Publications by authors named "Wei-Kuang Wang"

28 Publications

  • Page 1 of 1

Shift of bacterial communities in heavy metal-contaminated agricultural land during a remediation process.

PLoS One 2021 23;16(7):e0255137. Epub 2021 Jul 23.

Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan.

Anthropogenic activities accompanied by heavy metal waste threaten the environment. Heavy metal pollution alters the soil microbial community composition, and the microorganisms that adapt to this stress increase in abundance. The remediation process of contaminated soil not only reduces the concentration of heavy metals but also alters the bacterial communities. High-throughput 16S rDNA sequencing techniques were applied to understand the changes in soil microbial communities. Using the remediation approach of the soil mixing, the concentrations of heavy metals in the contaminated areas were diluted and the soil environment was changed. The change of soil environment as a disturbance contributed to the alteration of microbial diversity of the remediated areas. The pH and heavy metals (Cr, Cu, Ni, and Zn) were the most influential factors driving the changes in community structure. The bacterial community structure was significantly different among sample areas. The decrease of heavy metals in soil may be the important factors that changed the microbial composition. This study provides the better understanding of the changes in composition of microbial communities affected by the remediation process in heavy metal-contaminated soil.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255137PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8301633PMC
November 2021

Enhancing the compost maturation of swine manure and rice straw by applying bioaugmentation.

Sci Rep 2021 03 17;11(1):6103. Epub 2021 Mar 17.

Department of Environmental Engineering and Science, Feng Chia University, Taichung, 40724, Taiwan.

Microorganisms capable of decomposing cellulose, xylan, starch and protein were individually isolated from swine manure compost and soil in this study. The correlations with pH, carbon source concentration, C/N ratio and enzyme activity among these isolated microorganisms were also investigated. Furthermore, the effect of additional inoculation in the compost was studied by measuring variations in the C/N ratio, enzyme activity and compost maturation rate. The inoculated microorganisms used in this study included four bacterial isolates and one commercial microorganism Phanerochaete chrysosporium. The results indicated that the isolated Kitasatospora phosalacinea strain C1, which is a cellulose-degraded microorganism, presented the highest enzyme activity at 31 ℃ and pH 5.5, while the C/N ratio was 0.8%. The isolated xylan-degraded microorganism Paenibacillus glycanilyticus X1 had the highest enzyme activity at 45 ℃ and pH 7.5, while the C/N ratio was 0.5%. The starch-degraded microorganism was identified as Bacillus licheniformis S3, and its highest enzyme activities were estimated to be 31 ℃ and pH 7.5 while the C/N ratio was 0.8%. The highest enzyme activity of the protein-degraded microorganism Brevinacillus agri E4 was obtained at 45 ℃ and pH 8.5, while the C/N ratio was 1.0%. The rate of temperature increase in the compost inoculated with P. chrysosporium was only higher than that of the compost without inoculation, and its compost maturation level was also lower than that of other composts with additional inoculation. The optimal initial C/N ratio of the compost was 27.5 and the final C/N ratio was 18.9. The composting results also indicated that the secondary inoculation would benefit compost maturation, and the lowest final C/N ratio of 17.0 was obtained.
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http://dx.doi.org/10.1038/s41598-021-85615-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971061PMC
March 2021

Transcriptomic analysis elucidates the molecular processes associated with hydrogen peroxide-induced diapause termination in Artemia-encysted embryos.

PLoS One 2021 19;16(2):e0247160. Epub 2021 Feb 19.

Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan.

Treatment with hydrogen peroxide (H2O2) raises the hatching rate through the development and diapause termination of Artemia cysts. To comprehend the upstream genetic regulation of diapause termination activated by exterior H2O2 elements, an Illumina RNA-seq analysis was performed to recognize and assess comparative transcript amounts to explore the genetic regulation of H2O2 in starting the diapause termination of cysts in Artemia salina. We examined three groupings treated with no H2O2 (control), 180 μM H2O2 (low) and 1800 μM H2O2 (high). The results showed a total of 114,057 unigenes were identified, 41.22% of which were functionally annotated in at least one particular database. When compared to control group, 34 and 98 differentially expressed genes (DEGs) were upregulated in 180 μM and 1800 μM H2O2 treatments, respectively. On the other hand, 162 and 30 DEGs were downregulated in the 180 μM and 1800 μM H2O2 treatments, respectively. Cluster analysis of DEGs demonstrated significant patterns among these types of 3 groups. GO and KEGG enrichment analysis showed the DEGs involved in the regulation of blood coagulation (GO: 0030193; GO: 0050818), regulation of wound healing (GO:0061041), regulation of hemostasis (GO: 1900046), antigen processing and presentation (KO04612), the Hippo signaling pathway (KO04391), as well as the MAPK signaling pathway (KO04010). This research helped to define the diapause-related transcriptomes of Artemia cysts using RNA-seq technology, which might fill up a gap in the prevailing body of knowledge.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0247160PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894940PMC
September 2021

Complete mitochondrial genome of the freshwater fish (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis.

