Advances in data analysis in Metabolomics: towards a dynamic view of responses in plant cell cultures

Metabolite profiling of plant cell cultures under stress is an important approach towards the understanding of the biology of stress responses in plants by identifying by-products of the stress metabolism, either stress signal transduction molecules or molecules that are involved in adaptive responses. To model in a comprehensive way such complex biological phenomena, it is important to analyse the time-dependent behaviour of the cell metabolism in response to external stimuli. A single point measurement indeed gives only a snapshot of the cellular state in which all the dynamical information is not captured. In this respect, high resolution time-course experiments are expected to provide more information in the phase of data analysis than a series of measurements collected only at a few time-points. The main objective of this thesis is to study the metabolic response of grapevine cell cultures subjected to an external stimulus, designed to mimic the interaction of the plant with environment factors. The PhD thesis firstly describes the optimization of the sample preparation method, extraction protocol and targeted metabolomics analysis of compounds isolated from the grape cells. This optimized metabolomics protocol was then applied to study the long-term dynamic response of elicited grapevine (Vitis vinifera cv. Gamay) cell suspension cultures treated by methyl jasmonate or sodium nitroprusside. Generalized additive models were applied to study the time dependent profile of secondary metabolites in grapevine cell suspension cultures. The results suggested that this class of non-parametric statistical models in combination with metabolomics could be an effective tool to explore the complete time-dependent changes of secondary metabolites and their responses to external stimuli in plant cells and foundation for further integrative omics studies

Conceptual design of a gripper for a first-aid robot

First aid is the tentative care for anyone who is injured or ill before definitive medical care arrives. Advancements in technology offer robots the potential to be used extensively in first aid to replace human workers. Currently, many elderly people live alone and absence of care can increase risks of illness- or injury-induced unconsciousness. Due to this, it would be useful to investigate if robots could be employed to perform first-aid care. However, their application in aiding humans in such circumstances is still relatively rare due to complexities concerning safety, communication and ability to interact with humans. This thesis is part of a project to design a first-aid robot to manipulate an unconscious human from any position to the recovery position. The only direct contact with human is through gripper of the robot. An attempt to develop a conceptual design of cost-effective grippers has been undertaken. This will enable a robot to perform the handling and manipulation of human segments to achieve the recovery position. For the purpose of robotic application, a research into the feasibility of human body manipulation is being conducted. Initial stage of research is to identify the limit of physical robot-human interaction; the biomechanical characteristics of human body that decide these limits and essential gripper specifications required to theoretically carry out robot-human interactions to those limits. The research is focused on the geometric properties of various human body parts, defined as body segments, and the minimum gripper specification needed to manipulate these segments. A novel systematic design approach has been applied to the gripper by utilizing a design tool known as the Theory of Inventive Problem Solving (TRIZ). Results ii obtained from this study have substantiated design work to derive an enhanced design solution, which will enable the gripper to perform delicate tasks. The gripper‟s main priorities have been identified and concluded that fundamental issues are: safely engaging human segments and preventing pain exceeding the recommended pain threshold. This work could form the basis of developing and integrating the First Aid Robotic System (FAROS) and pave a way for further developments and innovations

Molecular dynamics simulations and photoluminescence measurements of annealed ZnO surfaces

The effect of thermal annealing on wurtzite ZnO, terminated by two surfaces, (0 0 0 $\bar 1$) (which is oxygen-terminated) and (0 0 0 1) (which is Zn-terminated), is investigated via molecular dynamics simulation using reactive force field (ReaxFF). As a result of annealing at a threshold temperature range of 700~K < T_{\mbox{\small t}} \leq 800~K, surface oxygen atoms begin to sublimate from the (0 0 0 $\bar 1$) surface, while no atom leaves the (0 0 0 1) surface. The ratio of oxygen leaving the surface increases with temperature $T$ (for T \geq T_{\mbox{\small t}}). The relative luminescence intensity of the secondary peak in the photoluminescence (PL) spectra, interpreted as a measurement of amount of vacancies on the sample surfaces, qualitatively agrees with the threshold behavior as found in the MD simulations. Our simulations have also revealed the formation of oxygen dimers on the surface and evolution of partial charge distribution during the annealing process. Our MD simulation based on the ReaxFF is consistent with experimental observations.Comment: 26 pages, 11 figures. Manuscript submitted to Physica

Earthquakes and slip rate of the southern Sagaing fault: insights from an offset ancient fort wall, lower Burma (Myanmar)

Field investigations of an ancient fortress wall in southern Myanmar reveal an offset of ~6 m across the Sagaing fault, the major right-lateral fault between the Sunda and Burma plates. The fault slip rate implied by offset of this 16th-century fortress is between 11 and 18 cm yr^(–1). A palaeoseismological excavation within the fortress reveals at least two major fault ruptures since its construction. The slip rate we obtained is comparable to geodetic and geological estimates farther north, but is only 50 per cent of the spreading rate (38 mm yr^(–1)) at the Andaman Sea spreading centre. This disparity suggests that other structures may be accommodating deformation within the Burma Plate. We propose two fault-slip scenarios to explain the earthquake-rupture history of the southern Sagaing fault. Using both small offset features along the fault trace and historical records, we speculate that the southern Sagaing fault exhibits a uniform-fault-slip behaviour and that one section of the fault could generate a M7+ earthquake within the next few decade

Early childhood caries and its associated factors among 5-years-old Myanmar children

