Browsing by Author "Chen, Lin"
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Item AKR2A interacts with KCS1 to improve VLCFAs contents and chilling tolerance of Arabidopsis thaliana(2020) Chen, Lin; Hu, Wenjun; Mishra, Neelam; Wei, Jia; Lu, Hongling; Hou, Yuqi; Qiu, Xiaoyun; Yu, Shaofang; Wang, Changlu; Zhang, Hong (TTU); Cai, Yifan (TTU); Sun, Chunyan; Shen, GuoxinArabidopsis thaliana AKR2A plays an important role in plant responses to cold stress. However, its exact function in plant resistance to cold stress remains unclear. In the present study, we found that the contents of very long-chain fatty acids (VLCFAs) in akr2a mutants were decreased, and the expression level of KCS1 was also reduced. Overexpression of KCS1 in the akr2a mutants could enhance VLCFAs contents and chilling tolerance. Yeast-2-hybrid and bimolecular fluorescence complementation (BIFC) results showed that the transmembrane motif of KCS1 interacts with the PEST motif of AKR2A both in vitro and in vivo. Overexpression of KCS1 in akr2a mutants rescued akr2a mutant phenotypes, including chilling sensitivity and a decrease of VLCFAs contents. Moreover, the transgenic plants co-overexpressing AKR2A and KCS1 exhibited a greater chilling tolerance than the plants overexpressing AKR2A or KCS1 alone, as well as the wild-type. AKR2A knockdown and kcs1 knockout mutants showed the worst performance under chilling conditions. These results indicate that AKR2A is involved in chilling tolerance via an interaction with KCS1 to affect VLCFA biosynthesis in Arabidopsis.Item AKR2A participates in the regulation of cotton fibre development by modulating biosynthesis of very-long-chain fatty acids(2020) Hu, Wenjun; Chen, Lin; Qiu, Xiaoyun; Wei, Jia; Lu, Hongling; Sun, Guochang; Ma, Xiongfeng; Yang, Zuoren; Zhu, Chunquan; Hou, Yuqi; Han, Xiao; Sun, Chunyan; Hu, Rongbin (TTU); Cai, Yifan (TTU); Zhang, Hong (TTU); Li, Fuguang; Shen, GuoxinThe biosynthesis of very-long-chain fatty acids (VLCFAs) and their transport are required for fibre development. However, whether other regulatory factors are involved in this process is unknown. We report here that overexpression of an Arabidopsis gene ankyrin repeat-containing protein 2A (AKR2A) in cotton promotes fibre elongation. RNA-Seq analysis was employed to elucidate the mechanisms of AKR2A in regulating cotton fibre development. The VLCFA content and the ratio of VLCFAs to short-chain fatty acids increased in AKR2A transgenic lines. In addition, AKR2A promotes fibre elongation by regulating ethylene and synergizing with the accumulation of auxin and hydrogen peroxide. Analysis of RNA-Seq data indicates that AKR2A up-regulates transcript levels of genes involved in VLCFAs’ biosynthesis, ethylene biosynthesis, auxin and hydrogen peroxide signalling, cell wall and cytoskeletal organization. Furthermore, AKR2A interacted with KCS1 in Arabidopsis both in vitro and in vivo. Moreover, the VLCFA content and the ratio of VLCFAs to short-chain fatty acids increased significantly in seeds of AKR2A-overexpressing lines and AKR2A/KCS1 co-overexpressing lines, while AKR2A mutants are the opposite trend. Our results uncover a novel cotton fibre growth mechanism by which the critical regulator AKR2A promotes fibre development via activating hormone signalling cascade by mediating VLCFA biosynthesis. This study provides a potential candidate gene for improving fibre yield and quality through genetic engineering.Item Co-overexpressing a Plasma Membrane and a Vacuolar Membrane Sodium/Proton Antiporter Significantly Improves Salt Tolerance in Transgenic Arabidopsis Plants(2016) Pehlivan, Necla; Sun, Li (TTU); Jarrett, Philip (TTU); Yang, Xiaojie; Mishra, Neelam (TTU); Chen, Lin; Kadioglu, Asim; Shen, Guoxin; Zhang, Hong (TTU)The Arabidopsis gene AtNHX1 encodes a vacuolar membrane-bound sodium/proton (Na+/H+) antiporter that transports Na+ into the vacuole and exports H+ into the cytoplasm. The Arabidopsis gene SOS1 encodes a plasma membrane-bound Na+/H+ antiporter that exports Na+ to the extracellular space and imports H+ into the plant cell. Plants rely on these enzymes either to keep Na+ out of the cell or to sequester Na+ into vacuoles to avoid the toxic level of Na+ in the cytoplasm. Overexpression of AtNHX1 or SOS1 could improve salt tolerance in transgenic plants, but the improved salt tolerance is limited. NaCl at concentration >200 mM would kill AtNHX1-overexpressing or SOS1-overexpressing plants. Here it is shown that co-overexpressing AtNHX1 and SOS1 could further improve salt tolerance in transgenic Arabidopsis plants, making transgenic Arabidopsis able to tolerate up to 250 mM NaCl treatment. Furthermore, co-overexpression of AtNHX1 and SOS1 could significantly reduce yield loss caused by the combined stresses of heat and salt, confirming the hypothesis that stacked overexpression of two genes could substantially improve tolerance against multiple stresses. This research serves as a proof of concept for improving salt tolerance in other plants including crops.Item Ensemble summarization models to leverage performance on CoronaNet(2021-05) Zhou, Fei; Sheng, Victor; Chen, Lin; Chi, SabrinaThe COVID-19 pandemic is the most fast-spreading and devastating event in recent history. CoronaNet Research Project produced the COVID-19 dataset regarding how governments responded to this pandemic. The dataset has given hand-written summaries for each recorded case and source URL links. The text data from the links are generally long articles, and we intend to apply