Polymorphism of MHC class IIB in an acheilognathid species, Rhodeus sinensis shaped by historical selection and recombination.

BACKGROUND: Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer meaningful insights into evolutionary processes in this species as well as other bitterlings. RESULTS: Using cDNA and gDNA samples from 50 individuals, we discovered classical 140 allelic sequences that could be allocated into either DAB1 (Rhsi-DAB1) or DAB3 (Rhsi-DAB3). DAB sequences completely lacking the intron, but identical or similar to Rhsi-DAB1, were also discovered from our gDNA samples, and this intron loss likely originated from the retrotransposition events of processed mDNA. The ß1 domain was the most polymorphic in both Rhsi-DAB1 and -DAB3. Putative peptide biding residues (PBRs) in Rhsi-DAB1, but not in Rhsi-DAB3, exhibited a significant dN/dS, presumably indicating that different selection pressures have acted on those two DABs. Recombination between different alleles seemed to have contributed to the increase of diversity in Rhsi-DABs. Upon phylogenetic analysis, Rhsi-DAB1 and -DAB3 formed independent clusters. Several alleles from other species of Cypriniformes were embedded in the clade of Rhsi-DAB1, whereas Rhsi-DAB3 clustered with alleles from the wider range of taxa (Cyprinodontiformes), indicating that these two Rhsi-DABs have taken different historical paths. CONCLUSIONS: A great deal of MHC class IIB allelic diversity was found in R. sinensis, and gene duplication, selection and recombination may have contributed to this diversity. Based on our data, it is presumed that such historical processes have commonly or differently acted on the polymorphism of Rhsi-DAB1 and -DAB3.

Population genetic structure of endangered Mongolian racerunner (Eremias argus) from the Korean Peninsula.

The Mongolian racerunner (Eremias argus) is a small lacertid lizard species, and its distribution range encompasses the Korean Peninsula, Mongolia, China and Russia. Eremias argus is widespread, but populations on the Korean Peninsula are small and declining, provoking concerns that genetic diversity is being lost. This species is currently listed under the Protection of Wild Fauna and Flora Act in South Korea. In this study, nine novel microsatellites for E. argus were developed with a biotin-enrichment method and used to understand its population genetic structure and delineate conservation units on the Korean Peninsula. Overall, low intrapopulation genetic diversity was observed (mean number of alleles per locus = 2.463; mean H E = 0.398) from 10 populations investigated (n = 110). Two populations (among five with n≥ 10) showed an excess of heterozygosity expected under HWE relative to that expected at mutation-drift equilibrium, indicating severe reduction in population sizes. With only a few exceptions, the overall genetic differentiation among populations was substantial with the high levels of pairwise-F ST (0.006-0.746) and -R ST (0.034-0.940) values. The results of Bayesian STRUCTURE analysis showed that E. argus populations on the Korean Peninsula were most likely partitioned into three genetic clusters. Taken all together, such low levels of gene flow and strong genetic structuring have critical implications for the conservation of this endangered species and its management.

Phylogeography of the Korean endemic Coreoleuciscus (Cypriniformes: Gobionidae): the genetic evidence of colonization through Eurasian continent to the Korean Peninsula during Late Plio-Pleistocene.

BACKGROUND: Freshwater endemism is thought to have been formed through the vicariance of connected water systems or the process by which ancestral populations colonized specific areas. The Korean Peninsula is well recognized for its high level of freshwater endemism with about 40% of freshwater fish species being endemic. OBJECTIVE: In this study, we attempted to reconstruct the process of speciation and phylogenetic dispersal of Coreoleuciscus species, which is endemic in the Korean Peninsula. METHODS: We used fossil-calibrated divergence time estimation and ancestral distributional reconstruction to infer phylogeographic reconstruction of Coreoleuciscus based on mitochondrial cytochrome c oxidate subunit I (COI) sequences (1551 bp). RESULTS: Our phylogeographic analysis based on a total of 626 individuals revealed that the two Coreoleuciscus species have originated from the independent colonization of different lineages in the ancestral populations, probably during the Late Plio-Pleistocene. The full-scale expansion of Coreoleuciscus populations appears to have taken place after major river structures were completed on the Korean Peninsula. We also provided evidence that the common ancestors of Coreoleuciscus was distributed in Eastern Eurasian continent and subsequently dispersed into the tip of East Asia. High genetic diversity was mainly concentrated in large drainage populations, while small populations showed an monomorphism, which could give important implications for planning the conservation and management of Coreoleuciscus. CONCLUSIONS: The phylogenetic background of the rheophilic Coreoleuciscus species can be explained by the colonizer hypothesis that the endemic freshwater fish originated from the common ancestor in continental region.

