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The CRISPR/Cas9 gene-editing system is the third-generation gene-editing technology that has been widely used in biomedical applications. However, off-target effects occurring CRISPR/Cas9 system has been a challenging problem it faces in practical applications. Although many predictive models have been developed to predict off-target activities, current models do not effectively use sequence pair information. There is still room for improved accuracy. This study aims to effectively use sequence pair information to improve the model's performance for predicting off-target activities. We propose a new coding scheme for coding sequence pairs and design a new model called CRISPR-IP for predicting off-target activity. Our coding scheme distinguishes regions with different functions in the sequence pairs through the function channel. Moreover, it distinguishes between bases and base pairs using type channels, effectively representing the sequence pair information. The CRISPR-IP model is based on CNN, BiLSTM, and the attention layer to learn features of sequence pairs. We performed performance verification on two data sets and found that our coding scheme can represent sequence pair information effectively, and the CRISPR-IP model performance is better than others. Data and source codes are available at https://github.com/BioinfoVirgo/CRISPR-IP.

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Resumen El objetivo de este trabajo fue evaluar la calidad nutricional en 3 cultivares de alfalfa, pertenecientes a diferentes grupos de reposo invernal (GRI), sometidos a dos frecuencias de corte, durante un año del cultivo, fundamentado en que es abundante la información existente en estudios realizados en productividad, cobertura y persistencia, no así en la determinación de calidad de forraje sometidos a diferentes frecuencias de cortes y de GRI contrastantes. Se utilizaron tres cultivares (GR6-Verzy), (GR9-Mecha) y (GR10-Ruano). El diseño experimental fue de parcelas divididas con cuatro repeticiones. Se establecieron 2 tratamientos definidos por los intervalos entre cortes: T1: 25 días y T2: 35 días. Estos fueron precisados para las estaciones de primavera, verano y otoño. En invierno el intervalo fue de 45 y 55 días en T1 y T2, respectivamente. Las variables evaluadas fueron: porcentaje de materia seca (% MS), porcentaje de proteína bruta (% PB), porcentaje de fibra detergente neutro (% FDN) y porcentaje de fibra detergente ácido (% FDA). Se encontraron diferencias significativas para todas las variables nutricionales estudiadas, para ambos tratamientos. Se observó interacción entre cultivares y tratamiento para % PB. Los cultivares estudiados con diferentes GRI, no expresaron diferencias significativas en los parámetros de calidad evaluados para ninguna de las frecuencias de corte realizadas. La frecuencia de corte de 35 días arrojó los menores % PB y mayores % FDN y % FDA, por lo cual el forraje resulta para esta frecuencia de menor calidad, llevando a la disminución de la digestibilidad y aprovechamiento de la pastura para el ganado.

Abstract The objective of this work was to evaluate the nutritional quality in 3 cultivars of alfalfa, belonging to different winter dormancy (GRI), subjected to two cutting frequencies during one year of cultivation, based on the abundant information existing in studies carried out in productivity, coverage and persistence, not so in the determination of quality of forage subjected to different frequencies of cuts and contrasting GRI. Three cultivars (GR6-Verzy), (GR9-Mecha) and (GR10-Ruano) were tested. The experimental design was a complete split plot with four repetitions. Two treatments defined by the cutting intervals were established: T1: 25 days and T2: 35 days. These were specified for spring, summer and fall seasons. For winter the interval was 45 and 55 days in T1 and T2, respectively. The evaluated variables were: percentage of dry matter (% DM), percentage of crude protein (% PB), percentage of neutral detergent fiber (% FDN) and percentage of acid detergent fiber (% FDA). Significant differences were found for all the nutritional variables studied, for both treatment with p <0.05 with InfoStat program. Interaction between cultivars and treatment was observed for % PB. The 35 days cutoff frequency of yielded the lowest percentages of PB and the highest percentages of FDN and FDA. Hence the forage resulting from this frequency is of a lower quality, leading to decreased digestibility and lower performance of pasture for livestock.

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The soil-dwelling larvae of several Scarabaeidae species (white grubs), like the cockchafer (Melolontha melolontha) and the garden chafer (Phyllopertha horticola), are serious pests in European cultivated grassland, reducing grass yield and destroying the turf by root-feeding. Nevertheless, the factors responsible for the development of large grub populations and the associated damage risk are poorly understood. The objectives of the study were to survey grub densities in grassland sites with different damage histories and find correlations with environmental and management variables. Data on grub densities were collected at 10 farms in the eastern Austrian Alps in September and October 2011. At each farm, one recently damaged site (high risk) and one site at which grub damage had never been observed by the farmers (undamaged site = low risk; each site: 500 m(2)) were sampled. All sites were dominated by P. horticola (99% of 1,422 collected individuals; maximum density 303 grubs/m(2)), which indicates that grub damage there is mainly caused by that species. Recently damaged sites tended to higher grub densities than undamaged sites. However, 3 out of 10 undamaged sites harbored high grub populations as well. Humus content together with the depth of the A-horizon significantly explained 38% of P. horticola grub density variance, with highest densities in deeper humus-rich soils. The risk of grub damage was positively connected to the humus content and negatively related to the cutting frequency. For the investigated mountainous grassland sites, these results suggest an important role of humus for the development of high grub densities and an effect of management intensity on grub damage.

