A 9 bp cis-element in the promoters of class I small heat shock protein genes on chromosome 3 in rice mediates L-azetidine-2-carboxylic acid and heat shock responses

In rice, the class I small heat shock protein (sHSP-CI) genes were found to be selectively induced by L-azetidine-2-carboxylic acid (AZC) on chromosome 3 but not chromosome 1. Here it is shown that a novel cis-responsive element contributed to the differential regulation. By serial deletion and computational analysis, a 9 bp putative AZC-responsive element (AZRE), GTCCTGGAC, located between nucleotides –186 and –178 relative to the transcription initiation site of Oshsp17.3 was revealed. Deletion of this putative AZRE from the promoter abolished its ability to be induced by AZC. Moreover, electrophoretic mobility shift assay (EMSA) revealed that the AZRE interacted specifically with nuclear proteins from AZC-treated rice seedlings. Two AZRE–protein complexes were detected by EMSA, one of which could be competed out by a canonical heat shock element (HSE). Deletion of the AZRE also affected the HS response. Furthermore, transient co-expression of the heat shock factor OsHsfA4b with the AZRE in the promoter of Oshsp17.3 was effective. The requirement for the putative AZRE for AZC and HS responses in transgenic Arabidopsis was also shown. Thus, AZRE represents an alternative form of heat HSE, and its interaction with canonical HSEs through heat shock factors may be required to respond to HS and AZC

Heterologous expression analyses of rice OsCAS in Arabidopsis and in yeast provide evidence for its roles in cyanide detoxification rather than in cysteine synthesis in vivo

While most dicot plants produce little ethylene in their vegetative stage, many monocots such as rice liberate a relatively large amount of ethylene with cyanide as a co-product in their seedling stage when etiolated. One of the known functions of β-cyanoalanine synthase (CAS) is to detoxify the co-product cyanide during ethylene biosynthesis in higher plants. Based on a tryptic peptide sequence obtained from a partially purified CAS activity protein preparation in etiolated rice seedlings, the full-length putative rice CAS-encoding cDNA sequence (OsCAS), which is homologous to those O-acetylserine sulphydrylase (OASS) genes, was cloned. Unlike most of the CAS genes reported from dicots, the transcription of OsCAS is promoted by auxins but suppressed by ethylene. To address the function and the subcellular localization of this gene product in planta, a binary vector construct consisting of this gene appended with a yellow fluorescent protein-encoding sequence was employed to transform Arabidopsis. Specific activities on CAS and OASS of the purified recombinant protein from transgenic Arabidopsis were 181.04 μmol H2S mg−1 protein min−1 and 0.92 μmol Cys mg−1 protein min−1, respectively, indicating that OsCAS favours CAS activity. The subcellular localization of OsCAS was found mostly in the mitochondria by immunogold electron-microscopy. Chemical cross-linking and in-gel assay on a heterodimer composed of functional and non-functional mutants in a yeast expression system on OsCAS suggested that OsCAS functions as a homodimer, similar to that of OASS. Despite the structural similarity of OsCAS with OASS, it has also been confirmed that OsCAS could not interact with serine-acetyltransferase, indicating that OsCAS mainly functions in cyanide detoxification

Old Technique -New Evidence: Topical agents for musculo-skeletal injuries

The popular use of topical agents for the treatment of musculoskeletal injuries has persisted for centuries but not much scientific evaluations have been done. Since medicinal herbs are particularly popular in Asia, we started a systematic exploration on their choices, and their pharmacological activities; whether transcutaneous transport of bioactive components occur and above all, whether quality clinical evidences could be generated. We found that a search on the vast literature pool would reveal the favourable choices of herbal agents. Biological screening of those selected herbs showed that they probably follow three major common pathways to help with healing after injury, viz, anti-inflammation, pro-angiogenesis and cellular proliferation. Using a simple formula of selected herbs with the ideal bioactivities, evidence based clinical trials could be organized to further prove the efficacy. We have created two such formulae to be put on clinical trial. Our early pilot clinical trials on two minor injuries on the foot and one chronic inflammatory condition have yielded positive data on the value of such topical agents on pain and oedema control, as well as functional maintenance. There was also suggestion of more rapid bone healing. Although limitations exist clear with the small number of study subjects, the positive data and safe application support more studies