Diversification and colonization processes in Gobioidei predicted based on mitochondrial 12S rRNA with focusing on Oxudercidae.

Gobioidei is one of the largest vertebrate taxa with over 2000 species observed around the globe. The largest group in Gobioidei is gobies that had been classified as one family, Gobiidae, based on morphological features. Molecular phylogenetic studies revealed that gobies consisted of two monophyletic families, Gobiidae and Oxudercidae, in which 19 lineages have been proposed, despite some claims arisen about the relationship among these lineages or species. We analyzed 58 Gobioidei species, including 45 East Asian oxudercids, based on 12S rRNA sequences to reconstruct the spatiotemporal diversification history of gobies. Our analysis yielded the results compatible with the previous reports in a large framework. The common ancestor of Gobiidae and Oxudercidae were estimated to appear at 38.66 Mya. Genus-level splits occurred in Gobiidae and Oxudercidae predominantly at Miocene and late Miocene to early Pleistocene, respectively. Gobies have likely originated in many parts of the northern and western Pacific Ocean, of which a large proportion of Oxudercidae have adapted to various environments in the North Pacific.

Differential patterns of diversity at neutral and adaptive loci in endangered Rhodeus pseudosericeus populations.

Given the fact that threatened species are often composed of isolated small populations, spatial continuity or demography of the populations may be major factors that have shaped the species' genetic diversity. Thus, neutral loci have been the most commonly-used markers in conservation genetics. However, the populations under the influence of different environmental factors may have evolved in response to different selective pressures, which cannot be fully reflected in neutral genetic variation. Rhodeus pseudosericeus, a bitterling species (Acheilognathidae; Cypriniformes) endemic to the Korean Peninsula, are only found in some limited areas of three rivers, Daecheon, Han and Muhan, that flow into the west coast. Here, we genotyped 24 microsatellite loci and two loci (DAB1 and DAB3) of MHC class II peptide-binding ß1 domain for 222 individuals collected from seven populations. Our microsatellite analysis revealed distinctive differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, and populations were structured into two subgroups within the Han River. Apparent positive selection signatures were found in the peptide-binding residues (PBRs) of the MHC loci. The allelic distribution of MHC showed a degree of differentiation between the populations of Daecheon and Muhan Rivers and the Han River populations, partially similar to the results obtained for microsatellites, however showed rather complex patterns among populations in the Han River. Considering the apparent differences in the distribution of supertypes obtained based on the physicochemical differences induced by the polymorphisms of these PBRs, the differentiation in DAB1 between the two regional groups may result in the differences in immune function. No differentiation between these two regions was observed in the supertyping of DAB3, probably indicating that only DAB1 was associated with the response to locally specialized antigenic peptides.

The complete mitochondrial genome information of Rana uenoi (Amphibia, Anura, Ranidae) and the phylogenetic implication.

We determined the complete mitochondrial genome of Rana uenoi (Anura: Ranidae) for the first time. The whole sequences were 17,370 bp and included 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene arrangement was completely identical to those observed from other Ranidae species. We used 11 protein-coding genes to examine the phylogenetic placement of this species in the genus Rana. Rana dybowskii was the closest sister species to R. uenoi. The clade of R. uenoi and R. dybowskii formed a cluster with Rana huarensis, which had a sister relationship with the group of Rana amurensis, Rana coreana, and Rana kunyuensis.

Isolation of a novel strain, Sphingorhabdus sp. YGSMI21 and characterization of its enantioselective epoxide hydrolase activity.

