Apoplast proteome reveals that extracellular matrix contributes to multistress response in poplar

<p>Abstract</p> <p>Background</p> <p>Riverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological components. We have little understanding of mechanisms by which riverine plant species have developed adaptive strategies to cope with stress in dynamic environments while maintaining growth and development.</p> <p>Results</p> <p>We report that poplar (<it>Populus </it>spp.) has evolved a systems level "stress proteome" in the leaf-stem-root apoplast continuum to counter biotic and abiotic factors. To obtain apoplast proteins from <it>P. deltoides</it>, we developed pressure-chamber and water-displacement methods for leaves and stems, respectively. Analyses of 303 proteins and corresponding transcripts coupled with controlled experiments and bioinformatics demonstrate that poplar depends on constitutive and inducible factors to deal with water, pathogen, and oxidative stress. However, each apoplast possessed a unique set of proteins, indicating that response to stress is partly compartmentalized. Apoplast proteins that are involved in glycolysis, fermentation, and catabolism of sucrose and starch appear to enable poplar to grow normally under water stress. Pathogenesis-related proteins mediating water and pathogen stress in apoplast were particularly abundant and effective in suppressing growth of the most prevalent poplar pathogen <it>Melampsora</it>. Unexpectedly, we found diverse peroxidases that appear to be involved in stress-induced cell wall modification in apoplast, particularly during the growing season. Poplar developed a robust antioxidative system to buffer oxidation in stem apoplast.</p> <p>Conclusion</p> <p>These findings suggest that multistress response in the apoplast constitutes an important adaptive trait for poplar to inhabit dynamic environments and is also a potential mechanism in other riverine plant species.</p

Expression of TLP-3 gene without signal peptide in tobacco plants using Agrobacterium mediated transformation

Plants are exploited as a source of food by a wide range of parasites, including viruses, bacteria, fungi, nematodes, insects and even other plants. So paying attention to their protection is very important. One of the most important groups of defensive gene is pathogenesis-related (PR) proteins. PR proteins are a group of plant proteins which accumulate as a result of different types of pathogens attack. Thaumatinlike proteins (TLPs) belonging to the PR proteins, plays an important role in plant defense against pathogen invasions. Agrobacterium-mediated transformation is routinely used for the transformation of many plants. In the present study, thaumatin-like TLP-3 gene without signal peptide was transferred into tobacco plants through Agrobacterium-mediated technology. The PCR and RT-PCR assays confirmed the presence of TLP-3 gene and TLP-3 mRNA in transgenic tobacco plants, respectively. The bioassay results showed the activity of TLP-3 against Alternaria alternata in microscopic experiment. This is the first report of the expression of TLP-3 gene without signal peptide in tobacco plants using Agrobacterium mediated transformation and it confirmed the ability of the gene action in another plant.Key words: Thaumatin like protein, Agrobacterium, signal peptide, Alternaria alternate

Sequence queries on temporal graphs

Graphs that evolve over time are called temporal graphs. They can be used to describe and represent real-world networks, including transportation networks, social networks, and communication networks, with higher fidelity and accuracy. However, research is still limited on how to manage large scale temporal graphs and execute queries over these graphs efficiently and effectively. This thesis investigates the problems of temporal graph data management related to node and edge sequence queries. In temporal graphs, nodes and edges can evolve over time. Therefore, sequence queries on nodes and edges can be key components in managing temporal graphs. In this thesis, the node sequence query decomposes into two parts: graph node similarity and subsequence matching. For node similarity, this thesis proposes a modified tree edit distance that is metric and polynomially computable and has a natural, intuitive interpretation. Note that the proposed node similarity works even for inter-graph nodes and therefore can be used for graph de-anonymization, network transfer learning, and cross-network mining, among other tasks. The subsequence matching query proposed in this thesis is a framework that can be adopted to index generic sequence and time-series data, including trajectory data and even DNA sequences for subsequence retrieval. For edge sequence queries, this thesis proposes an efficient storage and optimized indexing technique that allows for efficient retrieval of temporal subgraphs that satisfy certain temporal predicates. For this problem, this thesis develops a lightweight data management engine prototype that can support time-sensitive temporal graph analytics efficiently even on a single PC

