Ferrimonas pelagia sp. nov., isolated from seawater.

A Gram-stain-negative bacterium, designated strain CBA4601(T), was isolated from a seawater sample obtained off the coast of Jeju Island, Korea. The organism grew in the presence of 0-4% (w/v) NaCl and at 20-35 °C and pH 7.0-9.0, with optimal growth in 2% NaCl, and at 25 °C and pH 8.0. Phylogenetic trees based on 16S rRNA gene sequences showed that strain CBA4601(T) was related to the genus Ferrimonas within the class Gammaproteobacteria. 16S rRNA gene sequence similarity between strain CBA4601(T) and Ferrimonas marina A4D-4(T), the most closely related species, was 96.9%. The G+C content of the genomic DNA from strain CBA4601(T) was 54.2 mol%, and the isoprenoid quinones menaquinone 7 (MK-7), ubiquinone 7 (Q-7) and ubiquinone 8 (Q-8) were detected. The major fatty acids were C(17:1)ω8c, C(18:1)ω9c and C(16:0), and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified ninhydrin-positive phospholipid. On the basis of this taxonomic study using a polyphasic approach, strain CBA4601(T) represents a novel species of the genus Ferrimonas, for which the name Ferrimonas pelagia sp. nov. is proposed. The type strain is CBA4601(T) ( =KACC 16695(T) =KCTC 32029(T) =JCM 18401(T)).

Changes of parafoveal retinal nerve fiber layer thickness analyzed by spectral-domain optical coherence tomography after pars plana vitrectomy.

PURPOSE: To use spectral-domain optical coherence tomography to evaluate the postoperative retinal nerve fiber layer (RNFL) thickness changes in eyes undergoing vitrectomy. METHODS: This is a retrospective study of 44 patients (44 eyes) who underwent monocular vitrectomy for an epiretinal membrane (19 eyes), macular hole (12 eyes), or vitreous hemorrhage (13 eyes). Quantitative analysis of the peripapillary RNFL by spectral-domain optical coherence tomography was performed before surgery and for 6 months postoperatively on both eyes. RESULTS: Mean patient age was 62.72 ± 9.11 years. Mean preoperative RNFL thickness did not differ significantly between vitrectomized eyes (88.33 ± 13.23 µm) and nonvitrectomized fellow eyes (87.49 ± 13.18 µm; P > 0.05). In vitrectomized eyes, the preoperative mean RNFL thickness in the superior quadrant was significantly different from that at 6 months after surgery (P = 0.02). Vitrectomized eyes with a macular hole showed significant changes in the mean RNFL thickness in the inferior quadrant (P = 0.04). CONCLUSION: Retinal nerve fiber layer thickness was reduced in some of the quadrants of the vitrectomized eye during the 6-month postoperative follow-up period. Spectral-domain optical coherence tomography can be clinically useful for detection of localized RNFL defects in patients who underwent vitrectomy. Future prospective studies with more patients and longer follow-up duration are required.

Association between fundus autofluorescence and visual outcome in surgically closed macular holes.

PURPOSE: To investigate the association between fundus autofluorescence (FAF) and visual acuity, recovery of foveal microstructure, and FAF in surgically closed macular holes. METHODS: Twenty-six eyes with surgically closed macular hole were classified into two groups based on foveal FAF: normal autofluorescence (NAF) or increased autofluorescence (IAF). The association between foveal FAF and visual acuity was analyzed. In addition, we examined the relationship between recovery of the foveal microstructure assessed by spectral domain optical coherence tomography and FAF after macular hole surgery. RESULTS: At 1 month and 6 months after surgery, there were 9 NAF eyes and 17 IAF eyes. There were no differences between NAF and IAF eyes at 1 month and 6 months after surgery. Preoperative best-corrected visual acuity (logarithm of the minimum angle of resolution) did not differ between groups. Best-corrected visual acuity was significantly higher in the NAF group than in the IAF group at 1 month postoperatively (0.59 ± 0.34 vs. 0.91 ± 0.36, P = 0.044) and tended to be higher at 6 months (0.37 ± 0.38 vs. 0.69 ± 0.53, P = 0.126). Restoration of photoreceptor external limiting membrane differed significantly in 8 NAF eyes (89%) and 4 IAF eyes (24%) at postoperation 1 month (P = 0.001). After 6 months, external limiting membrane was restored in all 9 NAF eyes (100%) and in only 11 IAF eyes (65%) (P = 0.042). CONCLUSION: Fundus autofluorescence findings observed in surgically closed macular holes correlated with visual improvement and photoreceptor status. Eyes with visual improvement had restoration of normal foveal autofluorescence and retinal microstructure, whereas eyes with persistent foveal hyperautofluorescence did not achieve complete restoration of the retinal microstructure, and visual improvement was not as significant.