Sphingorhabdus sp. YGSMI21, a novel microbial strain with an enantioselective epoxide hydrolase activity, was isolated from tidal samples contaminated by accidental oil spills subjected to enriched culture with polycyclic aromatic hydrocarbon. This strain was able to optically decompose (R)-styrene oxide (SO) and showed 100% optical purity. In addition, it showed a good enantioselectivity for the derivatives of (S)-SO, (S)-2-chlorostyrene oxide (CSO), (S)-3-CSO and (S)-4-CSO. For (S)-2-CSO, (S)-3-CSO and (S)-4-CSO, 99.9%ee was obtained with the yield of 26.2%, 24.8%, and 11.0%, respectively, when using 10 mg cells of Sphingorhabdus sp. YGSMI21 at pH 8.0 with 4 mM racemic substrates at pH 8.0 and 25°C. The values obtained in this study for (S)-2-CSO, particularly the yield of 26.2%, is noteworthy, considering that obtaining an enantiomerically pure form is difficult. Taken together, Sphingorhabdus sp. YGSMI21 can be regarded as a whole-cell biocatalyst in the production of various (S)-CSO with the chlorine group at a different position.

The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion.

The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene. Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure of K. koreana using mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size of K. koreana was also small, these results suggest that the small, restricted populations of K. koreana are extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation.

The land snail Ellobium chinense (L. Pfeiffer, 1855) (Eupulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense. The results analyzed with COI and microsatellites revealed that E. chinense population exhibit metapopulation characteristics, retaining under the influence of the Kuroshio warm currents through expansion of the Late-Middle and Late Pleistocene. We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

Evidence of an ancient connectivity and biogeodispersal of a bitterling species, Rhodeus notatus, across the Korean Peninsula.

The modern-day distribution of freshwater fishes throughout multiple rivers is likely the result of past migration during times when currently separate drainages were once connected. Here, we used mitochondrial and microsatellite analyses for 248 individuals of Rhodeus notatus collected from seven different rivers to obtain better understand historical gene flow of freshwater fish on the Korean Peninsula. Based on our phylogenetic analyses, this Korean species originated through the paleo-Yellow River from China and first colonized near the west coast. These genetic data also provided evidence of estuary coalescences among the rivers flowing to the west and southwest coast on well-developed continental shelf. In addition, the pattern of population structure revealed the biogeodispersal route from the west coast to the south coast. It could be inferred that massive migration was not involved in the formation of southern populations, since the signature of historical genetic drift was clearly observed. Our study is the first genetic attempt to confirm hypotheses describing the migration of freshwater species towards the end of East Asia, which have previously been developed using only geological reasoning.

White matter and neurological disorders.

The central nervous system is simply divided into two distinct anatomical regions based on the color of tissues, i.e. the gray and white matter. The gray matter is composed of neuronal cell bodies, glial cells, dendrites, immune cells, and the vascular system, while the white matter is composed of concentrated myelinated axonal fibers extending from neuronal soma and glial cells, such as oligodendrocyte precursor cells (OPCs), oligodendrocytes, astrocytes, and microglia. As neuronal cell bodies are located in the gray matter, great attention has been focused mainly on the gray matter regarding the understanding of the functions of the brain throughout the neurophysiological areas, leading to a scenario in which the function of the white matter is relatively underestimated or has not received much attention. However, increasing evidence shows that the white matter plays highly significant and pivotal functions in the brain based on the fact that its abnormalities are associated with numerous neurological diseases. In this review, we will broadly discuss the pathways and functions of myelination, which is one of the main processes that modulate the functions of the white matter, as well as the manner in which its abnormalities are related to neurological disorders.

Hemistepsin A Inhibits Cell Proliferation and Induces G0/G1-Phase Arrest, Cellular Senescence and Apoptosis Via the AMPK and p53/p21 Signals in Human Hepatocellular Carcinoma.

