Transcriptional Characterization of Cysteine Protease Genes against Xanthomonas oryzae pv. oryzae in Rice (Oryza sativa L.)

NINO, MARJOHN CENEZA 충북대학교 2018 국내박사

This study aimed to examine cysteine protease genes (CPs) at molecular and genetic level in rice. Gain-of-function and down-regulation analysis were performed to uncover their biological significance especially in response to biotic stress. The whole-transcriptome shotgun sequencing screen of the OsCP3 overexpression and RNAi-mediated knockdown transgenic lines revealed the intrinsic transcriptional dynamics during early interaction between Xanthomonas oryzae pv. oryzae and rice. In chapter 1, database-searching for rice cysteine protease resulted in the identification of six families of OsCPs. Each family is distinctly represented by different proteolytic enzyme, including the 51 papain-like gene members of C1 family, single calpain-2-type member of C2, 7 ubiquitinyl hydrolase-L1 members of C12, 6 legumain members of C13, 2 caspase-1 members of C14, and 7 pyroglutamyl-peptidase 1 members of C15. Subsequent in-depth molecular analysis of cysteine protease members revealed the genomic rearrangement and expansion especially of papain-like cysteine proteases (C1 family) as indicated by a large number of members distributed across 12 chromosomes of the rice genome, as well as extensive variation in intron number and phase. Further investigation of physicochemical properties, gene and protein structure, motif, and cis-element highlighted the common and distinct characteristics of members of each family. It was found that 59.2% of the total numbers of cysteine protease in rice are stable. Protein type prediction based on subcellular localization revealed that all members of C1A, C13, C14, and C15 are globular proteins, whereas single member of C2 and 2 members of C12 are membrane proteins. Highest number and most variable motifs are evident in C1 and C2 family members, while the rest of CP families shared distinct set of few motifs. Gene expression analysis of selected C1 members including OsCP2 (LOC_Os01g67980), OsCP3 (LOC_Os05g01810), and OsCP5 (LOC_Os02g27030) showed that both OsCP2 and OsCP3 are tissue-specific, while OsCP5 is constitutively expressed in all tissues. Transcripts of all three genes were highly induced by Xanthomonas oryzae pv. oryzae (Xoo) race K3a, 100 μM salicylic acid (SA), and 100 μM methyl jasmonate (MeJA) at 12 hours post-inoculation. Moreover, mRNA of OsCP2 and OsCP3 were activated 6 to 12 hours after imposing salinity stress, while OsCP5 was up-regulated by both heat and salt at 6 hours after treatment. In Chapter 2, three selected papain-like cysteine protease members were cloned for functional analysis in rice. Evolutionary divergence analysis revealed that OsCP2 (LOC_01g73980.1) and OsCP3 (LOC_Os05g01810) are related (0.229) and are both associated (0.401 and 0.400) to XCP2 (At1g20850), a papain-type cysteine endopeptidase also known as xylem cysteine peptidase 2 in Arabidopsis, while OsCP5 (LOC_Os02g27030) is related (0.404) to RD19B (At2g21430). Biological investigation of cysteine protease was carried out using overexpression and RNAi transgenic lines. The total number of overexpression transgenic rice generated was six in OsCP2ox, nine in OsCP3ox, and nine in OsCP5ox. Moreover, five OsCP3RNAi transgenic rice plants were also developed. Stable inheritance of each transgene to T1 generation was verified by resistance to hygromycin for overexpression transgenic lines and phosphinothricin for RNAi lines with segregation that conformed (p<0.05) to 3:1 Mendelian ratio. Disease screening with Xoo race K3a resulted in significantly (p<0.05) shorter lesion length (OsCP2ox, 6.82 – 9.13 cm; OsCP3ox, 5.55 – 7.49 cm; and OsCP5ox, 5.40 – 5.68 cm) than that in Dongjin (16.07cm), while OsCP3RNAi lines exhibited significantly longer lesions (17.1 – 18.3 cm) than overexpression lines. Bacterial growth analysis taken at 0, 7, and 14 days post-inoculation (dpi) strongly corroborated with the phenotype data. This indicates that OsCP genes confered resistance to Xoo. Although all transgenic plants were highly sensitive to drought stress, OsCP3ox showed improved tolerance (5.0 – 5.3 score; rating scale from 1, highly tolerant to 9, highly sensitive) to salinity stress. Measurements of agronomic traits of the overexpression lines showed altered phenotype especially in plant height wherein OsCP2ox (123.8 – 132.7 cm) and OsCP5ox (117.9 – 119.6 cm) transgenic lines were significantly taller than the wild type Dongjin (109.8 cm), whereas OsCP3ox lines were significantly shorter (95.9 – 102.8 cm). In chapter 3, sufficient transcript data were generated by employing de novo transcriptome profiling to investigate changes in gene expression during early response to X. oryzae pv. oryzae infection. Early interaction with the pathogen was inferred from the cDNA library of OsCP3ox-3 overexpression transgenic line infected with Xoo race K3a for 30 min representing incompatible interaction and from the cDNA library of infected OsCP3RNAi-56 transgenic line and Dongjin which represent compatible interaction. The total number of genes identified from the clean reads matching to the reference genome is 35,666. By implementing the log2FC≥1 and p<0.05 statistical thresholds, a