Browsing by Author "Lin, Hsuan-Yu"

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A Rapid Fatigue Test Method on Micro Structures for High-Cycle Fatigue
(2016-03)
Shieh, Yi-Chueh
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Lin, Hsuan-Yu
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Hsu, Wensyang
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Lin, Yu-Hsin
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機械工程學系
Here, a rapid fatigue test method for micro structure is proposed, where the test sample is excited at its resonant frequency by an external actuator. Due to the scaling effect, a micro cantilever beam has high resonant frequency, so the testing time can be greatly reduced. In addition, no complicated built-in micro actuator is needed; therefore, it is easy to fabricate the test sample. Single-crystal silicon (SCS) beams are fabricated to demonstrate the proposed method here with two types of beams. A notch is designed near the fixed end to have stress concentration effect. The input voltage of the piezoelectric patch is adjusted to excite the cantilever beams at its resonant frequency to have different amplitudes to find the corresponding fatigue life, where a laser Doppler vibrometer is used to monitor displacements of the cantilever beam to control the stress amplitude. Then, the stress-life (S/N) curve of the silicon beam can be obtained. It is found that the fatigue limit of the SCS beam is about 1.33 GPa, and it takes only about 5.2 h to test 1.35 x 10(9) cycles at a resonant frequency of 72 kHz. Comparing with previous fatigue test methods with an external probe, testing 10(9) cycles at a frequency of 20 Hz will need 1.58 years, which indicates that the proposed rapid fatigue test method is particularly suitable for high-cycle fatigue test of micro structure.
Assessing Determinants of Exonic Evolutionary Rates in Mammals
(2012-10-01)
Chen, Feng-Chi
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Liao, Ben-Yang
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Pan, Chia-Lin
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Lin, Hsuan-Yu
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Chang, Andrew Ying-Fei
From studies investigating the differences in evolutionary rates between genes, gene compactness and gene expression level have been identified as important determinants of gene-level protein evolutionary rate, as represented by nonsynonymous to synonymous substitution rate (d(N)/d(S)) ratio. However, the causes of exon-level variances in d(N)/d(S) are less understood. Here, we use principal component regression to examine to what extent 13 exon features explain the variance in d(N), d(S), and the d(N)/d(S) ratio of human-rhesus macaque or human-mouse orthologous exons. The exon features were grouped into six functional categories: expression features, mRNA splicing features, structural-functional features, compactness features, exon duplicability, and other features, including G + C content and exon length. Although expression features are important for determining d(N) and d(N)/d(S) between exons of different genes, structural-functional features and splicing features explained more of the variance for exons of the same genes. Furthermore, we show that compactness features can explain only a relatively small percentage of variance in exon-level d(N) or d(N)/d(S) in either between-gene or within-gene comparison. By contrast, d(S) yielded inconsistent results in the human-mouse comparison and the human-rhesus macaque comparison. This inconsistency may suggest rapid evolutionary changes of the mutation landscape in mammals. Our results suggest that between-gene and within-gene variation in d(N)/d(S) (and d(N)) are driven by different evolutionary forces and that the role of mRNA splicing in causing the variation in evolutionary rates of coding sequences may be underappreciated.
Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs
(2014-01-01)
Chen, Feng-Chi
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Pan, Chia-Lin
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Lin, Hsuan-Yu
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生物科技學系
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Department of Biological Science and Technology
Long intergenic noncoding RNAs (lincRNAs) have been suggested as playing important roles in human gene regulation. The majority of annotated human lincRNAs include multiple exons and are alternatively spliced. However, the connections between alternative RNA splicing (AS) and the functions/regulations of lincRNAs have remained elusive. In this study, we compared the sequence evolution and biological features between single-exonic lincRNAs and multi-exonic lincRNAs (SELs and MELs, respectively) that were present only in the hominoids (hominoid-specific) or conserved in primates (primate-conserved). The MEL exons were further classified into alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs) for evolutionary analyses. Our results indicate that SELs and MELs differed significantly from each other. Firstly, in hominoid-specific lincRNAs, MELs (both CSEs and ASEs) evolved slightly more rapidly than SELs, which evolved approximately at the neutral rate. In primate-conserved lincRNAs, SELs and ASEs evolved slightly more slowly than CSEs and neutral sequences. The evolutionary path of hominid-specific lincRNAs thus seemed to have diverged from that of their more ancestral counterparts. Secondly, both of the exons and transcripts of SELs were significantly longer than those of MELs, and this was probably because SEL transcripts were more resistant to RNA splicing than MELs. Thirdly, SELs were physically closer to coding genes than MELs. Fourthly, SELs were more widely expressed in human tissues than MELs. These results suggested that SELs and MELs represented two biologically distinct groups of genes. In addition, the SEL-MEL and ASE-CSE differences implied that splicing might be important for the functionality or regulations of lincRNAs in primates.
Independent Effects of Alternative Splicing and Structural Constraint on the Evolution of Mammalian Coding Exons
(2012-01-01)
Chen, Feng-Chi
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Pan, Chia-Lin
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Lin, Hsuan-Yu
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生物科技學系
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Department of Biological Science and Technology
Alternative splicing (AS) is known to significantly affect exon-level protein evolutionary rates in mammals. Particularly, alternatively spliced exons (ASEs) have a higher nonsynonymous-to-synonymous substitution rate (dN/dS) ratio than constitutively spliced exons (CSEs), possibly because the former are required only occasionally for normal biological functions. Meanwhile, intrinsically disordered regions (IDRs), the protein regions lacking fixed 3D structures, are also reported to have an increased evolutionary rate due to lack of structural constraint. Interestingly, IDRs tend to be located in alternative protein regions. Yet which of these two factors is the major determinant of the increased dN/dS in mammalian ASEs remains unclear. By comparing human-macaque and human-mouse one-to-one orthologous genes, we demonstrate that AS and protein structural disorder have independent effects on mammalian exon evolution. We performed analyses of covariance to demonstrate that the slopes of the (dN/dS-percentage of IDR) regression lines differ significantly between CSEs and ASEs. In other words, the dN/dS ratios of both ASEs and CSEs increase with the proportion of IDR (PIDR), whereas ASEs have higher dN/dS ratios than CSEs when they have similar PIDRs. Since ASEs and IDRs may less frequently overlap with protein domains (which also affect dN/dS), we also examined the correlations between dN/dS ratio and exon type/PIDR by controlling for the density of protein domain. We found that the effects of exon type and PIDR on dN/dS are both independent of domain density. Our results imply that nature can select for different biological features with regard to ASEs and IDRs, even though the two biological features tend to be localized in the same protein regions.
Interactions between Inter Partes Review and Hatch-Waxman Litigations
(2019-01-01)
Chen, Feng-Chi
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Lee, Pin-Shen
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Huang, Yun-Yu
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Wu, Huang-Chi
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Lin, Hsuan-Yu
Generic drug development in the United States is governed by the Hatch-Waxman Act (HWA), which sets forth the "patent linkage" system requiring resolution of patent disputes before a generic drug can be approved for marketing. The emergence of Inter Partes Review (IPR), an effective administrative proceeding to weed out low-quality patents, is believed by some to have endangered the HWA balance between brand-name and generic drug makers. Here we describe an empirical analysis profiling the influences of IPR on patent linkage. Our results indicate that fewer than 10% of the HWA-litigated patents are subject to parallel IPR challenges. Importantly, IPR yields a slightly higher claim invalidation rate but a much lower settlement rate than court litigations, which may not benefit generic drug makers. Furthermore, IPR is employed by non-first generic drug makers, presumably to break into the market occupied by brand-name and the first generic makers. Overall, IPR seems not to play a dominant role, but to serve strategic functions in HWA disputes.
NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events
(2017-04-03)
Hsu, Min-Kung
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Lin, Hsuan-Yu
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Chen, Feng-Chi
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生物科技學系
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Department of Biological Science and Technology
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
Selective Constraint on Human Pre-mRNA Splicing by Protein Structural Properties
(2012)
Gelly, Jean-Christophe
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Lin, Hsuan-Yu
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de Brevern, Alexandre G.
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Chuang, Trees-Juen
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Chen, Feng-Chi
Alternative splicing (AS) is a major mechanism of increasing proteome diversity in complex organisms. Different AS transcript isoforms may be translated into peptide sequences of significantly different lengths and amino acid compositions. One important question, then, is how AS is constrained by protein structural requirements while peptide sequences may be significantly changed in AS events. Here, we address this issue by examining whether the intactness of three-dimensional protein structural units (compact units in protein structures, namely protein units [PUs]) tends to be preserved in AS events in human. We show that PUs tend to occur in constitutively spliced exons and to overlap constitutive exon boundaries. Furthermore, when PUs are located at the boundaries between two alternatively spliced exons (ASEs), these neighboring ASEs tend to co-occur in different transcript isoforms. In addition, such PU-spanned ASE pairs tend to have a higher frequency of being included in transcript isoforms. ASE regions that overlap with PUs also have lower nonsynonymous-to-synonymous substitution rate ratios than those that do not overlap with PUs, indicating stronger negative selection pressure in PU-overlapped ASE regions. Of note, we show that PUs have protein domain- and structural orderness-independent effects on messenger RNA (mRNA) splicing. Overall, our results suggest that fine-scale protein structural requirements have significant influences on the splicing patterns of human mRNAs.
The evolution of the coding exome of the Arabidopsis species - the influences of DNA methylation, relative exon position, and exon length
(2014-06-25)
Chen, Feng-Chi
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Chuang, Trees-Juen
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Lin, Hsuan-Yu
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Hsu, Min-Kung
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生物科技學系
Background: The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript isoforms may (1) mutate at different rates due to variations in DNA methylation level; and (2) serve distinct biological roles, and thus be differentially targeted by natural selection. Furthermore, intrinsic exonic features, such as exon length, may also affect the evolution of individual exons. Importantly, the evolutionary effects of these intrinsic/extrinsic features may differ significantly between animals and plants. Such inter-lineage differences, however, have not been systematically examined. Results: Here we examine how DNA methylation at CpG dinucleotides (CpG methylation), in the context of intrinsic exonic features (exon length and relative exon position in the transcript), influences the evolution of coding exons of Arabidopsis thaliana. We observed fairly different evolutionary patterns in A. thaliana as compared with those reported for animals. Firstly, the mutagenic effect of CpG methylation is the strongest for internal exons and the weakest for first exons despite the stringent selective constraints on the former group. Secondly, the mutagenic effect of CpG methylation increases significantly with length in first exons but not in the other two exon groups. Thirdly, CpG methylation level is correlated with evolutionary rates (d(S), d(N), and the d(N)/d(S) ratio) with markedly different patterns among the three exon groups. The correlations are generally positive, negative, and mixed for first, last, and internal exons, respectively. Fourthly, exon length is a CpG methylation-independent indicator of evolutionary rates, particularly for d(N) and the d(N)/d(S) ratio in last and internal exons. Finally, the evolutionary patterns of coding exons with regard to CpG methylation differ significantly between Arabidopsis species and mammals. Conclusions: Our results suggest that intrinsic features, including relative exonic position in the transcript and exon length, play an important role in the evolution of A. thaliana coding exons. Furthermore, CpG methylation is correlated with exonic evolutionary rates differentially between A. thaliana and animals, and may have served different biological roles in the two lineages.