Zookeys 2020 18;1005:57-72. Epub 2020 Dec 18.

Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan.

The cyprinid genus Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of , which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of , and . The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the and groups, respectively. Species of , and are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.
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http://dx.doi.org/10.3897/zookeys.1005.57592DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7765746PMC
December 2020

Genetic diversity of (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan.

Mitochondrial DNA A DNA Mapp Seq Anal 2021 01 10;32(1):12-19. Epub 2020 Nov 10.

The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan.

Mitochondrial DNA cytochrome and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation ( =0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, , and , our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.
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http://dx.doi.org/10.1080/24701394.2020.1844678DOI Listing
January 2021

A full-scale study of high-rate anaerobic bioreactors for whiskey distillery wastewater treatment with size fractionation and metagenomic analysis of granular sludge.

Bioresour Technol 2020 Feb 18;306:123032. Epub 2020 Feb 18.

Department of Environmental Engineering and Science, Feng Chia University, Taichung 40724, Taiwan.

Two full-scale high-rate bioreactors, i.e. external circulation sludge bed (ECSB) and expanded granular sludge bed (EGSB), were monitored for three years. Their performances for treating wastewater in a whiskey distillery were compared in terms of COD, pH, alkalinity and VFA. Even though feed flowrate highly fluctuated, COD removals of ECSB and EGSB were both excellent (95.7 ± 1.3% and 94.8 ± 3.0%, respectively). The influent and effluent characteristics of ECSB reactor were profiled and urea and urethane were also detected. High-strength properties of raw spent wash were exhibited in TOC, soluble COD and BOD of 13500, 37750, and 1950 mg·L, respectively and characterized by GC-MS. Anaerobic granular sludge sampled from different heights of ECSB reactor were fractionated for demonstrating vertical size distributions. Moreover, major species found by next-generation sequencing technique were archaea, i.e. Methanosaeta and Methanolinea, while major bacteria were Bacteroidetes with minor Nitrospiraceae. This metagenomic analysis provided an insight of anaerobic microbial consortium.
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http://dx.doi.org/10.1016/j.biortech.2020.123032DOI Listing
February 2020

Population structure of : phylogeography and systematics.

Zookeys 2019 26;872:77-90. Epub 2019 Aug 26.

Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan.

(Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of using sequences of the mitochondrial DNA control region and cytochrome gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices N (0.532) and G (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus were estimated.
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http://dx.doi.org/10.3897/zookeys.872.33105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718371PMC
August 2019

Salmonella-Mediated Cytolethal Distending Toxin Transfer Inhibits Tumor Growth.

Hum Gene Ther 2018 11 23;29(11):1327-1335. Epub 2018 Jul 23.

3 Department of Biological Sciences, National Sun Yat-sen University , Kaohsiung, Taiwan .

The Salmonella enterica serovar Choleraesuis (S.C.) has potential as an antitumor agent because of its tumor-targeting characteristics. S.C. can also be used for specific delivery of therapeutic agents and continuous release during replication. Previously, we successfully used S.C. as a vector to transfer a therapeutic gene and oncolytic virus, which suggested that modified S.C. is suitable for incorporating other antitumor agents into a single system. Cytolethal distending toxin B (CdtB) produced by Campylobacter jejuni can induce tumor cell apoptosis. Here we coated CdtB with poly(allylamine hydrochloride) (PAH) to yield PAH-CdtB. Treatment of cells with PAH-coated CdtB induced apoptosis, demonstrating that the compound retained antitumor activity. Furthermore, S.C. coated with PAH-CdtB (CdtB-S.C.) maintained tumor-targeting activity and had an enhanced antitumor effect. Measurement of the cytotoxic effect of CdtB-S.C. in vitro in a tumor cell line showed increased apoptosis whereas treatment of tumor-bearing mice with CdtB-S.C. reduced tumor growth and prolonged survival. Taken together, our results provide evidence that Salmonella carrying CdtB could have application for the treatment of tumors.
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http://dx.doi.org/10.1089/hum.2018.030DOI Listing
November 2018

Mitochondrial diversity and phylogeography of Acrossocheilus paradoxus (Teleostei: Cyprinidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2018 12 31;29(8):1194-1202. Epub 2018 Jan 31.

j The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan.