total of 1,597 combined differentially expressed genes (DEGs) were identified in three libraries, 1,147 of which are exclusively regulated only in OsCP3ox-3, 111 in Dongjin, and 122 in OsCP3RNAi-56 sample. In all library samples, the frequency of activated genes is higher (925 in OsCP3ox-3, 194 in Dongjin, and 191 in OsCP3RNAi-56) than suppressed ones (511, 61, and 31, respectively). The 148 common genes between three samples were found to enrich (FDR<0.05) 27 biological process; among them high number of genes was assigned to metabolic process, primary metabolic process, response to stimulus, and response to stress. Enrichment analysis of unique set of DEGs in each library revealed more over-represented biological processes that are crucial in resistance response in OsCP3ox-3 library (n=50) over Dongjin (n=12) and OsCP3RNAi-56 (n=13) samples. Interestingly, defense response, response to stress, response to osmotic stress, response to hormone, ROS metabolic process, and signal transduction are exclusively identified only in OsCP3ox-3. A total of 548 OsCP3ox-3-specific genes are assigned into 35 Kyoto encyclopedia of genes and genomes (KEGG) pathways, 8 Dongjin-specific genes into 2 pathways, and 32 OsCP3RNAi-56-specific genes into 6 pathways. Mapman visualization of core biotic stress responsive genes in OsCP3ox-3 sample highlights signaling by receptor-like kinases (RLKs), calcium signals, G-proteins, and hormones, as well as transcription activity by members of ERF, bZIP, MYB and DOF as drastic early response upon infection which orchestrate downstream responses including activation of 13 putative pathogenesis-related (PR) proteins and 37 putative secondary metabolites-related genes. Moreover, high H2O2 production and elevated accumulation of free SA are integral part of defense mechanism exhibited by OsCP3ox lines. Protein-protein interaction network analysis further depicted a more significant biological connection among proteins in OCP3ox-3 line with 11,696 (p<1.0e-16) predicted interactions over 132 (p=0.0152) and 167 (p=0.00213) interactions predicted in Dongjin and OsCP3RNAi-56, respectively. In chapter 4, comparative transcriptional profile was analyzed in response to Xoo race K2 and K3a response in rice. The K2-DEG gene set was derived from the cDNA oligo microarray of RNA collected from 48-hour infected Jinbaek (representing intermediate to late incompatible interaction; R-K2) while the K3a-DEG gene set was generated using the RNA-sequencing of the 30 min post-inoculated RNA of OsCP3ox-3 overexpression transgenic line (representing early incompatible interaction, R-K3a). A huge gap in the magnitude of DEGs was found, wherein K3a, being the most recent race and more virulent induced more (n=1,355) DEGs than K2 (n=789). In both libraries, activated genes are more abundant which indicate extensive regulation of larger gene network that led to resistance. A total of 127 overlapping genes was identified, 43 of which enriched peroxidase activity (p=0.041), defense response (p=0.025), transcription factor activity (p=0.006), cell redox homeostasis (p=0.048), metal-binding (p=0.000), and secondary metabolites biosynthesis (p=0.033). Mapman provides an overview on extensive activation of signaling and transcription factor activity as conserved cellular response to both Xoo races. The number of activated genes was 45 in R-K2 and 37 in R-K3a for receptor kinase-signaling, 6 in R-K2 and 12 in R-K3a for calcium signaling, 3 in R-K2 and 3 in R-K3a for G-protein signaling, and 11 in R-K2 and 25 in R-K3a for hormone signaling. Activation of downstream mechanism in response to both races commonly rely on WRKY, however K3a infection also requires substantial activation by ERF, MYB, and DOF, whereas K2-induced response also depends on MAPK signal transduction. It also appears that activation of multiple pathogenesis-related proteins were conserved cellular and physiological responses to K2 (n=11) and K3a (n=13) infection. Interestingly, response to two races differs in terms of cell wall-related functions and lignin biosynthesis with K3a infection inducing 14 isoprenoids, 7 phenylpropanoids, 6 lignin, 1 wax, 8 flavonoids, and 2 alkaloid-like, while response to K2 only involves up-regulation of 6 terpenoids, 2 phenylpropanoids, and 2 flavonoids. In summary, the analyses presented in this dissertation provide a detailed annotation of cysteine protease genes in rice. Using gain-of-function and RNAi-mediated knockdown of PLCP, I was able to demonstrate the functional aspect of this gene particularly against bacterial blight infection in rice. The analyses presented by RNA-sequencing, which is the first transcriptional investigation ever done on PLCPs in response to pathogen infection in rice, provide a global view of the transcriptome modulation response to Xoo mediated by cysteine protease. Substantial findings revealed that overexpression of cysteine protease allowed rice to circumvent Xoo infection through extensive activation of transduction signal and transcription that orchestrate downstream responses including up-regulation of multiple pathogenesis-related proteins and biosynthesis of secondary metabolites. Thus, rice PLCPs are valuable gene resource that can be employed in rice breeding programs for biotic stress.

