<Emphasis Type="Italic">Dankookia rubra</Emphasis> gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream

WS-10^T–a Gram-negative, non-motile, and aerobic bacterial strain–was isolated from the sediment of a shallow stream in Korea. The optimum ranges of temperature and pH for growth were 20–40°C (optimum 28°C) and pH 6.0–8.0 (optimum pH 7.0), respectively. The DNA G+C content of strain WS-10^T was 72.7 mol%. The major fatty acids (>5%) were summed feature 8 (C_18:1ω7c), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0, and C_18:1 2-OH. The major polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminolipids. Q-10 was the predominant respiratory quinone. The highest similarities in the 16S rRNA gene sequence were shown with Paracraurococcus ruber (95.3%), Belnapia soli (95.3%), B. moabensis (95.1%), and B. rosea (95.0%). A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain WS-10T formed a distinct line within a clade containing the genera Paracraurococcus, Craurococcus, and Belnapia in the family Acetobacteraceae. On the basis of polyphasic evidence, strain WS-10^T represents a novel species of a new genus in the family Acetobacteraceae, for which the name Dankookia rubra gen. nov., sp. nov. is proposed. The type strain of the type species is WS-10^T (= KACC 18533^T = JCM 30602^T).     

Influence of polymorphisms of UDP-glycosyltransferases (UGT) 2B family genes UGT2B15, UGT2B17 and UGT2B28 on the development of prostate cancer in Korean men

Prostate cancer is known as the fifth most common cancer in Korean male. The etiology of the prostate cancer remains unknown, but age, race, drug, family history, dietary habit and steroid hormone levels have been suggested as causative factors. Among these factors, variations in androgen hormone levels have been suggested as one of risk factors for the cancer. The glucuronidation is a major pathway of detoxification process of toxin and hormones within human body by UDP-glucuronosyltransferase (UGT) enzymes. Known as the androgen inactivating UGT2B enzyme family, UGT2B17 and UGT2B28 have common deletion region by copy number variation (CNV) and UGT2B15 has a single nucleotide polymorphism (SNP) (rs1902023: G > T) locus which contains the change from Asp to Tyr on exon 1. These polymorphisms were analyzed with genomic DNA extracted from 555 prostate cancer cases and 404 control males. There was no difference in the frequency of CNV and SNP of each UGT2B genes between prostate cancer cases and control males. In this study, we found the decreased risk (OR, 0.39; 95 % CI, 0.19–0.83; P = 0.011) of prostate cancer in individuals with UGT2B17 del/del type, UGT2B28 in/del type and UGT2B15 SNP TT type. Additionally, we found the length polymorphisms of the short tandem repeat (STR) in the allelic loci of UGT2B28 deletion regions and suggest that this locus can be used for a personal identification marker.     

MHC expression in a human adult stem cell line and its down-regulation by hCMV US gene transfection

Due to their unique capacity to self-renew and for multiple differentiation, stem cells are considered promising candidates for cell replacement therapy in many devastating diseases. However, studies on immune rejection, which is a major problem facing successful stem cell therapy, are rare. In this study, we examined MHC expression in the M13SV1 cell line, which has previously been shown to have stem cell properties and to be non-tumorigenic, in order to determine whether human adult stem cells might be rejected after transplantation. Our results show low expression levels of MHC class I molecules on the surface of these cells. An induction of MHC class I expression was observed when the cells were treated with IFN-gamma. Maximal induction of MHC class protein expression was observed at 48 h after treatment with concentrations above 5 ng/ml of IFN-gamma. Elevated MHC class I levels were sustained for 72 h after withdrawing IFN-gamma. Therefore, we introduced human cytomegalovirus (hCMV) US genes, which are known to be able to reduce MHC class I expression on the cell surface after infection, into M13SV1 cells. Cells transfected with the hCMV US2, US3, US6 or US11 genes exhibited a reduction (40-60%) of MHC class I expression compared with mock-transfected cells. These results suggest that human adult stem cells are capable of expressing high levels of MHC class I proteins, and thus may be rejected on transplantation unless they are modified. In addition, viral stealth mechanisms can be exploited for stem cell transplantation.     

