159 Works

Data from: A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts

Shang-Lin Chang, Jun-Yi Leu & Tien-Hsien Chang
Microbes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double-stranded RNA viruses is one such prominent example. Although the killer behaviour has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co-evolve with viruses remains limited. We investigated these issues using a panel of 81...

Data from: Ecologically differentiated, stress tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species.

Todd C. LaJeunesse, Drew C. Wham, D. Tye Pettay, John Everett Parkinson, Shashank Keshavmurthy & Chaolun Allen Chen
We used an integrative genetics approach using sequences of (1) nuclear ribosomal rDNA (internal transcribed spacers and partial large subunit rDNA), (2) single-copy microsatellite nuclear DNA, (3) chloroplast-encoded 23S rDNA, (4) mitochondrial cytochrome b, and (5) repeat variation at eight microsatellite markers, to test the hypothesis that the stress-tolerant, ‘morphologically cryptic’ Clade D Symbiodinium (Dinophyceae) was composed of more than one species. Concordant phylogenetic and population genetic evidence clearly differentiate separately evolving, reproductively isolated lineages....

Data from: Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior?

Viet-Dai Dang, Amir B. Cohanim, Silvia Fontana, Eyal Privman & John Wang
Queen discrimination behavior in the fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. In contrast, monogyne workers, all SB/SB, reject all additional queens...

Body size, light intensity and nutrient supply determine plankton stoichiometry in mixotrophic plankton food webs

Pei-Chi Ho, Chun-Wei Chang, Fuh-Kwo Shiah, Pei-Ling Wang, Chih-Hao Hsieh & Ken H. Andersen
Trophic strategy determines stoichiometry of plankton. In general, heterotrophic zooplankton have lower and more stable C:N and C:P ratios than photoautotrophic phytoplankton whereas mixotrophic protists, which consume prey and photosynthesize, have stoichiometry between zooplankton and phytoplankton. As trophic strategies change with cell size, body size may be a key trait influencing eukaryotic plankton stoichiometry. However, the relationship between body size and stoichiometry remains unclear. Here, we measured plankton size-fractionated C:N ratios under different intensities of...

Data from: Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

Jan Attig, Igor Ruiz De Los Mozos, Nejc Haberman, Zhen Wang, Warren Emmett, Kathi Zarnack, Julian König & Jernej Ule
Alu elements are retrotransposons that frequently form new exons during primate evolution. Here, we assess the interplay of splicing repression by hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and evolution of new Alu-exons. We identify 3100 new Alu-exons and show that NMD more efficiently recognises transcripts with Alu-exons compared to other exons with premature termination codons. However, some Alu-exons escape NMD, especially when an adjacent intron is retained, highlighting the importance of...

Genetic architecture associated with familial short stature

Ying-Ju Lin, Chi-Fung Cheng, Chung-Hsing Wang, Wen-Miin Liang, Chih-Hsin Tang, Li-Ping Tsai, Chien-Hsiun Chen, Jer-Yuarn Wu, Ai-Ru Hsieh, Ming Ta Michael Lee, Ting-Hsu Lin, Chiu-Chu Liao, Shao-Mei Huang, Yanfei Zhang, Chang-Hai Tsai & Fuu-Jen Tsai
Context Human height is an inheritable, polygenic trait under complex and multi-locus genetic regulation. Familial short stature (FSS; also called genetic short stature) is the most common type of short stature and is insufficiently known. Objective To investigate the FSS genetic profile and develop a polygenic risk predisposition score for FSS risk prediction. Design and Setting The FSS case group of Han Chinese ancestry was diagnosed by pediatric endocrinologists in Taiwan. Patients and Interventions The...

Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Flavia Termignoni-Garcia, Juan P. Jaramillo-Correa, Juan Chablé-Santos, Mark Liu, Allison J. Shultz, Scott V. Edwards, Patricia Escalante Pliego & Patricia Escalante-Pliego
Identifying the genetic basis of phenotypic variation and its relationship with the environment is key to understanding how local adaptations evolve. Such patterns are especially interesting among populations distributed across habitat gradients, where genetic structure can be driven by isolation by distance (IBD) and/or isolation by environment (IBE). Here, we used variation in ~1,600 high-quality SNPs derived from paired-end sequencing of double-digest restriction site-associated DNA (ddRAD-Seq) to test hypotheses related to IBD and IBE in...