Hemistepsin A (HsA), a natural sesquiterpene lactone isolated from Hemistepta lyrata, has been known as a wide range of anti-tumor effects. The aim of this study was to determine whether HsA suppresses hepatocellular carcinoma (HCC) and to figure out the cellular signaling pathways involved in the anti-HCC activities by experiments using the Huh7 cells (a human HCC cell line) and a xenograft HCC model. In this study, HsA completely inhibited HCC cell proliferation, presumably because it induced G0/G1 cell cycle arrest and mitochondrial-related apoptosis. HsA up-regulated p53, p21, cleaved caspase-3 and cleaved PARP (poly (ADP-ribose) polymerase), but reduced cyclin D, CDK6 and Bcl-2 expressions, and it disrupted mitochondrial membrane potential (ΔΨm). Moreover, phosphorylation of AMP-activated protein kinase (AMPK) was increased by HsA as did the resveratrol and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR, positive controls). Inhibition of AMPK by using compound C, a competent inhibitor of AMPK, attenuated the loss of ΔΨm, p53 up-regulation and cellular senescence. The efficacy of HsA to reduce HCC cell proliferation, compared to that of other known anti-HCC agents, appears to be similar or slightly better. The anti-tumor effect of HsA was also determined in mice, showing reduced growth of xenografted tumors with no weight loss. Overall, the results suggest that HsA should be considered as a candidate anti-HCC drug.

Early Life History of Coreoperca herzi in Han River, Korea.

This study aimed to investigate early life of Coreoperca herzi living in Han River and compare morphological differences between different groups during the development in order to provide basic data for relevant taxonomic research. On average, one female individual spawned 541 to 861 eggs (average 701) at once. After 259 hours, the tail broke out of the egg membrane and hatching began. Immediately after hatching, the larvae were average 7.81±0.10 mm (n=5) in total length. 60 days the juvenile was average 35.9±1.30 mm (n=5) in total length. The white spots spread to the rest of the body, rending the same pattern as that on the body of their broodstock fish.

Molecular phylogenetic, population genetic and demographic studies of Nodularia douglasiae and Nodularia breviconcha based on CO1 and 16S rRNA.

Freshwater mussels belonging to the genus Nodularia (Family Unionidae) are known to be widely distributed in East Asia. Although phylogenetic and population genetic studies have been performed for these species, there still remain unresolved questions in their taxonomic status and biogeographic distribution pathways. Here, the nucleotide sequences of CO1 and 16S rRNA were newly determined from 86 N. douglasiae and 83 N. breviconcha individuals collected on the Korean Peninsula. Based on these data, we revealed the following results: (1) N. douglasiae can be divided into the three genetic clades of A (only found in Korean Peninsula), B (widely distributed in East Asia), and C (only found in the west of China and Russia), (2) the clade A is not an independent species but a concrete member of N. douglasiae given the lack of genetic differences between the clades A and B, and (3) N. breviconcha is not a subspecies of N. douglasiae but an independent species apart from N. douglasiae. In addition, we suggested the plausible scenarios of biogeographic distribution events and demographic history of Nodularia species.

Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula.

BACKGROUND: The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions. OBJECTIVES: To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius. METHODS: Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus. RESULTS: A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used. CONCLUSION: Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.

The complete mitochondrial genome information of Hynobius unisacculus (Amphibia, Caudata, Hynobiidae) and the phylogenetic implication.

Hynobius unisacculus is a hynobiid salamander species found only in a limited area at the southernmost part of the Korean Peninsula. Here, we characterized the complete mitochondrial genome of this species that was used to identify the phylogenetic relationship with other Hynobius species. The whole sequence was 16,411 bp and included 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene arrangement was completely identical to those observed in other Hynobius species. Upon robust phylogenetic tree reconstructed based on 13 protein-coding genes, Hynobius species living on the Korean Peninsula showed close phylogenetic affinity; H. unisacculus and H. quelpaertensis formed a cluster that was the sister to the cluster of H. leechii and H. yangi.

The complete mitochondrial genome information of Phoxinus phoxinus (Cypriniformes: Cyprinidae) on the Korean Peninsula and the phylogenetic implication.

