Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

The influence of genetics factor on key growth traits and quantitative genetic analysis of sea cucumber <Emphasis Type="Italic">Apostichopus Japonicus</Emphasis> (Selenka) heat-resistant and fast-growing strain

Using incomplete diallels cross and North Carolina II design, this study established sea cucumber families with heat-resistant and fast-growing Apostichopus japonicus strains from different ecological areas. Then, this study analyzed the influence of paternal and maternal genetic effects on the growth of A. japonicus, evaluated the growth effect of different A. japonicus families in the early growth stage and estimated the combining ability and heritability. The study showed that, in the early growth stage of A. japonicus, the influence of paternal genetic effects on the growth was higher than that of maternal effects. The best five parents and eight offspring families in terms of genetic potential breeding and growth were selected. The 3-month weight, 9-month weight, 12-month weight, 5-month to 9-month specific growth rate, 9-month coefficient of variation (CV) and 12-month CV of A. japonicus are at moderate heritability level, in order, 28.18, 40.82, 43.56, 27.87, 44.39 and 38.59 %, respectively; these traits played a leading role in parental additive gene effect on the formation of hybrids offspring traits.     

Effect of sublethal α-cypermethrin exposure on main macromolecules concentration,energy content,and malondialdehyde concentration in free-feeding <Emphasis Type="Italic">Danio rerio</Emphasis> larvae

α-Cypermethrin (Cyp) is a synthetic insecticide used to control pests in agricultural crops and to protect human health against noxious insects; this toxic can reach aquatic systems through ground infiltration or by runoff and could affect the aquatic biota. The present study was aimed at evaluating the acute toxicity of Cyp on zebrafish (Danio rerio) exogenous feeding larvae of 10 and 20 days post-fertilization (dpf), and of sublethal concentrations on only 10-dpf larvae. Proteins, lipids, carbohydrates, glycogen concentration, and total energy contents, as well as malondialdehyde (MDA) quantification, through thiobarbituric acid reactive substances, as a lipid peroxidation biomarker, were assessed in free-feeding larvae exposed to sublethal Cyp concentrations. The LC₅₀ for 10-dpf larvae was 1.94 µg L^?1, and these were more sensitive than 20-dpf larvae (3.56 µg L^?1). The amount of protein, carbohydrates, and glycogen were not significantly affected (p > 0.05), but sublethal Cyp concentrations exposure caused decrement in lipids from 9.05 to 3.74 µg larva^?1, as well as a reduction in MDA and in the total energy content, which affected significantly the development of this fish. Although Cyp is considered an insecticide of reduced residual effect in the environment, the present study revealed that relatively low Cyp concentrations produced significant toxic effects on exogenous feeding fish larvae, a situation that could contribute to increase deaths during this already critical developmental stage in which high mortality is observed frequently.     

Quantitative loop-mediated isothermal amplification method for the detection of <Emphasis Type="Italic">Vibrio nigripulchritudo</Emphasis> in shrimp

Vibrio nigripulchritudo is considered one of the major pathogens threatening shrimp aquaculture. In this study, we developed a novel and highly specific quantitative loop-mediated isothermal amplification (Q-LAMP) assay. A set of four specific primers were designed targeting the V. nigripulchritudo intergenic spacer region. The reaction time and temperature were optimized for 60 min at 63°C. Quantitative analysis was then performed by measuring the turbidity of the reaction solution using a real-time turbidimeter, allowing for quantification of the initial DNA concentration with a sensitivity of 10² copy numbers equivalent to 2.3 colony forming units/ml or 0.3 fg/μl. The LAMP assay was able to specifically detect two representative strains of V. nigripulchritudo, whereas other Vibrio and non-Vibrio species were not amplified. A standard curve was generated for V. nigripulchritudo by plotting the threshold time (T _t) versus the log of bacterial number. A high correlation coefficient (R ² = 0.9749) was observed for the Q-LAMP reaction. In conclusion, Q-LAMP assay is a sensitive, rapid, and simple tool that can be used for the detection and quantification of V. nigripulchritudo in shrimp, thereby facilitating surveillance of vibriosis infection.     

