Analysis of changes in microbiome compositions related to the prognosis of colorectal cancer patients based on tissue-derived 16S rRNA sequences.

BACKGROUND: Comparing the microbiome compositions obtained under different physiological conditions has frequently been attempted in recent years to understand the functional influence of microbiomes in the occurrence of various human diseases. METHODS: In the present work, we analyzed 102 microbiome datasets containing tumor- and normal tissue-derived microbiomes obtained from a total of 51 Korean colorectal cancer (CRC) patients using 16S rRNA amplicon sequencing. Two types of comparisons were used: 'normal versus (vs.) tumor' comparison and 'recurrent vs. nonrecurrent' comparison, for which the prognosis of patients was retrospectively determined. RESULTS: As a result, we observed that in the 'normal vs. tumor' comparison, three phyla, Firmicutes, Actinobacteria, and Bacteroidetes, were more abundant in normal tissues, whereas some pathogenic bacteria, including Fusobacterium nucleatum and Bacteroides fragilis, were more abundant in tumor tissues. We also found that bacteria with metabolic pathways related to the production of bacterial motility proteins or bile acid secretion were more enriched in tumor tissues. In addition, the amount of these two pathogenic bacteria was positively correlated with the expression levels of host genes involved in the cell cycle and cell proliferation, confirming the association of microbiomes with tumorigenic pathway genes in the host. Surprisingly, in the 'recurrent vs. nonrecurrent' comparison, we observed that these two pathogenic bacteria were more abundant in the patients without recurrence than in the patients with recurrence. The same conclusion was drawn in the analysis of both normal and tumor-derived microbiomes. CONCLUSIONS: Taken together, it seems that understanding the composition of tissue microbiomes is useful for predicting the prognosis of CRC patients.

Preparation of stabilized magnetic nanoparticles with polymerizable lipid and anchor compounds.

Although the lipid-based method for coating of magnetic nanoparticles (MNPs) is rapid and simple, the unstable state of the lipid layer is a major limitation for the practical application of this method. We devised a method to prepare stabilized MNPs by covalent modifications such as lipid polymerization and anchoring of the lipid layer. The stability of the modified lipid layer was demonstrated by the stable status of enzymes immobilized on the MNPs and the resistance of the MNPs to aggregation. We also determined the maximum ratio of nonpolymerizable lipophilic compounds that can be included in the layer without significantly reducing stability.

A lipid-based method for the preparation of a piezoelectric DNA biosensor.

A piezoelectric DNA biosensor was prepared by immobilizing DNA probes on a quartz crystal microbalance (QCM) using a lipid-based method. A QCM electrode was coated with a hybrid bilayer membrane composed of an octadecanethiol monolayer and a lipid monolayer containing biotinylated lipids to establish biotin groups on the electrode surface. A DNA biosensor was prepared by sequentially immobilizing avidin and the biotinylated probe. The DNA biosensor was stable throughout repeated surface regeneration and showed higher sensitivity than that prepared by the conventional chemical method using diimide. We also optimized the surface regeneration conditions and flow rate for flow injection analysis.

Functionalization of quartz crystal microbalances with liposomes containing the N-hydroxysuccinimide ester of palmitic acid.

We developed a fast and simple method to functionalize a quartz crystal microbalance (QCM) with liposomes composed of phosphatidylcholine lipid and the N-hydroxysuccinimide (NHS) ester of palmitic acid. The liposome was applied directly to a bare gold surface of a QCM to prepare the lipid bilayer presenting NHS groups on the surface. The whole functionalization process was completed within 1 h using stored lipid films. Streptavidin immobilization efficiency of the method was comparable to the 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)/NHS chemical method, and the activity of the biotinylated antibody immobilized through the streptavidin was stably retained in repeated surface regeneration with the dissociation buffer.

Detection of Edwardsiella tarda by fluorometric or biosensor methods using a peptide ligand.

In this study, we identified a peptide ligand for Edwardsiella tarda from a phage peptide library and tested two approaches for sensitive detection of the bacteria with the peptide labeled with fluorescein or biotin. At first, the fluorescent peptide was proved to be advantageous in the fluorescence polarization (FP) assay because sensitivity of the assay is maximized when a fluorophore is linked to a small molecule. The FP assay using the fluorescent peptide enabled detection of E. tarda in a range from 5.2×10(3) to 2.1×10(5) cells. Second, we devised a new assay method using a quartz crystal microbalance (QCM) biosensor connected to a filter module. When a mixture of E. tarda and the biotinylated peptide was injected into the filter module, the E. tarda-peptide complex was separated from the unbound peptide by a filter and detected with a streptavidin-coated QCM sensor chip. On injection of samples containing the biotinylated peptide and E. tarda, concentration-dependent frequency change was observed in a range from 8×10(2) to 8×10(6) cells. The two approaches are expected to facilitate development of assay methods using other bacteria-binding peptides.

