Genome sequence of Leuconostoc fallax KCTC 3537

Leuconostoc fallax is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain Leuconostoc fallax KCTC 3537 (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large contigs (>100 bp in size).     

Genome sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167

Lactobacillus coryniformis subsp. coryniformis is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of Lactobacillus coryniformis subsp. coryniformis type strain KCTC 3167 (2,964,752 bp, with a G+C content of 42.8%), which consists of 55 scaffolds.     

Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade

Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5 clade and is closely related to clone OM241, Congregibacter litoralis, and strain HTCC2080. Here, the genome sequence of strain IMCC3088 is presented, showing the absence of photosynthetic gene clusters and the presence of proteorhodopsin.     

Inference of population mutation rate and detection of segregating sites from next-generation sequence data

We live in an age in which our ability to collect large amounts of genome-wide genetic variation data offers the promise of providing the key to the understanding and treatment of genetic diseases. Over the next few years this effort will be spearheaded by so-called next-generation sequencing technologies, which provide vast amounts of short-read sequence data at relatively low cost. This technology is often used to detect unknown variation in regions that have been linked with a given disease or phenotype. However, error rates are significant, leading to some nontrivial issues when it comes to interpreting the data. In this article, we present a method with which to address questions of widespread interest: calling variants and estimating the population mutation rate. We show performance of the method using simulation studies before applying our approach to an analysis of data from the 1000 Genomes project.     

Genome sequence of Lactobacillus suebicus KCTC 3549

Lactobacillus suebicus is important in the generation of particular flavors and in other ripening processes associated with apple mash. Here, we present the draft genome sequence of the type strain Lactobacillus suebicus KCTC 3549 (2,656,936 bp, with a G+C content of 39.0%), which consists of 143 large contigs (>100 bp).     

Genome sequence of Leuconostoc inhae KCTC 3774, isolated from Kimchi

Leuconostoc inhae strain KCTC 3774 is a Gram-positive, non-spore-forming, heterofermentative, spherical or lenticular lactic acid bacterium. Here we announce the draft genome sequence of Leuconostoc inhae KCTC 3774, isolated from traditional Korean kimchi, and describe major findings from its annotation.     

Draft genome sequence of Lactobacillus zeae KCTC 3804

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cow's milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).     

Genome sequence of Lactobacillus johnsonii PF01, isolated from piglet feces

Lactobacillus johnsonii PF01, an autochthonous bacterium of the gastrointestinal tract, was isolated from a fecal sample from a piglet. The strain adhered specifically to the duodenal and jejunal epithelial cells of the piglet and had high bile resistance activity. Here we report the genomic sequence of L. johnsonii PF01.     

Ginsenoside metabolite compound K differentially antagonizing tumor necrosis factor-α-induced monocyte-endothelial trafficking

Human leukocyte endothelial adhesion and transmigration occur in the early stage of the pathogenesis of atherosclerosis. Vascular endothelial cells are targeted by pro-inflammatory cytokines modulating many gene proteins responsible for cell adhesion, thrombosis and inflammatory responses. This study examined the potential of compound K to inhibit the pro-inflammatory cytokine TNF-α induction of monocyte adhesion onto TNF-α-activated human umbilical vein endothelial cells (HUVEC). HUVEC were cultured with 10 ng/ml TNF-α with individual ginsenosides of Rb1, Rc, Re, Rh1 and compound K (CK). Ginsenosides at doses of ?50 μM did not show any cytotoxicity. TNF-α induced THP-1 monocyte adhesion to HUVEC, and such induction was attenuated by Rh1 and CK. Consistently, CK suppressed TNF-α-induced expression of HUVEC adhesion molecules of VCAM-1, ICAM-1 and E-selectin, and also Rh1 showed a substantial inhibition. Rh1 and CK dampened induction of counter-receptors, α4/β1 integrin VLA-4 and αL/β2 integrin LFA-1 in TNF-α-treated THP-1 cells. Additionally, CK diminished THP-1 secretion of MMP-9 required during transmigration, inhibiting transendothelial migration of THP-1 cells. CK blunted TNF-α-promoted IL-8 secretion of HUVEC and CXCR1 expression of THP-1 monocytes. Furthermore, TNF-α-activated endothelial IκB phosphorylation and NF-κB nuclear translocation were disturbed by CK, and TNF-α induction of α4/β1 integrin was abrogated by the NF-κB inhibitor SN50. These results demonstrate that CK exerts anti-atherogenic activity with blocking leukocyte endothelial interaction and transmigration through negatively mediating NF-κB signaling.