Mitochondrial DNA cytochrome b sequences (1141 bp) in 229 specimens of Acrossocheilus paradoxus from 26 populations were identified as four lineages. The pairwise genetic distances among these four lineages ranged from 1.57 to 2.37% (mean= 2.00%). Statistical dispersal-vicariance analysis suggests that the ancestral populations were distributed over mainland China and Northern and Western Taiwan. Approximate Bayesian computation approaches show that the three lineages in Taiwan originated from the lineage in mainland China through three colonization routes during two glaciations. The results indicated that during the glaciation and inter-glacial periods, the Taiwan Strait was exposed and sank, which contributed to the dispersion and differentiation of populations. Furthermore, the populations of A. paradoxus colonized Taiwan through a land bridge to the north of the Formosa Bank, and the Miaoli Plateau in Taiwan was an important barrier that limited gene exchange between populations on both the sides.
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http://dx.doi.org/10.1080/24701394.2018.1431227DOI Listing
December 2018

The inhibition of indoleamine 2, 3-dioxygenase 1 by connexin 43.

Int J Med Sci 2017 19;14(12):1181-1188. Epub 2017 Sep 19.

Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.

Upregulation of connexin 43 (Cx43) showed potential in enhancing immune surveillance that was suppressed in the tumor microenvironment. The expression of indoleamine 2, 3-dioxygenase (IDO) is one of the crucial factors contributing to tumor immune tolerance by depletion of tryptophan and IDO-mediated tryptophan metabolites. Here, we aim to investigate the role of Cx43 in IDO production in murine tumor by using Cx43 inducers. Resveratrol (trans-3, 5, 4 '-trihydroxystilbene) is a natural plant-derived polyphenol possessing positive effect against cancer. serovar choleraesuis (S.C.) was proved to target and inhibit tumor growth. Both of them regulated Cx43 expression in tumor cells and led to either chemosensitizing or immune-activating. In this study, the correlation between Cx43 and IDO were determined by the treatment of resveratrol and S.C. Our data showed an increase in Cx43 while IDO protein and IDO-mediated inhibited effects on T cell decreased after tumor cells are given with resveratrol and S.C.

Treatments: All of which could be inhibited once the expression of Cx43 was blocked. Cx43 involved in IDO regulation might be useful in developing IDO-targeted cancer immune therapy.
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http://dx.doi.org/10.7150/ijms.20661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666550PMC
June 2018

Spatial genetic structure of the cyprinid fish Onychostoma lepturum on Hainan Island.

Mitochondrial DNA A DNA Mapp Seq Anal 2017 11 8;28(6):901-908. Epub 2016 Sep 8.

a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Lingang New City, Shanghai , P.R. China.

Population genetic structure of Onychostoma lepturum on Hainan Island was investigated based on mitochondrial CR + cyt b region in 63 specimens collected from four populations. Population analyses indicated significant genetic structure (F = 0.749) and displayed a significant relationship between phylogeny and geography (N = 0.750 and G = 0.140). Thirty-one mtDNA haplotypes were classified into four lineages, and these lineages had an almost allopatric distribution. The results of a statistical dispersal-vicariance analysis suggest that the ancestral populations were distributed widely on Hainan Island, and the rising of the central mountainous area of Hainan Island, the Wuzhi and Yinggeling Mountain Range, separated these four drainages into independent lineages. According to a spatial analysis of molecular variance analysis, we divided these populations into three units: ND, CH and WQ + LS, running into Qiongzhou Strait, the Gulf of Tokin and the South China Sea, respectively. According to our study, the exposure of straits and shelf under water retreat gave chances for population dispersion during the glaciations.
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http://dx.doi.org/10.1080/24701394.2016.1209193DOI Listing
November 2017

Origins of Semisulcospira libertina (gastropoda: semisulcospiridae) in Taiwan.

Mitochondrial DNA A DNA Mapp Seq Anal 2017 07 8;28(4):518-525. Epub 2016 Mar 8.

f Department of Biology, The Affiliated School of National Tainan First Senior High School , Tainan , Taiwan.

