Ji-Min Park

Sulfitobacter undariae sp. nov., isolated from a brown algae reservoir.

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, W-BA2(T), was isolated from a brown algae reservoir in Wando of South Korea. Strain W-BA2(T) grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of approximately 2.0-3.0% (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain W-BA2(T) fell within the clade comprising the type strains of species of the genus Sulfitobacter , clustering coherently with the type strains of Sulfitobacter donghicola and Sulfitobacter guttiformis showing sequence similarity values of 98.0-98.1%. Sequence similarities to the type strains of the other species of the genus Sulfitobacter were 96.0-97.4%. Strain W-BA2(T) contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain W-BA2(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain W-BA2(T) was 55.0 mol% and its DNA-DNA relatedness values with the type strains of Sulfitobacter donghicola , Sulfitobacter guttiformis and Sulfitobacter mediterraneus were 16-23%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain W-BA2(T) is separated from other species of the genus Sulfitobacter . On the basis of the data presented, strain W-BA2(T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter undariae sp. nov. is proposed. The type strain is W-BA2(T) ( = KCTC 42200(T) = NBRC 110523(T)).

Pontibacter litorisediminis sp. nov., isolated from a tidal flat.

A Gram-stain-negative, aerobic, non-flagellated, motile by gliding and ovoid or rod-shaped bacterial strain, designated YKTF-7T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. Strain YKTF-7T grew optimally at pH 7.0-8.0, at 30-37 °C and in the presence of 0.5-2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YKTF-7T fell within the clade comprising the type strains of species of the genus Pontibacter, clustering with the type strains of Pontibacterodishensis and Pontibacterkorlensis with which it exhibited 98.0-98.7 % sequence similarity. Strain YKTF-7T exhibited 16S rRNA gene sequence similarities of 94.7-96.8 % to the type strains of the other species of the genus Pontibacter and of less than 91.7 % to those of other recognized species. Strain YKTF-7T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain YKTF-7T was 54.0 mol%, and its mean DNA-DNA relatedness values with the type strains of P. odishensis and P. korlensis were 25 and 14 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain YKTF-7T is separated from recognized species of the genus Pontibacter. On the basis of the data presented, strain YKTF-7T is considered to represent a novel species of the genus Pontibacter, for which the name Pontibacterlitorisediminis sp. nov. is proposed. The type strain is YKTF-7T(=KCTC 52252T=NBRC 112298T).

Pedobacter lignilitoris sp. nov., isolated from wood falls

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated W-WS13T, was isolated from wood falls collected around Wando, an island in the South Sea of South Korea, and subjected to a polyphasic taxonomic study. Strain W-WS13T grew optimally at 30 °C, at pH 7.5 and in the presence of 0.5 % NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-WS13T belonged to the genus Pedobacter, clustering robustly with the type strain of Pedobacter arcticus, sharing 95.9 % sequence similarity. Strain W-WS13T exhibited 16S rRNA gene sequence similarity of 90.1–95.6 % to the type strains of the other species of the genus Pedobacter. Strain W-WS13T contained MK-7 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipid detected in strain W-WS13T was phosphatidylethanolamine. The DNA G+C content of strain W-WS13T was 36.9 mol%. Phylogenetic distinctiveness and differential phenotypic properties of strain W-WS13T revealed that the novel strain is separated from recognized species of the genus Pedobacter. On the basis of the data presented, strain W-WS13T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter lignilitoris sp. nov. is proposed. The type strain is W-WS13T ( = KCTC 42500T = CECT 8725T).

Aliiroseovarius pelagivivens gen. nov., sp. nov., isolated from seawater, and reclassification of three species of the genus Roseovarius as Aliiroseovarius crassostreae comb. nov., Aliiroseovarius halocynthiae comb. nov. and Aliiroseovarius sediminilitoris comb. nov.