IntroductionChildren's oral health plays a crucial role in their overall well-being and there is a significant gap in our understanding of early childhood caries (ECC) in Myanmar. This study aims to bridge this knowledge deficit by investigating the prevalence, causes, and potential interventions for ECC in the Myanmar population, providing crucial insights for future dental health policies and practices.MethodsGenerally healthy 5-year-old kindergarten children from 7 districts in city were recruited. ECC was assessed through clinical examinations using decayed, missed, filled teeth (dmft). Additionally, demographic data of the children and their caregivers, along with information about the children's oral health-related behaviors, were gathered using a structured questionnaire.ResultsOut of the 496 children, the overall prevalence of dental caries was 87.1% (mean dmft score: 5.57, SD: 4.6). Caries experience was categorized as severe (45.8%) and non-severe (41.3%). Decayed teeth constituted the major component of the dmft index (97.8%). Multiple logistic regression analysis revealed two significant factors associated with ECC prevalence: late toothbrushing initiation (OR: 2.54, p = 0.001) and dental visit experience (OR: 2.46, p = 0.010).DiscussionThe study highlights the alarming ECC prevalence in 5-year-old children in Mandalay, Myanmar, with mostly untreated decayed teeth. The findings emphasize early preventive oral health measures for young children to reduce ECC burden in Myanmar

Collaborative Exploration of Legume Crops and Wild Vigna Genetic Resources in Sagaing Region, Myanmar 2019

To collect legume genetic resources, a field survey was conducted in the Sagaing Region, Myanmar, from November 1 to 17, 2019. We concentrated on the collection of wild legumes belonging to genus Vigna. As a result, we collected a total of 43 seed samples from 23 survey sites and recorded three additional survey sites from where no seed samples could be collected. Collected seed samples consisted of 2 accessions of domesticated Glycine max (soybean), 2 of domesticated Lablab purpureus (hyacinth bean), 1 of domesticated Psophocarpus tetragonolobus (winged bean), 20 of Vigna angularis var. nipponensis (wild azuki bean), 6 of Vigna hirtella complex (wild Vigna), 6 of Vigna tenuicaulis (wild Vigna), 3 of domesticated Vigna umbellata (rice bean), and 3 of domesticated Vigna unguiculata (cowpea/yardlong bean). The collected seed samples have been primarily conserved in the seed bank of the Department of Agricultural Research in Myanmar, and the subset was transferred to the National Agriculture and Food Research Organization (NARO) Genebank in Japan under the Standard Material Transfer Agreement of the International Treaty on Plant Genetic Resources for Food and Agriculture. After the multiplication of seeds in Tsukuba Japan, the NARO Genebank plans to conserve them as distributable genetic resources for research, breeding, and training purposes for food and agriculture.マメ科作物の遺伝資源を収集するために，2019年11月1日から17日にかけてミャンマー連邦共和国ザガイン地方域における二国間共同現地調査を実施した．調査は，特にササゲ属野生種遺伝資源を主対象として行われた．その結果，合計43サンプルの遺伝資源を収集し，それに加えて3地点の遺伝資源生育地情報を記録した．収集品の内訳は，ダイズ（Glycine max） 2点，フジマメ（Lablab purpureus） 2点，シカクマメ（Psophocarpus tetragonolobus）1点，ツルアズキ（Vigna umbellata）3点，ササゲ/ジュウロクササゲ（Vigna unguiculata）3点，野生アズキ（Vigna angularis var. nipponensis）20点, Vigna属野生植物（Vigna hirtella complex）6点，Vigna属野生植物（Vigna tenuicaulis）6点である．収集した遺伝資源は，原産国ミャンマーのシードバンクに保存し，そのサブセットをITPGRFAのSMTAを用いてNAROジーンバンクに移転した．NAROジーンバンクでは，本調査で収集した種子を用いて増殖・特性評価を行った後，食糧農業に関する教育・研究・育種利用目的のために配布可能な遺伝資源として公開予定である（https://www.gene.affrc.go.jp/index_en.php）．Figure 3点, Table 4点, Photo 91点, Seed Photo 4

Collaborative Exploration of Cucurbitaceae Vegetable Genetic Resources in Myanmar\nin 2019

This study describes the exploration of genetic resources of cucurbitaceous vegetables in northwestern Myanmar, Sagaing region, and this study was jointly conducted by the National Agriculture and Food Research Organization (NARO), Japan, and the Department of Agriculture Research, Myanmar. A field survey was conducted in northwestern Myanmar from November 1 to 17, 2019. We collected a total of 24 accessions, 16 from Cucumis sativus L., two from Cucumis melo L., three from Cucurbita moschata Duchense, one from Cucurbita maxima Duchense ex Lam., one from Luffa acutangula (L.) Roxb., and one from Momordica charantia L. The collected accessions were stored as seeds at the Myanmar Seed Bank and subsets were transferred to the Genetic Resources Center, NARO, using a standard material transfer agreement.本報告は農林水産省委託プロジェクト研究「海外植物遺伝資源の収集・提供強化」の予算により実施され，国立研究開発法人農業・食品産業技術総合研究機構とミャンマー植物遺伝資源センターとの間で行われたミャンマー北西部ザガイン管区におけるウリ科野菜遺伝資源の探索・収集に関わる調査報告書である．調査は2019年11月1日～17日にかけて行った．カムティ省のカムティ郡、ラヘ郡、レイシ郡において探索・調査を行った．その結果，キュウリ（Cucumis sativus）16点，ニホンカボチャ（Cucurbita moschata）3点，メロン（Cucumis melo）2点，セイヨウカボチャ（Cucurbita maxima），トカドヘチマ（Luffa acutangula）およびツルレイシ（Momordica charantia）の計24点の野菜遺伝資源を収集した．収集された遺伝資源種子の半分はミャンマー農業研究局シードバンクで保存され，残りはSMTAを用いて国立研究開発法人農業・食品産業技術総合研究機構ジーンバンクに移転された．Figure 1点, Table 3点, Photo 12点, Sample Photo 17