The most accepted hypothesis has suggested that the fauna in Taiwan Island originated from South China, but some studies supported the Japan, Ryukyu Archipelago, and Taiwan Islands as a unique biogeographical district. This study examines whether the populations of freshwater snail Semisulcospira libertina in Taiwan are closer to those in Japan based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Our study shows the populations in North Taiwan originated from Japan and the cyclic glacial caused the migrations among islands and continent repeatedly; the populations in South Taiwan might originate from South China or South Asia. Our results will not only affect the conclusions in phylogeography of freshwater species in Taiwan but also change the sampling plans in the future studies about evolutionary of freshwater species in East Asia.
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http://dx.doi.org/10.3109/24701394.2016.1149823DOI Listing
July 2017

Hinokitiol Inhibits Melanogenesis via AKT/mTOR Signaling in B16F10 Mouse Melanoma Cells.

Int J Mol Sci 2016 Feb 18;17(2):248. Epub 2016 Feb 18.

Department of Microbiology, School of Medicine, China Medical University, Taichung 404, Taiwan.

H inokitiol purified from the heartwood of cupressaceous plants has had various biological functions of cell differentiation and growth. Hinokitiol has been demonstrated as having an important role in anti-inflammation and anti-bacteria effect, suggesting that it is potentially useful in therapies for hyperpigmentation. Previously, hinokitiol inhibited the production of melanin by inhibiting tyrosinase activity. The autophagic signaling pathway can induce hypopigmentation. This study is warranted to investigate the mechanism of hinokitiol-induced hypopigmentation through autophagy in B16F10 melanoma cells. The melanin contents and expression of microthphalmia associated transcription factor (MITF) and tyrosinase were inhibited by treatment with hinokitiol. Moreover, the phosphorylation of the protein express levels of phospho-protein kinase B (P-AKT) and phospho-mammalian targets of rapamycin (P-mTOR) were reduced after hinokitiol treatment. In addition, the microtubule associated protein 1 light chain 3 (LC3) -II and beclin 1 (autophagic markers) were increased after the B16F10 cell was treated with hinokitiol. Meanwhile, hinokitiol decreased cellular melanin contents in a dose-dependent manner. These findings establish that hinokitiol inhibited melanogenesis through the AKT/mTOR signaling pathway.
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http://dx.doi.org/10.3390/ijms17020248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783978PMC
February 2016

The treatment of mouse colorectal cancer by oral delivery tumor-targeting Salmonella.

Am J Cancer Res 2015 15;5(7):2222-8. Epub 2015 Jun 15.

Graduate Institute of Basic Medical Science, School of Medicine, China Medical University Taichung 40404, Taiwan ; Department of Microbiology, School of Medicine, China Medical University Taichung 40404, Taiwan.

Systemic administration of Salmonella to tumor-bearing mice leads to its preferential accumulation in tumor sites, the enhancement of host immunity, and the inhibition of tumor growth. However, the underlying mechanism for Salmonella-induced antitumor immune response via oral delivery remained uncertain. Herein, we used mouse colorectal cancer (CT26) as tumor model to study the therapeutic effects after oral delivery of Salmonella. When orally administered into tumor-bearing mice, Salmonella significantly accumulated in the tumor sites, inhibited tumor growth and extended the survival of mice. No obvious toxicity was observed during orally administered Salmonella by examining body weight and inflammatory cytokines. As indoleamine 2, 3-dioxygenase 1 (IDO) is a crucial mediator for tumor-mediated immune tolerance, we examined the expression of IDO. We demonstrated that Salmonella inhibited IDO expression in mouse cancer cells. Furthermore, immunohistochemical studies of the tumors revealed the infiltration of neutrophils and T cells in mice treated with Salmonella. In conclusion, our results indicate that Salmonella exerts its tumoricidal effects and stimulates T cell activities by inhibiting IDO expression. Oral delivery of Salmonella may, represent a potential strategy for the treatment of tumor.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548333PMC
September 2015

Connexin 43 suppresses tumor angiogenesis by down-regulation of vascular endothelial growth factor via hypoxic-induced factor-1α.

Int J Mol Sci 2014 Dec 26;16(1):439-51. Epub 2014 Dec 26.

Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung 40404, Taiwan.

