Complete chloroplast genome of Angelica hirsutiflora Liu et al. 1961 (Apiaceae).

Angelica hirsutiflora Liu et al.1961, is a perennial herb in the Apiaceae family that is endemic to Taiwan. In this study, the complete circular chloroplast genome of A. hirsutiflora was reconstructed and annotated using Illumina sequencing. The size of the chloroplast genome is 154,266 bp, consisting of two inverted repeats (IRs, 25,075 bp) separated by a large single-copy region (LSC, 86,569 bp) and a small single-copy region (SSC, 17,547 bp). The GC content of the chloroplast genome is 37.6%. There are 114 different genes in the chloroplast genome of A. hirsutiflora, including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that A. hirsutiflora forms a distinct clade, and separated from other species within the genus Angelica. This study provided insights into the evolutionary relationships among different species of Angelica.

Complete chloroplast genome and phylogenetic analysis of Bupleurum kaoi Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

Bupleurum kaoi Liu, Chao, and Chuang is an endemic and endangered herb in Taiwan. In this study, the complete circular chloroplast genome of B. kaoi was reconstructed and annotated using Illumina sequencing. The genome size of B. kaoi is 155,938 bp, including a pair of inverted repeat regions (IRs: 26308 bp), separated by a large single-copy (LSC) region of 85,784 bp and a small single-copy (SSC) region of 17,538 bp. The GC content of the chloroplast genome is 37.6%. There are 113 different genes in the chloroplast genome of B. kaoi, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that Bupleurum species is the monophyletic group, and B. kaoi belongs to subgenus Bupleurum and is closely related to B. scorzonerifolium.

Demographic history and population genetic structure of Anisakis pegreffii in the cutlassfish Trichiurus japonicus along the coast of mainland China and Taiwan.

Studying the genetic diversity of nematode parasite populations is crucial to gaining insight into parasite infection dynamics and informing parasite phylogeography. Anisakiasis is a zoonotic disease caused by the consumption of infectious third-stage larvae (L3) of Anisakis spp. carried by marine fish. In the present study, a total of 206 mitochondrial DNA sequences (cytochrome c oxidase 2, cox2) were used to study the genetic diversity, genetic structure, and historical demography of twelve A. pegreffii populations from Trichiurus japonicas along the coast of mainland China and Taiwan. Two distinct evolutionary lineages of A. pegreffii and no significant genealogical structures corresponding to sampling localities suggested that isolation in the marginal seas shaped their patterns of phylogeographic distribution along the coast of mainland China and Taiwan during glaciation with lower sea levels. Furthermore, pairwise FST values and AMOVA did not indicate any significant genetic differentiation among groups with no relation to the geographic area, which might be attributed to fewer barriers to gene flow as well as large population sizes. The results of the neutrality test, mismatch distribution, and Bayesian skyline plot analyses showed that entire population underwent population expansion during the late Pleistocene. Analysis of the demographic history revealed that A. pegreffii underwent historical lineage diversification and admixture due to secondary contact based on ABC analysis. The present research represents the first definitive population structure and demographic history across sampling locations of A. pegreffii along the coast of mainland China and Taiwan.

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

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.

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

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 â„ƒ 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 â„ƒ 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 â„ƒ 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 â„ƒ 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.

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

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.

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

Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus 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 (FST=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 R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, 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.

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

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 BOD5,20°C of 13500, 37750, and 1950 mg·L-1, 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.

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

The cyprinid genus Onychostoma 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 O. lepturum, 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 Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis 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.

Population structure of Aphyocypris normalis: phylogeography and systematics.

Aphyocypris normalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A. normalis using sequences of the mitochondrial DNA control region and cytochrome b 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 A. normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices NST (0.532) and GST (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 Aphyocypris were estimated.

Salmonella-Mediated Cytolethal Distending Toxin Transfer Inhibits Tumor Growth.

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.

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

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.

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

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. Salmonella enterica 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.

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

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 (FST = 0.749) and displayed a significant relationship between phylogeny and geography (NST = 0.750 and GST = 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.

Origins of Semisulcospira libertina (gastropoda: semisulcospiridae) in 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.

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

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.

Hinokitiol induces autophagy in murine breast and colorectal cancer cells.

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.

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

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%.

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

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%.

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

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.