A Gram-stain-negative, non-motile, aerobic and ovoid or rod-shaped bacterium, designated GYSW-22T, was isolated from seawater off Geoje Island in the South Sea, South Korea. Strain GYSW-22T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain GYSW-22T and the type strains of Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris form a coherent cluster, independent of phylogenetic lineages or clusters comprising the type strains of other species of the genus Roseovarius. Strain GYSW-22T exhibited 16S rRNA gene sequence similarities of 97.2, 96.6 and 96.3% to R. halocynthiae MA1-10T, R. crassostreae CV919-312T and R. sediminilitoris M-M10T, respectively, and of 92.6-94.7% to the type strains of other species of the genus Roseovarius. Strain GYSW-22T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain GYSW-22T was 59.0 mol% and its mean DNA-DNA relatedness value with R. halocynthiae MA1-10T was 15 %. On the basis of the data presented, we propose strain GYSW-22T represents a novel species of a new genus, Aliiroseovarius pelagivivens gen. nov., sp. nov. The type strain of the type species is GYSW-22T ( = KCTC 42459T = CECT 8811T). In this study, it is also proposed that Roseovarius crassostreae, Roseovarius halocynthiae and Roseovarius sediminilitoris be reclassified into the new genus as Aliiroseovarius crassostreae comb. nov. (type strain CV919-312T = ATCC BAA-1102T = DSM 16950T), Aliiroseovarius halocynthiae comb. nov. (type strain MA1-10T = KCTC 23462T = CCUG 60745T) and Aliiroseovarius sediminilitoris comb. nov. (type strain M-M10T = KCTC 23959T = CCUG 62413T), respectively.

Maribacter confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring.

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, SSK2-2(T), was isolated from the place where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK2-2(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0% (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain SSK2-2(T) fell within the clade comprising the type strains of species of the genus Maribacter, joining the type strain of Maribacter sedimenticola with which it shared 99.4% similarity. Sequence similarities to the type strains of other Maribacter species were 94.6-98.2%. Strain SSK2-2(T) contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0) as the major fatty acids. The major polar lipids of strain SSK2-2(T) were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-2(T) was 38.2 mol% and mean levels of DNA-DNA relatedness with the type strains of four phylogenetically related species of the genus Maribacter were 11-24%. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK2-2(T) is separate from other Maribacter species. On the basis of the data presented, strain SSK2-2(T) is considered to represent a novel species of the genus Maribacter, for which the name Maribacter confluentis sp. nov. is proposed. The type strain is SSK2-2(T) ( = KCTC 42604(T) = CECT 8869(T)).

PINK1 positively regulates HDAC3 to suppress dopaminergic neuronal cell death

Deciphering the molecular basis of neuronal cell death is a central issue in the etiology of neurodegenerative diseases, such as Parkinsons and Alzheimers. Dysregulation of p53 levels has been implicated in neuronal apoptosis. The role of histone deacetylase 3 (HDAC3) in suppressing p53-dependent apoptosis has been recently emphasized; however, the molecular basis of modulation of p53 function by HDAC3 remains unclear. Here we show that PTEN-induced putative kinase 1 (PINK1), which is linked to autosomal recessive early-onset familial Parkinsons disease, phosphorylates HDAC3 at Ser-424 to enhance its HDAC activity in a neural cell-specific manner. PINK1 prevents H2O2-induced C-terminal cleavage of HDAC3 via phosphorylation of HDAC3 at Ser-424, which is reversed by protein phosphatase 4c. PINK1-mediated phosphorylation of HDAC3 enhances its direct association with p53 and causes subsequent hypoacetylation of p53. Genetic deletion of PINK1 partly impaired the suppressive role of HDAC3 in regulating p53 acetylation and transcriptional activity. However, depletion of HDAC3 fully abolished the PINK1-mediated p53 inhibitory loop. Finally, ectopic expression of phosphomometic-HDAC3(S424E) substantially overcomes the defective action of PINK1 against oxidative stress in dopaminergic neuronal cells. Together, our results uncovered a mechanism by which PINK1-HDAC3 network mediates p53 inhibitory loop in response to oxidative stress-induced damage.

