Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the adhesion of Flavobacterium columnare (Flexibacter columnaris) to gill tissue.

Flavobacterium columnare (Flexibacter columnaris) is an important cause of gill and skin disease in freshwater fish species, often causing high mortality. In previous studies, virulence of F. columnare was correlated with the ability to adhere to the gill tissue. To gain insight into the factors responsible for adherence, a gill perfusion model was used. The bacterial cells of the high virulence strain AJS 1 were exposed to various treatments, after which they were added to the organ bath of an isolated gill arch and adherence to the gill tissue assessed. Adherence capabilities were significantly reduced following treatment of the bacteria with sodium metaperiodate or incubating them with d-glucose, N-acetyl-d-glucosamine, d-galactose and d-sucrose. Incubation of the bacteria with trypsin and pronase did not significantly inhibit adherence. The binding sites for F. columnare on the gill tissue were also partially characterised. Treatment of the gill with sodium metaperiodate reduced adhesion, but treatment with pronase or trypsin did not cause any significant reduction, indicating that the major component of the receptor is of carbohydrate nature. Adherence ability of the bacteria correlated well with their haemagglutination capacity using chicken and guinea pig erythrocytes. Higher haemagglutination titres were obtained with the highly virulent strain AJS 1 than with strain AJS 4, a strain with low virulence and adherence capacity. Haemagglutination was partially inhibited after incubation of the bacteria with d-glucose and N-acetyl-d-glucosamine and after treatment of the bacteria at 41_°C for 10_min (minor heat treatment). It was completely abolished following incubation of the bacterial cells with sodium metaperiodate and intensive heat treatment (65_°C, 25_min). Haemagglutination was also in-sensitive to pronase and trypsin treatment. Transmission electron microscopy (TEM) revealed that the high virulence strain had a thick capsule (120–130_nm) with a regular, dense appearance, whereas the capsule of the low virulence strain was much thinner (80–90_nm) and less dense. TEM also demonstrated the loss of the capsule of the high virulence strain after treatment of the bacterial cells with minor heat and sodium metaperiodate. These results indicate that a lectin-like carbohydrate-binding substance incorporated in the capsule is responsible for the attachment of F. columnare to the gill tissue.
N2O emissions from a cultivated mineral soil under different soil drainage conditions

In poorly drained (PD) soils, fertilizer N containing NO3 is easily denitrified. To determine emissions of N2O-N from PD, imperfectly drained (ID) and moderately well drained (MD) mineral soils, soil moisture and groundwater levels were monitored, and gas samples were collected from closed gas chambers during two crop growing seasons (i.e. April to August 2011 and 2012) in the South East of Norway. The gas samples were analyzed for N2O-N flux using gas chromatograph. In 2011, the depth to groundwater table ranged between 1 and 40 cm in PD, 50 and 89 cm in ID and 74 and 96 cm in MD soils during the growing seasons. In 2012, the depths were 11–51 cm in PD, 55–81 cm in ID and 46–78 cm in MD soil. Daily mean water filled pore space (WFPS) ranged between 51% and 70% in PD, 44% and 62% in ID and 38% and 72% in MD soils in 2011 and in 2012, the WFPS felled within this range. During the growing season, N2O flux rate (µg N m−2 h−1) varied from 20 to 635 (6–878) in PD, 22 to 112 (11–1607) in ID and 4 to 33 (8–92) in MD soils in 2011–2012 (mean of five chambers). Peak N2O-N fluxes in PD and ID soils were detected one week after fertilizer applications and immediately after rain events. Cumulative N2O-N emissions (kg N ha−1) from PD (6–10), from ID (4–12) and from MD soils (0.2–0.9) were emitted during (2011–2012) growing season. In general, PD soils emitted more N2O-N compared to MD soils mainly due to higher soil moisture and relatively shallow ground water table.
Fate and activity of microorganisms introduced into soil.

