Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system.

Strain designated DB0510T was isolated from an automobile evaporator core collected in Korea. Cells are gram-stain-positive, aerobic, and coccoid. The strain grew at 15-45 â„ƒ, pH 5.0-8.5 and 0-8.0% (w/v) NaCl. Growth occurs on R2A, trypticase soy agar, Luria-Bertani agar, and nutrient agar. Phylogenetic analysis showed that the strain belongs to the family Dermacoccaceae and strain DB0510T was distinctly separated from validly named genera of this family. Signature nucleotides in 16S rRNA gene sequence revealed that the strain contained the Dermacoccaceae family-specific 16S rRNA signature nucleotides patterns. The major fatty acids were C17:0 and C17:1 cis-9. The only menaquinone was MK-8 (H4). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, and two unidentified lipids. The diagnostic cell-wall amino acid at position 3 of the peptide subunit was found to be lysine. The cell-wall peptidoglycan contained alanine, aspartic acid, glutamic acid, glycine, lysine, and serine and thus the peptidoglycan type was concluded to be of A4α type with Lys-Gly-Ser-Asp interpeptide bridge. The genome size was 3.49 Mbp and G + C content of the genome DNA was 69.4 mol%. On the basis of the phenotypic, genomic, and chemotaxonomic characteristics, strain DB0510T is considered to represent a novel genus and species within the family Dermacoccaceae, for which the name Metallococcus carri gen. nov., sp. nov. is proposed. The type strain of Metallococcus carri is DB0510T (= KACC 19663 T = NBRC 113349 T).

Widespread occurrence of the tfd-II genes in soil bacteria revealed by nucleotide sequence analysis of 2,4-dichlorophenoxyacetic acid degradative plasmids pDB1 and p712.

Variovorax sp. strain DB1 and Pseudomonas pickettii strain 712 are 2,4-dicholorophenoxy-acetic acid (2,4-D)-degrading bacteria, which were isolated from agricultural soils in Republic of Korea and USA, respectively. Each strain harbors a 2,4-D degradative plasmid and is able to utilize 2,4-D as the sole source of carbon for its growth. The 2,4-D degradative plasmid pDB1 of strain DB1 consisted of a 65,269-bp circular molecule with a G+C content of 66.23% and had 68 ORFs. The 2,4-D degradative plasmid p712 of strain 712 was composed of a 62,798-bp circular molecule with a 62.11% G+C content and had 62 ORFs. The plasmids pDB1 and p712 share significantly homologous 2,4-D degradative genes with high similarity to the tfdR, tfdB-II, tfdC-II, tfdD-II, tfdE-II, tfdF-II, tfdK and tfdA genes of plasmid pJP4 of Alcaligenes eutrophus isolated from Australia. In a phylogenetic analysis with trfA, traL, and trbA genes, pDB1 belonged to IncP-1ß with pJP4, while p712 belonged to IncP-1ε with pKJK5 and pEMT3. The results indicated that, in spite of the differences in their backbone regions, the 2,4-D catabolic genes of the two plasmids were closely related and also related to the well-known 2,4-D degradative plasmid pJP4 even though all were isolated from different geographic regions. Other similarities in the genetic organization and the presence of IS1071 suggested that these catabolic genes may be on a transposable element, leading to widespread occurrence in soil bacteria.

Complete genome sequence of the fenitrothion-degrading Burkholderia sp. strain YI23.

Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23.

Complete genome sequence of Mycobacterium intracellulare strain ATCC 13950(T).

Here we report the first complete genome sequence of Mycobacterium intracellulare ATCC 13950(T), a Mycobacterium avium complex (MAC) strain. This genome sequence will serve as a valuable reference for understanding the epidemiologic, biological, and pathogenic aspects of the disparity between MAC members.

Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-02.

Here, we report the first complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-02, which was previously grouped in the INT2 genotype of M. intracellulare. This genome sequence will serve as a valuable reference for improving the understanding of the disparity in the virulence and epidemiologic traits between M. intracellulare genotypes.

Complete genome sequence of Mycobacterium intracellulare clinical strain MOTT-64, belonging to the INT1 genotype.

Here, we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-64, previously grouped into the INT1 genotype among five genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in the virulence and epidemiologic traits among M. intracellulare genotypes.

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.

Complete genome sequence of Burkholderia gladioli BSR3.

We report the complete genome sequence of Burkholderia gladioli BSR3, isolated from a diseased rice sheath in South Korea.

Complete genome sequence of Japanese erwinia strain ejp617, a bacterial shoot blight pathogen of pear.

The Japanese Erwinia strain Ejp617 is a plant pathogen that causes bacterial shoot blight of pear in Japan. Here, we report the complete genome sequence of strain Ejp617 isolated from Nashi pears in Japan to provide further valuable insight among related Erwinia species.

Comparison of analytical methods and residue patterns of pymetrozine in Aster scaber.

