MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences

The application of high-throughput techniques such as genomics, proteomics or transcriptomics means that vast amounts of heterogeneous data are now available in the public databases. Bioinformatics is responding to the challenge with new integrated management systems for data collection, validation and analysis. Multiple alignments of genomic and protein sequences provide an ideal environment for the integration of this mass of information. In the context of the sequence family, structural and functional data can be evaluated and propagated from known to unknown sequences. However, effective integration is being hindered by syntactic and semantic differences between the different data resources and the alignment techniques employed. One solution to this problem is the development of an ontology that systematically defines the terms used in a specific domain. Ontologies are used to share data from different resources, to automatically analyse information and to represent domain knowledge for non-experts. Here, we present MAO, a new ontology for multiple alignments of nucleic and protein sequences. MAO is designed to improve interoperation and data sharing between different alignment protocols for the construction of a high quality, reliable multiple alignment in order to facilitate knowledge extraction and the presentation of the most pertinent information to the biologist

Estrogen receptor transcription and transactivation: Structure-function relationship in DNA- and ligand-binding domains of estrogen receptors

Estrogen receptors are members of the nuclear receptor steroid family that exhibit specific structural features, ligand-binding domain sequence identity and dimeric interactions, that single them out. The crystal structures of their DNA-binding domains give some insight into how nuclear receptors discriminate between DNA response elements. The various ligand-binding domain crystal structures of the two known estrogen receptor isotypes (α and β) allow one to interpret ligand specificity and reveal the interactions responsible for stabilizing the activation helix H12 in the agonist and antagonist positions

MAO: a Multiple Alignment Ontology for nucleic

acid and protein sequence

Sci Rep

Retinoid X receptors (RXRs) act as homodimers or heterodimerisation partners of class II nuclear receptors. RXR homo- and heterodimers bind direct repeats of the half-site (A/G)G(G/T)TCA separated by 1 nucleotide (DR1). We present a structural characterization of RXR-DNA binding domain (DBD) homodimers on several natural DR1s and an idealized symmetric DR1. Homodimers displayed asymmetric binding, with critical high-affinity interactions accounting for the 3' positioning of RXR in heterodimers on DR1s. Differing half-site and spacer DNA sequence induce changes in RXR-DBD homodimer conformation notably in the dimerization interface such that natural DR1s are bound with higher affinity than an idealized symmetric DR1. Subtle changes in the consensus DR1 DNA sequence therefore specify binding affinity through altered RXR-DBD-DNA contacts and changes in DBD conformation suggesting a general model whereby preferential half-site recognition determines polarity of heterodimer binding to response elements

