Algal and fungal diversity in Antarctic lichens.

The composition of lichen ecosystems except mycobiont and photobiont has not been evaluated intensively. In addition, recent studies to identify algal genotypes have raised questions about the specific relationship between mycobiont and photobiont. In the current study, we analyzed algal and fungal community structures in lichen species from King George Island, Antarctica, by pyrosequencing of eukaryotic large subunit (LSU) and algal internal transcribed spacer (ITS) domains of the nuclear rRNA gene. The sequencing results of LSU and ITS regions indicated that each lichen thallus contained diverse algal species. The major algal operational taxonomic unit (OTU) defined at a 99% similarity cutoff of LSU sequences accounted for 78.7-100% of the total algal community in each sample. In several cases, the major OTUs defined by LSU sequences were represented by two closely related OTUs defined by 98% sequence similarity of ITS domain. The results of LSU sequences indicated that lichen-associated fungi belonged to the Arthoniomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes of the Ascomycota, and Tremellomycetes and Cystobasidiomycetes of the Basidiomycota. The composition of major photobiont species and lichen-associated fungal community were mostly related to the mycobiont species. The contribution of growth forms or substrates on composition of photobiont and lichen-associated fungi was not evident.

Complete genome sequence analysis of Leuconostoc kimchii IMSNU 11154.

Leuconostoc kimchii IMSNU 11154, isolated from kimchi, a traditional Korean fermented food, is known to be an important antimicrobial lactic acid bacterium with probiotic potential. Here we announce the complete genome sequence of L. kimchii IMSNU 11154 consisting of a 2,101,787-bp chromosome and five plasmids. The strain has genes for dextran formation from sucrose and for mannitol formation from fructose. Antimicrobial and antioxidative functions of L. kimchii IMSNU 11154 could be attributed to a leucosin B-like peptide and multiple enzymes to reduce hydrogen peroxide and oxidized thiols, respectively.

Phosphorylation of p300 by ATM controls the stability of NBS1.

Acetyltransferase, p300 is a transcriptional cofactor of signal-responsive transcriptional regulation. The surveillance kinase ataxia-telangiectasia mutated (ATM) plays a central role in regulation of a wide range of cellular DNA damage responses. Here, we investigated whether and how ATM mediates phosphorylation of p300 in response to DNA damage and how p300 phosphorylation is functionally linked to DNA damage. ATM-phosphorylated p300 in vitro and in vivo, in response to DNA damage. Phosphorylation of p300 proteins was observed upon gamma-irradiation in ATM(+) cells but not ATM(-) cells. Importantly, expression of nonphosphorylatable serine to alanine form of p300 (S106A) destabilized both p300 and NBS1 proteins, after DNA damage. These data demonstrate that ATM transduces a DNA damage signal to p300, and that ATM-dependent phosphorylation of p300 is required for stabilization of NBS1 proteins in response to DNA damage.

IM-412 inhibits transforming growth factor beta-induced fibroblast differentiation in human lung fibroblast cells.

Pulmonary fibrosis is a type of interstitial lung disease that causes progressive scarring in lung tissues. Although there have been many studies on fibrosis, there is no standard treatment for fibrotic disease. Thus, there is an urgent need for the development of effective anti-fibrotic drugs. Transforming growth factor beta (TGF-beta) is a major fibrotic mediator known to stimulate fibrosis. To identify small molecules that inhibit TGF-beta responses, we performed cell-based chemical screening using genetically engineered HEK293 reporter cells. Among 8000 chemical compounds containing biologically active natural products and synthetic or clinically used compounds, we found that 3-(2-chlorobenzyl)-1,7-dimethyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione (IM-412) significantly decreased TGF-beta stimulated reporter activity in a dose-dependent manner. In addition, IM-412 inhibited TGF-beta-induced expression of the fibrotic markers alpha-smooth muscle actin (alpha-SMA) and fibronectin, and collagen accumulation in CCD-18Lu human normal lung fibroblasts without cell cytotoxicity. IM-412 decreased Smad2 and -3 phosphorylation as well as JNK and ERK activity. Moreover, expression levels of TGF-beta receptor I (TbetaRI) and receptor II (TbetaRII) were down-regulated by IM-412 in a dose-dependent manner. Thus, our findings indicate that the small molecule IM-412 attenuated TGF-beta-mediated fibroblast differentiation through inhibition of the overall TGF-beta response and may be a promising novel agent for the treatment of pathological fibrotic conditions.