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients.

ABBREVIATIONS: LT, liver transplantation; HCC, hepatocellular carcinoma; IS, immunosuppressants; DC, dendritic cells; Treg, regulatory T; Th17, T helper 17; AST, aspartate transaminase; ALT, alanine transaminase; OUT, operational taxonomic unit; LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis; IL, interleukin; TGF, transforming growth factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; TNF-α, tumor necrosis factor-α; MIP-1α, macrophage inflammatory protein-1α; IP-10, interferon γ-induced protein; MCP-1, monocyte chemoattractant protein-1; ACR, acute cellular rejection; NF-κB, nuclear factor κB; PT INR, prothrombin time; QC, quality check; PBMC, peripheral blood mononuclear cells; PBS, phosphate-buffered saline; ELISA, enzyme-linked immunosorbent assay.

Identification of a polymeric ß-cyclodextrin-binding peptide from a phage-displayed peptide library.

In this work, a phage-displayed peptide library was applied to identification of ß-cyclodextrin (CD)-binding peptide tag, capable of being combined to target peptides or proteins in a homogeneous way by established methods such as peptide synthesis and the recombinant DNA technique. Four enriched sequences were obtained after five rounds of biopanning against polymeric ß-CD beads. One of the sequences showed high binding affinity to ß-CD beads with a dissociation constant of approximately 7×10(-6)M. The ß-CD-binding sequence was used for immobilization of a hepatitis C virus (HCV) antigenic peptide on ß-CD beads. The functionalized ß-CD beads were successfully used for immunoassay of anti-HCV antibody with a detection limit of 1 ng. These results demonstrate that the identified peptide sequence has the potential of being used as an affinity tag to ß-CD-containing surfaces.

Draft genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle.

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species and a winter economic aquaculture resource in South Korea. Because of its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summers. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) vs. warm (HT, 23°C) conditions to identify heat stress-induced genes and gene categories. We observed a total of 1987 contigs with N50 of 0.46 Mbp, with the largest contig (3.03 Mbp) in the assembled genome. A total of 20,644 protein-coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology terms and 11,560 genes for KEGG Orthology. We conducted the lost and gained genes analysis compared with three species that: human, zebrafish, and salmon. In the lost genes analysis, we detected that smelt lost 4461 (22.16%), 2825 (10.62%), and 1499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed that smelt gained 1133 (5.49%), 1670 (8.09%), and 229 (1.11%) genes compared with the above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with a false discovery rate <0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that upregulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and genes were downregulated by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, upregulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001), and calcium-release channel activity (GO:0015278, P < 0.01), and genes were downregulated for a nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of molecular mechanisms and heat responses and be useful for predicting survival of the smelt and its closely related species under global warming.

Rapid single-cell detection of pathogenic bacteria for in situ determination of food safety.

A highly sensitive in situ method to detect bacterial pathogens is of utmost importance in preventing the outbreak of foodborne diseases. In this study, a simple method enabling the detection of a single bacterial cell in a sample was developed based on magnetic capture particles (CPs), and europium-fluorescent labeling particles (LPs) functionalized with antibodies. After mixing the sample with the particles in a sample tube, the sample tube was connected to an assay chip, where the CP-bacteria-LP complex was transported from the sample chamber to a detection chamber using a simple assay device. The number of bacteria was quantitatively determined by measuring the fluorescence emitted from the detection chamber. This assay method enabled the detection of a single cell of Vibrio parahaemolyticus from 0.1 mL pure broth culture samples within 30 min. A simple enrichment method that can be performed using only the vibrating action of the assay device without any additional instruments was also developed for the analysis of food samples. By analyzing the enriched sample using the assay method, we could detect V. parahaemolyticus quantitatively with a detection limit of 1 colony forming unit from oyster samples within 130 min. Due to simplicity of this methodology and the instrumentation involved, and its capability of rapid single-cell detection, it may be considered as an in situ method for the determination of food safety.

Draft Genome Sequence of Lactobacillus plantarum EBKLp545, Isolated from Piglet Feces.

Lactobacillus plantarum strain EBKLp545 was isolated from piglet feces in South Korea and sequenced using an Illumina HiSeq system. This draft genome of strain EBKLp545 consists of 3,306,513 bp with 3,049 protein-coding genes in 138 contigs (≥500 bp), 54 noncoding RNA genes, and a 44.3% G+C content.

