Hsiao-Che KuoPureCare Innovation · Research & Development
Hsiao-Che Kuo
PhD
About
77
Publications
10,636
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
859
Citations
Publications
Publications (77)
Environmental factors can cause changes in the content of the fungal genome during evolution. In this study, a fungus used as a biocontrol agent, Trichoderma virens FT-333 (from a tropical marine climate) has been isolated. The genome (38.6 Mbp; GC content, 49.43%) has a total of 12 751 proteins. Gene ontology (GO) terms (cellular component and mol...
Hypocrea jecorina is the sexual form of the industrial workhorse fungus Trichoderma reesei that secretes cellulases and hemicellulases to degrade lignocellulosic biomass into simple sugars, such as glucose and xylose. H. jecorina CBS999.97 is the only T. reesei wild isolate strain that is sexually competent in laboratory conditions. It undergoes a...
Neurospora crassa has a long history as an excellent model for genetic, cellular, and biochemical research. Although this fungus is known as a saprotroph, it normally appears on burned vegetations or trees after forest fires. However, due to a lack of experimental evidence, the nature of its association with living plants remains enigmatic. Here we...
The industrially important cellulolytic filamentous fungus Trichoderma reesei is the anamorph of the pantropical ascomycete Hypocrea jecorina. H. jecorina CBS999.97 strain undergoes a heterothallic reproductive cycle, and the mating yields fertilized perithecia imbedded in stromata. Asci in the perithecia contain 16 linearly arranged ascospores. He...
Fungi belonging to the Cordyceps species have long been used as food and herbal medicines in Asia and are especially popular as commercially available powdered supplements. Despite this acceptance and use, little is known of the phylogenetic relationships of the genus. Presently, the neighbor-joining method based on the ITS1, 5.8S rRNA, and ITS2 re...
Sexual reproduction is a key process influencing the evolution and adaptation of animals, plants, and many eukaryotic microorganisms, such as fungi. However, the sequential cell biology of fertilization and the associated nuclear dynamics after plasmogamy are poorly understood in filamentous fungi. Using histone-fluorescent parental isolates, we tr...
Sexual reproduction is a key process influencing the evolution and adaptation of animals, plants and many eukaryotic microorganisms, such as fungi. Mycologists have described the different fungal fruiting bodies, while geneticists have partly unravelled the regulation of sexual development. However, the sequential fungal cell biology of fertilisati...
Cancer is a major cause of death. The outcomes of current therapeutic strategies against cancer often ironically lead to even increased mortality due to the subsequent drug resistance and to metastatic recurrence. Alternative medicines are thus urgently needed. Cumulative evidence has pointed out that pterostilbene (trans-3,5-dimethoxy-4-hydroxysti...
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Fi...
List of the syntenic gene sets between the two genomes of Heterobasidion spp.
Cordyceps sensu lato (s.l.) species have been used as herbal medicines and one of their main constituents is cordycepin. As the genome sequencing techniques become cheaper and more popular, more entomogenous fungal genomes have been sequenced and published. Here, we constructed a phylogenetic tree based on 18S rRNA sequences from Cordyceps fungi an...
Analysis of D-loop region in mitochondria of 20 groupers collected from two different regions shows that there are 18 single nucleotide polymorphic (SNP) sites which made up 8 different haplotypes. Giant grouper broodstocks from Malaysia (M-type) and Philippine (P-type) coastal regions do not share common haplotypes and 2 distinctive haplogroups ca...
Laccases, multi-copper-containing proteins, can catalyze the oxidation of phenolic substrates and have diverse functions such as a virulence factor in fungi. However, limited information can be found on the role of laccases in the interaction of Heterobasidion annosum s.s. to its host plant. Due to genome availability of the close-related species H...
NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bio...
Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals' fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as...
The process of mating in Basidiomycota is regulated by homeodomainencoding genes (HD) and pheromones and G protein-coupled pheromone receptor genes (P/R). Whether these genes are actually involved in determining mating type distinguishes mating systems that are considered tetrapolar (two locus) from bipolar (one locus). Polyporales are a diverse gr...