Characteristics and phylogenetic analysis of the complete mitochondrial genome of Microstomus achne.

Microstomus achne (Jordan and Starks, 1904) is an economically valuable flatfish belonging to the family Pleuronectidae and the only flatfish that inhabits Korea. Here, we report on the complete mitochondrial genome of M. achne and the phylogenetic relationship between close species. The mitogenome is 16,971 bp long and encodes 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The phylogenetic analysis showed that M. achne clustered with Glyptocephalus stelleri, which supports the conclusion that M. achne belongs to the family Pleuronectidae. The results of this study provide a better understanding of M. achne.

The study on the complete mitochondrial genome of Acanthopsetta nadeshnyi and its phylogenetic position.

Pleuronectidae is a well-studied familyin the order Pleuronectiformes. In contrast, genetic research on the flatfish Acanthopsetta nadeshnyi of the Pleuronectidae family is limited. This study reports the complete mitogenome of A. nadeshnyi. The mitogenome was 17,206 bases long and included 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region. Phylogenetic analysis based on the nucleotide sequences of the 13 PCGs confirmed that A. nadeshnyi belongs to the Pleuronectidae family.

Detection and molecular characterization of adenoviruses in Korean children hospitalized with acute gastroenteritis.

Human adenoviruses (HAdVs) are an important cause of acute gastroenteritis in children. However, few studies on the epidemiology or types of HAdVs associated with acute gastroenteritis have been conducted in Korea. Therefore, in the present study, the incidence of HAdV in 2064 stool samples from Korean children hospitalized with acute gastroenteritis (2004-2006) was assessed and the types of viruses present determined. Polymerase chain reaction, sequencing, and phylogenic analyses revealed that 113 samples (5.5%) were HAdV-positive. While HAdVs were mainly detected during July to October, no seasonal difference between the enteric and non-enteric viruses in the incidence of HAdV was observed. HAdV-41 and HAdV-40 were found in 54 (47.8%) and 3 (2.6%) HAdV-positive samples, respectively. HAdV-3, HAdV-7, HAdV-2, HAdV-31, HAdV-4, and HAdV-37 were detected in 11 (9.7%), 5 (4.4%), 2 (1.7%), 2 (1.7%), 1 (0.8%), and 1 (0.8%) of sample(s), respectively. Thus, not only enteric, but also non-enteric, HAdVs may play an important role in acute gastroenteritis in Korean children.

Cloning, heterologous expression, and enzymatic characterization of cathepsin L from starfish (Asterina pectinifera).

To determine the role of cathepsin L in Echinoderms, starfish (Asterina pectinifera) cathepsin L (ApCtL) was cloned. The results of RT-PCR analysis indicated that the expression of ApCtL in all of the tissues. The pro-mature enzyme of ApCtL, proApCtL, was expressed in Escherichia coli, and cathepsin activity was detected by cleaving of synthetic fluorogenic peptide substrates and gelatin zymography.

Molecular identification and real-time quantitative PCR (qPCR) for rapid detection of Thelohanellus kitauei, a Myxozoan parasite causing intestinal giant cystic disease in the Israel carp.