Previous work showed that connexin 43 (Cx43) reduced the expression of hypoxic-induced factor-1α (HIF-1α) in astrocytes. HIF-1α is a master transcription factor for angiogenesis in tumor. Angiogenesis is essential for tumor progression. Here, we investigated the role of Cx43 in vascular endothelial growth factor (VEGF) production and angiogenesis in murine tumor. In the study, mouse B16F10 and 4T1 cells were overexpressed or knockdown with Cx43. The expression profiles as well as activity of the treated cells were examined. Furthermore, reduced Cx43 expression in B16F10 and 4T1 cells causes increased expression of VEGF and enhanced the proliferation of endothelial cells. On the contrary, the expression of VEGF and the proliferation of endothelial were increased in the conditioned medium of Cx43-knockdown tumor cells. We subcutaneously transplanted Cx43-overexpressing B16F10 cells into mice to evaluate the roles of Cx43 in the tumor angiogenesis. Both tumor size and the number of vessels growing in the tumor were markedly decreased compare with control group. Our findings suggest that Cx43 inhibited tumor growth by reducing angiogenesis.
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http://dx.doi.org/10.3390/ijms16010439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307255PMC
December 2014

Hinokitiol induces autophagy in murine breast and colorectal cancer cells.

Environ Toxicol 2016 Jan 12;31(1):77-84. Epub 2014 Jul 12.

Department of Microbiology, School of Medicine, China Medical University, Taichung, Taiwan.

Hinokitiol is found in the heartwood of cupressaceous plants and possesses several biological activities. Hinokitiol may play an important role in anti-inflammation and antioxidant processes, making it potentially useful in therapies for inflammatory-mediated disease. Previously, the suppression of tumor growth by hinokitiol has been shown to occur through apoptosis. Programmed cell death can also occur through autophagy, but the mechanism of hinokitiol-induced autophagy in tumor cells is poorly defined. We used an autophagy inhibitor (3-methyladenine) to demonstrate that hinokitiol can induce cell death via an autophagic pathway. Further, we suggest that hinokitiol induces autophagy in a dose-dependent manner. Markers of autophagy were increased after tumor cells were treated with hinokitiol. In addition, immunoblotting revealed that the levels of phosphoprotein kinase B (P-AKT), phosphomammalian target of rapamycin (P-mTOR), and phospho-p70 ribosomal s6 kinase (P-p70S6K) in tumor cells were decreased after hinokitiol treatment. In conclusion, our results indicate that hinokitiol induces the autophagic signaling pathway via downregulation of the AKT/mTOR pathway. Therefore, our findings show that hinokitiol may control tumor growth by inducing autophagic signaling.
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http://dx.doi.org/10.1002/tox.22023DOI Listing
January 2016

Complete mitochondrial DNA genome of Metzia mesembrinum (Cypriniformes: Cyprinidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 13;27(1):214-5. Epub 2014 Feb 13.

g Department of Biotechnology , Asia University , Taichung , Taiwan.

In this study, we sequenced the complete mitochondrial genome of Metzia mesembrinum (Cypriniformes, Cyprinidae), an Endangered pelagic primary freshwater fish distributed in South China. This mitochondrial genome, consisting of 16,611 base pairs (bp), encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 936 bp long, was located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 26.83%, C 25.48%, A 32.01% and G 15.68%, with a slight AT bias of 58.84%.
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http://dx.doi.org/10.3109/19401736.2014.880894DOI Listing
September 2016

Complete mitochondrial DNA genome of Parazacco spilurus (Cypriniformes: Cyprinidae).

Mitochondrial DNA A DNA Mapp Seq Anal 2016 13;27(1):165-6. Epub 2014 Feb 13.

c Department of Environmental Engineering and Science .

In this study, we sequenced the complete mitochondrial genome of Parazacco spilurus (Cypriniformes, Cyprinidae). This mitochondrial genome, consisting of 16,612 base pairs (bp), encoded 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene synteny identical to that of typical vertebrates. Control region (D-Loop), of 926 bp in length, is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand shows T 26.91%, C 26.01%, A 30.45% and G 16.63%, with an AT bias of 57.36%.
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http://dx.doi.org/10.3109/19401736.2013.878926DOI Listing
September 2016

Resveratrol Enhances Chemosensitivity in Mouse Melanoma Model Through Connexin 43 Upregulation.

Environ Toxicol 2015 Jul 21;30(8):877-86. Epub 2014 Jan 21.

Graduate Institute of Basic Medical Science, School of Medicine, China Medical University, Taichung, Taiwan.