Phoxinus phoxinus is a small Leuciscinae species predominantly found in cool and well-oxygenated streams throughout a wide area encompassing Europe, Siberia and East Asia. It is believed that the populations in Korea hold important clues to how the species has been distributed south along the Eurasian continent to the Korean Peninsula. We characterized the complete mitochondrial genomes of two individual fin-clip samples collected from the two Korean river systems. The whole sequences were 17,665 and 18,220 bp, respectively, and included 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The genome size difference was due to the considerably different sizes of the control region. The overall genome structures were identical to those observed in other Leuciscinae species.

Development of microsatellite markers and the genetic diversity of Myocastor coypus introduced to South Korea.

The nutria (Myocastor coypus) was introduced to South Korea in 1987 for breeding of individuals for fur and meat industry, and was accidentally released into the wild. Here, we report the development of microsatellites for the nutria collected from South Korea using Illumina MiSeq genome sequencing to identify the genetic variability and demographic history of these introduced populations. A total of 626,282 microsatellite sequences were identified, and nine polymorphic loci were characterized. We used four novel loci developed and three previously known loci to investigate the genetic diversity of twelve South Korean populations. A low level of diversity was found, and no signature of genetic structuring was revealed among populations, indicating that Korean nutria individuals originated from a single population or a highly inbred reared herd.

Liquiritigenin inhibits hepatic fibrogenesis and TGF-ß1/Smad with Hippo/YAP signal.

BACKGROUND: Recent reports highlighted the possibility that Yes-associated protein (YAP) and transforming growth factor-ß1 (TGF-ß1) can act as critical regulators of hepatic stellate cells (HSCs) activation; therefore, it is natural for compounds targeting Hippo/YAP and TGF-ß1/Smad signaling pathways to be identified as potential anti-fibrotic candidates. PURPOSE: Liquiritigenin (LQ) is an aglycone of liquiritin and has been reported to protect the liver from injury. However, its effects on the Hippo/YAP and TGF-ß1/Smad pathways have not been identified to date. METHODS: We conducted a series of experiments using CCl4-induced fibrotic mice and cultured LX-2 cells. RESULT: LQ significantly inhibited liver fibrosis, as indicated by decreases in regions of hepatic degeneration, inflammatory cell infiltration, and the intensity of α-smooth muscle actin (α-SMA) staining in mice. Moreover, LQ blocked the TGF-ß1-induced phosphorylation of Smad 3, and the transcript levels of plasminogen activator inhibitor-1 (PAI-1) and matrix metalloproteinase-2 (MMP-2) in LX-2 cells, which is similar with resveratrol and oxyresveratrol (positive controls). Furthermore, LQ increased activation of large tumor suppressor kinase 1 (LATS1) with the induction of YAP phosphorylation, thereby preventing YAP transcriptional activity and suppressing the expression of exacerbated TGF-ß1/Smad signaling molecules. CONCLUSION: These results clearly show that LQ ameliorated experimental liver fibrosis by acting on the TGF-ß1/Smad and Hippo/YAP pathways, indicating that LQ has the potential for effective treatment of liver fibrosis.

Taxonomic characterization of Tanakia species (Acheilognathidae) using DNA barcoding analyses.

Tanakia is a bitterling genus with six species found in Far East Asia. Our aim was to construct the standard DNA barcode database available for the identification of six Tanakia species by comparing the range of intra- and inter-specific genetic distances, identifying the phylogenetic placement of each Tanakia species and providing the unique barcode characteristics that are specific to each species, using cytochrome oxidase I (COI) and cytochrome b (cyt b). Both loci failed to create a perfect barcoding gap between the ranges of inter- and intra-specific genetic distances, though interspecific COI distances were sufficiently greater than intraspecific values with only a few exceptions. In our phylogenetic analyses, T. koreensis and T. signifer did not form a monophyletic cluster of haplotypes in both loci. COI provided clear nucleotide characteristics that distinguish each species, whereas relatively fewer informative sites were found within the range of cyt b. Overall, COI could be regarded as appropriate species identification solution in Tanakia. Our analyses yielded some taxonomic issues that need the further investigation, and are expected to be helpful in the examination for the conservation status of Tanakia species that are on the verge of being endangered.