287 genes are at least two-fold up-regulated (p value <0.05) under 4 sexually potent conditions (i.e., W-12L12D, W-12D12L, W-24D and E-24D) in comparison with those under the three sexually impotent conditions (i.e., E-12D12L, E-12L12D, E-24D).
(XLS)
193 genes were at least two-fold down-regulated (p value <0.05) under 4 sexually potent conditions (i.e., W-12L12D, W-12D12L, W-24D and E-24D) in comparison with those under the four sexually impotent conditions (i.e., E-12D12L, E-12L12D, E-24L and W-24L).
(XLS)
Nucleotide sequence of primers used for preparing DNA probes in Northern blot analysis and for qRT-PCR analysis.
(DOC)
Groupers of the Epinephelus spp. are an important aquaculture species of high economic value in the Asia Pacific region. They are susceptible to piscine nodavirus infection, which results in viral nervous necrosis disease. In this study, a rapid and sensitive automated microfluidic chip system was implemented for the detection of piscine nodavirus;...
Electropherograms of the RT-PCR products from purified RNA. A. Slab-gel electropherograms for the amplified PCR products from fish tissues using the newly developed micro PCR module. (Lane M: 100-bp DNA ladders; 1: RT-PCR products from brain tissues of E. lanceolatus). B. Electropherograms of the RT-PCR products (203 bps) from purified RNA. The min...
Fish farming protocols. A. Indoor protocol; the temperature and the pH of the seawater are controlled. The fish tank is isolated from outside elements, including fish-feeding birds and sunlight. B. Semi-outdoor protocol; the fish tank is isolated from fish-feeding birds, but sunlight can penetrate inside. C. Outdoor protocol; the culturing tank is...
Virus isolates from infected grouper fish in four different fish farms.
(DOC)
Examination of grouper fish farms in Cigu, Jiading, Kunshen and Linyuan for nervous necrosis virus (NNV) infection by microfluidic chip analysis.
(DOC)
Three examinations (Batch I, II, and III) of the Linyuana grouper fish farm for nervous necrosis virus (NNV) infection by microfluidic chip analysis.
(DOC)
The detection of virus on slab-gel electropherograms by using direct lysis method. A. Slab-gel electropherograms of RT-PCR products. Lane M: 100-bp DNA ladders (Yeastern Biotech Corp., Taiwan); Lanes 1–5 contain samples with different viral RNA concentrations of 104, 103, 102, 50, and 25 (copies·µL−1), respectively. B. Comparison of pure RNA (isola...
Examination of the Anping grouper fish farm for nervous necrosis virus (NNV) infection by microfluidic chip analysis.
(DOC)
Comparison of microfluidic chip and conventional RT-PCR methods for nervous necrosis virus (NNV) detection.
(DOC)
Specificity of the microfluidic chip method.
(DOC)
The locations of sampling grouper fish farms in Taiwan. Taiwan is located between tropical and subtropical regions. The grouper aquacultures are mainly gathered in southern Taiwan due to the grouper fish preferred warm water temperature. Black circles indicate five major regions of sampling grouper aquaculture farms. The open circle indicates the l...
The electropherograms of the RT-PCR products from purified RNA. The minimum concentration detected on the CE module was 3 copies/µL (Kuo et al. unpublished). Each sample includes a mixture of DNA markers and RT-PCR products obtained from the infected grouper. Eleven peaks (corresponding to the DNA markers, added to samples post-amplification) and a...
Evaluation of multiplex RT-PCR with ex vivo samples (infected fish). M. DNA marker; lane 1, NNV (nodavirus); lane 2, V. anguillarum; lane 3, iridovirus; lane 4, NNV (nodavirus)+V. anguillarum; lane 5, NNV (nodavirus)+iridovirus; lane 6, V. anguillarum+iridovirus; lane 7, NNV (nodavirus)+V. anguillarum+iridovirus.