Data from: Origins of East Asian Summer Monsoon Seasonality

John Chiang, Wenwen Kong, Chi-Hua Wu & David Battisti
Climatological model output used in Chiang et al. (2019), "Origins of East Asian Summer Monsoon Seasonality".

Eggs survive through avian guts—A possible mechanism for transoceanic dispersal of flightless weevils

Hui-Yun Tseng, Si‐Min Lin, Tsui‐Wen Li, Chia‐Hsin Liou, Ace Kevin S. Amarga & Analyn Cabras
How flightless animals disperse to remote oceanic islands is a key unresolved question in biogeography. The flightless Pachyrhynchus weevils represent repetitive colonization history in West Pacific islands, which attracted our interests about how some weevils have successfully dispersed in the reverse direction against the sea current. Here, we propose endozoochory as a possible mechanism that the eggs of the weevils might be carried by embedded in the fruits as the food of frugivorous birds. In...

Full-length fruit transcriptomes of southern highbush (Vaccinium sp.) and rabbiteye (V. virgatum Ait.) blueberry

Yi-Wen Wang & Savithri U. Nambeesan
Abstract Background Blueberries (Vaccinium sp.) are native to North America and breeding efforts to improve blueberry fruit quality are focused on improving traits such as increased firmness, enhanced flavor and greater shelf-life. Such efforts require additional genomic resources, especially in southern highbush and rabbiteye blueberries. Results We generated the first full-length fruit transcriptome for the southern highbush and rabbiteye blueberry using the cultivars, Suziblue and Powderblue, respectively. The transcriptome was generated using the Pacific Biosciences...

Additional file 3 of Genome-wide analyses identify novel risk loci for cluster headache in Han Chinese residing in Taiwan

Shih-Pin Chen, Chia-Lin Hsu, Yen-Feng Wang, Fu-Chi Yang, Ting-Huei Chen, Jia-Hsin Huang, Li-Ling Hope Pan, Jong-Ling Fuh, Hsueh-Chen Chang, Yi-Lun Lee, Hung-Ching Chang, Ko-Han Lee, Yu-Chuan Chang, Cathy Shen-Jang Fann & Shuu-Jiun Wang
Additional file 3: Supplemental Figure 2. Principal component analysis (PCA) plot. The horizontal and vertical axes are the first and second dimensions from principal component analysis based on the cluster headache GWAS samples. Blue dots indicate controls and red dots indicate patients.

Additional file 5 of Genome-wide analyses identify novel risk loci for cluster headache in Han Chinese residing in Taiwan

Shih-Pin Chen, Chia-Lin Hsu, Yen-Feng Wang, Fu-Chi Yang, Ting-Huei Chen, Jia-Hsin Huang, Li-Ling Hope Pan, Jong-Ling Fuh, Hsueh-Chen Chang, Yi-Lun Lee, Hung-Ching Chang, Ko-Han Lee, Yu-Chuan Chang, Cathy Shen-Jang Fann & Shuu-Jiun Wang
Additional file 5: Supplemental Figure 4. Q-Q plot of the gene-based test computed by MAGMA. The horizontal axis shows -log10 p values expected under the null distribution. The vertical axis shows observed -log10 p values.

Additional file 5 of Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas

Chia-Hui Lo, Deng-Chyang Wu, Shu-Wen Jao, Chang-Chieh Wu, Chung-Yen Lin, Chia-Hsien Chuang, Ya-Bo Lin, Chien-Hsiun Chen, Ying-Ting Chen, Jiann-Hwa Chen, Koung-Hung Hsiao, Ying-Ju Chen, Yuan-Tsong Chen, Jaw-Yuan Wang & Ling-Hui Li
Additional file 5. Genera included in co-abundance groups with significant alteration. T-test results and genera of the co-abundance groups with significant alteration among cancer tissues, polyp tissues, and non-neoplastic colon tissues.

Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas

Chia-Hui Lo, Deng-Chyang Wu, Shu-Wen Jao, Chang-Chieh Wu, Chung-Yen Lin, Chia-Hsien Chuang, Ya-Bo Lin, Chien-Hsiun Chen, Ying-Ting Chen, Jiann-Hwa Chen, Koung-Hung Hsiao, Ying-Ju Chen, Yuan-Tsong Chen, Jaw-Yuan Wang & Ling-Hui Li
Abstract Background Owing to the heterogeneity of microbiota among individuals and populations, only Fusobacterium nucleatum and Bacteroides fragilis have been reported to be enriched in colorectal cancer (CRC) in multiple studies. Thus, the discovery of additional bacteria contributing to CRC development in various populations can be expected. We aimed to identify bacteria associated with the progression of colorectal adenoma to carcinoma and determine the contribution of these bacteria to malignant transformation in patients of Han...

Additional file 7 of Enrichment of Prevotella intermedia in human colorectal cancer and its additive effects with Fusobacterium nucleatum on the malignant transformation of colorectal adenomas

Chia-Hui Lo, Deng-Chyang Wu, Shu-Wen Jao, Chang-Chieh Wu, Chung-Yen Lin, Chia-Hsien Chuang, Ya-Bo Lin, Chien-Hsiun Chen, Ying-Ting Chen, Jiann-Hwa Chen, Koung-Hung Hsiao, Ying-Ju Chen, Yuan-Tsong Chen, Jaw-Yuan Wang & Ling-Hui Li
Additional file 7: Figure S2. Silver staining of conditioned medium collected from Prevotella intermedia.

Real-world treatment patterns and outcomes among patients with advanced non-small-cell lung cancer with spindle cell and/or giant cell carcinoma

Chia-Ling Chang, Min-Shu Hsieh, Jin-Yuan Shih, Yi-Hsuan Lee, Wei-Yu Liao, Chia-Lin Hsu, Ching-Yao Yang, Kuan-Yu Chen, Jih-Hsiang Lee, Chao-Chi Ho, Tzu-Hsiu Tsai, James Chih-Hsin Yang & Chong-Jen Yu
Objectives:A definitive diagnosis of pulmonary sarcomatoid carcinoma cannot be made with small biopsies. In clinical practice, a diagnosis of advanced non-small-cell lung cancer with spindle cell and/or giant cell carcinoma (NSCLCsg), or possible sarcomatoid carcinoma, is acceptable. Therefore, we aimed to investigate the treatment patterns and outcomes of advanced NSCLCsg.Materials and methods:Between 01 January 2012 and 01 April 2021, patients with pathologically proven advanced NSCLCsg were enrolled. The choice of treatment was based on clinician...

A novel RBD-protein/peptide vaccine elicits broadly neutralizing antibodies and protects mice and macaques against SARS-CoV-2

Shixia Wang, Chang Yi Wang, Hui-Kai Kuo, Wen-Jiun Peng, Juin-Hua Huang, Be-Shen Kuo, Feng Lin, Yaw-Jen Liu, Zhi Liu, Huang-Ting Wu, Shuang Ding, Kou-Liang Hou, Jennifer Cheng, Ya-Ting Yang, Ming-Han Jiang, Min-Sheng Wang, Tony Chen, Wei Guo Xia, Ed Lin, Chung Ho Hung, Hui-Jung Chen, Zhonghao Shih, Yi Ling Lin, Valorie Ryan, Mei Mei Hu … & Farshad Guirakhoo
The development of safe and effective vaccines to respond to COVID-19 pandemic/endemic remains a priority. We developed a novel subunit protein-peptide COVID-19 vaccine candidate (UB-612) composed of: (i) receptor binding domain of SARS-CoV-2 spike protein fused to a modified single-chain human IgG1 Fc; (ii) five synthetic peptides incorporating conserved helper and cytotoxic T lymphocyte (Th/CTL) epitopes derived from SARS-CoV-2 structural proteins (three from S2 subunit, one from membrane and one from nucleocapsid), and one universal...

Additional file 1 of Genome-wide analyses identify novel risk loci for cluster headache in Han Chinese residing in Taiwan

Shih-Pin Chen, Chia-Lin Hsu, Yen-Feng Wang, Fu-Chi Yang, Ting-Huei Chen, Jia-Hsin Huang, Li-Ling Hope Pan, Jong-Ling Fuh, Hsueh-Chen Chang, Yi-Lun Lee, Hung-Ching Chang, Ko-Han Lee, Yu-Chuan Chang, Cathy Shen-Jang Fann & Shuu-Jiun Wang
Additional file 1: Supplementary Table 1. Demographics and of headache characteristics in patients with cluster headache.