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Symbiotic N2 fixation is of primordial significance in sustainable agro-forestry management as it allows reducing the use of mineral N in the production of mixed stands and by protecting the soils from degradation. Thereby, on a 2-year basis, N2 fixation was evaluated in four oak woodlands under Mediterranean conditions using a split-plot design and three replicates. (15)N technique was used for determination of N2 fixation rate. Variations in environmental conditions (temperature, rainfall, radiation) by the cork tree canopy as well as the age of stands and pasture management can cause great differences in vegetation growth, legume N2 fixation, and soil rhizobial abundance. In the present study, non-legumes dominated the swards, in particular beneath the tree canopy, and legumes represented only 42% of total herbage. A 2-fold biomass reduction was observed in the oldest sown pasture in relation to the medium-age sward (6 t DW ha(-1)yr(-1)). Overall, competition of pasture growth for light was negligible, but soil rhizobial abundance and symbiotic N2 fixation capacity were highly favored by this environmental factor in the spring and outside the influence of tree canopy. Nitrogen derived from the atmosphere was moderate to high (54-72%) in unsown and sown swards. Inputs of fixed N2 increased from winter to spring due to more favorable climatic conditions (temperature and light intensity) for both rhizobia and vegetation growths. Assuming a constant fixation rate at each seasonal period, N2 fixation capacity increased from about 0.10 kg N ha(-1) per day in the autumn-winter period to 0.15 kg N ha(-1) per day in spring. Belowground plant material contributed to 11% of accumulated N in pasture legumes and was not affected by canopy. Size of soil fixing bacteria contributed little to explain pasture legumes N.

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As a rule, communities consist of few abundant and many rare species, which is reflected in the characteristic shape of species abundance distributions (SADs). The processes that shape these SADs have been a longstanding problem for ecological research. Although many studies found strong negative effects of increasing land-use intensity on diversity, few reports consider land-use effects on SADs. Arthropods (insects and spiders) were sampled on 142 grassland plots in three regions in Germany, which were managed with different modes (mowing, fertilization and/or grazing) and intensities of land use. We analysed the effect of land use on three parameters characterizing the shape of SADs: abundance decay rate (the steepness of the rank abundance curve, represented by the niche-preemption model parameter), dominance (Berger-Parker dominance) and rarity (Fisher's alpha). Furthermore, we tested the core-satellite hypothesis by comparing the species' rank within the SAD to their distribution over the land-use gradient. When data on Araneae, Cicadina, Coleoptera, Heteroptera and Orthoptera were combined, abundance decay rate increased with combined land-use intensity (including all modes). Among the single land-use modes, increasing fertilization and grazing intensity increased the decay rate of all taxa, while increasing mowing frequency significantly affected the decay rate only in interaction with fertilization. Results of single taxa differed in their details, but all significant interaction effects included fertilization intensity. Dominance generally increased with increasing fertilization and rarity decreased with increasing grazing or mowing intensity, despite small differences among taxa and regions. The majority of species found on <10% of the plots per region were generally rare (<10 individuals), which is in accordance with the core-satellite hypothesis. We found significant differences in the rarity and dominance of species between plots of low and high intensity for all three land-use modes and for the combined land-use intensity. We conclude that effects of land-use intensity on SADs lead to a stronger dominance of the most abundant species. Furthermore, species which have restricted distributions are more likely to also be rare species in the local SAD and therefore are at high risk of being lost under intensive land use.

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O experimento foi conduzido em casa de vegetação, na Embrapa Arroz e Feijão, com o objetivo de avaliar o intervalo de corte na produção de massa seca, altura de planta e composição químico-bromatológica da Brachiaria brizantha cv. MG-5. O delineamento utilizado foi o inteiramente casualizado. Os tratamentos constituíram de quatro intervalos de corte (15, 20, 30 e 60 dias), com cinco repetições, totalizando 20 parcelas. Foram aplicados 100 mg dm-3 de nitrogênio, utilizando como fonte o sulfato de amônio, em todas as parcelas. A adubação nitrogenada foi parcelada, de acordo com os cortes de avaliações. Foram realizados quatro cortes para o intervalo de 15 dias, três cortes para o de 20 dias, dois cortes para o de 30 dias e um corte para o de 60 dias. A forrageira foi cortada a uma altura de 5 cm do solo. O aumento no intervalo de corte na Brachiaria brizantha cv. M-5 determina acréscimos na produção de massa seca e teores de FDN e FDA. Contudo, o inverso pode ser observado no teor de PB e concentrações de P, Cu e Fe.

The experiment was carried out in a green house, at Embrapa Arroz e Feijão. It aimed to evaluate the offect of cutting period on dry mass production and bromatologic- chemical composition of Brachiaria brizantha cv. MG-5. The experimental design was completely randomized, with five replications. The treatments were constituted by four cutting intervals (15, 20, 30 and 60 days). After cuttings at a distant from soil, of ammonium sulfate (100 mg dm-3) was applied to all treatments. Four cuttings were carried out at 15 - day intervals, three at 20 day-intervals, two at 30 - day intervals and one at a 60 day-interval. Increases in cutting intervals caused dry mass production, neutral detergent fiber and acid detergent fiber rase. However, the opposite was observed for bromatologic composition and phosphorus, copper and iron concentrations.