Reflexivization strategies in Georgian

Amiridze, Nino LOT(Landelijke Onderzoekschool Taalwetenschap) 2006 국내박사

Production of xylose-based C4 and C5 platform chemicals by engineering the Dahms pathway in Escherichia coli

Kris Nino G. Valdehuesa 명지대학교 대학원 2015 국내박사

Characterization of two-phase flow in microchannels

Nino, Victor German University of Illinois at Urbana-Champaign 2002 해외박사(DDOD)

Aluminum multi-port microchannel tubes are currently utilized in automotive air conditioners for refrigerant condensation. Recent research activities are directed toward developing other air conditioning and refrigeration systems with microchannel condensers and evaporators. Three parameters are necessary to analyze a heat exchanger performance: heat transfer, pressure drop, and void fraction. The purpose of this investigation is the experimental investigation of void fraction and frictional pressure drop in microchannels. A flow visualization analysis is another important goal for two-phase flow behavior understanding and experimental analysis. Experiments were performed with a 6-port and a 14-port microchannel with hydraulic diameters of 1.54 mm and 1.02 mm, respectively. Mass fluxes from 50 to 300 kg/s.m<super>2</super> (range of most typical automotive applications) are operated, with quality ranging from 0% to 100% for two-phase flow experiments. R410A, R134a, and air-water mixtures are used as primary fluids. The results from the flow visualization studies indicate that several flow configurations may exist in multi-port microchannel tubes at the same time while constant mass flux and quality flow conditions are maintained. Flow mapping of the fluid regimes is accomplished by developing functions that describe the fraction of time or the probability that the fluid exists in an observed flow configuration. Experimental analysis and flow observations suggest that pressure drop and void fraction in microchannel is dependent on the most probable flow regime at which the two-phase mixture is flowing. In general, correlations for void fraction and pressure drop predictions are based in a separated flow model and do not predict the experimental results in the range of conditions investigated. A flow regime based model is developed for pressure drop and void fraction predictions in microchannels.

Context and Behavioral Analysis for Pedestrians in the Domain of Self-Driving

Nino, Jose Antonio Cornell University ProQuest Dissertations & Theses 2023 해외박사(DDOD)