The Watershed Transformation Applied to Image Segmentation

Image segmentation by mathematical morphology is a methodology based upon the notions of watershed and homotopy modification.This paper aims at introducing this methodology through various examples of segmentation in materials sciences, electron microscopy and scene analysis. First, we defined our basic tool, the watershed transform. We showed that this transformation can be built by implementing a flooding process on a greytone image. This flooding process can be performed by using elementary morphological operations such as geodesic skeleton and reconstruction. Other algorithms are also briefly presented (arrows representation). Then, the use of this transformation for image segmentation purposes is discussed. The application of the watershed transform to gradient images and the problems raised by over-segmentation are emphasized. This leads, into the third part, to the introduction of a general methodology for segmentation, based on the definition of markers and on a transformation called homotopy modification. This complex tool is defined in detail and various types of implementations are given. Many examples of segmentation are presented. These examples are taken from various fields: transmission electron microscopy, scanning electron microscopy (SEM), 3D holographic pictures, radiography, non destructive control and so on. The final part of this paper is devoted to the use of the watershed transformation for hierarchical segmentation. This tool is particularly efficient for defining different levels of segmentation starting from a graph representation of the images based on the mosaic image transform. This approach will be explained by means of examples in industrial vision and scene analysis

Simulation-Based Graph Similarity

We present symmetric and asymmetric similarity measures for labeled directed rooted graphs that are inspired by the simulation and bisimulation relations on labeled transition systems. Computation of the similarity measures has close connections to discounted Markov decision processes in the asymmetric case and to perfect-information stochastic games in the symmetric case. For the symmetric case, we also give a polynomial-time algorithm that approximates the similarity to any desired precision

Automatic gridding of DNA microarray images.

Microarray (DNA chip) technology is having a significant impact on genomic studies. Many fields, including drug discovery and toxicological research, will certainly benefit from the use of DNA microarray technology. Microarray analysis is replacing traditional biological assays based on gels, filters and purification columns with small glass chips containing tens of thousands of DNA and protein sequences in agricultural and medical sciences. Microarray functions like biological microprocessors, enabling the rapid and quantitative analysis of gene expression patterns, patient genotypes, drug mechanisms and disease onset and progression on a genomic scale. Image analysis and statistical analysis are two important aspects of microarray technology. Gridding is necessary to accurately identify the location of each of the spots while extracting spot intensities from the microarray images and automating this procedure permits high-throughput analysis. Due to the deficiencies of the equipment that is used to print the arrays, rotations, misalignments, high contaminations with noise and artifacts, solving the grid segmentation problem in an automatic system is not trivial. The existing techniques to solve the automatic grid segmentation problem cover only limited aspect of this challenging problem and requires the user to specify or make assumptions about the spotsize, rows and columns in the grid and boundary conditions. An automatic gridding and spot quantification technique is proposed, which takes a matrix of pixels or a microarray image as input and makes no assumptions about the spotsize, rows and columns in the grid and is found to effective on datasets from GEO, Stanford genomic laboratories and on images obtained from private repositories. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2004 .V53. Source: Masters Abstracts International, Volume: 43-03, page: 0891. Adviser: Luis Rueda. Thesis (M.Sc.)--University of Windsor (Canada), 2004