Additional file 3 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 3. Extended Results and Methods.

Additional file 3 of Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Daphne Z. Hoh, Hsin-Han Lee, Naohisa Wada, Wei-An Liu, Min R. Lu, Cheng-Kuo Lai, Huei-Mien Ke, Pei-Feng Sun, Sen-Lin Tang, Wen-Hsin Chung, Ying-Lien Chen, Chia-Lin Chung & Isheng Jason Tsai
Additional file 3. Extended Results and Methods.

sj-docx-1-vmj-10.1177_1358863X221136163 – Supplemental material for Neighborhood characteristics and arterial stiffness among Black adults – Results from the Jackson Heart Study and Morehouse-Emory Cardiovascular Center for Health Equity

Shabatun J Islam, Jeong Hwan Kim, Xiaona Li, Yi-An Ko, Peter Baltrus, Gary F Mitchell, Ervin R Fox, Mahasin S Mujahid, Viola Vaccarino, Tené T Lewis, Herman A Taylor, Mario Sims & Arshed A Quyyumi
Supplemental material, sj-docx-1-vmj-10.1177_1358863X221136163 for Neighborhood characteristics and arterial stiffness among Black adults – Results from the Jackson Heart Study and Morehouse-Emory Cardiovascular Center for Health Equity by Shabatun J Islam, Jeong Hwan Kim, Xiaona Li, Yi-An Ko, Peter Baltrus, Gary F Mitchell, Ervin R Fox, Mahasin S Mujahid, Viola Vaccarino, Tené T Lewis, Herman A Taylor, Mario Sims and Arshed A Quyyumi in Vascular Medicine

Neighborhood characteristics and arterial stiffness among Black adults – Results from the Jackson Heart Study and Morehouse-Emory Cardiovascular Center for Health Equity

Shabatun J Islam, Jeong Hwan Kim, Xiaona Li, Yi-An Ko, Peter Baltrus, Gary F Mitchell, Ervin R Fox, Mahasin S Mujahid, Viola Vaccarino, Tené T Lewis, Herman A Taylor, Mario Sims & Arshed A Quyyumi
Introduction:Poor quality neighborhood environments are independent risk factors for cardiovascular disease (CVD) but are understudied in Black adults, who face large CVD health disparities. Arterial stiffness, a marker of early vascular aging, precedes development of hypertension and adverse CVD events but the effect of neighborhood on arterial stiffness among Black adults remains unknown.Objective:We compared the association between neighborhood environment and arterial stiffness among Black adults in Jackson, MS and Atlanta, GA.Methods:We studied 1582 Black adults...

Table S2: Zircon U–Pb geochronology and Hf isotopic compositions of igneous rocks from Sumatra: implications for the Cenozoic magmatic evolution of the western Sunda Arc

Yu-Ming Lai, Ping-Ping Liu, Sun-Lin Chung, Azman A. Ghani, Hao-Yang Lee, Long Xiang Quek, Shan Li, Muhammad Hatta Roselee, Sayed Murtadha, Lediyantje Lintjewas & Yoshiyuki Iizuka
Zircon U–Pb ages used in this study.

Influenza vaccination is associated with a reduced risk of invasive aspergillosis in high-risk individuals in Taiwan: a population-based cohort study

Yi-Jyun Chen, I-Feng Lin, Jen-Hsiang Chuang, Hung-Ling Huang & Ta-Chien Chan
Invasive aspergillosis (IA) has become the emerging life-threatening disease in recent years. Influenza has been identified as an independent risk factor for IA. Vaccination is the most effective way to prevent influenza, while whether it can reduce IA in high-risk population still uncertain. We aimed to investigate the association between influenza vaccination and the risk of IA in high-risk population. We performed a population-based cohort study of people who qualified for government-funded influenza vaccination and...

Data from: NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss

Tracey A. Ruhlman, Wang-Jung Chang, Jeremy J. W. Chen, Yao-Ting Huang, Ming-Tsair Chan, Jin Zhang, De-Chih Liao, John C. Blazier, Xiaohua Jin, Ming-Che Shih, Robert K. Jansen & Choun-Sea Lin
Background: Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes...

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