CNC工具機PES加工應用專家系統之開發與研究

The papper of this study is tried to build-up a process-oriented expert system(PES) such that the operators can easily select a block within this system according to process requirement. In this system, the process control parameters are being categorized into three main index, speed, accuracy, and surface finish with totally 16 different blocks. Here, speed means having shortest process time. Accuracy means having smallest right angle error and radius reducing error. While, surface finish means having smallest oscillating magnitude and jerk along the process contour. Taguchi method is applied to find the influence of each control parameter. According to the importance of these parameters, the parameters setting in each block on the expert system are being determined. Two three-axis machine tools A and B with SYNTEC controllers and DELTA servo systems are being used for the experiment. From the experiment results, they are found that the PES is being successful established. At the testing machine tool A, the process time for the speed setting is 1.11 s. The right angle error for the accuracy setting is 4.5 um and radius reducing error is 2.5 um. The oscillating magnitude for the surface finish is 2.1 um and the jerk is 92.7 m/s3. At the testing machine tool B, the process time for the speed setting is 2.18 s. The right angle error for the accuracy setting is 5.8 um and radius reducing error is 1.1 um. The oscillating magnitude for the surface finish is 5.7 um and the jerk is 26.2 m/s3. They are all fulfilled with the requirements.PES(Process-oriented Expert System)加工應用專家系統目的在於建立最佳參數系統，將機台、控制器、進給系統...等與加工相關的參數最佳化，並依照當前加工需求選擇最適合的參數套用，讓人員無須進行參數測試和調校，就能得到良好的加工結果。 本論文所使用的系統規畫採用SYNTEC科技公司的10系列控制器搭配台達電(delta)的驅動器馬達與工具機測試機台，因此目前專家系統先針對控制器的部分建立，將控制器中的參數找出與快準穩有直接關聯，再依照田口實驗法規劃實驗，計算出各參數對快準穩的趨勢及貢獻度，再依照此貢獻度與趨勢製作成PES加工應用專家系統，最後以實際測試機台A、B進行系統驗證並調整。 從測試機台A結果能得知：快的比例為最高的參數其加工路徑時間為1.11秒，準的比例為最高的參數其直角誤差為2.5微米、圓半徑內縮量2.5微米，穩的比例為最高的參數其路徑振盪量為2.1微米、JERK值為92.7 m/s3。 從測試機台B結果能得知：快的比例為最高的參數其加工路徑時間為2.18秒，準的比例為最高的參數其直角誤差為5.8微米、圓半徑內縮量1.1微米，穩的比例為最高的參數其路徑振盪量為5.7微米、JERK值為26.2 m/s3。致謝 I 摘要 II Abstract III 目錄 IV 圖目錄 VI 表目錄 VIII 第一章 緒論 1 1.1 研究背景 1 1.2 文獻回顧 1 1.3 研究動機與目地 4 1.4 研究方法 4 1.5 論文架構 5 第二章 CNC控制器 7 2.1 SYNTEC控制器 7 2.2 控制器的加減速規劃 7 2.3 控制器的參數 9 第三章 田口法 15 3.1 決定品質特性 15 3.2 選擇實驗因子 15 3.3 定義因子的水準數 16 3.4 選擇直交表 17 3.5 變異數分析 19 第四章 實驗分析與結果 20 4.1 實驗設備 20 4.2 實驗路徑 24 4.3 實驗分析 25 4.4 PES加工應用專家系統 27 4.5 測試機台A的實驗結果 28 4.5.1. 快的趨勢與貢獻度 30 4.5.2. 準的趨勢與貢獻度 32 4.5.3. 穩的趨勢與貢獻度 33 4.5.4. 測試機台A的PES加工應用專家系統結果 35 4.6 測試機台B的實驗結果 39 4.6.1 快的趨勢與貢獻度 41 4.6.2 準的趨勢與貢獻度 42 4.6.3 穩的趨勢與貢獻度 44 4.6.4 測試機台B的PES加工應用專家系統結果 46 4.6.5 測試機台B實際加工 51 第五章 結論與未來展望 56 5.1 結論 56 5.2 未來展望 57 參考文獻 5

Reconstruction of Quaternary Structure from X-ray Scattering by Equilibrium Mixtures of Biological Macromolecules

A recent renaissance in small-angle X-ray scattering (SAXS) made this technique a major tool for the low-resolution structural characterization of biological macromolecules in solution. The major limitation of existing methods for reconstructing 3D models from SAXS is imposed by the requirement of solute monodispersity. We present a novel approach that couples low-resolution 3D SAXS reconstruction with composition analysis of mixtures. The approach is applicable to polydisperse and difficult to purify systems, including weakly associated oligomers and transient complexes. Ab initio shape analysis is possible for symmetric homo-oligomers, whereas rigid body modeling is applied also to dissociating complexes when atomic structures of the individual subunits are available. In both approaches, the sample is considered as an equilibrium mixture of intact complexes/oligomers with their dissociation products or free subunits. The algorithms provide the 3D low-resolution model (for ab initio modeling, also the shape of the monomer) and the volume fractions of the bound and free state(s). The simultaneous fitting of multiple scattering data sets collected under different conditions allows one to restrain the modeling further. The possibilities of the approach are illustrated in simulated and experimental SAXS data from protein oligomers and multisubunit complexes including nucleoproteins. Using this approach, new structural insights are provided in the association behavior and conformations of estrogen-related receptors ERRalpha and ERRgamma. The possibility of 3D modeling from the scattering by mixtures significantly widens the range of applicability of SAXS and opens novel avenues in the analysis of oligomeric mixtures and assembly/dissociation processes