Physicochemical and rheological properties of a novel emulsifier,EPS-R,produced by the marine bacterium<Emphasis Type="Italic">Hahella chejuensis</Emphasis>

The rheological properties of an exopolysaccharide, EPS-R, produced by the marine bacteriumHahella chejuensis strain 96CJ10356 were investigated. The E₂₄ of 0.5% EPS-R was 89.2%, which was higher than that observed in commercial polysaccharides such as xanthan gum (67.8%), gellan gum (2.01%) or sodium alginate (1.02%). Glucose and galactose are the main sugars in EPS-R, with a molar ratio of ∼1∶6.8, xylose and ribose are minor sugar components. The average molecular mass, as determined by gel filtration chromatography, was 2.2×10³ KDa. The intrinsic viscosities of EPS-R were calculated to be 16.5 and 15.9 dL/g using the Huggins and Kraemer equations, respectively, with a 2.3 dL/g overlap. In terms of rigidity, the conformation of EPS-R was similar to that of caboxymethyl cellulose (5.0×10⁻²). The rheological behavior of EPS-R dispersion indicated that the formation of a structure intermediate between that of a random-coil polysaccharide and a weak gel. The aqueous dispersion of EPS-R at concentrations ranging from 0.25 to 1.0% (w/w) showed a marked shear-thinning property in accordance with Power-law behavior. In aqueous dispersions of 1.0% EPS-R, the consistency index (K) and flow behavior index (n) were 1,410 and 0.73, respectively. EPS-R was stable to pH and salts.     

Antiviral Effects of Sulfated Exopolysaccharide from the Marine Microalga <Emphasis Type="Italic">Gyrodinium impudicum</Emphasis> Strain KG03

The sulfated exopolysaccharide p-KG03, which is produced by the marine microalga Gyrodinium impudicum strain KG03, exhibited impressive antiviral activity in vitro (EC₅₀ = 26.9 µg/ml) against the encephalomyocarditis virus (EMCV). Depending on the p-KG03 concentration, the development of cytopathic effects in EMCV-infected HeLa cells was either inhibited completely or slowed. Moreover, p-KG03 did not show any cytotoxic effects on HeLa cells, even at concentrations up to 1000 µg/ml. The polysaccharide was purified by repeated precipitation in ethanol, followed by gel filtration. The p-KG03 polysaccharide had a molecular weight of 1.87 × 10⁷, and was characterized as a homopolysaccharide of galactose with uronic acid (2.96% wt/wt) and sulfate groups (10.32% wt/wt). The biological activities of p-KG03 suggest that sulfated metabolites from marine organisms are a rich source of antiviral agents. This is the first reported marine source of antiviral sulfated polysaccharides against EMCV. The p-KG03 polysaccharide may be useful in the development of marine bioactive exopolysaccharide for biotechnological and pharmaceutical products.     

Cetaceans evolution: insights from the genome sequences of common minke whales

Background

Whales have captivated the human imagination for millennia. These incredible cetaceans are the only mammals that have adapted to life in the open oceans and have been a source of human food, fuel and tools around the globe. The transition from land to water has led to various aquatic specializations related to hairless skin and ability to regulate their body temperature in cold water.

Results

We present four common minke whale (Balaenoptera acutorostrata) genomes with depth of ×13 ~ ×17 coverage and perform resequencing technology without a reference sequence. Our results indicated the time to the most recent common ancestors of common minke whales to be about 2.3574 (95% HPD, 1.1521 – 3.9212) million years ago. Further, we found that genes associated with epilation and tooth-development showed signatures of positive selection, supporting the morphological uniqueness of whales.

Conclusions

This whole-genome sequencing offers a chance to better understand the evolutionary journey of one of the largest mammals on earth.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1213-1) contains supplementary material, which is available to authorized users.     

The diagnostic application of targeted re-sequencing in Korean patients with retinitis pigmentosa

Background

Identification of the causative genes of retinitis pigmentosa (RP) is important for the clinical care of patients with RP. However, a comprehensive genetic study has not been performed in Korean RP patients. Moreover, the genetic heterogeneity found in sensorineural genetic disorders makes identification of pathogenic mutations challenging. Therefore, high throughput genetic testing using massively parallel sequencing is needed.

Results

Sixty-two Korean patients with nonsyndromic RP (46 patients from 18 families and 16 simplex cases) who consented to molecular genetic testing were recruited in this study and targeted exome sequencing was applied on 53 RP-related genes. Causal variants were characterised by selecting exonic and splicing variants, selecting variants with low allele frequency (below 1 %), and discarding the remaining variants with quality below 20. The variants were additionally confirmed by an inheritance pattern and cosegregation test of the families, and the rest of the variants were prioritised using in-silico prediction tools. Finally, causal variants were detected from 10 of 18 familial cases (55.5 %) and 7 of 16 simplex cases (43.7 %) in total. Novel variants were detected in 13 of 20 (65 %) candidate variants. Compound heterozygous variants were found in four of 7 simplex cases.