Introduced microorganisms are potentially powerful agents for manipulation of processes and/or components in soil. Fields of application include enhancement of crop growth, protection of crops against plant-pathogenic organisms, stimulation of biodegradation of xenobiotic compounds (bioaugmentation), and improvement of soil structure. Inoculation of soils has already been applied for decades, but it has often yielded inconsistent or disappointing results. This is caused mainly by a commonly observed rapid decline in inoculant population activity following introduction into soil, i.e., a decline of the numbers of inoculant cells and/or a decline of the (average) activity per cell. In this review, we discuss the available information on the effects of key factors that determine the fate and activity of microorganisms introduced into soil, with emphasis on bacteria. The factors addressed include the physiological status of the inoculant cells, the biotic and abiotic interactions in soil, soil properties, and substrate availability. Finally, we address the possibilities available to effectively manipulate the fate and activity of introduced microorganisms in relation to the main areas of their application.
Mass trapping wild Agriotes obscurus and Agriotes lineatus males with pheromone traps in a permanent grassland population reservoir

A study was conducted to determine whether arrays of pheromone traps could be used to reduce populations of male Agriotes obscurus (AO) and Agriotes lineatus (AL) adults in a confined nonfarmed habitat (grassy dyke). Traps placed 3 m apart in 15 × 2 arrays captured significantly more AL than AO, although the trap catch varied with location for both species and was inversely related to the number of nearby competing traps. Models of beetle movement indicated that a considerable proportion of males (AL: 18.4–71.8%; AO: 35.0–58.3%) collected in the arrays had moved in from elsewhere and that AL beetles are more active than AO beetles. AL beetles frequently entered AO traps unless both trap types were present in the array, whereas AO rarely entered AL traps. Concurrent catches in pitfall traps placed inside and outside pheromone trapping zones indicated the trap arrays significantly reduced male (but not female) AO and AL beetles inside their respective arrays, that AO traps reduced AL beetles in AO arrays, and that both AL and AO traps could potentially reduce the number of mating pairs in these arrays. The implications of these results in determining the efficacy of this approach as a click beetle management approach are discussed.
Distribution of barren‐ground caribou during winter in response to fire

We investigated the influence of past fires on the large-scale distribution of barren-ground caribou (Rangifer tarandus groenlandicus) in the Northwest Territories, Canada, during winter. We used an information-theoretic approach and data describing fire history, vegetation, and predation risk to develop resource selection functions that explained caribou distribution on early- and late-winter ranges. We evaluated multiple sets of models constructed across years for all caribou (pooled models) and for individual caribou by period (early and late winter). Winter range habitats important to caribou were characterized by a high percentage of ground cover of lichen and herbaceous forage and a close proximity to lakes and rivers. Although caribou avoided areas densely populated with burns, there was considerable use of early-seral habitats as well as areas adjacent to the burn boundary. Disparate selection strategies among caribou highlight the importance of investigating both individual and global resource selection models. These results suggest that at some spatial and temporal scales, individual barren-ground caribou may be less averse to fire than previously thought.
Improvement of the Nutritional Quality and Fibrinolytic Enzyme Activity of Soybean Meal by Fermentation of Bacillus subtilis

Solid-state fermentation condition of soybean meal (SBM) by Bacillus subtilis XZI125 for producing fibrinolytic enzyme and soybean peptides was optimized, and the effect of microbe fermentation on decreasing anti-nutritional factors was studied. The optimum fermentation conditions were obtained by one-factor-at-a-time and orthogonal array design as follows: fermentation temperature 30C, fermentation time 48 h, grinding particle size of soybean meal 40 mesh, pH 7.0, soybean meal loading 10 g in a 250-mL flask, 1.5% glucose, initial moisture content and inoculum sizes were 1.0 mL/g and 3%, respectively. Under the optimum fermentation condition, fibrinolytic activity and soybean peptides reached 1347.35 IU/g and 171.32 mg/g, respectively. Furthermore, the trypsin inhibitor, phytic acid and urease content were reduced by 33.57, 42.65 and 67.31%, respectively. In our knowledge, it was first reported that the nutritional quality of SBMs was improved and fibrinolytic enzyme in fermented soybean meal (FSBM) was produced by fermentation. Practical Applications Soybean meal (SBM) has traditionally been used as an important dietary protein in the feed industry. However, SBM may be used as food for human consumption if anti-nutritional factors are reduced by fermentation with food-grade microbes. Solid-state fermentation condition of SBM by Bacillus subtilis XZI125 to produce fibrinolytic enzyme and soybean peptides was optimized. The FSBM complemented the fibrinolytic enzyme and peptides, and simultaneously reduced anti-nutritional factors, such as trypsin inhibitor, phytic acid and urease, indicating that the nutritional and health function of FSBM was upgraded through fermentation, and it could become a potential health food.
Metapopulation processes and persistence in remnant water vole populations

