The DNA sequences diversity of Fusarium oxysporum

中文摘要 II 英文摘要 III 致謝 V 壹、 前人研究 2 一、 鐮孢菌介紹 2 二、 生理發育 3 三、 分類依據 4 四、 特異性核酸序列介紹 4 五、 生物資訊 5 六、 生物晶片 6 七、 研究方向 7 貳、 材料與方法 8 一、 材料 8 (一)、菌株來源、培養及保存 8 二、 真菌DNA萃取 8 三、 聚合酶連鎖反應 (polymerase chain reaction, PCR) 9 四、 PCR產物之純化 9 五、 PCR產物與質體之接合作用 9 六、 核酸轉型作用 10 七、 DNA定序與引子組設計 10 八、 生物資訊分析 11 參、 結果與討論 12 一、 鑑定相關性基因之分析 12 二、 β-Tubulin (BT2) 基因序列之相似度分析 12 三、 Elongation Factor ( EF )基因序列之相似度分析 13 四、 Fusarium Osmotin Resistance ( FOR3 ) 基因序列之相似度分析 13 五、 Internal Transcribed Spacer ( ITS ) 核酸序列之相似度分析 14 六、 生物晶片之設計 15 八、 引子組設計 16 肆、 文獻 18 圖表 23 表一、 NCBI資料庫中不同鐮孢菌菌株之ITS序列及其相關資料。 24 表二、NCBI資料庫中不同鐮孢菌菌株之EF序列及其相關資料。 25 表三、NCBI資料庫中不同鐮孢菌菌株之BT2序列及其相關資料。 26 表四、寡核苷酸生物晶片之設計。 27 表五A、BT2測試點對不同分宿主離株之雜合反應型。 29 表五B、EF測試點對不同宿主分離株之雜合反應型。 30 表五C、FOR測試點對不同宿主分離株之雜合反應型。 31 表五D、ITS測試點對不同宿主分離株之雜合反應型。 32 圖一、作物所分離Fusarium菌株的BT2核酸序列之相似度分析。 34 圖二、作物所分離Fusarium菌株的EF核酸序列之相似度分析。 35 圖三、不同來源之Fusarium染色體DNA以 FOR3-F及FOR3-R引子組所進行之PCR增幅。 36 圖四、不同來源Fusarium之FOR3基因序列以多序列比對軟體所進行之相似度分析。 37 圖五、作物所分離Fusarium菌株的ITS核酸序列之相似度分析。 38 圖六A、FOR基因之多序列比對及測試點所在位置。 39 圖六B、FOR基因之多序列比對及測試點所在位置。 40 圖七、EF基因之多序列比對及測試點所在位置。 41 圖八A、ITS基因之多序列比對及測試點所在位置。 42 圖八B、ITS基因之多序列比對及測試點所在位置。 43 圖八C、ITS基因之多序列比對及測試點所在位置。 44 圖九、BT2基因之多序列比對及測試點所在位置。 45 圖十、不同來源鐮孢菌JN995193-EF-30核酸序列之多序列比對及引子設計位置。 46 附錄 47 附錄二 49[[abstract]]鐮孢菌 (Fusarium oxysporum) 為台灣地區田間常見的病原真菌，造成多種農作物包括香蕉、西瓜、香瓜等高經濟作物之病害，為台灣重要病害之一。本病原菌在早期多以顯微鏡下觀察型態來進行分類，近年使用Polymerase chain reaction 、Restriction fragment length polymorphism、Amplified fragment length polymorphism等方法來進行分類。由於Fusarium oxysporum的宿主廣泛，對不同宿主產生分化型(Formae Special)，由於分化型日益增加，因此在分類工作需要有更多的資料來判斷分化型的差異所在。本研究利用核酸序列比對方法去分析不同來源之Internal Transcribed Spacer (ITS)、Intergenic Spacer (IGS)、Elongation Factor(EF)、Fusarium Osmotin Resistance (FOR)等之相似度分析，可了解不同分化型菌株核酸序列間之差異。研究成果顯示FOR3核酸序列及比對後相似度較高之序列資料的結果可區分成8個Divisions，定序後之序列以BLAST搜尋NCBI資料庫發現此序列與Nectria及Gibberella的相似度較高其中FDS與Nectria其相似度86% ；Fo. Tomato和Fo. Cucumber與Gibberella相似度80%。以NCBI搜尋作物的Fusarium oxysporum f. sp.的不同來源之宿主分離株統整後進行相似度分析，分別建立ITS、EF及BT2的小型資料庫，經多序列比對後可發現ITS資料庫可分為3個Divisions。EF資料庫可分為2個Divisions。BT2資料庫可分為2個Divisions。ITS、EF及BT2核酸序列對不同宿主之分離株不具差異性，但多序列比對仍有顯示特異性序列，將有差異性之序列開發生物晶片之測試點，希望可依測試點所預測之特定反應型以區分宿主間的差異。 