Browsing by Author "Kim, Dongjin"

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Colonization by the endophyte Piriformospora indica leads to early flowering in Arabidopsis thaliana likely by triggering gibberellin biosynthesis
(2017-09) Kim, Dongjin; Abdelaziz, Mohamad E.; Ntui, Valentine Otang; Guo, Xiujie; Al-Babili, Salim
Piriformospora indica is an endophytic fungus colonizing roots of a wide variety of plants. Previous studies showed that P. indica promotes early flowering and plant growth in the medicinal plant Coleus forskohlii. To determine the impact of P. indica on flowering time in Arabidopsis, we co-cultivated the plants with P. indica under long day condition. P. indica inoculated Arabidopsis plants displayed significant early flowering phenotype. qRT-PCR analysis of colonized plants revealed an up-regulation of flowering regulatory (FLOWERING LOCUS T, LEAFY, and APETALA1) and gibberellin biosynthetic (Gibberellin 20-Oxidase2, Gibberellin 3-Oxidase1 and Gibberellin requiring1) genes, while the flowering-repressing gene FLOWERING LOCUS C was down regulated. Quantification of gibberellins content showed that the colonization with P. indica caused an increase in GA4 content. Compared to wild-type plants, inoculation of the Arabidopsis ga5 mutant affected in gibberellin biosynthetic gene led to less pronounced changes in the expression of genes regulating flowering and to a lower increase in GA4 content. Taken together, our data indicate that P. indica promotes early flowering in Arabidopsis likely by increasing gibberellin content.
CRISPR/Cas9 genome editing in wheat
(2017-09) Kim, Dongjin; Alptekin, Burcu; Budak, Hikmet
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome. Here, we applied CRISPR/Cas9 genome editing system in wheat protoplast to conduct the targeted editing of stress-responsive transcription factor genes, wheat dehydration responsive element binding protein 2 (TaDREB2) and wheat ethylene responsive factor 3 (TaERF3). Targeted genome editing of TaDREB2 and TaERF3 was achieved with transient expression of small guide RNA and Cas9 protein in wheat protoplast. The effectiveness of mutagenesis in wheat protoplast was confirmed with restriction enzyme digestion assay, T7 endonuclease assay, and sequencing. Furthermore, several off-target regions for designed sgRNAs were analyzed, and the specificity of genome editing was confirmed with amplicon sequencing. Overall results suggested that CRISPR/Cas9 genome editing system can easily be established on wheat protoplast and it has a huge potentiality for targeted manipulation of wheat genome for crop improvement purposes.
Location-preserved contention-based routing in vehicular ad hoc networks
(Wiley, 2014-04) Qing, Yang; Lim, Alvin; Ruan, Xiaojun; Qin, Xiao; Kim, Dongjin
Location privacy protection in vehicular ad hoc networks considers preserving two types of information: the locations and identifications of users. However, existing solutions, which either replace identifications by pseudonyms or hide locations in areas, cannot be directly applied to geographic routing protocols because they degrade network performance. To address this issue, we proposed a location-preserved contention (LPC) based routing protocol, in which greedy forwarding is achieved using dummy distance to the destination information instead of users’ true locations. Unlike the contention-based forwarding protocol, the number of duplicated responses in LPC can be reduced by adjusting the parameter α, which is a timer scaling factor. To quantify the efficiency of location privacy protection, an entropy-based analytical method is proposed. LPC is compared with existing routing and location privacy protection protocols in simulations. Results show that LPC provides 11.7% better network performance and a higher level of location privacy protection than the second best protocol.