The genomic features that affect the lengths of 5 ' untranslated regions in multicellular eukaryotes
(2011-10-05)
Chen, Chun-Hsi
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Lin, Hsuan-Yu
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Pan, Chia-Lin
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Chen, Feng-Chi
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生物科技學系
Background: The lengths of 5'UTRs of multicellular eukaryotes have been suggested to be subject to stochastic changes, with upstream start codons (uAUGs) as the major constraint to suppress 5'UTR elongation. However, this stochastic model cannot fully explain the variations in 5'UTR length. We hypothesize that the selection pressure on a combination of genomic features is also important for 5'UTR evolution. The ignorance of these features may have limited the explanatory power of the stochastic model. Furthermore, different selective constraints between vertebrates and invertebrates may lead to differences in the determinants of 5'UTR length, which have not been systematically analyzed. Methods: Here we use a multiple linear regression model to delineate the correlation between 5'UTR length and the combination of a series of genomic features (G+C content, observed-to-expected (OE) ratios of uAUGs, upstream stop codons (uSTOPs), methylation-related CG/UG dinucleotides, and mRNA-destabilizing UU/UA dinucleotides) in six vertebrates (human, mouse, rat, chicken, African clawed frog, and zebrafish) and four invertebrates (fruit fly, mosquito, sea squirt, and nematode). The relative contributions of each feature to the variation of 5'UTR length were also evaluated. Results: We found that 14%similar to 33% of the 5'UTR length variations can be explained by a linear combination of the analyzed genomic features. The most important genomic features are the OE ratios of uSTOPs and G+C content. The surprisingly large weightings of uSTOPs highlight the importance of selection on upstream open reading frames (which include both uAUGs and uSTOPs), rather than on uAUGs per se. Furthermore, G+C content is the most important determinants for most invertebrates, but for vertebrates its effect is second to uSTOPs. We also found that shorter 5'UTRs are affected more by the stochastic process, whereas longer 5'UTRs are affected more by selection pressure on genomic features. Conclusions: Our results suggest that upstream open reading frames may be the real target of selection, rather than uAUGs. We also show that the selective constraints on genomic features of 5'UTRs differ between vertebrates and invertebrates, and between longer and shorter 5'UTRs. A more comprehensive model that takes these findings into consideration is needed to better explain 5'UTR length evolution.
Valence- and element-dependent water oxidation behaviors: in situ X-ray diffraction, absorption and electrochemical impedance spectroscopies
(2017-04-07)
Hsu, Chia-Shuo
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Suen, Nian-Tzu
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Hsu, Ying-Ya
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Lin, Hsuan-Yu
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Tung, Ching-Wei
Metal oxides of the spinel family have shown great potential towards the oxygen evolution reaction (OER), but the fundamental OER mechanism of spinel oxides is still far from being completely understood, especially for the role of the metal ions. Owing to various coordinated sites of divalent/trivalent metals ions and surface conditions (morphology and defects), it is a great challenge to have a fair assessment of the electrocatalytic performance of spinel systems. Herein, we demonstrated a series of MFe2O4 (M = Fe, Co, Ni, Zn) with a well-controlled morphology to achieve a comprehensive study of electrocatalytic activity toward OER. By utilizing several in situ analyses, we could conclude a universal rule that the activities for OER in the metal oxide systems were determined by the occurrence of a phase transformation, and this structural transformation could work well in both crystallographic sites (Td and Oh sites). Additionally, the divalent metal ion significantly dominated the formation of oxyhydroxide through an epitaxial relationship, which depended on the atomic arrangement at the interface of spinel and metal oxyhydroxide, while trivalent metal ions remained unchanged as a host lattice. The metal oxyhydroxide was formed during a redox reaction rather than being formed during OER. The occurrence of the redox reaction seems to accompany a remarkable increase in resistance and capacitance might result from the structural transformation from spinel to metal oxyhydroxide. We believe that the approaching strategies and information obtained in the present study can offer a guide to designing a promising electrocatalytic system towards the oxygen evolution reaction and other fields.