Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of <Emphasis Type="Italic">RbcS</Emphasis> promoter sequences from green microalga <Emphasis Type="Italic">Ankistrodesmus convolutus</Emphasis>

Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalga Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.     

Detection of Vibrio parahaemolyticus in cockle (Anadara granosa) by PCR

This study aimed to determine the occurrence of Vibrio parahaemolyticus in cockles (Anadara granosa) at a harvesting area and to detect the presence of virulent strains carrying the thermostable direct hemolysin (tdh) and TDH-related hemolysin genes (trh) using PCR. Of 100 samples, 62 were positive for the presence of V. parahaemolyticus with an MPN (most probable number) value greater than 3.0 (>1100 MPN per g). The PCR analysis revealed 2 samples to be positive for the tdh gene and 11 to be positive for the trh gene. Hence, these results demonstrate the presence of pathogenic V. parahaemolyticus in cockles harvested in the study area and reveal the potential risk of illness associated with their consumption.     

Transcriptomic Profiling of Rice Seedlings Inoculated with the Symbiotic Fungus Trichoderma asperellum SL2

The fungal species Trichoderma is reported to have a significant impact on the growth and physiological performance of rice plants. However, the molecular mechanisms that induce these effects remain unspecified. Using next-generation sequencing technology, this study compared the differential expression of genes in rice seedlings that had been inoculated with Trichoderma asperellum SL2 with the gene expression in seedlings that had no such inoculation. The study showed that many genes related to plant growth enhancement and physiological functioning are differentially expressed in seedlings which have been symbiotically colonized by T. asperellum SL2. In these seedlings, specific genes related to photosynthesis, RNA activity, stomatal activity, and root development were found to be up-regulated as others were down-regulated. Although the exact causal mechanisms at the molecular level remain to be identified, the presence of Trichoderma versus its absence was associated with almost ten times more significant up-regulations than down-regulations for specific genes that have been identified from previous genomic mapping. Such analysis at the molecular level can help to explain observed phenotypic effects at the organismic level, and it begins to illuminate the observed beneficial relationships expressed phenotypically between crop plants and certain symbiotic microbes.

     

Seasonal variability of inorganic and organic nitrogen in the North Sea

This study considers the cycling of nitrogen in the waters of the North Sea, particularly focussing on organic nitrogen. Dissolved inorganic nitrogen (DIN), dissolved organic nitrogen (DON) and particulate organic nitrogen (PON) were measured in the North Sea over a one-year period (autumn 2004–summer 2005). The surface water concentrations of nitrate, ammonium, DON and PON during the present study ranged from <0.1–7.2 μM, <0.1–2.0 μM, 1.9–11.2 μM and 0.3–5.6 μM, respectively, with DON the dominant fraction of total nitrogen at all times. These nutrients concentrations were significantly lower compared to previous studies in the southern North Sea. The seasonal variations showed high mean surface concentrations of nitrate (4.7 ± 0.6 μM) and DON (8.9 ± 0.9 μM), low ammonium (<0.1 μM) and PON (0.8 ± 0.1 μM) in winter, shifting to low nitrate (0.3 ± 0.3 μM) and DON (4.2 ± 1.2 μM) in summer, with high ammonium (0.8 ± 0.4 μM) in autumn and PON (2.5 ± 1.2 μM) in spring. Highest mean surface DON concentration was measured in winter and may be due to resuspension of the organic matter from the bottom sediments. For autumn and spring, phytoplankton DON release was likely to be the most significant source of DON as shown by high concentrations of low molecular weight (LMW) DON and its positive correlation to chlorophyll a. Low total and LMW DON concentrations during summer were likely to be due to the uptake of the LMW DON fraction by phytoplankton and bacteria and the stratification of the water column. DON is therefore shown to be a potentially important source of nitrogen in shelf seas especially after the spring bloom has depleted nitrate to limiting concentrations. Handling editor: L. Naselli-Flores     

Influence of silver nitrate (ethylene inhibitor) on cucumber in vitro shoot regeneration

The effect of addition of silver nitrate (AgNO₃) on organogenesis of proximal and distal cotyledon and hypocotyl explants of five cucumber (Cucumis sativus L.) cultivars was investigated. Distal cotyledon and hypocotyl were unresponsive while only poor shoot regeneration was observed in proximal cotyledon and hypocotyl explants of all cucumber cultivars. The addition of different concentrations of AgNO₃ (10, 30 and 50 μM) to the medium, however, induced shoot regeneration in distal cotyledon except Suyo Long cultivar and effectively increased shoot regeneration response as well as the number of shoots per explant in proximal cotyledon and hypocotyl of all cucumber cultivars. This revised version was published online in June 2006 with corrections to the Cover Date.     

Prevalence of antibodies to Pseudomonas pseudomallei exotoxin and whole cell antigens in military personnel in Sabah and Sarawak, Malaysia.

Sera from 420 military personnel serving in Sabah and Sarawk, Malaysia, were tested for antibodies to Pseudomonas pseudomallei exotoxin and whole cell antigens by enzyme-linked immunosorbent assay procedure (ELISA). Data showed that 54.4% of serum samples were positive for antibodies to P. pseudomallei exotoxin and 65.7% were positive for antibodies to the whole cell antigens. Samples gave much lower titers for anti-exotoxin antibodies compared to titers against crude whole cell antigens. The incidence of antibody to exotoxin was highest in the age groups ranging from 26 to 32 years, where the positive rates were higher than 40% and 30% for military personnel serving in Sarawak and Sabah, respectively.