimneys at the Endeavour Segment, Juan de Fuca Ridge to evaluate linkages among mineralogy, fluid chemistry, and microbial community composition within the chimneys. Mössbauer, midinfrared thermal emission, and visible-near infrared spectroscopies were utilized for the first time to characterize vent mineralogy, in addition to thin-section petrography, X-ray diffraction, and elemental analyses. A 282°C venting chimney from the Bastille edifice was composed primarily of sulfide minerals such as chalcopyrite, marcasite, and sphalerite. In contrast, samples from a 300°C venting chimney from the Dante edifice and a 321°C venting chimney from the Hot Harold edifice contained a high abundance of the sulfate mineral anhydrite. Geochemical modeling of mixed vent fluids suggested the oxic-anoxic transition zone was above 100°C at all three vents, and that the thermodynamic energy available for autotrophic microbial redox reactions favored aerobic sulfide and methane oxidation. As predicted, microbes within the Dante and Hot Harold chimneys were most closely related to mesophilic and thermophilic aerobes of the Betaproteobacteria and Gammaproteobacteria and sulfide-oxidizing autotrophic Epsilonproteobacteria. However, most of the microbes within the Bastille chimney were most closely related to mesophilic and thermophilic anaerobes of the Deltaproteobacteria, especially sulfate reducers, and anaerobic hyperthermophilic archaea. The predominance of anaerobes in the Bastille chimney indicated that other environmental factors promote anoxic conditions. Possibilities include the maturity or fluid flow characteristics of the chimney, abiotic Fe2+ and S2- oxidation in the vent fluids, or O2 depletion by aerobic respiration on the chimney outer wall.

Microbial life associated with low-temperature alteration of ultramafic rocks in the Leka ophiolite complex.

Water-rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10-160 cm) and groundwater from a 50-m-deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative-PCR. Different microbial communities were observed in the groundwater, the fracture-coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen-oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H2 produced by low-temperature water-rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer-Tropsch-type reactions, dominated in the fracture-coating material. Putative hydrogen-, ammonia-, manganese- and iron-oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water-rock reactions.

The shortening fraction of myocardial fibers and its layered distribution, as derived from cine-MR imaged left ventriculograms. An approach for evaluating globar left ventricular function.

PURPOSE: To evaluate the mean shortening fraction and its SD through the wall calculated from multiple cine-MR views, as an estimate of left ventricular globar function. MATERIAL AND METHODS: The average myocardial fiber shortening fraction was calculated by means of a simple truncated ellipsoid nested shell model. Left ventricular parameters, acquired by cine-MR imaging, from 20 healthy volunteers served as input. Fiber angles, ventricular torsion and a gradient increase in wall thickening from epicard to endocard were part of the model. RESULTS: The average fiber shortening fraction was 0.203 (0.158-0.246) +/- 0.021 diastolic lengths. It varied only moderately with variations in fiber angle values and not at all when the torsion angles were varied within physiological limits. The average shortening fraction correlates well with the systolic increase in chamber oblonguity (k = 0.837), with the ejection fraction (k = 0.877), and even better with the calculated wall thickening (k = 0.973). The average epicardial shortening fraction 0.169 (0.142-0.202) +/- 0.016 increased gradually through the wall to the endocardial value 0.250 (0.212-0.290) +/- 0.024. The increase in chamber length-width ratio from diastole to systole reduced the SD of the shortening fraction through the wall layers to a minimum. CONCLUSION: The fiber shortening fraction expresses the layered contraction of the myocardial wall, the wall thickening, and also the endocardial wall motion. The ejection fraction expresses only the latter. The shortening fraction and its SD through the wall may prove a valuable additional tool for estimating ventricular globar function.

A study of tobacco carcinogenesis, LIII: carcinogenicity of N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in mink (Mustela vison).

In an earlier study, young male and female mink (Mustela vison) were found to be highly susceptible to the carcinogenic effect of N'-nitrosonornicotine (NNN). In this follow-up study we tested (i) the importance of the age of the animals with regard to the carcinogenic effect of NNN, (ii) the carcinogenic activity of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and (iii) the combined carcinogenic effect of NNN plus NNK. (I) In the previous study, the latency of nasal tumor induction by NNN (11.9 mM) averaged 84 +/- 40 weeks upon twice weekly applications, starting at the age of 3 weeks and continuing for 38 weeks. In this bioassay, giving NNN in 28 weeks but starting at the age of 3 months, it took, on the average, 97 +/- 29 weeks to induce malignant nasal tumors, primarily esthesioneuroepithelioma with invasion of the brain. (ii) NNK (6.3 mM), given by s.c. injection, induced nasal carcinoma with invasion of the forebrain after 77 +/- 39 weeks. (iii) NNN (11.9 mM) plus NNK (6.3 mM) led to the same type of carcinoma but at an accelerated pace, namely after 71 +/- 57 weeks. This study supports the earlier observation that tobacco-specific N-nitrosamines induce malignant tumors of the nasal cavity with invasion of the brain, dependent to some degree on the age of the mink at first application. NNK appears to be a stronger carcinogen than NNN in mink which follows the observations made with mice, rats and hamsters. It is suggested that combined administration of NNN with NNK induces a stronger carcinogenic effect than NNN or NNK given alone.

A study of tobacco carcinogenesis XLVIII. Carcinogenicity of N'-nitrosonornicotine in mink (Mustela vison).