Growth,nutrient utilization,oxidative condition,and element composition of juvenile red sea bream <Emphasis Type="Italic">Pagrus major</Emphasis> fed with fermented soybean meal and scallop by-product blend as fishmeal replacement

A feeding trial was conducted to evaluate the effect of fermented soybean meal and scallop by-product blend (3:2) (FP) on the performance of juvenile red sea bream. Five isocaloric diets were prepared by replacing 0% (FP0), 15% (FP15), 30% (FP30), 45% (FP45), and 60% (FP60) fishmeal (FM) protein with FP, respectively. Triplicate groups of fish (initial mean weight 2.83 g) were fed the test diets for 45 days in a flowthrough seawater system. The results demonstrated that growth rates of fish fed FP0, FP15, and FP30 were similar, and significantly higher (P < 0.05) than those of FP45 and FP60. Nutrient utilization was significantly lower in FP60, with no differences found among the other groups. Dietary heavy-metal contents were affected by inclusion of FP, impacting on whole-body heavy-metal contents. In terms of oxidative stress, fish fed the FP30 diet were in the best condition, since this fish group showed the least oxidative-stressed condition as well as the highest tolerance against oxidation. In conclusion, the approach of utilizing this fermented mixture is promising and it could replace at least 30% FM protein in red sea bream diet without negative effects on performance, body composition or health of fish.     

Vulnerability of Community-Based Forest Management to Climate Variability and Extremes: Emerging Insights on the Contribution of REDD+

Climate change spurs havoc on social-ecological system. People and places vulnerable to climate change have been the focus of many discussions. However, in the forestry sector, limited studies have been conducted that link human vulnerability to recent initiatives, such as reducing emissions from deforestation and forest degradation or REDD+, especially in highly vulnerable countries. Using case studies from the Philippines, this paper focuses on the vulnerability of two community-based forest management (CBFM) organizations, with and without REDD+ readiness intervention, to show the impacts of climate variability and extremes. Two balance-weighted approaches, the livelihood vulnerability index and the IPCC-framework, were used in the vulnerability assessments. Results revealed high vulnerability of both CBFM organizations, although Malitbog Upland Developers for Sustainable Association (MUDSA) livelihood vulnerability is largely aggravated by its exposure to disaster, climate variability and extremes, accessibility to health facilities and water supply. The long history of CBFM implementation in both organizations have minimal contribution in enhancing the adaptive capacity of members to cope with and adapt to climate change impacts. REDD+ (readiness), does not insure reduced vulnerability to climate change, unless sustainable livelihood is achieved. As the State controls forest resources, the rights of CBFM-organizations to commercially benefit from these resources are limited, a disincentive to the development of new and viable development programs in CBFM areas, such as REDD+. This also constrains the achievement of climate resiliency.     

Validation of multi-frequency inversion method by using dummy scatterers of zooplankton

ABSTRACT:   High- and multi-frequency acoustic measurement systems and the multi-frequency inversion (MFI) method have been used to measure spatial distributions and abundances of zooplankton by size. In this study, the calibration method for high- and multi-frequency systems was developed and the validation of MFI method was carried out by scatterer measurement. The standard sphere calibration method that has not been applied to such high- and multi-frequencies was applied to calibrate our high- and multi-frequency system, TAPS-6 (Tracor Acoustic Profiling System, BAE Systems). An optimum size of standard sphere of tungsten carbide of 1 mm radius was derived to have a small target strength variation for the six frequencies of TAPS-6, and the practicability and precision of the standard sphere calibration method was confirmed for those frequencies. A school or cluster of dummy scatterers of zooplankton with small tungsten carbide spheres were designed to validate the MFI method, and volume back-scattering strength values were measured by the multi-frequency system. By comparing the result of the inversion with their real composition, the features of the MFI method could be validated and examined.     

Stem cell factor supports migration in canine mesenchymal stem cells

Adult Mesenchymal Stem Cells (MSC) are cells that can be defined as multipotent cells able to differentiate into diverse lineages, under appropriate conditions. These cells have been widely used in regenerative medicine, both in preclinical and clinical settings. Initially discovered in bone marrow, MSC can now be isolated from a wide spectrum of adult and foetal tissues. Studies to evaluate the therapeutic potential of these cells are based on their ability to arrive to damaged tissues. In this paper we have done a comparative study analyzing proliferation, surface markers and OCT4, SOX9, RUNX2, PPARG genes expression in MSC cells from Bone marrow (BMMSC) and Adipose tissue (ASC). We also analyzed the role of Stem Cell Factor (SCF) on MSC proliferation and on ASCs metalloproteinases MMP-2, MMP-9 secretion. Healthy dogs were used as BMMSC donors, and ASC were collected from omentum during elective ovariohysterectomy surgery. Both cell types were cultured in IMDM medium with or without SCF, 10% Dog Serum (DS), and incubated at 38 °C with 5% CO2. Growth of BMMSCs and ASCs was exponential until 25–30 days. Flow citometry of MSCs revealed positive results for CD90 and negative for CD34, CD45 and MCH-II. Genes were evaluated by RT-PCR and metalloproteinases by zymografy. Our findings indicate morphological and immunological similarities as well as expression of genes from both origins on analyzed cells. Furthermore, SCF did not affect proliferation of MSCs, however it up-regulated MMP-2 and MMP-9 secretion in ASCs. These results suggest that metalloproteinases are possibly essential molecules pivoting migration.