SUMO1 negatively regulates BRCA1-mediated transcription, via modulation of promoter occupancy.

BRCA1, a tumor suppressor gene, is implicated in the repression and activation of transcription via interactions with a diverse range of proteins. The mechanisms regulating the action of BRCA1 are not fully understood. Here, we use the promoters of Gadd45alpha, p27(KIP1) and p21(WAF1/CIP1) to demonstrate that SUMO1 represses transactivation potential of BRCA1 by causing BRCA1 to be released from the promoters and augmenting histone deacetylation via recruitment of histone deacetylase (HDAC) activity. Consistently, silencing of SUMO1 led to recruitment of BRCA1 and release of HDAC1 at the BRCA1 target promoters, and subsequent transcriptional activation of the BRCA1 target genes. Furthermore, a sumoylation-incompetent mutant missing the sumoylation donor site suppressed BRCA1-induced activation of transcription, whereas E2 UBC9 or the dominant-negative mutant UBC9 had no effect, implying that repression of BRCA1-mediated activation of transcription by SUMO1 is independent of sumoylation. Repression of BRCA1-mediated activation of transcription by SUMO1 was reversed by DNA damage by inducing the release of SUMO1 from the Gadd45alpha promoter and the recruitment of BRCA1, along with increased histone acetylation, to enhance activation of transcription. Together, our data provide evidence that SUMO1 plays a role in the activation-repression switch of BRCA1-mediated transcription via modulation of promoter occupancy.

An HDAC inhibitor, trichostatin A, induces a delay at G2/M transition, slippage of spindle checkpoint, and cell death in a transcription-dependent manner.

Histone deacetylases (HDACs), a promising target for cancer therapy, play a role in regulating cell-cycle progression. The mechanisms for HDAC inhibition-induced regulation of G(2)/M transition and mitotic progression remain to be elucidated. Herein, we report that trichostatin A (TSA), an HDAC inhibitor, induces a delay at the G(2)/M transition, chromosome missegregation and multi-nucleation, and thereby leads to cell death by promoting exit from aberrant mitosis without spindle checkpoint. These results are associated with a transcriptional modulation of key regulator genes of the cell cycle, including CyclinB1, Plk1, Survivin, and p21(WAF1/Cip1). Actinomycin D, a transcriptional inhibitor, abrogated the TSA-induced delay of G(2)/M transition and transcriptional modulation of cell-cycle regulator genes, indicating that the impact of TSA in this manner is transcription dependent. Overall, our findings indicate that TSA provides a barrier to cell-cycle progression for antiproliferation and promotes escape from mitotic catastrophe and cell death, by inhibiting an HDAC-mediated transcriptional action.

Evaluation system for an experimental study of low-pathogenic avian influenza virus (H9N2) infection in specific pathogen free chickens using lactic acid bacteria, Lactobacillus plantarum KFCC11389P.

In low-pathogenic avian influenza (LPAI) virus, the effects of prophylactic oral administration of Lactobacillus plantarum KFCC11389P on immunity, viral loads and levels of nitric oxide and interferon-gamma in splenocytes from specific pathogen free (SPF) chickens were investigated. For in vitro screening of the antiviral effect, haemagglutination activities of four different lactic acid bacterial strains by direct contact with virus were measured. L. plantarum KFCC11389P only neutralized the virus on the SPF eggs. For in vivo studies, four groups of chickens were fed with various L. plantarum KFCC11389P bacterial components and were then challenged with LPAI virus at 28 days. Additionally, two control groups were used as negative (virus-unchallenged) control and positive (virus-challenged) control. We show that some parameters such as nitric oxide production in serum and splenic adherent cells and interferon-gamma levels in splenic cells from SPF chickens could be used for the evaluation of LPAI virus infection. This is the first report demonstrating the interferon-gamma production in cultured splenic mononuclear cells and nitric oxide production in serum as well as virus shedding in trachea and cloacae in LPAI virus-infected SPF chickens fed specific lactic acid bacterial components.