Residues of the polar pesticide pymetrozine were compared using two methods: hydromatrix and liquid-liquid extraction (LLE). The biological half-life and the final residue level were investigated using Aster scaber over a 10-days cultivation period. The respective biological half-lives of the pesticide were 4.2 and 3.5 days at the recommended and double dose. The final residue levels were 1.28 and 1.98 mg kg(-1), respectively, at the same application rate of pymetrozine according to the GAP standard of the United Kingdom. Average recovery was higher with LLE than with the hydromatrix method. Dissipation curves of pymetrozine were influenced by the application amount and growth rate of A. scaber. The final residue level of pymetrozine could be predicted to be lower than the UK maximum residue limit for lettuce applying the GAP standard.

Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencing.

Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease, which is a chronic and debilitating disease in ruminants. MAP is also considered to be a possible cause of Crohn's disease in humans. However, few studies have focused on the interactions between MAP and human macrophages to elucidate the pathogenesis of Crohn's disease. We sought to determine the initial responses of human THP-1 cells against MAP infection using single-cell RNA-seq analysis. Clustering analysis showed that THP-1 cells were divided into seven different clusters in response to phorbol-12-myristate-13-acetate (PMA) treatment. The characteristics of each cluster were investigated by identifying cluster-specific marker genes. From the results, we found that classically differentiated cells express CD14, CD36, and TLR2, and that this cell type showed the most active responses against MAP infection. The responses included the expression of proinflammatory cytokines and chemokines such as CCL4, CCL3, IL1B, IL8, and CCL20. In addition, the Mreg cell type, a novel cell type differentiated from THP-1 cells, was discovered. Thus, it is suggested that different cell types arise even when the same cell line is treated under the same conditions. Overall, analyzing gene expression patterns via scRNA-seq classification allows a more detailed observation of the response to infection by each cell type.

High-throughput SNP discovery and assay development in common bean.

BACKGROUND: Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery. RESULTS: Using a multi-tier reduced representation library we discovered a total of 3,487 SNPs of which 2,795 contained sufficient flanking genomic sequence for SNP assay development. Using Sanger sequencing to determine the validation rate of these SNPs, we found that 86% are likely to be true SNPs. Furthermore, we designed a GoldenGate assay which contained 1,050 of the 3,487 predicted SNPs. A total of 827 of the 1,050 SNPs produced a working GoldenGate assay (79%). CONCLUSIONS: Through combining two next generation sequencing techniques we have developed a method that allows high-throughput SNP discovery in any diploid organism without the need of a whole genome sequence or the creation of normalized cDNA libraries. The need to only perform one 454 run and one GA sequencer run allows high-throughput SNP discovery with sufficient sequence for assay development to be performed in organisms, such as common bean, which have limited genomic resources.

The genome of the Java medaka (Oryzias javanicus): Potential for its use in marine molecular ecotoxicology.

The Java medaka (Oryzias javanicus) is distributed in tropical brackish water and is considered as an ecotoxicological experimental organism for assessing diverse pollutions and global climate change effects in the ocean. In this study, we sequenced and assembled the genome of O. javanicus using the Oxford Nanopore technique and anchored the scaffolds to the 24 genetic linkage map of a sister species Oryzias melastigma. The assembled genome consisted of 773 scaffolds including 24 LG-based scaffolds, and the estimated genome length was 846.3 Mb (N50 = 19.3 Mb), containing 24,498 genes. As detoxification processes are crucial in aquatic organisms, antioxidant-related genes including glutathione S-transferases, superoxide dismutase, catalase, and glutathione peroxidase were identified in this study. In the genome of O. javanicus, a total of 21 GSTs, 4 SODs, 1 CAT, and 7 GPxs were identified and showed high similarities between sister species O. melastigma and Oryzias latipes. In addition, despite having 8 classes of cytosolic GSTs family, medaka showed no presence of GST pi and sigma classes, which are predominantly found in carp and salmon, but not in neoteleostei. This study adds another set to genome-library of Oryzias spp. and is a useful resource for better understanding of the molecular ecotoxicology.

The complete chloroplast genome of Hemerocallis Fulva.

We have sequenced the complete chloroplast genome of Hemerocallis fulva, a species of the Asphodelaceae family, through Illumina HiSeq paired-end sequencing. The total size of chloroplast genome of Hemerocallis fulva was 155,855 bp with a large single-copy (LSC) region of 84,607 bp, a small single-copy (SSC) region of 18,508 bp, and a pair of identical inverted repeat regions (IRs) of 26,370 bp. The genome contained a total of 112 genes, including 79 protein-coding genes, 29 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The phylogenetic analysis of Hemerocallis fulva with 10 related species exhibited the closest taxonomical relationship with Aloe species in the Asphodelaceae family.

The complete chloroplast genome of Codonopsis lanceolata (Campanulaceae).

