• Korean Journal of Agricultural and Forest Meteorology
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• v.19 no.4
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• pp.270-279
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• 2017

Regional assessment of crop productivity using a gridded simulation approach could aid policy making and crop management. Still, little effort has been made to develop the systems that allows gridded simulations of crop growth using ORYZA 2000 model, which has been used for predicting rice yield in Korea. The objectives of this study were to develop a series of data processing modules for creating input data files, running the crop model, and aggregating output files in a region of interest using gridded data files. These modules were implemented using C++ and R to make the best use of the features provided by these programming languages. In a case study, 13000 input files in a plain text format were prepared using daily gridded weather data that had spatial resolution of 1km and 12.5 km for the period of 2001-2010. Using the text files as inputs to ORYZA2000 model, crop yield simulations were performed for each grid cell using a scenario of crop management practices. After output files were created for grid cells that represent a paddy rice field in South Korea, each output file was aggregated into an output file in the netCDF format. It was found that the spatial pattern of crop yield was relatively similar to actual distribution of yields in Korea, although there were biases of crop yield depending on regions. It seemed that those differences resulted from uncertainties incurred in input data, e.g., transplanting date, cultivar in an area, as well as weather data. Our results indicated that a set of tools developed in this study would be useful for gridded simulation of different crop models. In the further study, it would be worthwhile to take into account compatibility to a modeling interface library for integrated simulation of an agricultural ecosystem.

• Animal Bioscience
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• v.34 no.10
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• pp.1579-1589
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• 2021

Objective: This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions. Methods: A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5' labelled with biotin/6-FAM to determine the binding potential and binding pattern. Results: We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between -1.17 to -26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5'-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×10⁶ spermatozoa could trap almost 80% from the suspension. Conclusion: The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.