Draft Genome Sequence of Enterococcus plantarum Strain TRW2, Isolated from Lettuce.

We report the draft genome sequence for Enterococcus plantarum strain TRW2, isolated from the phyllosphere of romaine lettuce. The draft sequence consists of 3,383,441 bp, with a G+C content of 35.8% and 3,218 protein-coding genes. None of the 22,190 known antibiotic resistance genes were detected.

Pan-Genomics of Lactobacillus plantarum Revealed Group-Specific Genomic Profiles without Habitat Association.

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (L-arabinose, L-rhamnose, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

Sensitive immunoassay-based detection of Vibrio parahaemolyticus using capture and labeling particles in a stationary liquid phase lab-on-a-chip.

In the present study, a method was developed for detection of Vibrio parahaemolyticus based on a stationary liquid phase lab-on-a-chip (SLP LOC). The present SLP LOC comprises a sample chamber, washing chamber, and detection chamber connected by two channels. The method utilizes two types of particles: capture particles (CPs), which are magnetic nanoparticles functionalized with antibody; and labeling particles (LPs), which are silica nanoparticles functionalized with horseradish peroxidase and antibody. Samples were added to the sample chamber with CPs and LPs, forming a CP-bacteria-LP complex, and the complex was transported to the detection chamber containing chromogenic substrate solution. The method allowed the detection of V. parahaemolyticus in the range of 101-105cfu within 45min. Additionally, contamination of oyster samples with V. parahaemolyticus was detected within 2.5h, including 2h of culturing. The present method has the advantage of being highly rapid and facile, and enabling the detection of bacteria with high sensitivity. Moreover, the LOC and LOC processing device used in this method possess simple structures, making the detection process economical and allowing miniaturization. Therefore, the present SLP LOC detection method is potentially useful for in situ determination of food safety.

Beneficial effects of fermented black ginseng and its ginsenoside 20(S)-Rg3 against cisplatin-induced nephrotoxicity in LLC-PK1 cells.

BACKGROUND: Nephrotoxicity is a common side effect of medications. Panax ginseng is one of the best-known herbal medicines, and its individual constituents enhance renal function. Identification of its efficacy and mechanisms of action against drug-induced nephrotoxicity, as well as the specific constituents mediating this effect, have recently emerged as an interesting research area focusing on the kidney protective efficacy of P. ginseng. METHODS: The present study investigated the kidney protective effect of fermented black ginseng (FBG) and its active component ginsenoside 20(S)-Rg3 against cisplatin (chemotherapy drug)-induced damage in pig kidney (LLC-PK1) cells. It focused on assessing the role of mitogen-activated protein kinases as important mechanistic elements in kidney protection. RESULTS: The reduced cell viability induced by cisplatin was significantly recovered with FBG extract and ginsenoside 20(S)-Rg3 dose-dependently. The cisplatin-induced elevated protein levels of phosphorylated c-Jun N-terminal kinase (JNK), p53, and cleaved caspase-3 were decreased after cotreatment with FBG extract or ginsenoside 20(S)-Rg3. The elevated percentage of apoptotic LLC-PK1 cells induced by cisplatin treatment was significantly abrogated by cotreatment with FBG and the ginsenoside 20(S)-Rg3. CONCLUSION: FBG and its major ginsenoside 20(S)-Rg3, ameliorated cisplatin-induced nephrotoxicity in LLC-PK1 cells by blocking the JNK-p53-caspase-3 signaling cascade.

Identification of a deoxyribonuclease I inhibitor from a phage-peptide library.

Deoxyribonuclease I (DNase I) is a divalent cation dependent endonuclease and thought to be a significant barrier to effective gene delivery. The only known DNase I-specific inhibitor is monomeric actin which acts by forming a 1:1 complex with DNase I. Its use, however, is restricted because of tendency to polymerize under certain conditions. We screened two random phage peptide libraries of complexity 10(8) and 10(9) for DNase I binders as candidates for DNase I inhibitors. A number of DNase I-binding peptide sequences were identified. When these peptides were expressed as fusion proteins with Escherichia coli maltose binding protein, they inhibited the actin-DNase I interaction (IC50 = 0.1-0.7 microM) and DNA degradation by DNase I (IC50 = 0.8-8 microM). Plasmid protection activity in the presence of DNase I was also observed with the fusion proteins. These peptides have the potential to be a useful adjuvant for gene therapy using naked DNA.

Immunoassay of paralytic shellfish toxins by moving magnetic particles in a stationary liquid-phase lab-on-a-chip.