Although current studies indicate that resveratrol exhibits potential antitumor activities, the precise mechanisms of its beneficial effects combined with chemotherapy are not fully understood. This work is warranted to elucidate the underlying mechanism of antitumor effects by the combination therapy of resveratrol and cisplatin. The presence of functional gap junctions is highly relevant for the success of chemotherapy. Gap junctions mediate cell communication by allowing the passage of molecules from one cell to another. Connexin (Cx) 43 is ubiquitous and reduced in a variety of tumor cells. Cx43 may influence the response of tumor cells to treatments by facilitating the passage of antitumor drugs or death signals between neighboring tumor cells. Following resveratrol treatment, dose-dependent upregulation of Cx43 expressions was observed. In addition, gap junction intercellular communication was increased. To study the mechanism underlying these resveratrol-induced Cx43 expressions, we found that resveratrol induced a significant increase in mitogen-activated protein kinases (MAPK) signaling pathways. The MAPK inhibitors significantly reduced the expression of Cx43 protein after resveratrol treatment. Specific knockdown of Cx43 resulted in a reduction of cell death after resveratrol and cisplatin treatment. Our results suggest that treatment of resveratrol in tumor leads to increase Cx43 gap junction communication and enhances the combination of resveratrol and cisplatin therapeutic effects. © 2014 Wiley Periodicals, Inc. Environ Toxicol 30: 877-886, 2015.
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http://dx.doi.org/10.1002/tox.21952DOI Listing
July 2015

Genetic and physiological data suggest demographic and adaptive responses in complex interactions between populations of figs (Ficus pumila) and their pollinating wasps (Wiebesia pumilae).

Mol Ecol 2013 Jul;22(14):3814-32

Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, 100, Taiwan.

To study interactions between host figs and their pollinating wasps and the influence of climatic change on their genetic structures, we sequenced cytoplasmic and nuclear genes and genotyped nuclear microsatellite loci from two varieties of Ficus pumila, the widespread creeping fig and endemic jelly fig, and from their pollinating wasps, Wiebesia pumilae, found in Taiwan and on nearby offshore islands. Great divergence in the mitochondrial cytochrome c oxidase subunit I (mtCOI) with no genetic admixture in nuclear markers indicated that creeping- and jelly-fig wasps are genetically distinct. Compared with creeping-fig wasps, jelly-fig wasps also showed better resistance under cold (20 °C) than warm (25 and 30 °C) conditions in a survival test, indicating their adaptation to a cold environment, which may have facilitated population expansion during the ice age as shown by a nuclear intron and 10 microsatellite loci. An excess of amino acid divergence and a pattern of too many rare mtCOI variants of jelly-fig wasps as revealed by computer simulations and neutrality tests implied the effect of positive selection, which we hypothesize was associated with the cold-adaptation process. Chloroplast DNA of the two fig plants was completely segregated, with signs of genetic admixture in nuclear markers. As creeping- and jelly-fig wasps can pollinate creeping figs, occasional gene flow between the two figs is thus possible. Therefore, it is suggested that pollinating wasps may be playing an active role in driving introgression between different types of host fig.
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http://dx.doi.org/10.1111/mec.12336DOI Listing
July 2013

The extract of Rhodobacter sphaeroides inhibits melanogenesis through the MEK/ERK signaling pathway.

Mar Drugs 2013 Jun 3;11(6):1899-908. Epub 2013 Jun 3.

Asia-Pacific Biotech Developing, Inc., Kaohsiung 806, Taiwan.

Reducing hyperpigmentation has been a big issue for years. Even though pigmentation is a normal mechanism protecting skin from UV-causing DNA damage and oxidative stress, it is still an aesthetic problem for many people. Bacteria can produce some compounds in response to their environment. These compounds are widely used in cosmetic and pharmaceutical applications. Some probiotics have immunomodulatory activities and modulate the symptoms of several diseases. Previously, we found that the extracts of Rhodobacter sphaeroides (Lycogen™) inhibited nitric oxide production and inducible nitric-oxide synthase expression in activated macrophages. In this study, we sought to investigate an anti-melanogenic signaling pathway in α-melanocyte stimulating hormone (α-MSH)-treated B16F10 melanoma cells and zebrafish. Treatment with Lycogen™ inhibited the cellular melanin contents and expression of melanogenesis-related protein, including microphthalmia-associated transcription factor (MITF) and tyrosinase in B16F10 cells. Moreover, Lycogen™ reduced phosphorylation of MEK/ERK without affecting phosphorylation of p38. Meanwhile, Lycogen™ decreased zebrafish melanin expression in a dose-dependent manner. These findings establish Lycogen™ as a new target in melanogenesis and suggest a mechanism of action through the ERK signaling pathway. Our results suggested that Lycogen™ may have potential cosmetic usage in the future.
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http://dx.doi.org/10.3390/md11061899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721212PMC
June 2013

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae).

Gene 2012 May 9;499(1):194-201. Epub 2012 Mar 9.

Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.