During tobacco processing and smoking, nicotine and nornicotine give rise to N'-nitrosonornicotine (NNN), a highly abundant, strong carcinogen. NNN is known to exert carcinogenic activity in mice, rats and hamsters. Major target organs for NNN carcinogenicity in the rat are the esophagus and the nasal mucosa, and in the Syrian golden hamster trachea and nasal mucosa. In comparison with the rat, the mink (Mustela vison) has a markedly expanded nasal mucosa. Therefore, we explored in this study whether the mink could serve as a non-rodent model for nasal carcinogenesis using NNN as the carcinogen. Twenty random-bred mink, beginning at the age of 3 weeks, received twice weekly s.c. injections of NNN, a total dose of 11.9 mM per animal over a 38 week period. All of the 19 mink at risk developed malignant tumors of both the respiratory and the olfactory region of the nose within 3.5 years. In most animals the malignant tumors, primarily esthesioneuroepithelioma, invaded the brain. Remarkably, NNN induced no other tumors in the mink. None of the control animals developed nasal tumors nor tumors at other sites during the 3.5 years of the assay. The historical data from the farm did not reveal any spontaneous occurrence of nasal tumors in mink at any age. This study supports the concept that NNN is a proven carcinogen for multiple species of mammals and that the mink can serve as a non-rodent, non-inbred animal model for nasal carcinogenesis, especially since NNN induces only tumors in the nasal cavity in this species and not at other sites, as it does in mice, rats and hamsters.

[Changing food habits]. / Kostvaner i endring.

The main goal of the Norwegian policy on food and nutrition for the period 1975-1990 is to reduce the proportion of fat in the diet to 35 per cent of the energy supply. This should be achieved through a gradual change in diet. Figures on food supply and consumption show that this target has been reached. The dietary changes have probably contributed considerably to the decrease in cardiovascular disease since the early 1970s. It is most likely that public health can still gain much from further changes in the Norwegian diet.

Plasma glucose, ketone bodies, insulin, glucagon and enteroglucagon in cows: diurnal variations related to ketone levels before feeding and to the ketogenic effects of feeds.

Ingestions of a moderately ketogenic silage twice daily were followed by transient increments in plasma insulin and ketone bodies and decreases in plasma glucose. Ketone bodies and glucose were negatively correlated throughout the day, but the insulin elevations culminated before the maximal effects on ketone bodies and glucose were established. Cows with varying glucose levels before morning feeding reacted to a highly ketogenic silage by decreasing their glucose level uniformly to about 3 mmol/l, in spite of a widely varying feeding-induced insulin increment. Hay-feeding caused insulin increments of the same magnitude as silage-feeding, but the glucose decrease and the ketone increment was much smaller. The results indicate some direct action of ketone bodies on blood sugar regulation, in addition to effects mediated by insulin. The role of ketone bodies as the insulinotropic factor was not confirmed. The insulin level after feeding seems to be determined by the carbohydrate status of the animal before feeding. No significant changes in plasma glucagon were observed after feeding, and no consistent differences in plasma levels of this hormone were found when non-ketonemic, ketonemic, and clinically ketotic cows were compared. The plasma level of enteroglucagon (GLI) was positively correlated to the relative amount of concentrates consumed, but no relation to plasma glucose was found.

Nociception is enhanced after low doses and reduced after high doses of the serotonin receptor agonist 5-methoxy-N,N-dimethyltryptamine.

The effects on pain sensitivity of intracerebroventricular injections of 5-methoxy-N,N-dimethyltryptamine were tested by the tail-flick method. Following administration of 1.6, 3.1, 6.3, 12.5 and 25 micrograms (n = 8 for each dose), tail-flick latencies were reduced by 13-24%. Fifty and 100 micrograms caused a biphasic response (hyperalgesia followed by analgesia), whereas 400 micrograms increased mean latencies by 28-39%. The hyperalgesia observed after low doses was most likely due to reduced activity in descending serotonergic neurons following presynaptic stimulation. Higher doses caused analgesia, probably by stimulating spinal postsynaptic serotonergic receptors as well.

Nitrite as a food additive.

Nitrite is used for its colouring, antimicrobial and flavouring effects as a food additive for several meat, fish and cheese products. Nitrite combines readily with secondary amines to form carcinogenic nitrosamines. Nitrosamines are found in many food products after nitrite addition and sometimes even without addition. Nitrite is regarded as an effective growth inhibitor for Clostridium botulinum and thereby its production of the lethal toxin. Today this is considered to be the main reason for addition of nitrite to food products. It should be possible to limit the addition of nitrite to a few special food products where Cl botulinum really represents a hazard to human health, i e to canned meat that is not sterilized by heat and some cured and fermented products. In Norway the use of nitrite is limited to products where growth of clostridia is possible, but in a few products nitrite is also allowed as a colour stabilizer. It is reasonable to expect that other countries will decide upon similar regulations. The naturally occurring nitrates in vegetables have to be included in the discussion due to the possibility of microbial reduction to nitrites.

Mutagenicity of nitrovin--a nitrofuran feed additive.

Nitrovin, a nitrofuran feed additive, is shown to be directly mutagenic in Salmonella typhimurium TA 98 and TA 100 between 0.1 and 2.5 microgram per plate (0.09--2.3 micrometer). Addition of a rat-liver homogenate reduces the mutation rates. Nitrovin inhibits growth of the same bacteria in suspension cultures at concentrations above 0.09 micrometer.