Intestinal giant-cystic disease (IGCD) of the Israel carp (Cyprinus carpio nudus) has been recognized as one of the most serious diseases afflicting inland farmed fish in the Republic of Korea, and Thelohanellus kitauei has been identified as the causative agent of the disease. Until now, studies concerning IGCD caused by T. kitauei in the Israel carp have been limited to morphological and histopathological examinations. However, these types of diagnostic examinations are relatively time-consuming, and the infection frequently cannot be detected in its early stages. In this study, we cloned the full-length 18S rRNA gene of T. kitauei isolated from diseased Israel carps, and carried out molecular identification by comparing the sequence with those of other myxosporeans. Moreover, conventional PCR and real-time quantitative PCR (qPCR) using oligonucleotide primers for the amplification of 18S rRNA gene fragment were established for further use as methods for rapid diagnosis of IGCD. Our results demonstrated that both the conventional PCR and real-time quantitative PCR systems applied herein are effective for rapid detection of T. kitauei spores in fish tissues and environmental water.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Notostomum cyclostomum.

Notostomum cyclostomum is a parasite that lays eggs on the snow crab shells and causes various diseases by parasitizing fish. Although there have been some studies on the life history of this parasite and the associated fish diseases, little is known about the molecular biology of this parasite. Thus, here we report the mitochondrial genome of N. cyclostomum, which is 16,972 bp long and contains 13 mitochondrial protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region with a 92% AT-rich sequences between tRNA-R and tRNA-H. Phylogenetic analysis using 13 PCGs confirmed that N. cyclostoum belongs to the family Pisciodlidae. This is the first study revealing the complete mitochondrial genome sequence of N. cyclostomum.

The complete mitochondrial genome of Pseudopleuronectes herzensteini.

Pseudopleuronectes herzensteini belonging to Pleuronectiformes (family Pleuronectidae) is important in the fishery industry. However, the molecular biology of this valuable fish has hardly been reported. Thus, here we report the complete mitochondrial genome of P. herzensteini. The mitochondrial DNA (mtDNA) of P. herzensteini is 16,719 bp long and contains 13 mitochondrial protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region between tRNA-P and tRNA-F distinguished by a single short noncoding region. Phylogenetic analysis using PCGs confirmed that this mtDNA sequence belongs to the family Pleuronectidae. This is the first study reporting the complete mitochondrial genome sequence of P. herzensteini.

Photodynamic therapy combined with intravitreal injection of vascular endothelial growth factor antibody for polypoidal choroidal vasculopathy.

BACKGROUND/AIMS: To evaluate the efficacy of photodynamic therapy (PDT) combined with intravitreal injection of anti-vascular-endothelial-growth-factor (anti-VEGF) antibody in patients with polypoidal choroidal vasculopathy (PCV). METHODS: Twenty-two eyes of 22 patients with PCV followed for 12 months after combination therapy with PDT and anti-VEGF were retrospectively reviewed. Patients received intravitreal anti-VEGF (1.25 mg bevacizumab or 0.5 mg ranibizumab) within 7 days after PDT. Retreatment with PDT and intravitreal anti-VEGF injections, or with intravitreal anti-VEGF alone, was performed when indicated. The main outcome measures were best-corrected visual acuity (BCVA) and central foveal thickness (CFT). RESULTS: Mean logMAR BCVA was 0.43 at baseline and 0.45, 0.36, 0.30 and 0.28 at 1, 3, 6 and 12 months, respectively, after the initial combination therapy. Mean BCVA was significantly improved at 6 and 12 months after treatment (p < 0.05). Mean CFT was 269.4 µm at baseline and 180.1, 136.7, 127.5 and 139.6 µm at 1, 3, 6 and 12 months, respectively, after the initial combination therapy. CFT decreased significantly throughout the follow-up period. At 12 months, mean BCVA improved by 1.5 lines, and mean CFT decreased by 129.8 µm. Polypoidal lesions disappeared in 7 of the 13 eyes in which indocyanine green angiography was performed at 12 months. No changes in the branching vascular network were observed in any of these 13 eyes. Patients were treated with PDT a mean of 1.3 times and injected with intravitreal anti-VEGF a mean of 3.4 times over the 12-month period. CONCLUSION: Combined PDT and intravitreal anti-VEGF may improve visual acuity and decrease CFT at 12 months. Large long-term prospective studies are needed to evaluate the efficacy and safety of combination therapy.