Astragali Radix elicits anti-inflammation via activation of MKP-1, concomitant with attenuation of p38 and Erk.

Although Astragali Radix (Astragalus, AR), the root of Astragalus membranaceus (Fisch) Bunge, is widely used in oriental medicine for tonifying the immune response and improving circulation, the underlying mechanism(s) by which these effects are induced remains unclear. Here, we report that AR displays anti-inflammatory effects in zymosan air-pouch mice by reducing the expression of iNOS, COX-2, IL-6, IL-1beta and TNF-alpha and by decreasing the production of nitric oxide (NO). In a similar manner, AR reduces the expression of IL-6, iNOS, and COX-2 in lipopolysaccharide (LPS)-treated Raw 264.7 cells. We further demonstrate that AR attenuates the activity of p38 and Erk1/2 and stimulates mitogen-activated protein kinase phosphatase-1 (MKP-1) in LPS-treated Raw 264.7 cells. Additionally, AR interferes with the translocation of NFkappaB to the nucleus, subsequently resulting in NFkappaB-dependent transcriptional repression. Taken together, these data reveal that AR has an anti-inflammatory effect that is mediated by the MKP-1-dependent inactivation of p38 and Erk1/2 and inhibition of NFkappaB-mediated transcription. These results imply that the AR herb has a potential anti-inflammatory activity.

Hypoxia inhibits the SDF-1-dependent migration of human leukemic cell line HL-60 via blocking of Akt activation.

Hypoxia is known to regulate the expression of genes involved in the migration of various cell types. Although many studies have shown that hypoxia increases cell migration, it still remains unclear whether hypoxia could modulate the stromal cell derived factor-1 (SDF-1)-dependent migration of leukemic cell. Herein, we demonstrated that the SDF-1-dependent migration of HL-60, was reduced under hypoxia with no comparable decrease of CXC-type chemokine receptor CXCR4, a cognate receptor for SDF-1. Furthermore, we showed that migration toward SDF-1 was reduced by inactivation of either serine/threonine kinase Akt or extracellular signal regulated kinase Erk, which was confirmed by selective pathway inhibitor LY294002 and PD98059. In our results, phosphorylation of Erk was increased under hypoxia, but phosphorylation of Akt was attenuated on the contrary. These results led us to conclusion that hypoxia could inhibit the SDF-1-dependent migration of HL-60 via blocking of Akt activation.

Methyl CpG-binding domain protein 3 mediates cancer-selective cytotoxicity by histone deacetylase inhibitors via differential transcriptional reprogramming in lung cancer cells.

Histone deacetylase inhibitors (HDI) have been reported to inhibit the growth and survival of cancer cells while leaving normal cells untouched. However, the mechanisms underlying this selective cell death are poorly understood. Gene expression analysis revealed that HDI treatment induced up-regulation of p21(WAF1/Cip1) and down-regulation of ErbB2 in cancer cells but not normal cells. Overexpression of p21(WAF1/Cip1) and/or silencing of ErbB2 enhanced cancer cell growth inhibition, suggesting that HDI-induced up-regulation/down-regulation of these genes play critical roles in HDI-induced growth inhibition of cancer cells. Most importantly, we found that the gene silencing factor methyl CpG-binding domain protein 3 (MBD3) was not only released from cancer-selective promoter of the HDI up-regulated p21(WAF1/Cip1) gene but also recruited to that of the HDI-down-regulated ErbB2 gene. Furthermore, silencing of MBD3 by small interfering RNA abrogated the HDI-induced gene regulation and growth inhibition in lung cancer but not in normal cells. Together, our results support the critical potential of MBD3 in HDI-induced cancer-selective cell death via cancer differential gene expression.