Clostridium chauvoei, an evolutionary dead-end pathogen

Full genome sequences of 20 strains of Clostridium chauvoei, the etiological agent of blackleg of cattle and sheep, isolated from four different continents over a period of 64 years (1951–2015) were determined and analyzed. The study reveals that the genome of the species C. chauvoei is highly homogeneous compared to the closely related species C. perfringens, a widespread pathogen that affects human and many animal species. Analysis of the CRISPR locus is sufficient to differentiate most C. chauvoei strains and is the most heterogenous region in the genome, containing in total 187 different spacer elements that are distributed as 30 – 77 copies in the various strains. Some genetic differences are found in the 3 allelic variants of fliC1, fliC2 and fliC3 genes that encode structural flagellin proteins, and certain strains do only contain one or two alleles. However, the major virulence genes including the highly toxic C. chauvoei toxin A, the sialidase and the two hyaluronidases are fully conserved as are the metabolic and structural genes of C. chauvoei. These data indicate that C. chauvoei is a strict ruminant-associated pathogen that has reached a dead end in its evolution

애기장대 생체시계 고온 안정성과 환경 변화에 대한 숲개밀의 접촉형태형성 반응 기작 연구

학위논문(박사)--서울대학교 대학원 :자연과학대학 화학과,2019. 8. 박충모.식물은 주변 환경의 영향을 받는다는 것이 잘 알려져 있다. 대표적인 환경적 자극 요인으로는 빛과 온도의 변동, 바람이나 홍수, 동물의 움직임에 의한 물리적인 자극 등이 있다. 식물은 환경적 자극에 대응하여 다양한 적응 전략을 발달시켜왔다. 예를 들어, 생체시계는 외부의 환경 변화를 예측하고 인지함으로써 식물 내의 다양한 생리 발달 과정을 조절하고 식물의 생장을 최적화한다. 본 연구에서는 이러한 생체시계의 열 안정성과 관련된 분자 기작에 대해서 알아보았다. 한편, 접촉이나 바람과 같은 환경적 자극은 생체 시계뿐만 아니라 외형의 변화를 유도하기도 한다. 이러한 물리적 자극에 의한 외형적 변화를 접촉형태형성(thigmomorphogenesis)이라고 한다. 본 연구에서는 바람에 의한 숲개밀의 뿌리 형성에 대한 표현형을 분석하고, 외떡잎식물의 뿌리 발달 기작을 기반으로 호르몬의 조절 방법에 대해서 논의하였다. 제1 장에서는 열 스트레스 하에서 ZEITLUPE (ZTL)의 protein quality control 기능에 대해 다루었다. 세포 단백질은 고온 스트레스 하에서 변성 및 산화에 의한 손상을 받아 세포 내에 독성을 가지는 불용성 응집체를 형성한다. 변성된 단백질은 원래의 형태로 재생되거나 세포질 구획에서 제거된다. 이 과정을 protein quality control이라고 하며, heat shock protein (HSP)은 변성된 단백질 재생 과정을 돕는 분자 샤페론 역할을 한다. 본 연구에서는 고온에 의해 변성된 단백질 응집체가 애기장대의 생체시계 조절 인자인 ZTL에 의한 protein quality control 기작에 의해 제거됨을 증명하였다. ZTL은 변성된 단백질을 polyubiquitination 시킴으로써 proteasomal degradation 과정으로 유도한다. ZTL이 없는 돌연변이체(ztl)에서는 고온에 의해 유도되는 polyubiquitination이 충분히 일어나지 못하므로 insoluble한 단백질 응집체가 더욱 많이 쌓이게 되며, 고온에 취약한 표현형을 보인다. 또한, ztl 돌연변이체가 고온에서 생체시계 리듬이 깨지는 현상을 관찰한 바, ZTL을 통한 protein quality control이 식물 생체시계의 고온 안정성에 기여한다고 제안하였다. 나아가 샤페론인 HSP90과 ZTL단백질의 interaction이 고온에서도 유지되며, HSP90의 발현이 낮은 식물체의 polyubiquitination 정도와 생체시계 리듬의 고온 반응성이 ztl 돌연변이체와 유사한 양상을 보인다는 것을 통해 HSP90과 ZTL이 기능적인 측면에서 관련되어 있다는 것을 알 수 있었다. 제2 장에서는 부정근 형성에 대한 바람의 영향에 대해서 논의하였다. 바람에 의한 물리적 자극은 식물의 키를 작게 하고 방사형으로 넓고 튼튼하게 자라도록 한다. 또한 뿌리의 발달에서도 다양한 효과를 일으킨다고 알려져 있다. 그러나 식물이 어떤 기작으로 바람을 인지하고 적응 발달을 일으키는지는 알려지지 않았다. 본 연구에서는 외떡잎식물 종의 모델 식물인 숲개밀이 바람에 의한 자극에 적응하기 위해서 부정근을 형성한다는 것을 발견하였다. 부정근은 바람에 의한 식물체의 흔들림을 막고, 지면과 식물의 고착면을 넓힘으로써 뿌리가 안정적으로 식물을 지탱하도록 한다. 복합적인 환경적 자극인 바람을 물리적인 접촉 자극, 공기 압력 자극, 중력 자극 등으로 나누어 분석한 결과, 중경(mesocotyl)의 접힘 현상보다는 leaf node와 흙의 물리적 접촉이 부정근 형성을 유도한다는 것을 밝혔다. 또한, 오옥신과 에틸렌 신호 억제제를 처리한 후 식물의 부정근 형성 양상을 관찰함으로써, 에틸렌보다는 오옥신이 부정근의 접촉형태형성에 깊게 관여되어 있음을 알 수 있었다. 