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2,286 results on '"Liao, Hui"'

1. Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Author

Smith, Alexander, Fletcher, Jessica, Swinnen, Janne, Jonckheere, Karl, Bazzicalupo, Anna, Liao, Hui-Ling, Ragland, Greg, Colpaert, Jan, Lipzen, Anna, Tejomurthula, Sravanthi, Barry, Kerrie, Grigoriev, Igor V, Ruytinx, Joske, and Branco, Sara

Subjects
Microbiology, Biological Sciences, Genetics, Zinc, Mycorrhizae, Gene Expression Regulation, Fungal, Transcriptome, Gene Expression Profiling, Basidiomycota, Oxidative Stress, gene expression, metal, zinc, stress, tolerance, fungi, Biochemistry and cell biology, Statistics
Abstract

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in the expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.

Published
2024

4. Workplace Resilience and Stress Among Certified Nursing Assistants in Long-Term Care Institutions During the COVID-19 Pandemic

Author

Kuo, Ju-Chuan, Liao, Hui-Yen, Chen, Shiu-Ping, and Pai, Hsiang-Chu

Subjects
Geriatric nursing -- Practice, Epidemics -- Psychological aspects -- Social aspects -- United States, Job stress -- Risk factors -- Prevention, Resilience (Personality trait) -- Analysis, Health, Seniors
Abstract

Purpose: To explore the relationship among resilience, stress, and demographic factors in certified nursing assistants (CNAs) who worked in long-term care institutions during the coronavirus disease 2019 pandemic. Method: A cross-sectional correlation-based research design was used. Data were collected using a demographic questionnaire, Connor-Davidson Resilience Scale, and Occupational Stress Scale. CNAs from 21 long-term care institutions in Taiwan were recruited. Results: This study included 118 female and 26 male CNAs (response rate = 80%). Mean age was 46.8 years. A moderately negative correlation was found between workplace resilience and stress. Overall, being a woman and parent were found to be significantly correlated with CNAs' resilience. Furthermore, resilience and shift work were important predictors of stress. Conclusion: We suggest that leadership and management pay more attention to CNAs' basic demographic background information. Furthermore, timely, relevant strategies can be provided to enhance resilience and reduce workplace stress. [Journal of Gerontological Nursing, 50(7), 19–26.], The number of certified nursing assistants (CNAs) joining care teams has gradually increased owing to the increasing demand for long-term care. However, results of two systematic literature reviews indicated that [...]

Published
2024
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8. Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.

Author

Ke, Yi-Hong, Branco, Sara, Bazzicalupo, Anna, Nguyen, Nhu, Liao, Hui-Ling, Kennedy, Peter, Bruns, Thomas, Kuo, Alan, LaButti, Kurt, Barry, Kerrie, Grigoriev, Igor, and Vilgalys, Rytas

Subjects
Rhizopogon, Suillus, balancing selection, breeding system, evolution, fungi, homeodomain protein, mating, self-incompatibility, Evolution, Molecular, Plant Breeding, Basidiomycota, Genomics, Polymorphism, Genetic, Genes, Mating Type, Fungal, Phylogeny, Fungi
Abstract

Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.