Complete mitochondrial DNA sequence of Norwegian skates (Raja brachyuran Lafont, 1871) imported to Korea.

In this study, the complete mitochondrial genome of Norwegian skates imported to Korea was sequenced with a circular molecule of 17,121 bp, which consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNA genes, and a control region (D-loop). And among these sequences, 193 bp sequence in the D-loop of the genus Raja suggested the possibility of being used as a genetic marker for classification of Raja and Dipturus species. The BI phylogenetic tree by using the nucleotide sequences of 13 PCGs from 15 available mitogenomes of family Rajidae confirmed also that Norwegian skates imported to Korea form a group with Raja brachyura species with high branch value, and that this was a species of Raja brachyura. As above, these results would be expected to provide for the further understanding on the phylogenetic relationship, taxonomic classification and phylogeography of the family Rajidae.

The complete mitochondrial genome of Sardinella zunasi (Clupeiformes: Clupeidae).

The complete mitogenome of Sardinella zunasi was determined by next-generation sequencing. The S. zunasi mitogenome was a circular 16,307 bp molecule that contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region (D-loop). The gene arrangement was consistent with other Sardinella mitogenomes. The phylogenetic relationships of 29 Clupeoidei species based on 13 protein-coding genes from the available mitogenomes were analyzed. Sardinella zunasi clustered with Sardinella among Clupeidae, suggesting a closer relationship with this genus. These results will be useful for understanding the phylogenetic relationships, taxonomic classification, and phylogeography of the genus Sardinella relative to other genera of Clupeoidei.

The complete mitochondrial genome of an edible mushroom, Sparassis crispa.

Sparassis crispa, also known as cauliflower mushroom, is a widely used medicinal mushroom in traditional Chinese medicine due to the presence of bioactive substances with pharmacological activity. Here, we report a complete mitochondrial genome sequence of S. crispa consisting of 139,253 bp containing 47 genes including 15 protein-coding genes, 27 transfer RNA, and 5 ribosomal RNA genes obtained from 40.406 Mb genome containing 18,917 predicted contigs using raw data of next-generation sequencing having 85.4% Q30. The overall base composition of S. crispa was 26.47% G-C and 73.53% A-T. The phylogenetic tree based on atp6 sequence data showed its close relationship with Sparassis radicata. The complete mitochondrial genome sequence of S. crispa provides an essential and important DNA molecular data for further phylogenetic and evolutionary analysis of S. crispa.

Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker.

BACKGROUND: Pseudobagrus brevicorpus is an endangered species in Korea. The development of genetic markers and genetic information regarding the populations of this species are needed to establish conservation strategies. OBJECTIVE: As part of the conservation of P. brevicorpus, a 12-microsatellite marker was developed using next-generation sequencing (NGS) to provide current genetic population information. METHODS: Microsatellites from P. brevicorpus were identified by NGS analysis. Genetic diversity and genetic structure analysis of six populations (Seojeong Stream [SJ], Gokgang Stream [GK], Jaho Stream [JH], Daega Stream [DG], Nam River [NG], and Deokcheon River [DC]) of P. brevicorpus were conducted using the newly developed microsatellite marker. RESULTS: NGS generated 10,347,578 reads and identified 659,507 simple sequence repeats. Twelve microsatellites were successfully amplified and verified in 30 individuals of P. brevicorpus. The genetic diversity of the six P. brevicorpus populations in terms of the number of alleles ranged from 3.667 to 7.111. All populations except DG deviated significantly from Hardy-Weinberg equilibrium (HWE) at one or more loci. The genetic distances of the six populations showed the closest relationship between the SJ and GK populations (independent Stream populations), and there was a close relationship with the JH population among the Nakdong River. Structure analysis showed that P. brevicorpus is largely divided into two groups. CONCLUSIONS: The developed microsatellite marker will be used to provide basic genetic data of P. brevicorpus. Genetic diversity and structure analysis of the population will provide useful information for conservation management of P. brevicorpus.

Complete mitochondrial genome of Halocynthia hilgendorfi ritteri (Pyuridae) from Korea.