Combined application of rapamycin and atorvastatin improves lipid metabolism in apolipoprotein E-deficient mice with chronic kidney disease

Atherosclerosis arising from the pro-inflammatory conditions associated with chronic kidney disease (CKD) increases major cardiovascular morbidity and mortality. Rapamycin (RAPA) is known to inhibit atherosclerosis under CKD and non-CKD conditions, but it can cause dyslipidemia; thus, the co-application of lipid-lowering agents is recommended. Atorvastatin (ATV) has been widely used to reduce serum lipids levels, but its synergistic effect with RAPA in CKD remains unclear. Here, we analyzed the effect of their combined treatment on atherosclerosis stimulated by CKD in apolipoprotein E-deficient (ApoE^−/−) mice. Oil Red O staining revealed that treatment with RAPA and RAPA＋ ATV, but not ATV alone, significantly decreased the atherosclerotic lesions in the aorta and aortic sinus, compared to those seen in the control (CKD) group. The co-administration of RAPA and ATV improved the serum lipid profile and raised the expression levels of proteins involved in reverse cholesterol transport (LXRα, CYP7A1, ABCG1, PPARγ, ApoA1) in the liver. The CKD group showed increased levels of various genes encoding atherosclerosis-promoting cytokines in the spleen (Tnf-α, Il-6 and Il-1β) and aorta (Tnf-α and Il-4), and these increases were attenuated by RAPA treatment. ATV and RAPA＋ATV decreased the levels of Tnf-α and Il-1β in the spleen, but not in the aorta. Together, these results indicate that, in CKD-induced ApoE^−/− mice, RAPA significantly reduces the development of atherosclerosis by regulating the expression of inflammatory cytokines and the co-application of ATV improves lipid metabolism.     

Association between IL28B Polymorphisms and Spontaneous Clearance of Hepatitis B Virus Infection

Background/Aims

Single-nucleotide polymorphisms (SNPs) near the interleukin 28B gene (IL28B; interferon [IFN]-λ-3) are associated with outcomes of chronic hepatitis C virus (HCV) and hepatitis B virus (HBV) infection treated with peginterferon (PEG-IFN) alpha-based antiviral therapy. In this study, we investigated the influence of IL28B polymorphisms on spontaneous clearance of HBV infection in a large Korean cohort.

Methods

Between January 2007 and June 2010, a total of 208 patients with chronic HBV infection and newly diagnosed HBV-related hepatocellular carcinoma were recruited as the CC group [HBsAg(+) for >6 months, anti-HBc(+), and anti-HBs(-)]. In addition, 351 organ donors were stratified into the UE group [n = 106; HBsAg(-), anti-HBc(-), and anti-HBs(-)] or the SC group [n = 245; HBsAg(-), anti-HBc(+), and anti-HBs(+)]. The SNaPshot ddNTP Primer Extension Kit (Applied Biosystems, Foster City, CA) was used for SNP detection. Direct full sequencing of the IL28B coding region was attempted.

Results

Regardless of group, rs12979860 CC was most frequently identified (85.0% in UE, 85.9% in SC, and 93.5% in CC, respectively), whereas rs12979860 TT was not identified in any group. Similarly, rs12980275 AA and rs8099917 TT were most frequently identified (≥85%) regardless of group, whereas rs12980275 GG was identified in only one subject in the SC group. In addition, rs8099917 GG was not identified. The prevalences of CC in rs12979860, AA in rs12980275, and TT in rs8099917 were significantly higher in the CC group when compared with the UE and SC group (all P<0.05). Among 19 novel SNPs in the IL28B coding region, the proportions of 6 SNPs were significantly different among the UE, SC, and CC groups (all P<0.05).

Conclusions

The SNP upstream of IL28B that has the strongest genetic association with HCV recovery has an inverse influence on HBV recovery. Additional studies are needed to understand the mechanisms of this SNP in HBV infection.     

Population parameters and growth of Riptortus pedestris (Fabricius) (Hemiptera: Alydidae) under elevated CO2 concentrations

We evaluated the direct effects of three different CO₂ concentrations (400, 600 and 1,000 ppm) on the population parameters and growth of the bean bug, Riptortus pedestris, while being fed on soybean. The raw life history data from R. pedestris was analyzed using an age‐stage, two‐sex life table to take the viable development rate among individuals into account. Based on the age‐stage, two‐sex life table analysis, the population projections of R. pedestris provide the stage structure and variability of the population growth under different CO₂ treatments. Our results showed significantly shorter immature durations and higher pre‐adult survival rate under elevated CO₂ (1,000 ppm) than those under ambient CO₂ (400 ppm). The population of R. pedestris reared under elevated CO₂ conditions showed higher intrinsic and finite rates of increase but a lower mean generation time than R. pedestris reared under ambient CO₂ conditions. Our results show the population parameters and growth of R. pedestris are influenced by increased CO₂ relative to ambient CO₂ treatment. Further studies on the long‐term direct effects of different CO₂ levels on R. pedestris are essential to understand their population dynamics and to establish appropriate management strategies.     