NLP summarization in such a context. There are two approaches for summarization tasks. The abstractive methods, which extract the text from the source text to form summaries, are usually not very flexible but simpler. The other approach is abstractive techniques, which are usually more complicated than abstractive methods but more flexible in semantics. Since the deep learning field advancements, NLP summarization tasks have seen many successes and applications in our daily lives. In this thesis, we built a system that ensembles pre-training NLP models to leverage the abstractive summarization performance. We included focal loss function to improve performance by focusing on the samples with lower scores. Our proposed ensemble method improved the overall ROUGE scores compared to the individual models.Item Morphological, Physiological and Proteomic Analyses Provide Insights into the Improvement of Castor Bean Productivity of a Dwarf Variety in Comparing with a High-Stalk Variety(2016) Hu, Wenjun; Chen, Lin; Qiu, Xiaoyun; Lu, Hongling; Wei, Jia; Bai, Yueqing; He, Ningjia; Hu, Rongbin (TTU); Sun, Li (TTU); Zhang, Hong (TTU); Shen, GuoxinRicinus communis displays a broad range of phenotypic diversity in size, with dwarf, common, and large-sized varieties. To better understand the differences in plant productivity between a high-stalk variety and a dwarf variety under normal growth conditions, we carried out a comparative proteomic study between Zhebi 100 (a high stalk variety) and Zhebi 26 (a dwarf variety) combined with agronomic and physiological analyses. Over 1000 proteins were detected, 38 of which differed significantly between the two varieties and were identified by mass spectrometry. Compared with Zhebi 100, we found that photosynthesis, energy, and protein biosynthesis related proteins decreased in abundance in Zhebi 26. The lower yield of the dwarf castor is likely related to its lower photosynthetic rate, therefore we hypothesize that the lower yield of the dwarf castor, in comparing to high stalk castor, could be increased by increasing planting density. Consequently, we demonstrated that at the higher planting density in Zhebi 26 (36,000 seedlings/hm2) can achieve a higher yield than that of Zhebi 100 (12,000 seedlings/hm2). Proteomic and physiological studies showed that for developing dwarf R. communis cultivar that is suitable for large scale-production (i.e., mechanical harvesting), it is imperative to identify the optimum planting density that will contribute to higher leaf area index, higher photosynthesis, and eventually higher productivity.Item Photocatalytic radical defluoroalkylation of unactivated alkenes via distal heteroaryl ipso-migration(2020) Yuan, Xin; Zhuang, Kai Qiang; Cui, Yu Sheng; Qin, Long Zhou; Sun, Qi; Duan, Xiu; Chen, Lin; Zhu, Ning; Li, Guigen (TTU); Qiu, Jiang Kai; Guo, KaiCurrently, the selective activation of C(sp3)–F bonds and C–C bonds constitute one of the most widely used procedures for the synthesis of high-value products that range from pharmaceuticals to agrochemical applications. While numerous examples of these two methods have been reported in their respective fields, the processes which merge the activation of both single C(sp3)-F bonds and C–C bonds in one step still remain elusive. Here, we demonstrate the controllable defluoroalkylation–distal functionalization of trifluoromethylarenes with unactivated alkenes via distal heteroaryl migration. This is proposed to proceed via tandem C(sp3)–F and C–C bond cleavage using visible-light photoredox catalysis combined with Lewis acid activation. This strategy provides facile and flexible access to multiply functionalized α,α-difluorobenzylic ketones in useful yields (up to 88%) under mild conditions. The products can be further transformed into other valuable compounds, demonstrating the method’s utility.Item Preventing User Radicalization by Automatically Detecting Misinformation Videos(2022-12) Latif, Lawzeem; Sheng, Victor; Chen, Lin; Tianxi, JiOnline misinformation has become a very large problem with the rise in information sharing capabilities of social media. The rise in such misinformation has in turn influenced and lead to many cases of radicalization which has resulted in many unfortunate situations. Detecting misinformation is computationally expensive and usually by the time it is found and removed, the content has spread to many places. Additionally, online echo-chambers often exacerbate the spread of misinformation and without any oversight can lead to users getting radicalized. In this thesis, I will look at leading research papers on how to detect misinformation using multiple methods and how to detect potential echo-chambers. Using that knowledge, I will propose a video ranking algorithm that will attempt to prevent user radicalization by automatically detecting potential misinformation content.Item Protecting data privacy with anonymity: Quantifying instinctive measures and intelligent effective search for optimal anonymized data(2022-05) Arca, Sevgi; Hewett, Rattikorn; Serwadda, Abdul; Dang, Tommy; Salman, Tara; Chen, Lin; Yamazaki, KazuoData privacy entails the ability for individuals to control their personal data. With advanced technology in this digital era, users can lose control of their personal data without knowing as their data can be tracked, stored, and shared across multiple parties. Protecting online data privacy is a daunting task. Current consent-based privacy policies tend to be too elaborate and difficult to apply