Fusarium oxysporum is a common pathogenic fungus in the fields of Taiwan. It causes serious diseases on plants including crops such as bananas, watermelons, melons and other economic crops, and it is one of the serious plant diseases in Taiwan. In the early stage, Fusarium was identified by the patterns under microscope. In recent years, the identify method often used is Polymerase chain reaction, Restriction fragment length polymorphism and Amplified fragment length polymorphism, etc. Because of the wide range of hosts, different Formae Special of Fusarium oxysporum are very much which is specific to their hosts and the association interaction between Fusarium oxysporum f.sp toxicity and hosts will be established. Since the increasing number of Formae Special, it is more and more difficult in identifying the Fusarium oxysporum. In this study, we utilized bioinformatics to analysis the similarity of nucleic acid sequence including Internal Transcribed Spacer (ITS), Intergenic Spacer (IGS), Elongation Factor (EF) and Fusarium Osmotin Resistance (FOR), etc. It can help us to find out the difference between different strains. The result shows FOR3 nucleic acid sequence and similarity higher, and the sequence data results can be divided into eight divisions, after sequencing and comparing to NCBI database found this sequence are similar with Nectria and Gibberella. The FDS and Nectria of similarity is 86%; the Fo. Tomato, Fo. Cucumber and Gibberella of similarity is 80%. By searching Fusarium oxysporum f. sp.'s crop from different host on NCBI and integrating similarity analysis, we established small databases for ITS, EF and BT2. The multiple sequence alignment results can be obtained from ITS database and can be divided into three divisions; EF database can be divided into two divisions; BT2 database can be divided into two divisions. ITS, EF and BT2 nucleic acid sequences of different host does not have any diversity, but still have specific sequence, these specific sequence will be designed to development the bio-chip test points, hope distinguish the diversity between the host by these test point

