Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field

A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107^T was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107^T was found to occur at 4–37 °C (optimum, 20–30 °C), at pH 5.5–10 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107^T was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5^T (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107^T was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C_15:0 (26.3 %), iso-C_17:0 3OH (12.6 %) and summed feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107^T has β-glucosidase activity to convert ginsenosides Rb₁ and Rd into Gyp17 and F₂. DNA-DNA hybridization with F. denitrificans ED5^T was 52 %. Strain THG-107^T could be distinguished from F. denitrificans ED5^T and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107^T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107^T = KACC 16219^T = LMG 26575^T).     

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

Simple sequence repeat marker associated with a natural leaf defoliation trait in tetraploid cotton

Cotton (Gossypium hirsutum L.) leaf defoliation has a significant ecological and economical impact on cotton production. Thus the utilization of a natural leaf defoliation trait, which exists in wild diploid cotton species, in the development of tetraploid cultivated cotton will not only be cost effective, but will also facilitate production of very high-grade fiber. The primary goal of our research was to tag loci associated with natural leaf defoliation using microsatellite markers in Upland cotton. The F2 populations developed from reciprocal crosses between the two parental cotton lines--AN-Boyovut-2 (2n = 52), a late leaf defoliating type, and Listopad Beliy (2n = 52), a naturally early leaf defoliating type--demonstrated that the naturally early leaf defoliation trait has heritability values of 0.74 and 0.84 in the reciprocal F2 population. The observed phenotypic segregation difference in reciprocal crosses suggested a minor cytoplasmic effect in the phenotypic expression of the naturally early leaf defoliation trait. Results from the Kruskal-Wallis (KW) nonparametric test revealed that JESPR-13 (KW = 6.17), JESPR-153 (KW = 9.97), and JESPR-178 (KW = 13.45) Simple sequence repeat (SSR) markers are significantly associated with natural leaf defoliation in the mapping population having stable estimates at empirically obtained critical thresholds (P < .05-.0001). JESPR-178 revealed the highest estimates (P < .0001) for association with the natural leaf defoliation trait, exceeding maximum empirical threshold values. JESPR-178 was assigned to the short arm of chromosome 18, suggesting indirectly that genes associated with natural leaf defoliation might be located on this chromosome. This microsatellite marker may have the potential for use to introgress the naturally early leaf defoliation quantitative trait loci (QTL) from the donor line Listopad Beliy to commercial varieties of cotton through marker-assisted selection programs.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

ImmunoPET and biodistribution with human epidermal growth factor receptor 3 targeting antibody 89Zr-RG7116

The humanized monoclonal antibody with high affinity for the human epidermal growth factor receptor (HER) 3, RG7116, is a glycoengineered, IgG1 class antibody. By labeling RG7116 with zirconium-89 (⁸⁹Zr) we aimed to visualize in vivo HER3 expression and study the biodistribution of this antibody in human tumor-bearing mice. Biodistribution of ⁸⁹Zr-RG7116 was studied in subcutaneously xenografted FaDu tumor cells (HER3-positive). Dose-dependency of ⁸⁹Zr-RG7116 organ distribution and specific tumor uptake was assessed by administering doses ranging from 0.05 to 10 mg/kg RG7116 to SCID/Beige mice. Biodistribution was analyzed at 24 and 144 h after injection. MicroPET imaging was performed at 1, 3, and 6 days after injection of 1.0 mg/kg ⁸⁹Zr-RG7116 in the FaDu, H441, QG-56 and Calu-1 xenografts with varying HER3 expression. The excised tumors were analyzed for HER3 expression. Biodistribution analyses showed a dose- and time-dependent ⁸⁹Zr-RG7116 tumor uptake in FaDu tumors. The highest tumor uptake of ⁸⁹Zr-RG7116 was observed in the 0.05 mg/kg dose group with 27.5%ID/g at 144 h after tracer injection. MicroPET imaging revealed specific tumor uptake of ⁸⁹Zr-RG7116 in FaDu and H441 models with an increase in tumor uptake over time. Biodistribution data was consistent with the microPET findings in FaDu, H441, QG56 and Calu-1 xenografts, which correlated with HER3 expression levels. In conclusion, ⁸⁹Zr-RG7116 specifically accumulates in HER3 expressing tumors. PET imaging with this tracer provides real-time non-invasive information about RG7116 distribution, tumor targeting and tumor HER3 expression levels.     

Stratification,Blinding and Placebo Effect in a Randomized,Double Blind Placebo-controlled Clinical Trial of Gold Bead Implantation in Dogs with Hip Dysplasia

The purpose of this study was to investigate the need for and choice of stratification factors, and the effects of blinding and placebo in a clinical experiment. Eighty dogs with canine hip dysplasia (CHD) were included in a randomized, placebo-controlled and double blind clinical trial with stratified parallel group design, in which body weight and degree of CHD were used as stratification factors. Thirty-eight dogs were allocated to gold bead implantation and 42 to placebo. After six months, 33 of the 42 placebo-treated dogs received gold bead implantation in an open study lasting a further 18 months. The main outcome variable in the study was change in pain signs of CHD as assessed by the owner. No significant difference in the main outcome variable, regardless of the treatment given, could be detected in the two chosen stratification factors. The only factor to influence the main outcome variable significantly was age. The blinding procedure used in the study, in which 60% of the owners correctly guessed the treatment given, was found sufficient. Of those who guessed the treatment erroneously, 88% believed the treatment given was gold bead implantation. The treatment efficacy after six months in the blinded treatment group was found to be significantly larger compared to the efficacy obtained in the open study. A significant placebo effect was therefore detected. Conclusion and Clinical Relevance: The age of the dogs influenced the outcome of the CHD treatment, and is recommended as a stratification factor. A significant placebo effect has to be expected and an optimal blinding procedure is necessary in similar clinical studies.     

The role of induced mutation in conversion of photoperiod dependence in cotton

Wild cotton germplasm resources are largely underutilized because of photoperiod-dependent flowering of "exotic" cottons. The objectives of this work were to explore the genome-wide effect of induced mutation in photoperiod-converted induced cotton mutants, estimating the genetic change between mutant and wild-type cottons using simple sequence repeats (SSRs) as well as understand the pattern of SSR mutation in induced mutagenesis. Three groups of photoperiod-converted radiomutants ((32)P) including their wild-type parental lines, A- and D-genome diploids, and typically grown cotton cultivars were screened with 250 cotton SSR primer pairs. Forty SSRs revealed the same SSR mutation profile in, at least, 2 independent mutant lines that were different from the original wild types. Induced mutagenesis both increased and decreased the allele sizes of SSRs in mutants with the higher mutation rate in SSRs containing dinucleotide motifs. Genetic distance obtained based on 141 informative SSR alleles ranged from 0.09 to 0.60 in all studied cotton genotypes. Genetic distance within all photoperiod-converted induced mutants was in a 0.09-0.25 range. The genetic distance among photoperiod-converted mutants and their originals ranged from 0.28 to 0.50, revealing significant modification of mutants from their original wild types. Typical Gossypium hirsutum cultivar, Namangan-77, revealed mutational pattern similar to induced radiomutants in 40 mutated SSR loci, implying possible pressure to these SSR loci not only in radiomutagenesis but also during common breeding process. Outcomes of the research should be useful in understanding the photoperiod-related mutations, and markers might help in mapping photoperiodic flowering genes in cotton.