오옥신은 관련 유전자인 WUSCHEL RELATED HOMEOBOX와 LATERAL ORGAN BOUNDARIES DOMAIN 전사 인자들의 발현을 유도함으로써 바람에 의한 부정근 형성에 참여한다는 것을 밝혔다.It is widely perceived that plants are influenced by surrounding environment. The representative environmental stimuli are light, temperature fluctuation, and mechanical touch, such as rubbing and bending by passing animals, wind, and flooding. Plants have developed various adaptation strategies to cope with the environmental changes. For example, the circadian clock predicts the environmental changes and generates diurnal rhythms of numerous physiological and developmental processes in most living organisms to synchronize with surrounding conditions. In this study, I investigated the molecular mechanisms that contribute to thermostability of circadian clock in Arabidopsis. Otherwise, some environmental stimuli, such as touch or wind, induce the morphological changes as well as clock rhythm of plants. The adaptive growth which accompanies with morphological changes is termed thigmomorphogenesis. Thigmomorphogenesis has been reported in the early stage of plant research, but the noticeable studies are not shown recently. Here, I described the phenotypic analysis of Brachypodium root formation under windy conditions. And hormonal regulation underlying the root development mechanisms in monocotyledon plants was also proposed. In chapter 1, a role of ZEITLUPE (ZTL) in protein quality control under heat stress is described. Cellular proteins undergo denaturation and oxidative damages under heat stress, forming insoluble aggregates that are toxic to cells. Denatured proteins are either renatured to their native conformations or removed from cellular compartments, which are processes often termed as protein quality control. Heat shock proteins (HSPs) act as molecular chaperones that assist the renaturation-degradation process. Here, I demonstrated that heat-induced protein aggregates are removed by a protein quality control system that includes the ZTL, a central clock component in Arabidopsis. ZTL mediates the polyubiquitination of aggregated proteins, which leads to proteasomal degradation, and enhances the thermotolerance of plants growing at high temperatures. Insufficient heat-induced polyubiquitination in ztl-105 results in increased protein aggregates thus, thermosensitive phenotype. Notably, the circadian clock was hypersensitive to heat in the ztl-105 mutant. I propose that ZTL-mediated protein quality control contributes to thermal stability of the clock. Moreover, the reduced levels of polyubiquitination and thermosensitive circadian clock in HSP90 RNAi plants indicate that HSP90 and ZTL are functionally related at high temperatures. In chapter 2, influence of wind stimulation and adventitious root formation are discussed. Wind-driven mechanical stimulation is known to induce the incidence of radial expansion and shorter and stockier statue. Wind stimulation also affects the adaptive propagation of the root system in various plant species. However, it is unknown how plants sense and transmit the wind-derived mechanical signals to launch appropriate responses, leading to the wind-adaptive root growth. Here, I found that Brachypodium distachyon, a model grass widely used for studies on bioenergy crops and cereals, efficiently adapts to wind-driven mechanical stress by forming adventitious roots (ARs), which are formed from nonroot tissues. The ARs prevent the leaf flipping of the plants by anchoring in soil. Experimental dissection of wind stimuli revealed that not the bending of the