Dementia Assessment Using Mandarin Speech with an Attention-based Speech Recognition Encoder

Dementia diagnosis requires a series of different testing methods, which is complex and time-consuming. Early detection of dementia is crucial as it can prevent further deterioration of the condition. This paper utilizes a speech recognition model to construct a dementia assessment system tailored for Mandarin speakers during the picture description task. By training an attention-based speech recognition model on voice data closely resembling real-world scenarios, we have significantly enhanced the model's recognition capabilities. Subsequently, we extracted the encoder from the speech recognition model and added a linear layer for dementia assessment. We collected Mandarin speech data from 99 subjects and acquired their clinical assessments from a local hospital. We achieved an accuracy of 92.04% in Alzheimer's disease detection and a mean absolute error of 9% in clinical dementia rating score prediction.Comment: submitted to IEEE ICASSP 202

Estrogen Modulates the Sensitivity of Lung Vagal C Fibers in Female Rats Exposed to Intermittent Hypoxia

Obstructive sleep apnea is mainly characterized by intermittent hypoxia (IH), which is associated with hyperreactive airway diseases and lung inflammation. Sensitization of lung vagal C fibers (LVCFs) induced by inflammatory mediators may play a central role in the pathogenesis of airway hypersensitivity. In females, estrogen interferes with inflammatory signaling pathways that may modulate airway hyperreactivity. In this study, we investigated the effects of IH on the reflex and afferent responses of LVCFs to chemical stimulants and lung inflammation in adult female rats, as well as the role of estrogen in these responses. Intact and ovariectomized (OVX) female rats were exposed to room air (RA) or IH for 14 consecutive days. On day 15, IH enhanced apneic responses to right atrial injection of chemical stimulants of LVCFs (e.g., capsaicin, phenylbiguanide, and α,β-methylene-ATP) in intact anesthetized females. Rats subjected to OVX prior to IH exposure exhibited an augmented apneic response to the same dose of stimulants compared with rats subjected to other treatments. Apneic responses to the stimulants were completely abrogated by bilateral vagotomy or perivagal capsaicin treatment, which blocked the neural conduction of LVCFs. Electrophysiological experiments revealed that in IH-exposed rats, OVX potentiated the excitability of LVCFs to stimulants. Moreover, LVCF hypersensitivity in rats subjected to OVX prior to IH exposure was accompanied by enhanced lung inflammation, which was reflected by elevated inflammatory cell infiltration in bronchoalveolar lavage fluid, lung lipid peroxidation, and protein expression of inflammatory cytokines. Supplementation with 17β-estradiol (E2) at a low concentration (30 μg/ml) but not at high concentrations (50 and 150 μg/ml) prevented the augmenting effects of OVX on LVCF sensitivity and lung inflammation caused by IH. These results suggest that ovarian hormones prevent the enhancement of LVCF sensitivity and lung inflammation by IH in female rats, which are related to the effect of low-dose estrogen

A novel sol-gel Bi2-xHfxO3+x/2 radiopacifier for mineral trioxide aggregates (MTA) as dental filling materials

Funding Information: The authors would like to thank Taipei Medical University Hospital for financially sup-porting this work under grant no. 110TMU-TMUH-16 and partially supported by MOST 109-2221-E-038-014. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Mineral trioxide aggregate (MTA) is well known as an effective root canal filling material for endodontics therapy. Within MTA, bismuth oxide (Bi2O3) serving as the radiopacifier still has biocompatibility concerns due to its mild cytotoxicity. In the present study, we tried to modify the Bi2O3 radiopacifier by doping hafnium ions via the sol-gel process and investigated the effects of different doping ratios (Bi2-xHfxO3+x/2, x = 0–0.3) and calcination temperatures (400–800 °C). We mixed various precursor mixtures of bismuth nitrate (Bi(NO3)3·5H2O) and hafnium sulfate (Hf(SO4)2) and controlled the calcination temperatures. The as-prepared Hf-doped Bi2O3 radiopaci-fier powders were investigated by thermogravimetric analysis (TGA), X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), and transmission electron microscopy (TEM). Portland cement/radiopacifier/calcium sulfate (75/20/5) were mixed and set by deionized water (powder to water ratio = 3:1). Changes in radiopacity, diametral tensile strength (DTS), and in vitro cell viability of the hydrated MTA-like cement were carried out. The experimental results showed that the group containing radiopacifier from sol-gelled Bi/Hf (90/10) exhibited significantly higher radiopacity (6.36 ± 0.34 mmAl), DTS (2.54 ± 0.29 MPa), and cell viability (84.0±8.1%) (p < 0.05) when compared to that of Bi/Hf (100/0) powders. It is suggested that the formation of β-Bi7.78Hf0.22O12.11 phase with hafnium addition and calcining at 700 °C can prepare novel bismuth/haf-nium composite powder that can be used as an alternative radiopacifier for root canal filling mate-rials.publishersversionPeer reviewe

Mechanism of Evolution Shared by Gene and Language

We propose a general mechanism for evolution to explain the diversity of gene and language. To quantify their common features and reveal the hidden structures, several statistical properties and patterns are examined based on a new method called the rank-rank analysis. We find that the classical correspondence, "domain plays the role of word in gene language", is not rigorous, and propose to replace domain by protein. In addition, we devise a new evolution unit, syllgram, to include the characteristics of spoken and written language. Based on the correspondence between (protein, domain) and (word, syllgram), we discover that both gene and language shared a common scaling structure and scale-free network. Like the Rosetta stone, this work may help decipher the secret behind non-coding DNA and unknown languages.Comment: 15 pages, 13 figures, 3 tabl

Application of Multiple Sensors in Monitoring Land Subsidence in Central Taiwan

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Topical application of marine briarane-type diterpenes effectively inhibits 12-O-tetradecanoylphorbol-13-acetate-induced inflammation and dermatitis in murine skin