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Estimation of water storage and flood reduction benefits at the Taichung metropolitan park

山坡地開發利用，部分設施因施工與維護上的時效性、方便性與經濟性需求，設施舖面若採用不透水材料施作，將妨礙地表雨水之滲透變成地表逕流，導致原有公共排水設施增加負荷甚至不足，致使低窪地區每遇大雨即形成淹水問題。本研究透過常態化差異植生指標NDVI 推算台中都會公園開發前與開發後之綠覆率、並以降雨－逕流模式計算洪峰流量及綠建築設計技術之保水等配置效益，並探討其相互間之關連性，獲得基地開發後總保水量比開發前少了1,885,415 m3，綠覆率比開發前減少5.97％，洪峰總流量增加25.73 cms，但整體公園在開發配置截蓄保水及滯洪池、綠化等設施後，基地保水指標λ仍大於基地保水指標基準λc值，基地開發後未曾發生水患情形，顯示截蓄保水設施、滯洪池配置已獲得預期成效；基地保水深度與透水率、綠覆率之關係呈現正相關，而洪峰流量與綠覆率之關係則呈負相關。During the development and utilization of slope land, some facilities adopt impermeable materials as the ground surface construction for time effectiveness, convenience and/or economy, which may obstruct the infiltration of rainfall on the ground resulting in surface runoff and add to the load of the original public drainage facilities causing inundation problems in lowland areas in case of heavy rain. The purpose of this study is to calculate the vegetation coverage of Taichung Metropolitan Park before and after development by using normalized differences vegetation index (NDVI) to estimate the peak flow before implementation and the allocation effects of water storage of green architecture design technologies in the rainfall-runoff mode for finding out the relationships between them. Results show that water storage for Taichung Metropolitan Park is 1,885,415m³ which is less than that of before development. The vegetation coverage reduced by 5.97% and peak flow increased by 25.73cms comparing to before implementation. After setting up the facilities of interception, storage, flood detention ponds as well as afforest, the water storage index ( λ) of the whole park is still greater than the benchmark value (λc), and no flood occurred after development, which shows that the expected effectiveness of water interception and/or storage facilities and flood detention ponds have been achieved. There exits positive correlations between water storage depth and water permeability or vegetation coverage, while peak flow before implementation is negatively correlated to vegetation coverage.摘要 i Abstract ii 目次 iii 圖目次 v 表目次 vi 第一章 緒論 1 第一節 研究動機 1 第二節 研究目的 1 第三節 研究流程 2 第二章 前人研究與相關法令探討 4 第一節 基地保水 4 一、保水意義與功能 4 二、保水指標方法論述 6 第二節 降雨－逕流模式 9 一、線型逕流模式 9 二、非線型逕流模式 9 三、準非線型逕流模式 10 第三節 合理化公式 11 第四節 SPOT衛星影像應用 12 一、法國SPOT衛星影像簡介 12 二、遙感探測相關應用 13 三、常態化差異植生指標 14 第五節 綠覆率 15 一、綠化定義與功能 15 二、相關法規探討 18 第三章 研究材料與方法 21 第一節 研究樣區概況 21 一、地理位置 21 二、地形 22 三、地質與土壤 25 四、土地利用 27 五、氣候及水文 28 六、水系與截蓄保水設施 28 七、公園管理維護 32 第二節 研究方法 33 一、集水區劃分 33 二、基地保水指標計算 34 三、洪水減量計算 39 四、綠覆率指標計算 44 第四章 結果與討論 47 第一節 保水設施與保水量評估 47 第二節 洪水減量效益評估 49 第三節 綠覆率評估 51 第四節 綠覆率與保水量及洪水減量評估 53 第五章 結論與建議 59 第一節 結論 59 第二節 建議 60 參考文獻 6