mesocotyls but physical contact of leaf nodes with soil triggers AR formation. Moreover, it was observed that inhibition of auxin transport is critical for AR emergence and/or elongation. Wind stimulation triggers the transcriptional induction of a group of auxin-responsive genes encoding WUSCHEL RELATED HOMEOBOX and LATERAL ORGAN BOUNDARIES DOMAIN transcription factors, which are intimately associated with the induction of AR formation. My findings would contribute to further understanding molecular mechanisms governing the initiation and development of ARs, which will be applicable to crop agriculture in extreme wind climates.CONTENTS ABSTRACT i CONTENTS iv LIST OF FIGURES vii LIST OF TABLES x ABBREVIATIONS xi CHAPTER 1: ZEITLUPE contributes to a thermoresponsive protein quality control system in Arabidopsis INTRODUCTION 2 MATERIALS AND METHODS 6 Plant materials and growth conditions 6 Transcript abundance measurement 7 Thermotolerance assay 8 Measurement of chlorophyll contents 8 Detection of polyubiquitinated proteins 9 Fractionation of soluble and insoluble proteins 9 Protein stability assay 11 Bimolecular fluorescence complementation (BiFC) assay 11 Coimmunoprecipitation assay 12 Circadian rhythm measurement 13 RESULTS 15 The ztl-105 mutant exhibits reduced thermotolerance 15 Polyubiquitination is suppressed in the ztl-105 mutant under heat stress 24 Accumulation of protein aggregates is elevated in the ztl-105 mutant under heat stress 29 The clock function is hypersensitive to high temperatures in the ztl-105 mutant 38 DISCUSSION 45 ZTL and HSP90 mediate a thermoresponsive protein quality control mechanism 45 ZTL sustains the thermostability of the circadian clock 48 ACKNOWLEDGMENTS 50 CHAPTER 2: Auxin mediates the wind-induced development of adventitious roots in Brachypodium distachyon. INTRODUCTION 52 MATERIALS AND METHODS 56 Plant materials and growth conditions 56 Phenotypic analysis 56 Chemical treatments 57 Phylogenetic analysis 58 Gene transcript analysis 58 Statistical analysis 59 RESULTS 61 Brachypodium adapts to wind-induced mechanical stress by forming ARs 61 Wind-driven falling down of the shoots triggers AR formation 66 Direct contact of the fallen leaf nodes with soil particles triggers the induction of AR emergence 71 Auxin mediates the wind-mediated mechano-stimulation of AR emergence 75 WOX and LBD genes are auxin-responsive in artificially fallen plants 78 WOX and LBD genes are induced by the wind-mediated mechano-stimulation 82 DISCUSSION 87 AR as an adaptive developmental device in response to environmental fluctuations 87 Hormonal regulation of post-embryonic root formation 88 Induction of AR development by mechanical stimuli 92 ACKNOWLEDGMENTS 94 PUBLICATION LIST 111 ABSTRACT IN KOREAN 113 LIST OF FIGURES Figure 1. Molecular validation of ZTL-overexpressing plants. 17 Figure 2. Reduced basal thermotolerance in ztl-105 mutant. 18 Figure 3. Thermal responses depend on diurnal cycles. 19 Figure 4. Complementation of ztl-105 mutant. 20 Figure 5. Thermal responses are independent of long periodicity. 21 Figure 6. Reduced acquired thermotolerance in ztl-105 mutant. 22 Figure 7. Enhanced acquired thermotolerance in ZTL-overexpressing plants. 23 Figure 8. Quantification of the transcript levels of heat stress genes in ztl-105 mutant. 26 Figure 9. Heat-induced polyubiquitination is reduced in ztl-105 mutant. 