A lactic acid bacterium isolated from kimchi ameliorates intestinal inflammation in DSS-induced colitis.

Some species of lactic acid bacteria have been shown to be beneficial in inflammatory bowel disease (IBD). In the present study, a strain of lactic acid bacterium (Lactobacillus paracasei LS2) was isolated from the Korean food, kimchi, and was shown to inhibit the development of experimental colitis induced by dextran sulfate sodium (DSS). To investigate the role of LS2 in IBD, mice were fed DSS in drinking water for seven days along with LS2 bacteria which were administered intragastrically to some of the mice, while phosphate-buffered saline (PBS) was administered to others (the controls). The administration of LS2 reduced body weight loss and increased survival, and disease activity indexes (DAI) and histological scores indicated that the severity of colitis was significantly reduced. The production of inflammatory cytokines and myeloperoxidase (MPO) activity also decreased. Flow cytometry analysis showed that the number of Th1 (IFN-γ) population cells was significantly reduced in the LS2-administered mice compared with the controls. The administration of LS2 induced the increase of CD4+FOXP3+ Treg cells, which are responsible for IL-10. Numbers of macrophages (CD11b+ F4/80+), and neutrophils (CD11b+ Gr-1+) among lamina propria lymphocytes (LPL) were also reduced. These results indicate that LS2 has an anti-inflammatory effect and ameliorates DSS-induced colitis.

Protection of Staphylococcus aureus-infected septic mice by suppression of early acute inflammation and enhanced antimicrobial activity by ginsan.

Ginsan, an acidic polysaccharide prepared from Panax ginseng, demonstrated multiple immunomodulatory effects in previous studies. This study was conducted to elucidate the antiseptic mechanism induced by ginsan in mice infected with Staphylococcus aureus. When mice were treated with ginsan before the bacterial challenge with S. aureus, they were highly protected from sepsis-induced death. The numbers of S. aureus recovered from ginsan-treated mice were considerably lower than those recovered from nontreated mice. The in vivo depletion of monocytes/macrophages caused more S. aureus to be recovered from the bacteria-infected mice. Nevertheless, mice treated with both etoposide and ginsan were able to maintain an antibacterial activity. In addition, the phagocytic activity of ginsan-treated macrophage against S. aureus was considerably enhanced. The synthesis of inflammatory cytokines, such as tumor necrosis factor-alpha interleukin (IL)-1beta, IL-6, IFN-gamma, IL-12, IL-18 and interferon gamma, was significantly downregulated at the early phase of sepsis in mice that were treated with ginsan before the bacterial challenge. Expression of Toll-like receptors (TLRs), including TLR2, TLR4, and TLR9, as well as the adaptor molecule MyD88, was considerably reduced in peritoneal macrophages that were treated with ginsan before a subsequent contact with S. aureus. These data indicated that ginsan protected mice from S. aureus-induced sepsis through the suppression of acute inflammatory responses at an early phase and the enhancement of antimicrobial activities at subsequent phases of infection.

The histone deacetylase inhibitor trichostatin A sensitizes estrogen receptor alpha-negative breast cancer cells to tamoxifen.

Many cases of breast cancer show loss of estrogen receptor (ER) alpha expression, which leads to unresponsiveness to antihormonal treatment even though there is no loss of the structurally and biochemically similar ER beta. ER activity is positively and negatively regulated by transcriptional regulators such as histone deacetylase (HDAC), which is known to be a negative ER regulator. Here, we evaluated using ER beta as an alternative target for tamoxifen therapy by treating ER alpha-negative, beta-positive breast cancer cells with the HDAC inhibitor trichostatin A (TSA), and testing whether tamoxifen responsiveness increased following upregulation of ER beta. TSA enhanced the overall ER transcriptional activity in these cells, as visualized by estrogen response element-regulated reporter and the expression of progesterone receptor, a known ER target, without ER alpha restoration. Additionally, TSA induced the expression and nuclear translocation of ER beta but not alpha, suggesting that these actions leading to increase of ER transcriptional activity are mediated through ER beta rather than alpha. Furthermore, following treatment with TSA, the formerly unresponsive MDA-MB-231 and Hs578T breast cancer cells became responsive to tamoxifen. However, reduction of ER beta expression by short interfering RNA abrogated this TSA-induced sensitization effect in these cells. Together, these results show that the HDAC inhibitor TSA sensitized ER alpha-negative, antihormone-unresponsive breast cancer cells to tamoxifen treatment possibly by upregulating ER beta activity.