A fast algorithm for multilevel thresholding

Otsu reference proposed a criterion for maximizing the between-class variance of pixel intensity to perform picture thresholding. However, Otsu’s method for image segmentation is very time-consuming because of the inefficient formulation of the between-class variance. In this paper, a faster version of Otsu’s method is proposed for improving the efficiency of computation for the optimal thresholds of an image. First, a criterion for maximizing a modified between-class variance that is equivalent to the criterion of maximizing the usual between-class variance is proposed for image segmentation. Next, in accordance with the new criterion, a recursive algorithm is designed to efficiently find the optimal threshold. This procedure yields the same set of thresholds as the original method. In addition, the modified between-class variance can be pre-computed and stored in a look-up table. Our analysis of the new criterion clearly shows that it takes less computation to compute both the cumulative probability (zeroth order moment) and the mean (first order moment) of a class, and that determining the modified between-class variance by accessing a look-up table is quicker than that by performing mathematical arithmetic operations. For example, the experimental results of a five-level threshold selection show that our proposed method can reduce down the processing time from more than one hour by the conventional Otsu’s method to less than 107 seconds. Keywords: Otsu’s thresholding, image segmentation, picture thresholding, multilevel thresholding, recursive algorithm 1

Detection of lithospermate B in rat plasma at the nanogram level by LC/MS in multi reaction monitoring mode

Low bioavailability and high binding affinity to plasma proteins led to the difficulty for the quantitative detection of lithospermate B (LSB) in plasma. This study aimed to develop a protocol for detecting LSB in plasma. A method was employed to quantitatively detect LSB of 5–500 ng/mL by LC/MS spectrometry in multi reaction monitoring mode via monitoring two major fragments with m/z values of 519 and 321 in the MS2 spectrum. To set up an adequate extraction solution to release LSB captured by plasma proteins, recovery yields of LSB extracted from rat plasma acidified by formic acid or HCl in the presence or absence of EDTA and caffeic acid were detected and compared using the above quantitative method. High recovery yield (∼90%) was achieved when LSB (5–500 ng/mL) mixed in rat plasma was acidified by HCl (5 M) in the presence of EDTA (0.5 M) and caffeic acid (400 μg/mL). The lower limit of detection and the lower limit of quantification for LSB in the spiked plasma were calculated to be 1.8 and 5.4 ng/mL, respectively. Good accuracy (within ±10%) and precision (less than 10%) of intra- and inter-day quality controlled samples were observed. Oral bioavailability of LSB in rat model was detected via this optimized extraction method, and the maximum plasma concentration (Cmax) was found to be 1034.3 ± 510.5 μg/L at tmax around 10 min, and the area under the plasma concentration–time curve (AUC) was 1414.1 ± 851.2 μg·h/L

The effects of macromolecular crowding on the mechanical stability of protein molecules

Macromolecular crowding, a common phenomenon in the cellular environments, can significantly affect the thermodynamic and kinetic properties of proteins. A single-molecule method based on atomic force microscopy (AFM) was used to investigate the effects of macromolecular crowding on the forces required to unfold individual protein molecules. It was found that the mechanical stability of ubiquitin molecules was enhanced by macromolecular crowding from added dextran molecules. The average unfolding force increased from 210 pN in the absence of dextran to 234 pN in the presence of 300 g/L dextran at a pulling speed of 0.25 μm/sec. A theoretical model, accounting for the effects of macromolecular crowding on the native and transition states of the protein molecule by applying the scaled-particle theory, was used to quantitatively explain the crowding-induced increase in the unfolding force. The experimental results and interpretation presented could have wide implications for the many proteins that experience mechanical stresses and perform mechanical functions in the crowded environment of the cell