Autonomous Ground Vehicles (AGVs) have made their way into various industries, including transportation, delivery services, healthcare, and logistics handling. In order to thrive in these sectors, AGVs must possess the ability to accurately detect, track, anticipate, and navigate around pedestrians in their surroundings. Over time, a multitude of new tracking and forecasting algorithms have been developed to enhance the effectiveness and safety of AGVs. This progress has been largely facilitated by the availability of public datasets and challenges centered around self-driving technologies.However, it is important to note that most of these datasets and approaches primarily focus on cars, often neglecting the evaluation of pedestrian performance. This is primarily due to the limited number of pedestrian annotations compared to vehicle annotations within these datasets.In this dissertation, I present a series of studies aimed at enhancing the performance of pedestrian tracking, forecasting, and anomaly detection. To begin, I introduce a novel self-driving dataset designed to achieve a more balanced representation of pedestrians. The dataset captures data along a 15 km route, encompassing diverse scenes such as urban, highway, rural, and campus environments. It also contains various weather conditions such as snow, rain, and sun and incorporates different time periods, including day and night. Furthermore, the dataset covers a wide range of traffic conditions and compositions, including pedestrians, cyclists, and cars. To facilitate the training of machine learning models, the dataset includes road and object annotations utilizing amodal masks to capture partial occlusions and 3D bounding boxes effectively.Secondly, I delve into my research on priority tracking of pedestrians in self-driving scenarios. This work capitalizes on the concept of reachability to determine the priority of pedestrians based on safety considerations. This framework ensures efficient resource allocation and optimized tracking performance by employing computationally intensive tracking algorithms on agents that pose potential safety risks and utilizing computationally lightweight tracking approaches for pedestrians who do not present such concerns.Next, I introduce a novel prediction framework that capitalizes on pedestrian-focused contextual cues. Our approach involves an encoder-decoder Long-short-term memory (LSTM) network, which effectively encodes past behaviors, sequential appearance, pose features, and map context. By leveraging these elements, we can accurately forecast the future trajectory of a target pedestrian.Finally, I present my research on anomaly detection of pedestrians in the context of self-driving cars. We propose a framework for generating weak labels using raw data and repeated traversals, thereby alleviating the need for laborious and costly manual annotation of pedestrian data. This approach has the potential to enhance the training of algorithms specifically tailored to pedestrian-related tasks. We then introduce a probabilistic framework and train it to learn the typical behavior patterns of pedestrians utilizing weak labels. Lastly, we demonstrate the framework's qualitative ability to identify anomalies within a given scene.

Written in Blood: AIDS and the Politics of Genre

Testa, Nino Tufts University 2013 해외박사(DDOD)

This dissertation will argue that the AIDS text's tendency to explicitly place itself in specific generic histories and traditions is an effort to challenge or access the cultural fantasies associated with those traditions. Works produced in response to the AIDS epidemic are often explicitly marked as belonging or not belonging, challenging or embracing particular generic conventions for political aims in relation to the perceived needs of the specific reading publics to which they are addressed. It is not my aim to argue for or against the validity of these generic fantasies, but to demonstrate the ways in which they are an integral organizing principle of so many representations of AIDS in American cultural life. Each chapter will explore how AIDS was accommodated as a subject by a variety of generic traditions, and will follow a somewhat chronological structure. I begin with "ground zero" for AIDS writers grappling with genre in the early years of the epidemic: historically consolatory writing in honor of the dead in the form of obituaries and elegies. Secondly, I explore the uses of sentimentality and American quilting histories in the development of the NAMES Project AIDS Memorial Quilt. Next, I trace a developing tradition of AIDS novels as they respond to shifting historical and political realities and challenge the stability of a coherent narrative of the AIDS epidemic. Finally, a coda examines a spate of documentaries that were released around the 30<super>th</super> anniversary of what were thought to be the first reported cases of HIV infection. My focus on texts by mostly gay men is an attempt to trace the development of AIDS writing proper to queer reading publics and is not meant to erase the impact of the epidemic on other disenfranchised communities in its early years; people of color, women, IV drug users, the homeless, sex workers—many of whom also identified as gay—all have unique relationships to these genres. Likewise, the absence of such a relationship (for example, the lack of obituaries for the homeless) is worthy of its own study. An exploration of the generic traditions of AIDS texts is especially appropriate not just because, as I argue, the texts often beg for attention to their generic dimensions, but also because as a body of work itself, AIDS writing is obviously quite new and the conventions, fantasies and traditions which comprise it are relatively underexplored.