Published
2023

23. Thousands of small, novel genes predicted in global phage genomes

Author

Fremin, Brayon J, Bhatt, Ami S, Kyrpides, Nikos C, Consortium, Global Phage Small Open Reading Frame, Sengupta, Aditi, Sczyrba, Alexander, da Silva, Aline Maria, Buchan, Alison, Gaudin, Amelie, Brune, Andreas, Hirsch, Ann M, Neumann, Anthony, Shade, Ashley, Visel, Axel, Campbell, Barbara, Baker, Brett, Hedlund, Brian P, Crump, Byron C, Currie, Cameron, Kelly, Charlene, Craft, Chris, Hazard, Christina, Francis, Christopher, Schadt, Christopher W, Averill, Colin, Mobilian, Courtney, Buckley, Dan, Hunt, Dana, Noguera, Daniel, Beck, David, Valentine, David L, Walsh, David, Sumner, Dawn, Lymperopoulou, Despoina, Bhaya, Devaki, Bryant, Donald A, Morrison, Elise, Brodie, Eoin, Young, Erica, Lilleskov, Erik, Högfors-Rönnholm, Eva, Chen, Feng, Stewart, Frank, Nicol, Graeme W, Teeling, Hanno, Beller, Harry R, Dionisi, Hebe, Liao, Hui-Ling, Beman, J Michael, Stegen, James, Tiedje, James, Jansson, Janet, VanderGheynst, Jean, Norton, Jeanette, Dangl, Jeff, Blanchard, Jeffrey, Bowen, Jennifer, Macalady, Jennifer, Pett-Ridge, Jennifer, Rich, Jeremy, Payet, Jérôme P, Gladden, John D, Raff, Jonathan D, Klassen, Jonathan L, Tarn, Jonathan, Neufeld, Josh, Gravuer, Kelly, Hofmockel, Kirsten, Chen, Ko-Hsuan, Konstantinidis, Konstantinos, DeAngelis, Kristen M, Partida-Martinez, Laila P, Meredith, Laura, Chistoserdova, Ludmila, Moran, Mary Ann, Scarborough, Matthew, Schrenk, Matthew, Sullivan, Matthew, David, Maude, O'Malley, Michelle A, Medina, Monica, Habteselassie, Mussie, Ward, Nicholas D, Pietrasiak, Nicole, Mason, Olivia U, Sorensen, Patrick O, de los Santos, Paulina Estrada, Baldrian, Petr, McKay, R Michael, Simister, Rachel, Stepanauskas, Ramunas, Neumann, Rebecca, Malmstrom, Rex, Cavicchioli, Ricardo, Kelly, Robert, Hatzenpichler, Roland, Stocker, Roman, Cattolico, Rose Ann, Ziels, Ryan, and Vilgalys, Rytas

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Generic health relevance, Bacteriophages, Genome, Viral, Genomics, Microbiota, Phylogeny, Global Phage Small Open Reading Frame (GP-SmORF) Consortium, CP: Microbiology, MetaRibo-Seq, comparative genomics, gene families, microbiome, phage, sORFs, small genes, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Small genes (40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Published
2022

50. Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi

Author

Lofgren, Lotus A, Nguyen, Nhu H, Vilgalys, Rytas, Ruytinx, Joske, Liao, Hui‐Ling, Branco, Sara, Kuo, Alan, LaButti, Kurt, Lipzen, Anna, Andreopoulos, William, Pangilinan, Jasmyn, Riley, Robert, Hundley, Hope, Na, Hyunsoo, Barry, Kerrie, Grigoriev, Igor V, Stajich, Jason E, and Kennedy, Peter G

Subjects
Microbiology, Biological Sciences, Genetics, Biotechnology, Human Genome, Evolution, Molecular, Fungi, Genome, Fungal, Genomics, Mycorrhizae, Pinus, Specialization, genomics, G&#8208, protein coupled receptors, host specificity, secondary metabolites, small secreted proteins, Suillus, G-protein coupled receptors, Agricultural and Veterinary Sciences, Plant Biology & Botany, Plant biology, Climate change impacts and adaptation, Ecological applications
Abstract

While there has been significant progress characterizing the 'symbiotic toolkit' of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understood. We conducted a comparative genomic analysis of ECM fungal host specialists and generalists, focusing on the specialist genus Suillus. Global analyses of genome dynamics across 46 species were assessed, along with targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins (SSPs), secondary metabolites (SMs) and G-protein coupled receptors (GPCRs). Relative to other ECM fungi, including other host specialists, Suillus had highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions. Targeted analyses supported a role for SMs but not SSPs or GPCRs in Suillus host specificity. Phylogenomic-based ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches between white and red pine hosts. These results suggest that like other defining characteristics of the ECM lifestyle, host specificity is a dynamic process at the genome level. In the case of Suillus, both SMs and pathways involved in the deactivation of reactive oxygen species appear to be strongly associated with enhanced host specificity.

Published
2021

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