Recovering the genetic divergence between species is one of the major interests in the evolutionary biology. It requires accurate estimation of the neutral substitution rates. Arabidopsis thaliana, the first whole-genome sequenced plant, and its out-crossing relatives provide an ideal model for examining the split between sister species. In the study, rates of molecular evolution at markers frequently used for systematics and population genetics, including 14 nuclear genes spanning most chromosomes, three noncoding regions of chloroplast genome, and one intron of mitochondrial genome, between A. thaliana and four relatives were estimated. No deviation from neutrality was detected in the genes examined. Based on the known divergence between A. thaliana and its sisters about 8.0-17.6 MYA, evolutionary rates of the eighteen genes were estimated. Accordingly, the ratio of rates of synonymous substitutions among mitochondrial, chloroplast and nuclear genes was calculated with an average and 95% confidence interval of 1 (0.25-1.75): 15.77 (7.48-114.09): 74.79 (36.27-534.61). Molecular evolutionary rates of nuclear genes varied, with a range of 0.383-0.856×10(-8) for synonymous substitutions per site per year and 0.036-0.081×10(-9) for nonsynonymous substitutions per site per year. Compared with orthologs in Populus, a long life-span tree, genes in Arabidopsis evolved faster in an order of magnitude at the gene level, agreeing with a generation time hypothesis. The estimated substitution rates of these genes can be used as a reference for molecular dating.
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http://dx.doi.org/10.1016/j.gene.2012.02.037DOI Listing
May 2012

Genetic population structure of the alpine species Rhododendron pseudochrysanthum sensu lato (Ericaceae) inferred from chloroplast and nuclear DNA.

BMC Evol Biol 2011 Apr 19;11:108. Epub 2011 Apr 19.

Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.

Background: A complex of incipient species with different degrees of morphological or ecological differentiation provides an ideal model for studying species divergence. We examined the phylogeography and the evolutionary history of the Rhododendron pseudochrysanthum s. l.

Results: Systematic inconsistency was detected between gene genealogies of the cpDNA and nrDNA. Rooted at R. hyperythrum and R. formosana, both trees lacked reciprocal monophyly for all members of the complex. For R. pseudochrysanthum s.l., the spatial distribution of the cpDNA had a noteworthy pattern showing high genetic differentiation (FST=0.56-0.72) between populations in the Yushan Mountain Range and populations of the other mountain ranges.

Conclusion: Both incomplete lineage sorting and interspecific hybridization/introgression may have contributed to the lack of monophyly among R. hyperythrum, R. formosana and R. pseudochrysanthum s.l. Independent colonizations, plus low capabilities of seed dispersal in current environments, may have resulted in the genetic differentiation between populations of different mountain ranges. At the population level, the populations of Central, and Sheishan Mountains may have undergone postglacial demographic expansion, while populations of the Yushan Mountain Range are likely to have remained stable ever since the colonization. In contrast, the single population of the Alishan Mountain Range with a fixed cpDNA haplotype may have experienced bottleneck/founder's events.
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http://dx.doi.org/10.1186/1471-2148-11-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096940PMC
April 2011

Conservation genetics and phylogeography of endangered and endemic shrub Tetraena mongolica (Zygophyllaceae) in Inner Mongolia, China.

BMC Genet 2011 Jan 4;12. Epub 2011 Jan 4.

Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.

Background: Tetraena mongolica (Zygophyllaceae), an endangered endemic species in western Inner Mongolia, China. For endemic species with a limited geographical range and declining populations, historical patterns of demography and hierarchical genetic structure are important for determining population structure, and also provide information for developing effective and sustainable management plans. In this study, we assess genetic variation, population structure, and phylogeography of T. mongolica from eight populations. Furthermore, we evaluate the conservation and management units to provide the information for conservation.

Results: Sequence variation and spatial apportionment of the atpB-rbcL noncoding spacer region of the chloroplast DNA were used to reconstruct the phylogeography of T. mongolica. A total of 880 bp was sequenced from eight extant populations throughout the whole range of its distribution. At the cpDNA locus, high levels of genetic differentiation among populations and low levels of genetic variation within populations were detected, indicating that most seed dispersal was restricted within populations.

Conclusions: Demographic fluctuations, which led to random losses of genetic polymorphisms from populations, due to frequent flooding of the Yellow River and human disturbance were indicated by the analysis of BEAST skyline plot. Nested clade analysis revealed that restricted gene flow with isolation by distance plus occasional long distance dispersal is the main evolutionary factor affecting the phylogeography and population structure of T. mongolica. For setting a conservation management plan, each population of T. mongolica should be recognized as a conservation unit.
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http://dx.doi.org/10.1186/1471-2156-12-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025899PMC
January 2011

Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.

