Ai‐Ling Hour

Fu Jen Catholic University

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Yann‐Rong Lin

Hangzhou Normal University

Yue‐Ie Hsing

Institute of Plant and Microbial Biology, Academia Sinica

Qingyi Yu

Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center

Yong‐Pei Wu

Ministry of Agriculture and Rural Affairs

Ray Ming

Fujian Agriculture and Forestry University

Zhaohui Zeng

Hunan Normal University

Jingsheng Xu

Ministry of Agriculture and Rural Affairs

Tianqu Fan

Fujian Agriculture and Forestry University

Wei-Tzu Lin

Linkou Chang Gung Memorial Hospital

Zhichang Chen

Fujian Agriculture and Forestry University

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Academia Sinica

National Taiwan University

Fu Jen Catholic University

Taiwan Agricultural Research Institute Council of Agriculture, Executive Yuan

National Defense Medical Center

Chang Gung Memorial Hospital

Linkou Chang Gung Memorial Hospital

National Yang Ming Chiao Tung University

Fujian Agriculture and Forestry University

Institute of Molecular Biology, Academia Sinica

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Additional file 1: Table S1. of Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice

H. C. Chin Yong‐Pei Wu Ai‐Ling Hour Chwan‐Yang Hong Yann‐Rong Lin

Table (database)

Genetic Analysis

10.6084/m9.figshare.c.3630389_d1

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Citations (0)

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice (2020)

Ai‐Ling Hour Wei-hsun Hsieh Su-huang Chang Yong‐Pei Wu Han-shiuan Chin

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica . Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica ( F ST = 0.3751) but not in indica ( F ST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

Germ plasm

Genetic erosion

Gene pool

10.1186/s12284-020-00445-w

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The effects of Hd1, Hd6, and Ehd1 on rice heading date.

Chien HsiangTing Rong-Kuen Chen Ai‐Ling Hour Chen ChengSheng Lin YannRong

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A comprehensive evaluation of imidazole‐zinc reverse stain for current proteomic researches

PROTEOMICS (2009)

Ching‐Yu Lin Vinchi Wang Hao‐Ai Shui Rong‐Huay Juang Ai‐Ling Hour

In this paper, we comprehensively evaluated the capability of imidazole-zinc reverse stain (ZN) in comparative proteomics. Three commonly used protein gel staining methods, including silver (SN), SYPRO Ruby (SR), and CB stain were investigated alongside for comparison purpose. A transparency scanning procedure, which may deliver more even and contrasting gel images, was found best for documenting ZN stained gels. Our results showed that ZN was more sensitive than SN, SR, and CB. It may reveal as few as 1.8 ng of proteins in a gel. Moreover, ZN was found to provide a linear dynamic range of staining for revealing proteins up to 140 ng, and show an insignificant staining preference. To analyze a ZN stained 2-D gel image that generally comprises an apparent but even background, the Melanie 4 software was found more suitable than others. Furthermore, ZN demonstrated an equivalent or better MS compatibility than the other three staining methods. Intense and comprehensive MS profiles were frequently observed for ZN stained gel spots. Approximate two-third of ZN stained gel spots were successfully identified for protein identities. Taken together, our results suggest that the prompt, cost effective and versatile ZN is well suited for current proteomic researches.

Stain

Silver stain

10.1002/pmic.200700470

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Citations (22)

Investigation of the Correlation between Graves’ Ophthalmopathy and CTLA4 Gene Polymorphism

Journal of Clinical Medicine (2019)

Ding‐Ping Chen Yen-Chang Chu Ying-Hao Wen Wei-Tzu Lin Ai‐Ling Hour

Graves' disease (GD) is an autoimmune inflammatory disease, and Graves' ophthalmopathy (GO) occurs in 25-50% of patients with GD. Several susceptible genes were identified to be associated with GO in some genetic analysis studies, including the immune regulatory gene CTLA4. We aimed to find out the correlation of CTLA4 gene polymorphism and GO. A total of 42 participants were enrolled in this study, consisting of 22 patients with GO and 20 healthy controls. Chi-square or Fisher's exact test were used to appraise the association between Graves' ophthalmopathy and CTLA4 single nucleotide polymorphisms (SNPs). All regions of CTLA4 including promoter, exon and 3'UTR were investigated. There was no nucleotide substitution in exon 2 and exon 3 of CTLA4 region, and the allele frequencies of CTLA4 polymorphisms had no significant difference between patients with GO and controls. However, the genotype frequency of "TT" genotype in rs733618 significantly differed between patients with GO and healthy controls (OR = 0.421, 95%CI: 0.290-0.611, p = 0.043), and the "CC" and "CT" genotype in rs16840252 were nearly significantly differed in genotype frequency (p = 0.052). Haplotype analysis showed that CTLA4 Crs733618Crs16840252 might increase the risk of GO (OR = 2.375, 95%CI: 1.636-3.448, p = 0.043). In conclusion, CTLA4 Crs733618Crs16840252 was found to be a potential marker for GO, and these haplotypes would be ethnicity-specific. Clinical application of CTLA4 Crs733618Crs16840252 in predicting GO in GD patients may be beneficial.