Halocynthia hilgendorfi ritteri is an ascidian distributed on the coast of Geoje Island in Korea and found on rocks. The mitochondrial genome of Halocynthia hilgendorfi ritteri consists of 15,181 bp with 13 protein-coding genes, 2 ribosomal RNAs, 23 transfer RNA genes. The overall base composition of the complete genome is 22.94% A, 43.32% T, 25.72% G, and 8.02% C, with a high A + T content of 66.26%.

The complete mitochondrial genome sequence and phylogenetic analysis for Inimicus japonicus (Scorpaeniformes: Synanceiidae).

The complete mitochondrial genome (mitogenome) of the Inimicus japonicus was analyzed by next-generation sequencing in this study. The mitogenome is 16,978 base pairs (bp) long and codes for 22 transfer RNA (tRNA) genes, 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNA), and 1 non-coding control region. The overall nucleotide composition of the mitogenome is: 29.61% for A, 29.16% for T, 25.26% for C, and 15.97% for G. Twenty-two tRNAs range from 67 to 74 bp in length, and 2 rRNA (12S and 16S) were 953 and 1,687 bp long, respectively. Phylogenetic analysis by neighbor-joining (NJ) method indicated that I. japonicus showed considerable genetic similarity (82%), and had a closer relationship in the phylogenetic tree to Synanceia verrucosa.

The complete mitochondrial genome of Chionoecetes japonicus (Crustacea: Decapoda: Majoidea).

The complete mitochondrial genome of Chionoecetes japonicus was sequenced using a specimen collected offshore in the East Sea. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop), with a total length of 16,060 bp. The overall nucleotide composition was 34.91% A, 17.29% C, 10.93% G, and 36.87% T, with 71.78% A + T. In the phylogenetic tree was constructed using maximum-likelihood and Bayesian inference analyses, C. japonicus and C. japonicus pacificus formed a genetic clade that was sister to C. opilio.

The complete mitochondrial genome analysis and phylogenetic position of the short barbeled grunter Hapalogenys nigripinnis (Lobotiformes: Hapalogenyidae) from Jeju island, Korea.

This study analyzed the complete mitochondrial genome of the short barbeled grunter Hapalogenys nigripinnis (Accession number: MT374064). The complete mitogenome was 16,476 bp long and included 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Nucleotide composition of the genome was A: 28.70%, T:27.46%, G: 15.73%, and C: 28.11%. All genes were encoded on the H-strand, except for the NADH dehydrogenase subunit (ND6) and 8 tRNA genes. When compared this sequence with the mitogenome of Chinese black grunt, Korean short barbeled grunter showed difference of 64 bp of nucleotide sequence in 20 genes. Phylogenetic tree was constructed using the neighbor-joining (NJ) method and showed the phylogenetic position of the short barbeled grunter in Korea.

Molecular cloning, expression analysis and enzymatic characterization of cathepsin K from olive flounder (Paralichthys olivaceus).

We assessed the putative physiological roles of cathepsin K from a flatfish, olive flounder. We cloned a cDNA encoding for cathepsin K (PoCtK), a cysteine protease of the papain family from olive flounder, Paralichthys olivaceus. The tissue-specific expression pattern of PoCtK, determined via real-time PCR analysis, revealed ubiquitous expression in normal tissues with high levels of expression in the spleen and bone marrow. However, PoCtK expression was significantly increased in the muscle and gill at 3-24 h post-injection with bacterial lipopolysaccharide (LPS). The cDNA encoding for the mature enzyme of PoCtK was expressed in Escherichia coli using the pGEX-4T-1 expression vector system. Its activity was quantified via the cleavage of the synthetic peptide Z-Gly-Pro-Arg-MCA, zymography, and the collagen degradation assay. The optimum pH for the protease activity was 8, and the recombinant PoCtK enzyme degraded collagen types I, II, III, IV, and VI and acid-soluble collagen from olive flounder muscle in the presence of chondroitin 4-sulphate (C-4S). Therefore, our data indicate that cathepsin K may play a role in the immune system of fish skin and muscle, in addition to its principal bone-specific function as a collagenolytic enzyme.