<p>Abstract</p> <p>Background</p> <p>Skin is the largest organ in the body, and is directly exposed to extrinsic assaults. As such, the skin plays a central role in host defense and the cutaneous immune system is able to elicit specific local inflammatory and systemic immune responses against harmful stimuli. 12-O-tetradecanoylphorbol-13-acetate (TPA) can stimulate acute and chronic inflammation and tumor promotion in skin. TPA-induced dermatitis is thus a useful <it>in vivo </it>pharmacological platform for drug discovery. In this study, the inhibitory effect of briarane-type diterpenes (BrDs) from marine coral <it>Briareum excavatum </it>on TPA-induced dermatitis and dendritic cell (DC) function was explored.</p> <p>Methods</p> <p>Evans blue dye exudation was used to determine vascular permeability. H&E-stained skin section was used to determine the formation of edema in mouse abdominal skin. We also used immunohistochemistry staining and western blot assays to evaluate the activation of specific inflammation makers and key mediators of signaling pathway in the mouse skin. Furthermore, mouse bone marrow DCs were used to determine the relationship between the chemical structure of BrDs and their regulation of DC function.</p> <p>Results</p> <p>BrD1 remarkably suppressed TPA-induced vascular permeability and edema in skin. At the biochemical level, BrD1 inhibited TPA-induced expression of cyclooxygenase-2, inducible nitric oxide synthase and matrix metalloproteinase-9, the key indicators of cutaneous inflammation. This inhibition was apparently mediated by interference with the Akt/NF-κB-mediated signaling network. BrD1 also inhibited TNF-α and IL-6 expression in LPS-stimulated BMDCs. The 8, 17-epoxide of BrDs played a crucial role in the inhibition of IL-6 expression, and replacement of the C-12 hydroxyl group with longer esters in BrDs gradually decreased this inhibitory activity.</p> <p>Conclusions</p> <p>Our results suggest that BrDs warrant further investigation as natural immunomodulatory agents for control of inflammatory skin diseases.</p

Using UWB Sensor for Delta Robot Vibration Detection

Abstract-This study proposed the ultra-wideband(UWB) sensor to detect the vibration of the delta robot and the distance between UWB sensor and robot arm. Based on the radar propagating principle and the proposed algorithm, the vibration status of robot arm can be obtained. Besides, the vibration status can be reduced by feedback the information to the controller of the robot arm. The advantage of the proposed sensor is that without contacting to the robot arm, UWB sensor is more flexible to be used and will not cause any unnecessary payload as accelerometers. With proper calibration, the simulation of vibration frequency and the real-time absolute position of the robot arm were calculated and demonstrated. The experimental results show that the correlations for measured frequency and distance approximate to 1

Visfatin mediates malignant behaviors through adipose-derived stem cells intermediary in breast cancer

Adipose-derived stem cells (ADSCs) have been implicated in tumor growth and metastasis in breast cancer. ADSCs exhibit tumor tropism, and are of increasing clinical relevance due to the autologous fat grafting for breast reconstruction. Although we have previously shown that a high level of the adipocytokine visfatin in human breast cancer tissues correlated with tumor progression mediated by cAbl and STAT3, the effects of visfatin in the tumor microenvironment are unclear. To understand how visfatin modulates breast cancer within the tumor-stromal environment, we examined determinants of breast cancer progression using a visfatin-primed ADSCs-tumor co-culture model. ADSCs were isolated from tumor-free adipose tissue adjacent to breast tumors. ADSCs were treated with or without visfatin for 48 h and then collected for co-culture with breast cancer cell line MDA-MB-231 for 72 h in a transwell system. We found that the MDA-MB-231 cells co-cultured with visfatin-treated ADSCs (vADSCs) had higher levels of cell viability, anchorage independent growth, migration, invasion, and tumorsphere formation than that co-cultured with untreated ADSCs (uADSCs). Growth differentiation factor 15 (GDF15) upregulation was found in the co-culture conditioned medium, with GDF15 neutralizing antibody blocking the promoting effect on MDA-MB-231 in co-culture. In addition, a GDF15-induced AKT pathway was found in MDA-MB-231 and treatment with PI3K/AKT inhibitor also reversed the promoting effect. In an orthotopic xenograft mouse model, MDA-MB-231 co-injected with vADSCs formed a larger tumor mass than with uADSCs. Positive correlations were noted between visfatin, GDF15, and phosphor-AKT expressions in human breast cancer specimens. In conclusion, visfatin activated GDF15-AKT pathway mediated via ADSCs to facilitate breast cancer progression