effectively. There is a need for new approaches to protecting data privacy that go beyond user consent model. As more data are shared and publicly available, attackers can further infer confidential data from multiple query sources to commit malicious acts. This dissertation addresses the issues of how to better protect privacy of such published structured data, particularly, fundamental issues of anonymity quantification and practical issues on efficiency and optimality of automated anonymization. Anonymity is among the most widely used property for data privacy protection. It represents the state of indistinguishability. Thus, increasing users’ anonymity increases their indistinguishability that makes it harder for them to be re-identified. Anonymization ensures that each set of "critical" data values belongs to more than one individual so that the individual's identity can be protected. Many privacy-preserving approaches to anonymizing structured data involve transforming the original data into a more anonymous form (via generalization and suppression) while preserving the data integrity. Although techniques for anonymization have been studied extensively, to our surprise, most of them do not directly measure anonymity but use a measure specified to indirectly indicate the quality of anonymity (e.g., anonymity degree in k-anonymity). Most existing anonymity measures are indirect since they are based on entropy that estimates information loss, a partial consequence of anonymity. Anonymity measure is at the heart of anonymization and yet there is little research on quantifying a direct measure of anonymity. This dissertation models two direct anonymity measures: information-based and inference-based for the disclosure breach and re-identification attack, respectively. The unique aspect of the formulation is its instinctive articulation of opposing perspectives of victims (in concealing their identity) and attackers (in finding the disclosure or identity). Furthermore, unlike most other work, this study distinguishes the measure of an individual anonymity from that of the group. When dealing with large-scaled data, by using data distribution, this dissertation proposes measures of uniformity, variety, and diversity as anonymity indicators to quickly assess degrees of data privacy. On practical issues of anonymization, to improve efficiency, most general-purpose anonymization techniques aim to find "optimal" k-anonymization (or anonymized data satisfying k-anonymity requirements), e.g., by minimizing data distortion or the number of generalization steps. However, the problem of finding k-anonymization to maximize preserved information is NP-hard. This has led to greedy anonymization and special purpose techniques. Still, a common issue in anonymization is trade-offs between data privacy and informativeness. Generalization helps gain anonymity but can result in data that are not useful. Anonymization approaches are mostly designed to address specific goals (e.g., accurate classification, efficient algorithms) but none provides an integrated solution for efficiency, privacy, and preserved informativeness. This dissertation presents a general-purpose anonymization technique that applies generalization for securing privacy by satisfying user-specified anonymity requirements while optimizing information preservation. The proposed approach exploits the monotonicity property of generalization along with a heuristic search to efficiently find optimal generalized data that comply with the anonymity requirements. The approach is theoretically grounded as the search can be mapped to a well-known efficient optimal search in Artificial Intelligence. In addition, the approach can give the data quality for classification relatively well even though its intent is to keep the generalized data as close as possible to the original. Finally, this dissertation puts together a practical methodology for anonymity analytics and retention.Item The molecular chaperon AKR2A increases the mulberry chilling-tolerant capacity by maintaining SOD activity and unsaturated fatty acids composition(2018) Chen, Lin; Hou, Yuqi; Hu, Wenjun; Qiu, Xiaoyun; Lu, Hongling; Wei, Jia; Yu, Shaofang; He, Ning Jia; Zhang, Hong (TTU); Shen, GuoxinChilling is common in nature and can damage most plant species, particularly young leaves and buds. Mulberry (Morus spp.) is an economically important food source for the domesticated silkworm (Bombyx mori). However, weather and climatic extremes, such as “late spring coldness”, seriously damage mulberry buds and young leaves. The molecular mechanism involved in the differing mulberry chilling tolerance is unclear. In the present study, we found that mSOD1, mFADII, and mKCS1 interacted with mAKR2A and that the expression of mAKR2A, mSOD, mFAD, and mKCS1 in the chilling-tolerant mulberry variety was higher than that in the chilling-sensitive variety. Unsaturated fatty acids content and superoxide dismutase (SOD) activity in the chilling-tolerant variety was higher than that in the chilling-sensitive variety. After chilling treatment, mSOD1, mKCS1 and mAKR2A expression in the chilling-tolerant variety was reduced to lower than that in the chilling-sensitive variety, whereas mFADII expression increased in the chilling-tolerant variety compared with that in the chilling-sensitive variety, suggesting that the increased expression of the molecular chaperon mAKR2A helped to maintain or prompted the chilling-related proteins in the chilling-tolerant variety.