Directed Self-Assembly of Poly(2-vinylpyridine)-b-polystyrene-b-poly(2-vinylpyridine) Triblock Copolymer with Sub-15 nm Spacing Line Patterns Using a Nanoimprinted Photoresist Template.

Low molecular weight P2VP-b-PS-b-P2VP triblock copolymer (poly(2-vinlypyridine)-block-polystyrene-block-poly(2-vinylpyridine)] is doped with copper chloride and microphase separated into lamellar line patterns with ultrahigh area density. Salt-doped P2VP-b-PS-b-P2VP triblock copolymer is self-assembled on the top of the nanoimprinted photoresist template, and metallic nanowires with long-range ordering are prepared with platinum-salt infiltration and plasma etching.

Identification of Weissella species by the genus-specific amplified ribosomal DNA restriction analysis.

The Weissella species have been increasingly isolated from many food and meat samples. For rapid and systematic identification of Weissella species, an amplified ribosomal DNA restriction analysis (ARDRA) has been developed. This method employs both polymerase chain reaction (PCR) and restriction pattern analysis: first, PCR using the genus-specific primers that were designed from 16S rDNA sequence produces a 725-bp band only from Weissella species and next, restriction analysis using MnlI, MseI, and BceAI restriction enzymes identifies these Weissella-specific PCR fragments to the species level. This ARDRA method clearly identified six Weissella strains isolated from kimchi as well as 10 validly described Weissella type strains. Therefore, these results suggest that this ARDRA is a rapid and reliable method for identification of Weissella species.

Identification of Lactobacillus sakei and Lactobacillus curvatus by multiplex PCR-based restriction enzyme analysis.

Two closely related lactic acid bacteria, Lactobacillus sakei and Lactobacillus curvatus, are very difficult to be rapidly differentiated. Here we report multiplex polymerase chain reaction (PCR)-based restriction enzyme analysis that is useful for rapid and reliable identification of these two species. This method employs both polymerase chain reaction (PCR) and restriction enzyme analysis (REA). First, multiplex-PCR using three primers that were designed from 16S rDNA sequence produces two bands, a 433-bp and a 623-bp band. A 433-bp band represents only L. sakei and L. curvatus among lactobacilli and genetically related bacteria, and a 623-bp band is used for further identification by restriction analysis. Second, restriction analysis of 623-bp band using Hind III restriction enzyme discriminates L. sakei from L. curvatus. This method could identify 28 strains as L. sakei or L. curvatus, which were frequently isolated from kimchi, a traditional fermented cabbage product in South Korea. Therefore, these results suggest that this method is simple, rapid, and reliable for the identification of L. sakei and L. curvatus species.

On the self-assembly of brush block copolymers in thin films.

We describe a simple route to fabricate two dimensionally well-ordered, periodic nanopatterns using the self-assembly of brush block copolymers (brush BCPs). Well-developed lamellar microdomains oriented perpendicular to the substrate are achieved, without modification of the underlying substrates, and structures with feature sizes greater than 200 nm are generated due to the reduced degree of chain entanglements of brush BCPs. A near-perfect linear scaling law was found for the period, L, as a function of backbone degree of polymerization (DP) for two series of brush BCPs. The exponent increases slightly from 0.99 to 1.03 as the side chain molecular weight increases from ∼2.4 to ∼4.5 kg/mol(-1) and saturated with further increase in the side chain molecular weight due to the entropic penalty associated with the packing of the side chains. Porous templates and scaffolds from brush BCP thin films are also obtained by selective etching of one component.

