149 research outputs found
The Landscape of Chromatin Accessibility and ChIP-seq Analysis of a bZIP Transcription Factor AaHY5 in Artemisia annua
No full textGlandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Critical artemisinin biosynthetic genes are expressed explicitly in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules can interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, I investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). I identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR and CYP71AV1, showed higher accessible regions in GT than in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the GT high and artemisinin biosynthetic genes associated accessible regions, indicating the important role of these transcription factor types in artemisinin biosynthesis.ChIP-seq (Chromatin immunoprecipitation with sequencing) is the gold standard for determining genome-wide in vivo transcription factor binding sites, which is the first step for whole-genome targets prediction and network construction. For non-model plants, ChIP-seq is challenging to perform due to the obstacle of transgenic plant construction. AaHY5 is a positive regulator in artemisinin biosynthesis, with detailed molecular mechanisms elusive. In the second part of my work, I established the protoplast transformation procedure for Artemisia annua and performed AaHY5 ChIP-seq based on the transient expression system. An AaHY5 target AaWRKY14 was identified as a potential transcription factor linking AaHY5 and the artemisinin biosynthetic gene regulation. AaWRKY14 is highly expressed in glandular trichomes and can be induced by light and AaHY5. Furthermore, AaWRKY14 could promote the expression of two artemisinin biosynthetic genes, ADS and CYP71AV1, and has transcriptional activation activity on the promoter region of CYP71AV1.In summary, I applied ATAC-seq and ChIP-seq in Artemisia annua and revealed the epigenetic regulation of artemisinin biosynthesis in GT and the molecular mechanism for AaHY5-mediated artemisinin biosynthetic gene regulation.腺毛是青蒿中青蒿素合成的主要場所，青蒿素合成的關鍵基因在腺毛中特異表達。但是，基因在腺毛和其他組織類型之間差異表達的分子機制仍不甚清楚。染色質可及性，即核分子能夠與染色質DNA相互作用的程度，在一定程度上反映了基因表達的能力。我們利用ATAC-seq技術比較研究了青蒿葉和腺毛中染色質可及性的情況。我們鑒定到5413個腺毛高可及性區域和4045個腺毛低可及性區域，腺毛高可及性區域可能有助於解釋腺毛特定的生物學功能。腺毛特有的青蒿素生物合成基因，如DBR2和CYP71AV1在腺毛中顯示出比在葉片中更高的可及性，這表明它們在腺毛中的表達可能受到染色質可及性的調控。此外，MYB，bZIP，C2H2和AP2的轉錄因子結合基序在腺毛高可及性區和青蒿素合成基因相关的开放区富集，暗示著這幾類轉錄因子對於青蒿素表达调控有较为重要的意义。ChIP-seq（染色質免疫沉澱測序）是確定全基因組體內轉錄因子結合位點的金標準，也是預測全基因組靶標和構建網絡的第一步。對於非模式植物，由於轉基因植物構建困難，ChIP-seq難以實施。AaHY5是青蒿素合成的正調節因子之一，但其具體的分子機制尚不清楚。在這裡，我們建立了基於原生質體的瞬時轉化系統，並基於該體系進行了AaHY5的ChIP-seq。我們鑒定到一個AaHY5靶標AaWRKY14，可能是直接連接AaHY5和青蒿素生物合成調控的轉錄因子。AaWRKY14在腺毛中高表達，並受光信号和AaHY5誘導。此外，AaWRKY14可以促进青蒿素生物合成基因ADS和CYP71AV1的表達，並对CYP71AV1的啟動子區域具有轉錄激活活性。综上，我們在青蒿中應用了ATAC-seq和ChIP-seq，並揭示了青蒿素生物合成的表觀遺傳調控機制以及AaHY5介導的青蒿素生物合成基因調控的分子機制。ZHOU, Limeng.Ph.D. Chinese University of Hong Kong 2021.Includes bibliographical references (leaves )Abstracts in English and Chinese.Title from PDF title page (viewed on ...
Allelic analysis of sheath blight resistance with association mapping in rice
No full textCitation: Jia, Limeng, Wengui Yan, Chengsong Zhu, Hesham A. Agrama, Aaron Jackson, Kathleen Yeater, Xiaobai Li, et al. “Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice.” PLOS ONE 7, no. 3 (March 12, 2012): e32703. https://doi.org/10.1371/journal.pone.0032703.Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed
that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r =20.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to
indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice
Dynamic decision-making under uncertainties: algorithms based on linear decision rules and applications in operating models
No full textThis thesis is to propose efficient and robust algorithms based on Linear
Decision Rule (LDR), which expand the applicability of the existing LDR methods. Representative and complex operation models are analyzed and solved by the proposed approaches. The research motivation and scope are provided in Chapter 1.
Chapter 2 introduces the generic LDR method and the contributions of this thesis to the LDR literature. To extend the LDR method to nonlinear objectives, two methods are proposed. The first is an iterative LDR (ILDR) method that tackles general concave differentiable nonlinear terms in the objective function. The second treats quadratic terms in the objective function by a Second-Order Cone approximation. The details and implementation of the proposed methods are presented in Chapter 3 and Chapter 4.