In this study, we devised a stationary liquid-phase lab-on-a-chip (SLP LOC), which was operated by moving solid-phase magnetic particles in the stationary liquid phase. The SLP LOC consisted of a sample chamber to which a sample and reactants were added, a detection chamber containing enzyme substrate solution, and a narrow channel connecting the two chambers and filled with buffer. As a model system, competitive immunoassays of saxitoxin (STX), a paralytic shellfish toxin, were conducted in the SLP LOC using protein G-coupled magnetic particles (G-MPs) as the solid phase. Anti-STX antibodies, STX-horseradish peroxidase conjugate, G-MPs, and a STX sample were added to the sample chamber and reacted by shaking. While liquids were in the stationary state, G-MPs were transported from the sample chamber to the detection chamber by moving a magnet below the LOC. After incubation to allow the enzymatic reaction to occur, the absorbance of the detection chamber solution was found to be reciprocally related to the STX concentration of the sample. Thus, the SLP LOC may represent a novel, simple format for point-of-care testing applications of enzyme-linked immunosorbent assays by eliminating complicated liquid handling steps.

Microplate assay measurement of cytochrome p450-carbon monoxide complexes.

Cytochrome P450 in microsomes can be quantitated using the characteristic 450 nm absorption peak of the CO adduct of reduced cytochrome P450. We developed a simple microplate assay method that is superior to previous methods. Our method is less laborious, suitable for analyzing many samples, and less sensitive to sample aggregation. Microsome samples in microplate wells were incubated in a CO chamber rather than bubbled with CO gas, and then reduced with sodium hydrosulfite solution. This modification allowed a reliable and reproducible assay by effectively eliminating variations between estimations.

A colorimetric microplate assay method for high throughput analysis of lipase activity.

The present work describes a colorimetric microplate assay for lipase activity based on the reaction between 5,5'-dithiobis(2-nitro benzoic acid) (DTNB) and the hydrolysis product of 2,3-dimercapto-1-propanol tributyrate (DMPTB). Reaction mixtures containing DTNB, DMPTB, and lipase were prepared in microplate wells, and the absorbance at 405nm was recorded after incubation at 37 degrees C for 30 min. A linear relationship was obtained in the range of 0.1-1 U of lipase activity by this method. The reaction conditions were also optimized for the range of 0.01-0.1 U or 1-10 U. When assaying crude tissue extracts, the reaction of DTNB with non-specific reducing agents created a major source of error. However, this error was corrected by the use of blank samples that did not contain DMPTB.

Direct introduction of a hydrazide group into a quartz crystal microbalance surface with dodecanoic hydrazide embedded in a hybrid bilayer membrane.

Hydrazide group has a potential of immobilizing an antibody on a sensor surface in a way that ensures an optimal orientation and efficiency of the antibody. However, a multi-step chemical process, required for the preparation of a hydrazide group, is a barrier to its extensive application. This paper describes a new method to introduce a hydrazide group to a sensor surface by a one-step process using dodecanoic hydrazide. The method is based on an ability of the dodecanoic hydrazide to be incorporated into a hybrid bilayer membrane (HBM) layer, thereby presenting its hydrazide group to the surface. Liposome containing dodecanoic hydrazide was added to a hydrophobic self-assembled monolayer surface of a quartz crystal microbalance for the formation of a HBM. Then, the hydrazide group, presented in the surface of the HBM layer, was utilized for the oriented immobilization of an antibody via its carbohydrate moiety which was partially oxidized prior to the conjugation reaction. Activity and stable status of the incorporated dodecanoic hydrazide was revealed by the efficiency and reproducibility of the resulting immunosensor chip.

Optimization of the hybrid bilayer membrane method for immobilization of avidin on quartz crystal microbalance.

Hybrid bilayer membrane (HBM), comprising a lipid monolayer fused to a hydrophobic self-assembled monolayer (SAM), has a potential capability to provide a convenient tool for the preparation of functionalized sensor surfaces. In this work, the HBM approach was optimized for the preparation of avidin-containing quartz crystal microbalance (QCM) sensor chip which would be available for immobilization of biotinylated molecules. Lipid layer of HBM was composed of background lipid such as egg phosphatidyl choline and biotinylated lipid to which avidin was attached. Highest performance was obtained at 1:1 ratio of the biotinylated lipid and the background lipid, and sensitivity and stability of the resulting sensor chip was comparable to a sensor chip prepared by the conventional carbodiimide reaction. By utilizing the HBM method, construction of a stable avidin sensor chip was achieved within 40 min without any chemical steps. Thus the HBM method was proven to be a convenient and efficient way to immobilize avidin on sensor surfaces.