We examined the spatial distribution of water vole populations in four consecutive years and investigated whether the regional population processes of extinction, recolonisation and migration influence distribution and persistence. We examined how such regional processes are influenced by spatial variation in habitat quality. In addition, we assessed the relevance of metapopulation concepts for understanding the dynamics of species that deviate from classical metapopulation assumptions and developing conservation measures for them. Populations were patchy and discrete, and the patchy distribution was not static between years. Population turnover occurred even in the absence of predatory mink, which only influenced the network of populations at the end of the study. Most populations were clustered close together in the upper tributaries. Local population persistence was predominantly influenced by population size: large populations were more persistent. Recolonisation rates were influenced by isolation and habitat quality. The isolation estimates which best explained the distribution of water vole populations incorporated straight-line distances, suggesting water voles disperse overland. The distribution of recolonised sites indicated that dispersing voles actively selected habitat on the basis of its quality. Water voles depart from some of the assumptions made by frequently used metapopulation models. In particular there is no clear binary distinction between suitable and non-suitable habitat. Accounting for variation in habitat quality before investigating temporal changes in population distribution allowed us to demonstrate that the key metapopulation processes were important. The significance of regional population processes relative to local population processes may have increased in declining, fragmented populations compared to pristine regional populations. We hypothesise that although mink predation is likely to eventually cause regional extinction in many areas, metapopulation processes have delayed this decline. Consequently, conservation measures should take into account mink predation rates and regional population processes, before considering aspects of habitat quality.
Review of Nutrient Management in Freshwater Polyculture

Abstract One of the most important issues concerning fish-pond fertilization is the determination of the optimal amount of fertilizer to be applied to the pond system. Another important concern is the suitability of fish species for polyculture in order to optimize production. The dynamics of nutrients, phytoplankton, and fish is a complex subject and practitioners are often compelled to formulate solutions without detailed scientific and practical consideration. The primary objective of pond fertilization is to maintain an optimal nutrient concentration for sustained biological production. Current fertilization practices in the Asia-Pacific region include: a fixed rate of fertilization and fertilization based on water color. Individual pond ecology determines how fertilization affects pond productivity, not the pond's physical location in relation to international borders. There is no universal recipe of “maximal” fertilization rates due to pond-specific variability. There is also no clear guide in the literature with regard to many aspects of fish-food; the type of organisms consumed, mechanisms of food consumption, and the digestibility and nutritive value of plankton. The usual practice is to divide fish according to their foraging in natural habitats; feeding on phytoplankton, zooplankton, zoo benthos, or detritus. The distinction between different feeding habits is not always absolute as many species of fish may change food preference depending on the abundance of different food items. This paper reviews the nutrient (nitrogen, N and phosphorus, P) management in regard to pond fertilization; use of organic and inorganic fertilizer and the impacts on fish production; use of organic fertilizer from different organisms (pig, cow and buffalo) and their interactions with primary production and water quality; optimum N:P concentration in pond water; and individual pond factors and their influence on fish production. A significant interaction was evident with time between water quality variables such as pH and alkalinity, and other factors, including manure type and fish species composition. This was reflected in the difference between pig and cow manure treatments. A significant interaction between species composition and fish production has been demonstrated. Fish survival and biomass production was influenced by the stocking ratio of the: rohu, Labeo rohita; mrigal, Cirrhinus mrigala; and Nile tilapia, Oreochromis niloticus. The recommended nutrient level for pond fertilization based on the South Australian Research and Development Institute (SARDI) and Research Institute for Aquaculture No. 1 (RIA#1) study is 1 ppm N:0.5 ppm P. The required quantity of fertilizer varies significantly with time. However, regional research is highly recommended to optimize fish production focusing on significant climate variability, which affects both primary and secondary production.
The distribution of the eggs of Mammalian Lice on their hosts. 2. Analysis of the Oviposition behaviour of Damalinia ovis (L)

