A versatile endonuclease IV from Thermus thermophilus has uracil-excising and 3'-5' exonuclease activity

Apurinic/apyrimidinic (AP) sites arise in DNA through the spontaneous loss of bases or through the release of damaged bases from DNA by DNA glycosylases. AP sites in DNA can be catalyzed by AP endonucleases such as exonuclease III and endonuclease IV, generating a 3'-hydroxyl group and a 5'-terminal sugar phosphate. Here, we have identified and characterized a novel endonuclease IV from a hyperthermophilic bacterium Thermus thermophilus designated as TthNfo. TthNfo efficiently removed AP site from double-stranded oligonucleotide substrate. No significant difference was observed in the rate of reaction of four bases opposite AP site with TthNfo. In addition, TthNfo possesses a 3'-5' exonuclease activity similar to that of Escherichia coli exonuclease III. Surprisingly, we found that TthNfo also catalyzes the excision of uracil from DNA. In comparison with other endonuclease IV proteins, the removal of uracil residue was unique to TthNfo. Based on these observations and the absence of exonuclease III in T. thermophilus, we suggest that versatile enzyme activities of TthNfo play an important role in counteracting DNA base damage in vivo.     

Evaluation of light-harvesting complex proteins as senescence-related protein markers in detached rice leaves

Ten light-harvesting complex (Lhc) proteins were investigated to determine which was the most appropriate protein marker of senescence in detached rice leaves. The levels of Lhc proteins were monitored by immunoblot analysis, which was conducted using commercially available antibodies raised against each Lhc protein. Among the Lhc proteins evaluated in this study, Lhca1, Lhcb1, Lhcb2, Lhcb3, and Lhcb5 were not appropriate to be used as senescence markers while others can be used after optimization of the procedure.     

Influence of coronary collateral flow on coronary diagnostic parameters: An in vitro study

Functional severity of coronary stenosis is often assessed using diagnostic parameters. These parameters are evaluated from the combined pressure and/or flow measurements taken at the site of the stenosis. However, when there are functional collaterals operating downstream to the stenosis, the coronary flow-rate increases, and the pressure in the stenosed artery is altered. This effect of downstream collaterals on different diagnostic parameters is studied using a physiological representative in vitro coronary flow-loop.The three diagnostic parameters tested are fractional flow reserve (FFR), lesion flow coefficient (LFC), and pressure drop coefficient (CDP). The latter two were discussed in recent publications by our group (Banerjee et al., 2008, Banerjee et al., 2007, 2009). They are evaluated for three different severities of stenosis and tested for possible misinterpretation in the presence of variable collateral flows. Pressure and flow are measured with and without downstream collaterals. The diagnostic parameters are then calculated from these readings.In the case of intermediate stenosis (80% area blockage), FFR and LFC increased from 0.74 to 0.77 and 0.58 to 0.62, respectively, for no collateral to fully developed collateral flow. Also, CDP decreased from 47 to 42 for no collateral to fully developed collateral flow. These changes in diagnostic parameters might lead to erroneous postponement of coronary intervention. Thus, variability in diagnostic parameters for the same stenosis might lead to misinterpretation of stenosis severity in the presence of operating downstream collaterals.     

Production of plant-specific tyramine derivatives by dual expression of tyramine N-hydroxycinnamoyltransferase and 4-coumarate:coenzyme A ligase in Escherichia coli

Plant-specific bioactive compounds including feruloyltyramine (FT), 4-coumaroyltyramine (CT), and caffeoyltyramine (CaT) were simultaneously produced in Escherichia coli by heterologous expression of two biosynthetic genes encoding 4-coumarate:coenzyme A ligase and tyramine N-hydroxycinnamoyltransferase (THT) cloned from Arabidopsis thaliana and pepper, respectively. Simultaneous supplementation of substrates to the recombinant E. coli resulted in the secretion of multiple tyramine derivatives into the medium at high yield: CT (189 mg l⁻¹), FT (135 mg l⁻¹), CaT (40 mg l⁻¹). In addition, the recombinant E. coli also produced, albeit at low concentration, a range of dopamine derivatives such as feruloyldopamine due to THT’s ability to accept dopamine as a substrate.     

Reporting of Quantitative Protein Electrophoresis in Australia and New Zealand: a Call for Standardisation

Background

The lack of guidelines on reporting standards for protein electrophoresis may have led to significant differences in reports from different laboratories.

Objective

To determine the extent of variation in reporting of protein electrophoresis results in Australia and New Zealand.

Method

Questionnaires were distributed to laboratories throughout Australia and New Zealand asking about protein electrophoresis practices and reporting.

Results

Extensive variation was found in the following reporting practices: (a) units for urine Bence Jones protein (BJP); (b) reporting absence of a paraprotein rather than a normal pattern; (c) numerical reporting of all protein fractions or only the paraprotein; (d) warning of possible inaccuracy in the serum immunoglobulin result of the paraprotein type; (e) co-migration of a paraprotein with a normal serum protein; (f) use of a confirmatory test when a known paraprotein is no longer detectable.

Conclusions

A working party should be established to make recommendations on the reporting of protein electrophoresis. Implementation of such recommendations should reduce both report variation between laboratories and the risk of misinterpretation of reports.     

Effects of an exotic invasive macrophyte (tropical signalgrass) on native plant community composition,species richness and functional diversity

1. The issue of freshwater species being threatened by invasion has become central in conservation biology because inland waters exhibit the highest species richness per unit area, but apparently have the highest extinctions rates on the planet. 2. In this article, we evaluated the effects of an exotic, invasive aquatic grass (Urochloa subquadripara– tropical signalgrass) on the diversity and assemblage composition of native macrophytes in four Neotropical water bodies (two reservoirs and two lakes). Species cover was assessed in quadrats, and plant biomass was measured in further quadrats, located in sites where tropical signalgrass dominated (D quadrats) and sites where it was not dominant or entirely absent (ND quadrats). The effects of tropical signalgrass on macrophyte species richness, Shannon diversity and number of macrophyte life forms (a surrogate of functional richness) were assessed through regressions, and composition was assessed with a DCA. The effects of tropical signalgrass biomass on the likelihood of occurrence of specific macrophyte life forms were assessed through logistic regression. 3. Tropical signalgrass had a negative effect on macrophyte richness and Shannon and functional diversity, and also influenced assemblage composition. Emergent, rooted with floating stems and rooted submersed species were negatively affected by tropical signalgrass, while the occurrence of free‐floating species was positively affected. 4. Our results suggest that competition with emergent species and reduction of underwater radiation, which reduces the number of submersed species, counteract facilitation of free‐floating species, contributing to a decrease in plant diversity. In addition, homogenisation of plant assemblages shows that tropical signalgrass reduces the beta diversity in the macrophyte community. 5. Although our results were obtained at fine spatial scales, they are cause for concern because macrophytes are an important part of freshwater diversity.