Conclusion

Panel-based targeted re-sequencing can be used as an effective molecular diagnostic tool for RP.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1723-x) contains supplementary material, which is available to authorized users.     

Ecological development and genetic diversity of <Emphasis Type="Italic">Microcystis aeruginosa</Emphasis> from artificial reservoir in Russia

Microcystis aeruginosa is a well-known Cyanobacterium responsible for the formation of toxic water blooms around the world. Shallow, warm, and eutrophic reservoirs provide the most favourable conditions for M. aeruginosa development. Numerous studies have been devoted to this species, but there still is a necessity to develop additional approaches for the monitoring of cyanobacteria in reservoirs. In this study, M. aeruginosa in the water column of a hypereutrophic Siberian reservoir was investigated by fluorescence, light, and electron microscopy as well as genetic analysis using a mcyE marker. Here, we demonstrate the genetic diversity and features of the fluorescence spectra for different ecotypes of this species. We suggest that a fluorescence approach can be used to identify M. aeruginosa in a natural environment in order to increase the effectiveness of ecological monitoring and water quality evaluation.     

Physiological and psychological effects of walking on young males in urban parks in winter

Background

Interaction with nature has a relaxing effect on humans. Increasing attention has been focused on the therapeutic effects of urban green space; however, there is a lack of evidence-based field research. This study provided scientific evidence supporting the physiological and psychological effects of walking on young males in urban parks in winter.

Findings

Subjects (13 males aged 22.5 ± 3.1 years) were instructed to walk predetermined 15-minute courses in an urban park (test) and in the city area (control). Heart rate and heart rate variability (HRV) were measured to assess physiological responses. The semantic differential (SD) method, Profile of Mood States (POMS), and State-Trait Anxiety Inventory (STAI) were used to determine psychological responses.Heart rate was significantly lower and the natural logarithm of the high frequency component of HRV was significantly higher when walking through the urban park than through the city area. The results of three questionnaires indicated that walking in the urban park improved mood and decreased negative feelings and anxiety.

Conclusions

Physiological and psychological data from this field experiment provide important scientific evidence regarding the health benefits of walking in an urban park. The results support the premise that walking in an urban park has relaxing effects even in winter.     

Characterization of the thioredoxin peroxidase from Cryptosporidium parvum

Cryptosporidium parvum can survive exposure to harsh environmental conditions, various disinfectants, and high doses of γ-radiation. Recently, it was found that the expression of thioredoxin peroxidase (CpTPx) in C. parvum increased after a high dose of γ-irradiation to the parasite. CpTPx is a two-cysteine peroxiredoxin that contains cysteines at positions 49 and 170. Recombinant CpTPx fused to an N-terminal hexahistidine sequence, (His)₆-CpTPx, exhibited substantial thiol-dependent peroxidase activity that protected plasmid DNA from damage by metal-catalyzed oxidation in vitro. (His)₆-CpTPx was used to screen sera from C. parvum-infected mice and humans for antibodies against CpTPx. In Western blots, 10% of the mouse sera and 20% of the human sera reacted with (His)₆-CpTPx, suggesting that after infection by C. parvum CpTPx can induce a host-immune reaction but is not a major antigen. Immunolocalization studies revealed that CpTPx is expressed mainly in the cytoplasm of C. parvum at various developmental stages.     

Single‐molecule real‐time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.)

The diverse colours of mature pepper (Capsicum spp.) fruit result from the accumulation of different carotenoids. The carotenoid biosynthetic pathway has been well elucidated in Solanaceous plants, and analysis of candidate genes involved in this process has revealed variations in carotenoid biosynthetic genes in Capsicum spp. However, the allelic variations revealed by previous studies could not fully explain the variation in fruit colour in Capsicum spp. due to technical difficulties in detecting allelic variation in multiple candidate genes in numerous samples. In this study, we uncovered allelic variations in six carotenoid biosynthetic genes, including phytoene synthase (PSY1, PSY2), lycopene β‐cyclase, β‐carotene hydroxylase, zeaxanthin epoxidase and capsanthin‐capsorubin synthase (CCS) genes, in 94 pepper accessions by single‐molecule real‐time (SMRT) sequencing. To investigate the relationship between allelic variations in the candidate genes and differences in fruit colour, we performed ultra‐performance liquid chromatography analysis using 43 accessions representing each allelic variation. Different combinations of dysfunctional mutations in PSY1 and CCS could explain variation in the compositions and levels of carotenoids in the accessions examined in this study. Our results demonstrate that SMRT sequencing technology can be used to rapidly identify allelic variation in target genes in various germplasms. The newly identified allelic variants will be useful for pepper breeding and for further analysis of carotenoid biosynthesis pathways.