Graves' ophthalmopathy

Genotype frequency

10.3390/jcm8111842

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Five Different Piscidins from Nile Tilapia, Oreochromis niloticus: Analysis of Their Expressions and Biological Functions

PLoS ONE (2012)

Kuan-Chieh Peng Shu‐Hua Lee Ai‐Ling Hour Chieh‐Yu Pan Lin-Han Lee

Piscidins are antimicrobial peptides (AMPs) that play important roles in helping fish resist pathogenic infections. Through comparisons of tilapia EST clones, the coding sequences of five piscidin-like AMPs (named TP1∼5) of Nile tilapia, Oreochromis niloticus, were determined. The complete piscidin coding sequences of TP1, -2, -3, -4, and -5 were respectively composed of 207, 234, 231, 270, and 195 bases, and each contained a translated region of 68, 77, 76, 89, and 64 amino acids. The tissue-specific, Vibrio vulnificus stimulation-specific, and Streptococcus agalactiae stimulation-specific expressions of TP2, -3, and -4 mRNA were determined by a comparative RT-PCR. Results of the tissue distribution analysis revealed high expression levels of TP2 mRNA in the skin, head kidneys, liver, and spleen. To study bacterial stimulation, S. agalactiae (SA47) was injected, and the TP4 transcript was upregulated by >13-fold (compared to the wild-type (WT) control, without injection) and was 60-fold upregulated (compared to the WT control, without injection) 24 h after the S. agalactiae (SA47) injection in the spleen and gills. Synthesized TP3 and TP4 peptides showed antimicrobial activities against several bacteria in this study, while the synthesized TP1, -2, and -5 peptides did not. The synthesized TP2, -3, and -4 peptides showed hemolytic activities and synthesized TP3 and TP4 peptides inhibited tilapia ovary cell proliferation with a dose-dependent effect. In summary, the amphiphilic α-helical cationic peptides of TP3 and TP4 may represent novel and potential antimicrobial agents for further peptide drug development.

Nile tilapia

Vibrio vulnificus

10.1371/journal.pone.0050263

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Additional file 5: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Figshare (2019)

Yongjun Wang Xiuting Hua Jingsheng Xu Zhichang Chen Tianqu Fan

Amino acid sequences of 16 species. (FASTA 133 kb)

Saccharum

Divergence (linguistics)

10.6084/m9.figshare.7628036

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Additional file 10: of Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum

Figshare (2019)

Yongjun Wang Xiuting Hua Jingsheng Xu Zhichang Chen Tianqu Fan

The non-synonymous (Ka) and synonymous (Ks) substitution ratios of each MGTs from 10 representative plants. (XLSX 804 kb)

Saccharum

Functional divergence

Divergence (linguistics)

10.6084/m9.figshare.7627922

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Identification of the Nanogold Particle-Induced Endoplasmic Reticulum Stress by Omic Techniques and Systems Biology Analysis

ACS Nano (2011)

Yen-Yin Tsai Yi-Huei Huang Ya-Li Chao Kuang-Yu Hu Li‐Te Chin

Growth inhibition and apoptotic/necrotic phenotype was observed in nanogold particle (AuNP)-treated human chronic myelogenous leukemia cells. To elucidate the underlying cellular mechanisms, proteomic techniques including two-dimensional electrophoresis/mass spectrometry and protein microarrays were utilized to study the differentially expressed proteome and phosphoproteome, respectively. Systems biology analysis of the proteomic data revealed that unfolded protein-associated endoplasmic reticulum (ER) stress response was the predominant event. Concomitant with transcriptomic analysis using mRNA expression, microarrays show ER stress response in the AuNP-treated cells. The ER stress protein markers' expression assay unveiled AuNPs as an efficient cellular ER stress elicitor. Upon ER stress, cellular responses, including reactive oxygen species increase, mitochondrial cytochrome c release, and mitochondria damage, chronologically occurred in the AuNP-treated cells. Conclusively, this study demonstrates that AuNPs cause cell death through induction of unmanageable ER stress.

Proteome

10.1021/nn2027775

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Citations (111)

A rice phenomics study—phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population

Plant Molecular Biology (2007)

Chyr-Guan Chern Ming‐Jen Fan Su‐May Yu Ai‐Ling Hour Po-Chang Lu

With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. As an important crop and a model organism, rice provides major insights into gene functions important for crop growth or production. Phenomics with detailed information about tagged populations provides a good tool for functional genomics analysis. By a T-DNA insertional mutagenesis approach, we have generated a rice mutant population containing 55,000 promoter trap and gene activation or knockout lines. Approximately 20,000 of these lines have known integration sites. The T0 and T1 plants were grown in net "houses" for two cropping seasons each year since 2003, with the mutant phenotypes recorded. Detailed data describing growth and development of these plants, in 11 categories and 65 subcategories, over the entire four-month growing season are available in a searchable database, along with the genetic segregation information and flanking sequence data. With the detailed data from more than 20,000 T1 lines and 12 plants per line, we estimated the mutation rates of the T1 population, as well the frequency of the dominant T0 mutants. The correlations among different mutation phenotypes are also calculated. Together, the information about mutant lines, their integration sites, and the phenotypes make this collection, the Taiwan Rice Insertion Mutants (TRIM), a good resource for rice phenomics study. Ten T2 seeds per line can be distributed to researchers upon request.

Phenomics

Insertional mutagenesis

Functional Genomics

10.1007/s11103-007-9218-z

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Citations (55)