(TIF)
Infection of virus (such as nodavirus and iridovirus) and bacteria (such as Vibrio anguillarum) in farmed grouper has been widely reported and caused large economic losses to Taiwanese fish aquaculture industry since 1979. The multiplex assay was used to detect dual viral infection and showed that only nervous necrosis virus (NNV) can be detected t...
Chemokine (C-X-C motif) receptor 4 (CXCR4) from orange-spotted grouper (Epinephelus coioides) was identified and characterized in this study. gCXCR4 shared common features in protein sequence and predicted structure of CXCR4 family. This suggested that gCXCR4 is a member of G protein-coupled receptors with seven transmembrane domains. The expressio...
Viral nervous necrosis caused by nervous necrosis virus (NNV) exacts a high mortality and results in huge economic losses
in grouper aquaculture in Taiwan. The present study developed a real-time quantitative PCR (qPCR) method for NNV monitoring.
The assay showed a strong linear correlation (r2 = 0.99) between threshold cycle (CT) and RNA quantitie...
Perithecial neck phototropisms in response to unilateral light of different wavelengths. (A–C) Positive neck phototropisms in response to white light (A, fluence rate 3.4 µM/m2*s), blue light (B, wavelength: 470 nm; fluence rate 6.3 µM/m2*s), and green light (C, wavelength: 530 nm; fluence rate 3.4 µM/m2*s). (D, E) No neck phototropisms under red l...
Comparisons of different genomic regions.
(4.61 MB XLS)
OrthoMCL orthogroups.
(1.66 MB XLS)
Genome integrity genes.
(0.35 MB XLS)
Homologs to genes involved in light signaling and regulation.
(0.05 MB PDF)
Genes with putative functions in calcium signaling.
(0.07 MB PDF)
Phylogenetic analysis of orthogroups 49 (A) and 180 (B) and related orthogroups. With the exception of orthogroup 6050, which is split in two parts, all orthogroups that were found by OrthoMCL are supported by phylogenetic analysis. Most orthogroups contain one member each in S. macrospora, N. crassa, and N. discreta, but orthogroups 49 and 180 con...
Regions of high similarity within four fungal genomes. Each genome sequence was compared to itself with BLASTN with e-value <10−150. Dot plot visualization was done with Combo (Engels et al. 2006, Bioinformatics 22: 1782–1783). The M. grisea genome contains a high amount of repeated DNA (Dean et al. 2005, Nature 434 :980–986), and this is reflected...
Comparison of RIP indices in the S.macrospora and N. crassa genomes. (A) No evidence for large regions with RIP in the S. macrospora genome. The substrate ([CA+TG]/[AC+GT]; orange) and product (TpA/ApT; dark green) RIP indices were calculated for all unscaffolded contigs (nt 1 to 2,865,981), the mtDNA (nt 2,865,982 to 2,954,404) and random scaffold...
Orthologs between S. macrospora and N. crassa.
(1.02 MB XLS)
Next-generation sequencing of the S. macrospora genome. (A) Summary of the Illumina/Solexa and 454 sequences that were obtained. (B) Maximum contig lengths (N max) and N50 values for assemblies with different k-values (hash length in Velvet) for the Illumina/Solexa data alone or in combination with the 454 data. The combined assembly with the highe...
Assemblies with different coverage levels of short reads. Assemblies were done with Velvet 0.7.56 with k = 25. N50, maximum contig length (Nmax), the number of gaps that Velvet introduced within contigs and the total length of gaps within the assembly are given for different combinations of 454 coverage (x-axis), coverage from a 300 bp Solexa paire...
The mitochondrial genome of S. macrospora. (A) Schematic map of the mitochondrial genome. Size 88,423 bp, scale in kb indicated on the inner circle. Blue: ribosomal RNAs, green: tRNAs, red: protein coding genes, orange on the inner circle: open reading frames within introns of protein coding genes. Note that all predicted genes are encoded on the s...
Summary of all proteins in S. macrospora that are predicted to be PKSs or NRPSs.