Suppression of proinflammatory cytokine production by specific metabolites of Lactobacillus plantarum 10hk2 via inhibiting NF-κB and p38 MAPK expressions.

The objective of this study was to evaluate the immunomodulatory effects of specific bacterial metabolites of Lactobacillus plantarum 10hk2 to induce anti-inflammatory mediators in cell cultures of the murine macrophage cell line, RAW 264.7. The effects of the extracellular metabolites of this bacterial strain were examined by dividing them into protein and polysaccharide fractions. A specific protein fraction (8.7 kDa) was found to be a strong IL-10 inducer in LPS-stimulated RAW 264.7 cells and suppressed LPS-induced NF-κB induction and inhibited LPS-induced phosphorylation of I-κB and p38 MAPK. To the best of our knowledge, this was the first study that investigated the anti-inflammatory effects of an extracellular peptide derived from lactic acid bacteria. In addition, we characterized the inhibitory mode of this molecule in the induction of proinflammatory cytokines. Based on the findings presented in this study, this molecule holds promise for use as an agent to modulate inflammation related diseases.

Sustained expression of NADPH oxidase 4 by p38 MAPK-Akt signaling potentiates radiation-induced differentiation of lung fibroblasts.

Radiation-induced fibrosis (RIF) is a long-term adverse effect of curative radiotherapy; however, the distinct molecular mechanisms of RIF in neighboring normal tissue are not fully understood. We investigated the mechanisms underlying radiation-induced fibroblast differentiation into myofibroblasts. Lung fibroblasts produced reactive oxygen species (ROS) immediately after irradiation, the level of which remained increased for 24 h. The NADPH oxidase inhibitor, diphenyleneiodonium (DPI), suppressed ROS production and significantly decreased the radiation-induced expression of alpha-smooth muscle actin (alpha-SMA) and fibronectin (FN). The mRNA and protein expression of Nox4 was increased by radiation, and siRNA knockdown of Nox4 reduced alpha-SMA and FN levels. Increased phosphorylation of p38MAPK, Erk, and PI3k/Akt was observed after irradiation. Inhibitors of p38 MAPK and Akt, but not of Erk, reduced radiation-induced fibroblast differentiation and Nox4 expression. Notably, DPI partially decreased phosphorylation of p38MAPK and Akt, suggesting that p38MAPK, Akt, and Nox4 may cooperate in a positive feedback loop. Nox4 expression was also increased during bleomycin-induced fibroblast differentiation, and downregulation of Nox4 reduced alpha-SMA levels and extracellular matrix (ECM) accumulation. These results demonstrate that interfering Nox4 activation can be a potential strategy to disrupt fibrotic process.

ATM modulates transcription in response to histone deacetylase inhibition as part of its DNA damage response.

Chromatin structure has a crucial role in a diversity of physiological processes, including development, differentiation and stress responses, via regulation of transcription, DNA replication and DNA damage repair. Histone deacetylase (HDAC) inhibitors regulate chromatin structure and activate the DNA damage checkpoint pathway involving Ataxia-telangiectasia mutated (ATM). Herein, we investigated the impact of histone acetylation/deacetylation modification on the ATM-mediated transcriptional modulation to provide a better understanding of the transcriptional function of ATM. The prototype HDAC inhibitor trichostain A (TSA) reprograms expression of the myeloid cell leukemia-1 (MCL1) and Gadd45 genes via the ATM-mediated signal pathway. Transcription of MCL1 and Gadd45alpha is enhanced following TSA treatment in ATM(+) cells, but not in isogenic ATM(-) or kinase-dead ATM expressing cells, in the ATM-activated E2F1 or BRCA1- dependent manner, respectively. These findings suggest that ATM and its kinase activity are essential for the TSA-induced regulation of gene expression. In summary, ATM controls the transcriptional upregulation of MCL1 and Gadd45 through the activation of the ATM-mediated signal pathway in response to HDAC inhibition. These findings are important in helping to design combinatory treatment schedules for anticancer radio- or chemo-therapy with HDAC inhibitors.