Genetic variability and evolutionary dynamics of tomato black ring virus population

Tomato black ring virus (TBRV) is an important pathogen infecting a wide range of plant species worldwide. Phylogenetic studies of TBRV have already been conducted, although limited by the use of short genomic regions or a reduced amount of isolates. In the present study, we carried out an exhaustive phylogenetic and population genetic analysis based on the coat protein gene (CP) sequence of 57 TBRV isolates originating from different host plants and European geographic regions (47 isolates from Poland, 8 from Lithuania, one from the UK, and one from Hungary). Moreover, the selective pressure acting on particular codons and coevolution of amino acid residues in the CP were analysed. The results clearly showed that the TBRV population is being shaped by recombination and both positive and purifying selection. The analyses revealed that the placement of TBRV isolates in the phylogenetic trees was nonrandom, with isolates clustering according to host plant families and geographic origin.     

Characterization of two distinct Polish isolates of Pepino mosaic virus

In Poland in 2002 and 2005 two different isolates of Pepino mosaic virus signed PepMV-SW and PepMV-PK were obtained. Both isolates were compared on the basis of their symptomatology on a series of plant species. In addition, the isolates were characterized by the nucleotide sequence analysis of the triple gene block, coat protein and a part of the polymerase genes. The studies showed that the Polish isolates differ from each other and belong to two strains. PepMV-SW was highly similar to European isolates, showing extensive sequence identity, ca. 99%. Pairwise comparisons of PepMV-PK with other PepMV isolates from the GenBank database showed that the highest nucleotide sequence identity was with two isolates: Ch2 from Chile and US2 from the USA.     

Sperm characteristics of chub Leuciscus cephalus (L.) collected in artificial condition after Ovopel and Ovaprim treatment

The effect of two commercial preparations containing different GnRH analogues with dopamine antagonists on quantitative and qualitative parameters of semen from chub Leuciscus cephalus L. collected in artificial conditions were examined. Semen was collected after the application of [(D‐Ala⁶, Pro⁹ NEt)‐mGnRH + metoclopramide] (Ovopel, n = 9), [(D‐Arg⁶, Pro⁹ Net)‐sGnR + domperidone] (Ovaprim, n = 9) and from the control group (0.9% NaCl, n = 9). Afterwards, semen volume, sperm concentration, total sperm production and semen pH were determined. Osmolality and pH of seminal plasma were also determined. Using the Computer‐assisted sperm analysis system (CASA), selected sperm parameters such as sperm motility (MOT %), progressively motile sperm (PRG, %), curvilinear velocity (VCL, μm s^?1), straight‐line velocity (VSL, μm s^?1), movement linearity (LIN, %), wobbling index (WOB, %), amplitude of lateral head displacement (ALH, μm) and beat cross frequency (BCF, Hz) were analysed. While Ovopel can also be used to stimulate chub spermation, the application of Ovaprim was much more effective for obtaining higher amounts of semen.     

Effect of two commercial preparations containing different GnRH analogues with dopamine antagonists on barbel Barbus barbus (L.) sperm quantity and quality

The effectiveness of applying Ovaprim [(D-Arg⁶, Pro⁹NEt)-sGnRH + domperidone] and Ovopel [(D-Ala⁶, Pro⁹NEt)-mGnRH + metoclopramide] to male barbel Barbus barbus (L.) 6, 12 and 24 h after hormonal stimulation was analyzed. The control group (Control) during each time interval was stimulated with 0.9 % NaCl. Milt was collected from seven fish only once (n = 7) for Ovopel, Ovaprim and Control group in order to determine total volume of milt, volume of milt per kg of body weight, sperm concentration, total sperm production, seminal plasma osmotic pressure, pH of milt and pH of seminal plasma. Woynarovich’s solution (68 mM NaCl + 50 mM urea) with the addition of 0.5 % BSA (pH 7.7; 181 mOsm kg^?1) was used as the activating liquid. Selected parameters of sperm motility (MOT %) and progressively motile sperm (%), curvilinear velocity (VCL, μm s^?1), straight-line velocity (μm s^?1), movement linearity (%), wobbling index (%), amplitude of lateral head displacement (μm) and beat cross frequency (Hz) were determined using the Computer-assisted sperm analysis system. A time of 6 h proved to be too short to obtain milt from barbel following hormonal stimulation with Ovaprim and Ovopel. Extending the time to 12 h, however, resulted in 100 % spermiation in males, regardless of hormonal preparation used for stimulation. The stimulation of spermiation in barbel is best performed using Ovopel 12 h upon application. Extending the latency period to 24 h following the application of this preparation results in a significant decrease in the volume of milt obtained, sperm count and motility parameters, including MOT and VCL, which may influence sperm fertilization ability.     

Applying Chemometrics to Determine Dispersion of Mine Tailing-Affected Sediments from Submarine Tailing Disposal in Bøkfjorden,Northern Norway

Mine tailing management is one of the largest environmental issues related to mining operation. This study uses chemometrics to assess the dispersion of iron mine tailing-affected sediments in Bøkfjorden, Northern Norway. Metal concentrations (Al, As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, Zn) and physico-chemical sediment characteristics (conductivity, organic matter, sulphate, chloride, grain size, CaCO₃, pH) were analysed in seven sediment cores collected in a transect out of the fjord along with two reference cores. Results of hierarchical cluster analysis and principal component analysis allowed to distinguish between mine tailing-affected and non-affected sediments. Non-affected sediments were especially characterised by high levels of organic matter whilst mine tailing-affected sediments varied significantly in sediment characteristics depending on location in the fjord. Crucial parameters to reveal mine tailing-affected sediments varied between the target metal Fe along with metals of Cd and Mn, albeit less significant. Variations in mine tailing-affected sediment characteristics could be attributed to other anthropogenic activities in the fjord. Despite potential disturbances, chemometrics made it possible to identify dispersion of mine tailing-affected sediments to cover the inner and middle parts of the fjord. The study demonstrates the advantage of applying chemometrics on complex fjord systems, which in this case was used to distinguish mine tailing-affected sediments from areas with elevated levels of metals not necessarily related to the mine.     