Chapter 3 utilizes the Robust Optimization approach to derive an ILDR solution for a multi-period hydropower generation problem that has a nonlinear objective function. The methodology results in tractable second-order cone formulations. The performance of the ILDR approach is compared with the Sampling Stochastic Dynamic Programming (SSDP) policy derived using historical data.
In Chapter 4, a joint pricing and inventory control problem of a perishable product with a fixed lifetime is analyzed. Both the backlogging and lost-sales cases are discussed. The analytic results shed new light on perishable inventory management, and the proposed approach provides a significantly simpler proof of a classical structural result in the literature. Two heuristics were proposed, one of which is a modification and improvement of an existing heuristic. The other one is an LDR based approach, which approximates the dynamics and the objective function by robust counterparts. The robust counterpart for the backlogging case is tight, and it leads to a satisfactory performance of less than 1% loss of optimality. Although the robust counterpart for the lost-sales case is not tight in the current numerical study, the gap between the LDR method and the SDP benchmark is less than 5% on average.
Chapter 5 summarizes the contributions of the thesis and discusses about potential improvements. One important working project, an approximate dynamic programming based on LDR (ADP-LDR) approach, is introduced for future research.Item withdrawn by Mark Zulauf ([email protected]) on 2014-07-15T19:03:57Z
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Novel Clustering Method towards Identification of Activation Points for Atrial Fibrillation
No full textIn this paper, a novel approach to locate the activation points of atrial fibrillation (AF) is proposed. This new method is built upon machine learning, where common parameters, such as dominant frequency, first harmonic frequency, etc., are adopted. Features are extracted from the original electrocardiography (ECG) and then clustering is performed to classify the ECG signals into two groups, namely activation and nonactivation points. The experimental results are compared with those from the state-of-the-art system, Topera, used in East Jefferson General Hospital nowadays
Novel Hierarchical Tag-Recognition for RFID Systems
No full textIn this paper, we propose a new hierarchical radio-frequency identification (RFID) tag- recognition method based on the graph-based automatic modulation classification (AMC) and direct-sequence spread-spectrum (DSSS). In our proposed method, RFID tags can be modulated using different modulation schemes according to different scenarios (e.g., different users or different devices). For each modulation scheme, the direct-sequence spread-spectrum strategy is employed to allow simultaneous transmissions of multiple tags. In the first hierarchy, different modulation types are employed to distinguish different users, the graph-based AMC is built upon the periodicity of the modulated signals. The cyclic spectrum of the received signal is first established. The graph representation is then constructed according to the cyclic spectrum. Ultimately, robust features are extracted from the graph representation. In the second hierarchy, the DSSS scheme is utilized to differentiate the control or sensed data carried by individual tags, the signature sequence set with low cross- correlations is generated from Gold and Kasami sequences. In the third hierarchy, the information data sequences are thus spread by these signature sequences. In our proposed new RFID framework, multiple tags can transmit the signals simultaneously in the same frequency band where the dominant tag signal will be identified and its carried information can be recovered. Monte Carlo simulation results demonstrate the promising performance of our proposed new scheme
Step-like contrast structure of singularly perturbed optimal control problem
No full textIn this paper, the existence of step-like contrast structure for a class of singularly perturbed optimal control problem is shown by the contrast structure theory. By means of direct scheme of boundary function method, we construct the uniformly valid asymptotic solution for the singularly perturbed optimal control problem. Finally, an example is presented to show the result
Novel Automatic Human-Height Measurement Using a Digital Camera
No full textNowadays, automatic object-size measurement (AOSM) techniques are in high demand since there are numerous applications including three-dimensional multimedia entertainment games, cyber-physical interaction, and real-time geographical survey. When a scene is complex with many objects, the AOSM problem is quite challenging because it is very hard to describe the object of interest a priori. In this paper, we present a novel efficient automatic human-height measurement scheme using a single camera. Our proposed new scheme is very robust so that the heights of multiple persons within the scene can be estimated automatically and simultaneously. The experimental results demonstrate that the average error percentage is less than 2% in general
Novel automatic size measurement method using a digital camera
No full textAutomatic size measurements have been intriguing lately since they have a lot of applications such as cyber-physical interaction, three-dimensional multimedia entertainment games, navigation and target tracking, real-time surveying of the environment using artificial intelligence. Conventional accurate approaches are mostly based on the active techniques, including laser-beams, ultrasonics, radio-frequency transceivers, etc. These existing approaches can recognize neither the object nor the context of the scene; thus advanced image processing methods using visible-light digital cameras are more preferable on the other hand. In this paper, we utilize the basic visible-light propagation principles to build a novel efficient automatic size measurement algorithm, which can be employed by one or two digital cameras. The experimental results show that less than 3% of striking accuracy can be achieved on average using our proposed new method
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