A Shrimp Among the Whales : South Korea's Domestic Interests Shadowed By International Politics

Lortkipanidze Nino 고려대학교 국제대학원 2023 국내석사

On December 28, 2015, South Korean and Japanese Foreign Ministers announced that governments have reached the Japan–South Korea Comfort Women Agreement. The agreement that intended to solve the highly sensitive historical issues “finally and irreversibly”, eventually lead to the worst relations since 1965. This study analyzes various international factors, including North Korea's Nuclear Program, China-US Rivalry, and their impact on President Park and President Moon's Approaches to the comfort women issue and the Japan-South Korea Comfort Women Agreement. The paper first delves into the negotiation process of the 2015 Agreement and identifies its major flaws. Second, it examines President Park's initial approach to the Comfort Women issue and identifies the international factors that influenced her policy. Third, the paper analyzes President Moon’s policy on this historical issue and how international factors impacted it. The findings of his qualitative research suggest that international factors greatly influence South Korean leaders' approaches to historical issues with Japan. Regardless of their political ideologies, South Korean leaders are constrained by external factors to introduce stable policies on historical issues, that can satisfy domestic pressure. And this eventually hinders the reconciliation process between Japan and South Korea.

VOLATILITY AND PERFORMANCE ANALYSIS OF TWO PAST REAL ESTATE MARKETS: MORTGAGE BONDS OF THE 1920'S AND LAND WARRANTS OF THE 1850'S (NINETEEN TWENTIES, EIGHTEEN FIFTIES, SECURITIZATION, PRICING)

PEDRELLI, NINO DANTE THE UNIVERSITY OF WISCONSIN - MADISON 1999 해외박사(DDOD)

Mortgage bonds of the 1920's represent the first generation of securitized commercial and residential urban real estate in the U.S. At their peak, mortgage bond issues made up 20% of the total long term corporate debt market. Therefore, on a relative basis, this market was larger than the CUBS market of the 1990's. During the early 1850's the U.S. Government issued assignable land warrants to military veterans and their heirs. These warrants entitled holders to take possession of tracts of public domain land, at that time the area primarily between Wisconsin and Texas. An active secondary market in the trading of these warrants which existed between 1848 and 1861. Return volatility and mean reversion of both markets are examined utilizing the present value model for time varying returns of Campbell (1991); the variance decomposition methodology of Campbell and Ammer (1993); and the variance ratio of Lo and MacKinlay (1988). Mortgage bond volatility is found to be primarily driven by investors' revisions in expectations of the future real interest rate. The dominance of capital market factors provides a benchmark to understand the behavior of the CUBS market in 1998 which demonstrated similar characteristics. In a historical context the importance of the real interest rate contributes to the 'monetary hypothesis' theory of the Great Depression. Variance ratio results indicate that over longer holding periods, the return generating process is a sum of a random walk and a stationary mean reverting process. Land warrant volatility is found to have been driven primarily by investors' revisions in expectation of future returns. This dominance of expected future returns over 'fundamentals' is indicative of speculative bubbles. The return process can also be viewed in a price discovery model in which warrant pricing reflected the constant updating of information regarding the productivity of the land. In this context, the results am directly applicable to understanding land auctions in emerging market economies.

A Study of Otar Taktakishvili's Piano Suite: The Influence of the Georgian National Instruments Salamuri, Chonguri, Panduri, Duduki, and Doli

Bakradze, Nino ProQuest Dissertations & Theses The University of 2018 해외박사(DDOD)

Georgian composer, teacher, conductor, and musicologist Otar Taktakishvili (1924--1989) played a leading role in the revival of Georgian art music in the second half of the 20th century. Despite his multiple duties and close relationship with the USSR regime, Taktakishvili consistently wrote music based on Georgian traditional folk music, hence imprinting and preserving the national Georgian identity through his compositions. These nationalistic influences appear prominently in several of his Piano Suites and are ubiquitous in the Piano Suite written in 1973. In the Piano Suite (1973), Taktakishvili adapts and recreates the sonorities, registers, coloristic effects through textural layering and articulations, rhythmic patterns and performance practices of selected Georgian folk instruments at the piano. He creates a unified suite by evoking the sound characteristics of his national instruments. The Piano Suite is unique and likely the only suite in the piano literature based on the imitation of a group of folk instruments, and as such deserves a place in the scholarly literature on world piano music. An analysis of the pianistic resources used by Taktakishvili to imitate the unique musical qualities and performance practices of five popular Georgian folk instruments reveals a reliance on repetitive rhythmic figures, textural layering, imaginative articulation, and deft use of the registers of the piano. The composer also distinctively implements characteristic modes and harmonic language to evoke the flavor of Georgian folk music.