An assessment of soil bacterial community structure and physicochemistry in two microtopographic locations of a palustrine forested wetland

We studied redoximorphic features, field indicators and bacterial communities of soils in hummocks and hollows of a palustrine forested wetland in Virginia. We hypothesized that presence of hydric soils, soil physicochemistry and soil bacterial community structure would differ between hummocks and hollows. We fingerprinted soils collected from different microtopographic locations using Length Heterogeneity Polymerase Chain Reaction (LH-PCR) to study their bacterial community structures. Two hummocks had silty/sandy loam soils with mean chroma values of > 4, showing no indication of ‘hydric soils’ (i.e., wetland soils). Two hollows, however, had clay loam soils with mean chroma values of 2 with gleying and redox concentrations observed, indicative of seasonally inundated wetlands. The soils of hollows also had higher organic matter content and soil moisture compared to the soils of hummocks (P < 0.05). Multidimensional scaling (MDS) and Analysis of similarity (ANOSIM) of the fingerprints revealed differences in soil microbial community structures between hummocks and hollows (Global R = 0.30, P < 0.01). The diversity measures of the fingerprints (Shannon’s H′) were also different by microtopography with higher diversity in hollows relative to hummocks (P < 0.05). LH-PCR proves to be a useful tool in examining bacterial community composition of wetland soils in this study. However, cloning and sequencing of specific community LH-PCR profiles of interest is necessary to fully characterize the community down to genus/species level. With species identities we should be able to not only better explain differences observed in the community profiles, but study their relations to hydrologic and/or physicochemical conditions of wetlands.     

Simultaneous organics removal and bio-electrochemical denitrification in microbial fuel cells

Simultaneous organics removal and bio-electrochemical denitrification using a microbial fuel cell (MFC) reactor were investigated in this study. The electrons produced as a result of the microbial oxidation of glucose in the anodic chamber were transferred to the anode, which then flowed to the cathode in the cathodic chamber through a wire, where microorganisms used the transferred electrons to reduce the nitrate. The highest power output obtained on the MFCs was 1.7 mW/m(2) at a current density of 15 mA/m(2). The maximum volumetric nitrate removal rate was 0.084 mg NO(3)(-)-N cm(-2) (electrode surface area) day(-1). The coulombic efficiency was about 7%, which demonstrated that a substantial fraction of substrate was lost without current generation.     

Structural study of novel antimicrobial peptides, nigrocins, isolated from Rana nigromaculata.

Novel cationic antimicrobial peptides, named nigrocin 1 and 2, were isolated from the skin of Rana nigromaculata and their amino acid sequences were determined. These peptides manifested a broad spectrum of antimicrobial activity against various microorganisms with different specificity. By primary structural analysis, it was revealed that nigrocin 1 has high sequence homology with brevinin 2 but nigrocin 2 has low sequence homology with any other known antimicrobial peptides. To investigate the structure-activity relationship of nigrocin 2, which has a unique primary structure, circular dichroism (CD) and homonuclear nuclear magnetic resonance spectroscopy (NMR) studies were performed. CD investigation revealed that nigrocin 2 adopts mainly an alpha-helical structure in trifluoroethanol (TFE)/H(2)O solution, sodium dodecyl sulfate (SDS) micelles, and dodecylphosphocholine micelles. The solution structures of nigrocin 2 in TFE/H(2)O (1:1, v/v) solution and in SDS micelles were determined by homonuclear NMR. Nigrocin 2 consists of a typical amphipathic alpha-helix spanning residues 3-18 in both 50% TFE solution and SDS micelles. From the structural comparison of nigrocin 2 with other known antimicrobial peptides, nigrocin 2 could be classified into the family of antimicrobial peptides containing a single linear amphipathic alpha-helix that potentially disrupts membrane integrity, which would result in cell death.