The behaviour pattern of Damalinia ovis (L.) is adapted to the physical features of the environment in which the louse lives. In stage 1, the louse was attracted to temperatures between 35 and 40°C and this temperature zone was necessary for oviposition to proceed satisfactorily. Optimum temperature conditions were between 37 and 39°C. In stage 2, the louse orientated itself so that its head was directed towards the warm end of a temperature gradient or towards the saturated end of a humidity gradient, but when these gradients were antagonistic the orientation to temperature dominated. At the commencement of stage 3, the louse reversed its orientation to both temperature and humidity gradients but again the attraction to temperature was dominant. Before egg laying commenced, a fibre of suitable diameter had to be caught by a gonopod and held next to the abdomen. The resulting tactile stimulus was critical and its absence inhibited oviposition. Other factors which influenced oviposition were the depressant effect of high humidities, the orientation to light, and the attraction to other ovipositing lice and eggs.
Integrative analysis of ChIP-chipdatasets in Saccharomyces cerevisiae

ChIP-chip is a technology originally developed to determine the binding sites of proteins in chromatin on a genome wide scale. Its uses have since been expanded to analyse other genome features, such as epigenetic modifications and, in our laboratory, DNA damage. Datasets comprise many thousands of data points and therefore require bioinformatic tools for their analysis. Currently available tools are limited in their applications and lack the ability to normalise data so as to allow relative comparisons between different datasets. This has limited the analyses of multiple ChIP-chip datasets from different experimental conditions. The first part of the study presented here is bioinformatic, presenting a selection of tools written in R for ChIP-chip data analysis, including a novel normalisation procedure which allows datasets from different conditions to be analysed together, permitting comparisons of values between different experiments and opening up a new dimension of analysis of these datasets. A novel enrichment detection procedure is presented, suited to many formats of data, including protein binding (which forms peaks) and epigenetic modifications (which can form extended regions of enrichment). Graphical tools are also presented, to facilitate the analysis of these large datasets. A method of predicting the output of a ChIP-chip dataset is presented, which has been used to show that ChIP-chip is capable of detecting sequence dependent damage events. All functions work together, using a common data format, and are effcient and easy to use. The second part of this study applies these bioinformatic tools in a biological context. An analysis of Abf1 protein binding datasets has been undertaken, revealing many more binding sites than had previously been identified. Analysis of the sequences at these binding sites identifed the previously determined consensus binding motif in only a subset, with no novel motif identifiable in the remainder, suggesting binding may be in uenced by factors other than sequence.
Resistance of riverine macroinvertebrate assemblages to hydrological extremes

Macroinvertebrates were sampled in the lowland Drzewiczka River downstream from a dam reservoir and just below a whitewater slalom canoeing track. For over 20 years, pulse flow fluctuations of moderate intensity, an effect of two-three hour long releases of water per day to enable training of canoeists, induced a patchy mosaic in the tailwater riverbed compared to a natural site. After these regular disturbances, three accidental events of increased discharge of different magnitudes (three, five and sixteen times higher compared to a long-term median) occurred in two following years and we were able to investigate their impact on the habitat-specific processes.Two of the three events (in September 2000 and March 2001) had a minor effect on abiotic and biotic variables, while the third one (in February 2002, over 40 m3 s−1 discharge) destabilized the bed habitat, washing away the flood-sensitive macroinvertebrates of Ephemeroptera and Trichoptera. In the dominant benthic group, i.e. Chironomidae, varied resistance patterns were observed, depending on their mode of life and patch occupancy. In conclusion, biota in the Drzewiczka River have adapted their life history to long-term moderate flow disturbance, but the largest flood mobilized bed sediments together with most of their dwellers.
Outlaw fishing in Missouri.