27 Figure 10. Levels of polyubiquitinated proteins in ztl-105 complemented lines. 28 Figure 11. Levels of protein aggregates in ztl-105 mutant. 31 Figure 12. Levels of protein aggregates in ZTL-overexpressing OX-2 plants 32 Figure 13. Effects of high temperatures on ZTL transcript abundance and its protein stability. 33 Figure 14. Nano high resolution LC-MS/MS spectrometer analysis of protein aggregates at high temperatures. 36 Figure 15. HSP90 is associated with heat-induced polyubiquitination by interacting with ZTL. 37 Figure 16. Disruption of circadian rhythms in ztl-105 mutant at high temperatures. 41 Figure 17. Disruption of circadian rhythms in HSP90 RNAi plants. 42 Figure 18. Effects of MG132 on circadian rhythms. 43 Figure 19. Diurnal rhythmic accumulation of PRR5 and TOC1 is disrupted at high temperatures. 44 Figure 20. Adaptation of Brachypodium plants to wind-induced mechanical stimulation. 63 Figure 21. Induction of AR formation by wind stimulation. 64 Figure 22. Experimental set-up for phenotypic analysis of plants against mechanical and gravity stimuli. 68 Figure 23. Effects of wind-driven falling down on AR formation. 69 Figure 24 Effects of mechanical and gravity stimuli on AR formation. 70 Figure 25. Induction of AR formation by soil contact. 73 Figure 26. Induction of AR formation by sand-driven mechanical touch. 74 Figure 27. Auxin-mediated induction of AR formation in fallen plants. 76 Figure 28. Effects of ethylene inhibitor on AR formation. 77 Figure 29. Auxin-mediated stimulation of WOX gene expression in falling-induced AR formation. 80 Figure 30. Auxin-mediated stimulation of LBD gene expression in falling-induced AR formation. 81 Figure 31. Induction of WOX and LBD genes by wind-mediated mechanical stimulation. 84 Figure 32. Schematic model of auxin-mediated AR formation under windy conditions. 85 Figure 33. Effects of auxin and NPA on the transcription of ethylene-responsive genes. 86 LIST OF TABLES Table 1. Primers used in CHAPTER 1. 14 Table 2. Primers used in CHAPTER 2. 62Docto

Toxic elements in soil and rice in Ecuador

The concentration of trace toxic metals (Cr, Zn, As, Pb, Cd, Cu, and Ni) in soil and rice plants, including the stems, leaves, and grain, from the main rice-producing provinces in Ecuador, was determined. Additionally, the soils were analyzed to determine their properties, composition, total content, bioavailable fraction, and geochemical fractions of toxic elements. Approximately 30% of soil samples in the case of Cr and Cu and 10% of samples in the case of Ni exceeded the legal thresholds for Ecuador. Moreover, for Cr and Cu, approximately 4% and 13% of samples, respectively, exceeded the threshold value of 100 mg kg−1 proposed for these two elements in several international regulations. Concentrations of As, Pb, and Cd in the soils were below the threshold values established both by Ecuadorian laws and by other countries. The concentrations of metals in rice plants did not correlate linearly with the total metal concentrations in the soil, nor with their bioavailability. However, the bioconcentration factors for As, Cd, Cu, Ni, and Zn could be predicted from bioavailability by a power law with exponents ranging from −0.724 to −1.625, which is typical of accumulator plants, where trace metal homeostasis plays an important role.info:eu-repo/semantics/publishedVersio