The complete chloroplast genome sequence of Codonopsis lanceolata was determined by next generation sequencing. The total length of chloroplast genome of C. lanceolata was 169,447 bp long, including a large single-copy (LSC) region of 85,253 bp, a small single-copy (SSC) region of 8060 bp, and a pair of identical inverted repeat regions (IRs) of 38,067 bp. A total of 110 genes was annotated, resulting in 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenetic analysis of C. lanceolata with related chloroplast genome sequences in this study provided the taxonomical relationship of C. lanceolata in the genus Campanula.

Interfacial Energy-Controlled Top Coats for Gyroid/Cylinder Phase Transitions of Polystyrene-block-polydimethylsiloxane Block Copolymer Thin Films.

Block copolymers (BCPs) with a high Flory-Huggins interaction parameter (χ) can form well-defined sub-10 nm periodic structures and can be used as a template for fabrication of various functional nanostructures. However, the large difference of surface energy between the blocks commonly found in high-χ BCPs makes it challenging to stabilize a useful gyroid morphology in thin film form. Here, we used an interfacial-energy-tailored top-coat on a blended film of a polystyrene-block-polydimethylsiloxane (PS-b-PDMS) BCP and a low-molecular-weight PDMS homopolymer with a hydrophilic end functional group. The top coat consisted of a random mixture of 40% hydrolyzed poly(vinyl acetate)-random-poly(vinly alcohol) (PVA-r-PVAc, PVA40) and PVAc homopolymer. At the optimized top-coat composition, gyroid nanostructures with sub-10 nm strut width were achieved down to ∼125 nm film thickness, which is only 3 times the lattice parameter of the gyroid structure. This is in marked contrast with a mixed morphology of gyroid and cylinders obtained for other compositions of the top coat. Self-consistent field theoretic simulations were used to understand the effect of the interfacial energy between the top coat and BCP/homopolymer blends on the phase transition behavior of the BCP/homopolymer films.

Genetic and phenotypic diversity of (R/S)-mecoprop [2-(2-methyl-4-chlorophenoxy)propionic acid]-degrading bacteria isolated from soils.

Twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genus Sphingomonas. Ten different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 12 isolates. The isolates were found to be able to utilize the chiral herbicide mecoprop as a sole source of carbon and energy. While seven of the isolates were able to degrade both (R)- and (S)-mecoprop, four isolates exhibited enantioselective degradation of the (S)-type and one isolate could degrade only the (R)-enantiomer. All of the isolates were observed to possess plasmid DNAs. When certain plasmids were removed from isolates MP11, MP15, and MP23, those strains could no longer degrade mecoprop. This compelling result suggests that plasmid DNAs, in this case, conferred the ability to degrade the herbicide. The isolates MP13, MP15, and MP24 were identified as the same strain; however, they exhibited different plasmid profiles. This indicates that these isolates acquired different mecoprop-degradative plasmids in different soils through natural gene transfer.

Low-temperature, selective catalytic deoxygenation of vegetable oil in supercritical fluid media.

The effects of supercritical fluids on the production of renewable diesel-range hydrocarbons from natural triglycerides were investigated. Various supercritical fluids, which included CO2 (scCO2 ), propane (scC3 H8 ) and n-hexane (scC6 H14 ), were introduced with H2 and soybean oil into a fixed-bed reactor that contained pre-activated CoMo/γ-Al2 O3 . Among these supercritical fluids, scC3 H8 and scC6 H14 efficiently allowed the reduction of the reaction temperature by as much as 50 °C as a result of facilitated heat and mass transfer and afforded similar yields to reactions in the absence of supercritical fluids. The compositional analyses of the gas and liquid products indicated that the addition of scC3 H8 during the hydrotreatment of soybean oil promoted specific deoxygenation pathways, decarbonylation and decarboxylation, which consumed less H2 than the hydrodeoxygenation pathway. As a result, the quantity of H2 required to obtain a high yield of diesel-range hydrocarbons could be reduced to 57 % if scC3 H8 was used. As decarboxylation and decarbonylation are mildly endothermic reactions, the reduced heat transfer resistance in scC3 H8 may drive the deoxygenation reaction to thermodynamically favourable pathways.

Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses.

Burkholderia glumae is a causal agent of rice grain and sheath rot. Similar to other phytopathogens, B. glumae adapts well to the host environment and controls its biology to induce diseases in the host plant; however, its molecular mechanisms are not yet fully understood. To gain a better understating of the actual physiological changes that occur in B. glumae during infection, we analyzed B. glumae transcriptome from infected rice tissues using an RNA-seq technique. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2653 transcripts that were significantly altered. We then performed KEGG pathway and module enrichment of the DEGs. Interestingly, most genes involved bacterial chemotaxis-mediated motility, ascorbate and trehalose metabolisms, and sugar transporters including l-arabinose and d-xylose were found to be highly enriched. The in vivo transcriptional profiling of pathogenic B. glumae will facilitate elucidation of unknown plant-pathogenic bacteria interactions, as well as the overall infection processes.

Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production.

Mycobacterium bovis bacillus Calmette-Guérin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. Here, we report the complete genome sequence of M. bovis BCG Korea, the strain that will be actually used in Korea for vaccine production.