(0.44 MB TIF)
Overview of predicted S. macrospora genes.
(7.09 MB XLS)
OrthoMCL family species count.
(1.18 MB XLS)
Genes with putative functions as motor proteins.
(0.07 MB PDF)
Genes with putative functions in MAP kinase and phospholipid signaling.
(0.09 MB PDF)
Histograms of % pairwise identity between S. macrospora and N. crassa for different genomic regions. CDSs, introns, and regions upstream of CDSs (in 1 kb steps ranging from 1 to 4 kb) were used for comparison. Only those upstream regions were used that do not overlap with a protein coding region. Each region was used only once even if it is upstrea...
Expression of S. macrospora genes that are orthologs of genes involved in conidiation in N. crassa. Transcript levels were compared between sexual development and vegetative growth. Expression data are the results of two independent experiments and were determined by quantitative real time PCR. The red dashed line indicates two-fold upregulation. I...
The het-6/un-24 locus from S. macrospora is syntenic to the OR allele of N. crassa. (A) Region from S. macrospora scaffold 5 and N. crassa scaffold 8 containing het-6 and un-24 genes. Homologous genes are given in the same color. The two different allelic combinations of het-6 and un-24 in N. crassa, Oak Ridge (OR) and Panama (PA), are indicated. T...
Phylogenetic analysis of the UbiA prenyltransferase family proteins from 12 fungi. The S. macrospora protein SMAC_01190 clusters in a group of “outsider” proteins with not quite clear phylogenetic resolution (bootstrap support of only 60 % as indicated in a red circle), most likely due to gene family expansion in Aspergillus/Neosartorya/Stagonospor...
Assemblies with different coverage levels.
(0.19 MB PDF)
Orphan genes.
(0.37 MB XLS)
hmmpfam predictions.
(1.22 MB XLS)
Homologs to genes involved in senescence.
(0.07 MB PDF)
Known and putative meiosis genes.
(0.09 MB XLS)
S. macrospora homologs of genes involved in heterokaryon incompatibility from different ascomycetes.
(0.06 MB PDF)
Predicted subcellular localizations, signal peptides, and transmembrane domains for the S. macrospora proteins.
(0.08 MB PDF)
S. macrospora homologs of conidiation-related genes from different ascomycetes.
(0.07 MB PDF)
Predicted polyketide synthases (PKS), non-ribosomal peptide synthases (NRPS), and fatty acid synthases (FAS).
(0.06 MB PDF)
Parameters used for the assembly of the S. macrospora genome.
(0.05 MB PDF)
A putative polyketide biosynthesis cluster that is partly conserved in S. macrospora and Phaeosphaeria nodorum.
(0.06 MB PDF)
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic...
Neurospora crassa macroconidia form germ tubes that are involved in colony establishment and conidial anastomosis tubes (CATs) that fuse to
form interconnected networks of conidial germlings. Nuclear and cytoskeletal behaviors were analyzed in macroconidia, germ
tubes, and CATs in strains that expressed fluorescently labeled proteins. Heterokaryons...
A method for distinguishing isolates of the fungi belonging to genus Cordyceps, used as
food/medicine in Eastern Asia, was developed. A PCR-single stranded conformation
polymorphism-based profile was applied and established on the ITS2 region of rDNA
for molecular typing in 48 different isolates of Cordyceps species. Compared with the
DNA sequencin...
Cordyceps sinensis (Berk.) Sacc., which is a part of traditional Chinese medicine, has
been used as a tonic food and herbal medicine in Asia for centuries. C. sinensis is sold
as powders, and the quality is often questionable. To confirm the quality of C. sinensis,
products were purchased from different supermarkets in Taiwan. Product samples
were...
This study is aimed at evaluating the effect of Aspergillus oryzae fermentation extract (AFE) on corn silage fermentation characteristics. Trial included two groups of treatments, with or without AFE inclusion in corn ensilage. Sixty corn silage containers, including two treatments with thirty replicates each, were processed in a laboratory scale m...