Scots pine (Pinus sylvestris L.) roots and soil moisture did not affect soil thermal sensitivity

Through their effects on microbial metabolism, temperature and moisture affect the rate of decomposition of soil organic matter. Plant roots play an important role in SOM mineralization and nutrient cycling. There are reports that rhizosphere soil exhibits higher sensitivity to temperature than root-free soil, and this can have implications for how soil CO₂ efflux may be affected in a warmer world. We tested the effects of 1-week incubation under different combinations of temperature (5, 15, 30 ^°C) and moisture (15, 50, 100% WHC) on the respiration rate of soil planted with Scots pine and of unplanted soil. Soil respiration in both soils was the highest at moderate moisture (p < 0.0001) and, increased with temperature (p < 0.0001). There was also marginally significant effect of soil kind on respiration rate (p < 0.055), but the significant interaction of temperature effect with soil kind effect, indicated, that soil respiration of planted soil was higher than unplanted soil only at 5 ^°C (p < 0.05). The soil kind effect was compared also as Q₁₀ coefficients for respiration rate, showing the relative change in microbial activity with increased temperature. However, there was no difference in the thermal sensitivity of soil respiration between planted and unplanted soils (p = 0.99), irrespective of the level of soil moisture. These findings were similar to the latest studies and confirmed, that in various models, being useful tools in studying of soil carbon cycling, there is no need to distinguish between planted and unplanted soil as different soil carbon pools.     

Conception rates in farm mink (Neovison vison) in relation to first mating date,age and color variety

The aim of the study was to analyze the effects of the first mating date, age and color variety on the conception rates in farm mink. We analyzed female mink reproductive performance in 492 Sapphire and 463 Standard Black females over 3 or 4 years. The analysis included the number of inefficient matings, the interval between the first inefficient mating and the efficient mating (copulation) and the conception rates. The results show a significant effect of female's age and color variety on the conception rates. The youngest, yearling females of either color needed a higher number of matings per conception, as compared to older, 2‐ and 3‐year‐old females. Black females demonstrated a higher number of inefficient matings (1.066), as compared with Sapphires (0.730). Yearling females were most often mated from 1 to 10 March, and older females from 11 to 20 March. Older females achieved better conception rates than the yearlings. Dates between 11 and 25 March proved to be the optimum for the first mating, since the highest conception rates were observed if the females had mated during this period.     

The impact of installation of automatic milking system on production and reproduction traits of dairy cows

The objective of the research was the evaluation of change in the traditional milking system using automatic milking system in the scope of the selected reproduction features of dairy cows of the Polish Holstein–Friesian breed. Animal material consisted of 2,818 cows used on nine farms equipped with the automatic milking system Astronaut A4 made by Lely. The cows were controlled in the scope of services per conception, service period, length of pregnancy, calving interval and calving to conception period, milk yield, protein and fat content obtained in lactations of 305 days. The selected traits were observed between 2005 and 2015. In this period, the milking system was changed from the conventional to automated one. The collected data material was statistically processed, using the multifactorial analysis of variance. The period between the first calving and the second effective insemination was reduced by 11.8 days, and the period between the second calving and the third effective insemination was shortened by 4 days after the installation of the automatic milking system. The increase in milk yield by 466 kg during 305‐day lactation was observed among primiparous cows. The percentage of protein and fat content in the researched groups decreased; moreover, the fall of intergroup variability was noticeable, which may be a sign of the levelling of the yield within the herd.     

Over‐dispersed count data in crop and agronomy research

While evaluating plant response to biotic or abiotic stress and genotype–environment interactions and searching causes of yield gap, very often are observed data with non‐normal distributions. One of the commonly encountered types of variables with a non‐normal distribution is count data. Count data are defined as the type of observations which have a positive, non‐zero, integer value. The selection of appropriate probability distributions and model types is very important due to the risk of estimating the variance incorrectly—the phenomenon of over‐dispersion. Increasingly, biologists and agronomists have been using methods based on generalized linear models. However, sometimes, when including count data, they are not aware of or disregard their over‐dispersion. One of the solutions for over‐dispersed count data is to use probability distributions and model types which assume a more flexible mean and variance relationship. Thus, the aim of this study is to present various ways of assessing over‐dispersion. Additionally, we present alternative distributions and discuss other approaches to solve the problem of over‐dispersion in count data sets. As examples in this study are used real data sets from different agricultural experiments. In our study, in one out of the two data sets used, this phenomenon occurred. Thus, in the analysis of count data, instead of using default distribution (usually Poisson distribution), other distributions should be considered because of the possible occurrence of over‐dispersion. We also observed that there is not one universal distribution to use and each data set might need a separate assessment to choose its distribution. For an efficient and proper count data analysis, with potential over‐dispersion, it is important to explore several options, i.e. evaluate models with an alternative to Poisson probability distributions and then make an informed choice.