New Phytol 2010 Oct 28;188(2):488-500. Epub 2010 Jul 28.

Department of Life Sciences, National Cheng-Kung University, Tainan, Taiwan.

• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
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http://dx.doi.org/10.1111/j.1469-8137.2010.03383.xDOI Listing
October 2010

Population history in Arabidopsis halleri using multilocus analysis.

Mol Ecol 2010 Aug 28;19(16):3364-79. Epub 2010 Jul 28.

Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.

A. halleri is a psuedometallophyte with a patchy distribution in Europe and is often spread by human activity. To determine the population history and whether this history is consistent with potential human effects, we surveyed nucleotide variation using 24 loci from 12 individuals in a large A. halleri population. The means of total and silent nucleotide variation (theta(W)) are within the range expected for the species. The population genetic neutrality tests Tajima's D and Wall's B had significant composite results rejecting panmixia, and Approximate Bayesian Computation analysis revealed that a subdivision model better explained the variation than the standard neutral model, refugia (or admixture), bottleneck or change of population size models. A categorical regression analysis further supports the subdivision model, and under the subdivision model, the neutrality tests are no longer significant. The best support was for two source populations, a situation consistent with the mixing of two populations possibly mediated by human activity. This scenario might limit the genetic diversity and adaptive potential of the population. The non-neutral population variation described here should be considered in bioinformatic searches for adaptation.
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http://dx.doi.org/10.1111/j.1365-294X.2010.04761.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921003PMC
August 2010

Diverse selective modes among orthologs/paralogs of the chalcone synthase (Chs) gene family of Arabidopsis thaliana and its relative A. halleri ssp. gemmifera.

Mol Phylogenet Evol 2007 Aug 25;44(2):503-20. Epub 2007 May 25.

Department of Life Sciences, Cheng-Kung University, Tainan 701, Taiwan.

As a model system, Arabidopsis thaliana and its wild relatives have played an important role in the study of genomics and evolution in plants. In this study, we examined the genetic diversity of the chalcone synthase (Chs) gene, which encodes a key enzyme of the flavonoid pathway and is located on chromosome five, as well as two Chs-like genes on the first and fourth chromosomes of Arabidopsis. The objectives of the study are to determine if natural selection operates differentially on the paralogs of the Chs gene family in A. thaliana and Arabidopsis halleri ssp. gemmifera. The mode of selection was inferred from Tajima's D values from noncoding and coding regions, as well as from the ratio of nonsynonymous to synonymous substitutions. Both McDonald-Kreitman and HKA tests revealed the effects of selection on the allelic distribution, except for the chromosome 1 paralog in ssp. gemmifera. The Chs gene on chromosome 5 was under purifying selection in both species. Significant, negative Tajima's D values at synonymous sites and positive Fay and Wu's H values within coding region, plus reduced genetic variability in introns, indicated effects of background selection in shaping the evolution of this gene region in A. thaliana. The Chs paralog on chromosome 1 was under positive selection in A. thaliana, while interspecific introgression and balancing selection determined the fates of the paralog and resulted in high heterogeneity in ssp. gemmifera. Local adaptation differentiated populations of Japan and China at the locus. In contrast, the other Chs-paralog of chromosome 4 was shaped by purifying selection in A. thaliana, while under positive selection in ssp. gemmifera, as indicated by dn/ds>1. Moreover, these contrasting patterns of selection have likely resulted in functional divergence in Arabidopsis, as indicated by radical amino acid substitutions at the chalcone synthase/stilbene synthase motif of the Chs genes. Unlike previous studies of the evolutionary history of A. thaliana, the high levels of genetic diversity in most gene regions of Chs paralogs and nonsignificant Tajima's D in the intron sequences of the Chs gene family in A. thaliana did not reflect the effects of a recent demographic expansion.
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http://dx.doi.org/10.1016/j.ympev.2007.05.006DOI Listing
August 2007

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB-rbcL noncoding spacer cpDNA.

J Plant Res 2005 Feb 13;118(1):1-11. Epub 2005 Jan 13.

Division of Botany, Taiwan Endemic Species Research Institute, Chi-Chi, Taiwan, 551.

Genetic variation in the atpB-rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB-rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (theta = 0.00343+/-0.00041). The distribution of genetic variation among populations agrees with an "isolation-by-distance" model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.
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http://dx.doi.org/10.1007/s10265-004-0185-zDOI Listing
February 2005
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