Abstract This study describes hand fishers and their unique method of harvesting catfish. Although the Missouri state legislature outlawed hand fishing in 1919, a segment of anglers still practice this sport. In 2000, some of the participants met with officials from the Missouri Department of Conservation and requested a legalized hand fishing season. Their petition was denied, partly due to the lack of information about this activity. A mail-back questionnaire was administered to hand fishers in Missouri and nearly 5 6% of them responded to the survey. Results indicated that hand fishers were primarily males who lived in rural areas of the state. Participants went hand fishing about 13 times per year (x = 12.5) and caught approximately 10 catfish annually {x = 10.4). A profile of hand fishers was developed and sent to decision-makers to assist them with policy formation. Since hand fishers reported numerous ways of catching catfish (only 1 5% used their hands exclusively), a better description of these p.
Pluripotent Embryonal Stem Cell Lines Can Be Established from Disaggregated Mouse Morulae

Mouse pluripotent embryonal stem (ES) cell lines hitherto have been conventionally isolated from the ‘inner cell mass’ of mouse blastocysts. In this report, I describe a new and simplified method for establishing pluripotent cell lines from mouse morulae of the 16‐ to 20‐cell stage, which were disaggregated by the use of EDTA. From 17 cell lines established in such a way, 7 were characterized with respect to their differentiation potential:
Growth rates of five species of surf clams on a southern North Island beach, New Zealand

Abstract Growth rates of five species of surf clam were estimated on the Kapiti Coast, southern North Island, New Zealand. Length‐frequencies of sequential population samples were analysed by the computer program, MULTIFAN. Incremental growth of marked individuals was analysed by the computer program, GROTAG. The von Bertalanffy growth parameters k and L 8 estimated by MULTIFAN for Spisula aequilatera (Deshayes in Reeve, 1854) were 0.80 yr−1 and 52.1 mm; for Mactra murchisoni Deshayes in Reeve, 1854 were 0.60 yr−1 and 72.3 mm; and for M. discors Gray, 1837 were 0.35 yr−1 and 60.1 mm. MULTIFAN could not model growth of Paphies donacina (Spengler, 1793) and Dosinia anus (Philippi, 1848) from the population samples. The growth parameters estimated by GROTAG for D. anus were 0.53 yr−1 and 53.0 mm and for M. murchisoni 1.84 yr−1 and 72.4 mm. The growth rates of P. donacina, S. aequilatera, and M. discors were estimated for the size range of their incremental growth data and the estimates are usable for this limited size range only. Growth rates of each species varied with depth in the surf zone in the same way in the North and the South Island. The growth rate of two species was faster in the South Island and asymptotic size of all species was greater in the South Island.
Identification of Single Nucleotide Polymorphisms in PRNP Gene of Korean Native Goats

Prion protein (PRNP) is known to be a causative protein for transmissible spongiform encephalopathy (TSE), a disease occurring in human and animals. Previous results indicate that the genetic variability can affect the resistance and susceptibility of goat scrapie and can give the guideline for reducing the risk of this disease. Until now, 35 single nucleotide polymorphisms (SNPs) were identified in goat PRNP gene from many countries such as Great Britain, Italy, United States of America and Asian countries etc. In this study, SNPs in PRNP gene have been investigated to research the PRNP variations and their possible TSE risks in 60 Korean native goats. Based on the sequencing results, we identified four SNPs and three of those polymorphisms (G126A, C414T and C718T) were synonymous and the A428G polymorphism was non-synonymous which changes the amino acid histidine to arginine. Previously, all of these four SNPs were identified in Asian native goats. Specifically, five polymorphisms were identified in Asian native goats and two of them (G126A and C414T) were silent mutations, and the other SNPs (T304G, A428G and T718C) caused amino acid changes (W102G, H143R and S240P). Comparing with SNP results from other breeds, this study is an initial step to understand resistance and susceptibility of this disease in Korean native goats. (Key words : Korean native goats, Prion protein (PRNP), Single nucleotide polymorphism (SNP), Transmissible spongiform encephalopathy (TSE))