Winogradskyella wandonensis sp. nov., isolated from a tidal flat

A Gram-stain-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated WD-2-2T, was isolated from a tidal flat of Wando, an island of South Korea, and subjected to a polyphasic taxonomic analysis. Strain WD-2-2T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WD-2-2T belonged to the genus Winogradskyella, clustering coherently with the type strain of Winogradskyella litorisediminis. Strain WD-2-2T exhibited 16S rRNA gene sequence similarity of 97.4% to W. litorisediminis DPS-8T and 94.5-96.6% to the type strains of the other species of the genus Winogradskyella. Strain WD-2-2T contained MK-6 as the predominant menaquinone and iso-C15:1 G, iso-C17:0 3-OH and iso-C15:0 as the major fatty acids. The major polar lipids detected in strain WD-2-2T were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 36.4 mol%, and DNA-DNA relatedness with W. litorisediminis DPS-8T was 13%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain WD-2-2T is separate from recognized species of the genus Winogradskyella. On the basis of the data presented, strain WD-2-2T is considered to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella wandonensis sp. nov. is proposed. The type strain is WD-2-2T (=KCTC 32579T=CECT 8445T).

Rheinheimera arenilitoris sp. nov., isolated from seashore sand

A Gram-stain-negative, non-flagellated, aerobic and ovoid or rod-shaped bacterium, designated J-MS1(T), was isolated from seashore sand in the South Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain J-MS1(T) was found to grow optimally at 30 °C and pH 7.0-8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain J-MS1(T) belonged to the genus Rheinheimera, clustering coherently with the type strain of Rheinheimera chironomi and sharing 98.34% sequence similarity. Strain J-MS1(T) exhibited 16S rRNA gene sequence similarity of 94.26-96.98% to the type strains of the other species of the genus Rheinheimera. In the phylogenetic trees based on gyrB sequences, strain J-MS1(T) clustered with the type strain of R. chironomi, with which it shared the highest sequence similarity (86.97%). Strain J-MS1(T) contained Q-8 as the predominant ubiquinone and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c), C(16:0) and C(18:1)ω7c as the major fatty acids. The major polar lipids detected in strain J-MS1(T) and in the type strain of R. chironomi were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain J-MS1(T) was 49.8 mol% and its mean DNA-DNA relatedness value with R. chironomi LMG 23818(T) was 12%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain J-MS1(T) is separated from recognized species of the genus Rheinheimera. On the basis of the data presented, strain J-MS1(T) is considered to represent a novel species of the genus Rheinheimera, for which the name Rheinheimera arenilitoris sp. nov. is proposed. The type strain is J-MS1(T) ( =KCTC 42112(T) =CECT 8623(T)).

Retinal Angiogenesis Effects of TGF-β1 and Paracrine Factors Secreted From Human Placental Stem Cells in Response to a Pathological Environment.

Abnormal angiogenesis is a primary cause of many eye diseases, including diabetic retinopathy, age-related macular degeneration, and retinopathy of prematurity. Mesenchymal stem cells (MSCs) are currently being investigated as a treatment for several such retinal diseases based on their neuroprotective and angiogenic potentials. In this study, we evaluated the role of systemically injected human placental amniotic membrane-derived MSCs (AMSCs) on pathological neovascularization of proliferative retinopathy. We determined that AMSCs secrete higher levels of transforming growth factor-β (TGF-β1) than other MSCs, and the secreted TGF-β1 directly suppresses the proliferation of endothelial cells under pathological conditions in vitro. Moreover, in a mouse model of oxygen-induced retinopathy, intraperitoneally injected AMSCs migrated into the retina and suppressed excessive neovascularization of the vasculature via expression of TGF-β1, and the antineovascular effect of AMSCs was blocked by treatment with TGF-β1 siRNA. These findings are the first to demonstrate that TGF-β1 secreted from AMSCs is one of the key factors to suppress retinal neovascularization in proliferative retinopathy and further elucidate the therapeutic function of AMSCs for the treatment of retinal neovascular diseases.

Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat.

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis, showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola, Sulfitobacter porphyrae, Sulfitobacter mediterraneus and Roseobacter litoralis, respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria, for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).