Preferential amplification is minimised in long-PCR systems

The advent of long PCR (XL-PCR) has proven to be a major advance in PCR technology and is currently being utilised to investigate numerous biological systems. The analysis of mixed DNA populations is a particularly useful application for XL-PCR. For example, XL-PCR has been used to investigate the occurrence of heterogeneous mitochondrial DNA (mtDNA) rearrangement mutations. With XL-PCR it became possible to amplify the entire length of the mtDNA chromosome and detect any mtDNA deletion or insertion mutations based on a measurable change in overall sequence length. In the present communication, XL-PCR and conventional short-length PCR were used to amplify mitochondrial DNA sequences from several human vastus lateralis skeletal muscle samples. The experiments demonstrated that there was minimal preferential amplification of shorter DNA sequences with XL-PCR and was significantly less than the preferential amplification of shorter sequences observed with conventional PCR. Also, XL-PCR amplification of the complete mtDNA sequence from control DNA containing a single mtDNA template (leucocyte extracts) showed that the generation of PCR artefacts was not a predisposed failing of the system but was dependant on the standard rules that govern the set up and optimisation of any PCR reaction. In optimised systems, XL-PCR artefacts were not generated and a single PCR product was always recovered.     

Novel effect of plant lectins on the inhibition of Streptococcus mutans biofilm formation on saliva-coated surface

Aims:  Dental caries is caused by the disturbance in oral homeostasis, marked by a notable increase in the population of Streptococcus mutans . Lectins are a group of plant proteins that are capable of recognizing the glycoconjugates present on the bacterial surface. The aim of this study was to evaluate the effect of seven plant lectins on the growth and initial adhesion of S. mutans .
Methods and Results:  Lectins of different carbohydrate specificities were isolated from plant sources by conventional methods of protein purification. The effect on growth of S. mutans was evaluated following CLSI guidelines. None of the lectins used in this study inhibited the bacterial growth and multiplication. The adherence and biofilm formation of bacteria to saliva-coated polystyrene plates was tested in the presence of plant lectins. All the plant lectins tested, inhibited both the adherence and biofilm in a concentration dependent manner. Confocal microscopy and scanning electron microscopy were employed to assess the biofilm formation in the presence of plant lectin (glucose/mannose-specific) at sub-minimal inhibitory concentrations. These evaluations revealed that lectins inhibited the clumping and attachment of S. mutans .
Conclusions:  Lectins tested here inhibited initial biofilm formation by S. mutans. Glucose/Mannose-specific lectin altered the adhesion arrangement of the bacteria on the saliva-coated surfaces.
Significance and Impact of the Study:  The plant lectins used in this study may offer a novel strategy to reduce development of dental caries by inhibiting the initial adhesion and subsequent biofilm formation of S. mutans.     

Dairy manure and tillage effects on soil fertility and corn yields

Organic amendments have received renewed attention to improve soil fertility for crop production. A randomized complete block split plot experiment was conducted to evaluate the dairy manure (DM) amendments of soil for corn (Zea mays L. cv. Monsanto 919) production under different tillage systems. Main plot treatments were no-till (NT), conventional tillage (CT), and deep tillage (DT), and subplot treatments were chemical fertilization (DM(0)), and DM at 10Mgha(-1)yr(-1) (DM(10)) and 20Mgha(-1)yr(-1) (DM(20)) with supplemental chemical fertilization. Results show that tillage and DM had significantly reduced bulk density (rho(b)) with greater porosity (f(t)) and hydraulic conductivity (K(fs)) than soils under NT and DM(0). Manuring was effective to improve soil physical properties in all tillage treatments. While manure significantly increased C sequestration, the N concentration was influenced by both tillage and manure with significant interaction. The CT significantly increased P as did the addition of manure. However, with manure, K was significantly increased in all tillage treatments. While tilled soils produced taller plants with higher grain yields, and water-use efficiency than NT soils, manuring, in contrast, increased corn harvest index. Manure exerted significant quadratic effect on corn biomass N and K uptake. The variable effects of tillage and dairy manuring on soil properties and corn growth are most probably related to "transitional period" in which soil ecosystems may have adjusting to a new equilibrium.     

Cloning and molecular characterization of a cubilin-related serine proteinase from the hard tick Haemaphysalis longicornis

Serine proteinases are one of the largest proteolytic families of enzymes, and have diverse cellular activities in mammalian tissues. We report here the cloning and molecular characterization of a cDNA encoding the serine proteinase of the hard tick Haemaphysalis longicornis (HlSP). The HlSP cDNA is 1570 bp long and the deduced precursor protein consists of 464 amino acids with a predicted molecular mass of 50.4 kDa and a pI of 8.2. The preprotein, consisting of 443 amino acids, was predicted to include a complement C1r/C1s, Uegf, and bone morphogenic protein-1 domain, a low-density lipoprotein receptor class A domain, and a catalytic domain. HlSP sequence analysis showed high similarity to serine proteinases reported from arthropods and vertebrate animal species. Two-dimensional immunoblot analysis revealed endogenous HlSP in adult tick extracts at 50 kDa. Endogenous HlSP was also expressed in all lifecycle stages of H. longicornis. Immunohistochemical studies detected the endogenous enzyme in the midgut epithelial cells of an adult tick. The Escherichia coli-expressed recombinant HlSP was demonstrated to degrade bovine serum albumin and hydrolyze the substrate Bz-L-Arg-pNA at the rate of 30.2 micromol/min/mg protein. Further, HlSP expression was up-regulated during a blood-feeding process, indicating its involvement in the digestion of host blood components.     

Spinach-thylakoid phosphorylation: Studies on the kinetics of changes in photosystem antenna size, spill-over and phosphorylation of light-harvesting chlorophyll a/b protein

The kinetics of LHCP phosphorylation and associated changes in photosystem cross-section and energy ‘spill-over’ from PS II to PS I have been examined in isolated spinach chloroplasts. During an initial phosphorylation period of 3–6 min, in the presence of saturating concentrations of Mg²⁺, the increase in PS I and decrease in PS II cross-section are largely completed, as judged by both measurements of the steady-state redox state of Q and fluorescence yield changes. This corresponds to a period of rapid ³²P incorporation into the low-molecular weight LHCP polypeptide. Subsequent to this initial 3–6-min period there is substantial further phosphorylation of both LHCP polypeptides, which is not accompanied by significant changes in photosystem cross-section, even after the chloroplasts had been unstacked with extensive mixing of PS I and PS II by Mg-removal. It is suggested that there exists a specific ‘mobile’ population of LHCP molecules which is rapidly phosphorylated and which may be enriched in the low-molecular-weight polypeptide. In addition, measurements of the kinetics of the ‘spill-over’ changes upon either Mg²⁺ addition or removal indicate that the continued phosphorylation of LHCP is able to increase the ‘spill-over’ process under favourable ionic conditions.     

Pandemic strains of O3:K6 Vibrio parahaemolyticus in the aquatic environment of Bangladesh

A total of 1500 environmental strains of Vibrio parahaemolyticus, isolated from the aquatic environment of Bangladesh, were screened for the presence of a major V. parahaemolyticus virulence factor, the thermostable direct haemolysin (tdh) gene, by the colony blot hybridization method using a digoxigenin-labeled tdh gene probe. Of 1500 strains, 5 carried the tdh sequence, which was further confirmed by PCR using primers specific for the tdh gene. Examination by PCR confirmed that the 5 strains were V. parahaemolyticus and lacked the thermostable direct haemolysin-related haemolysin (trh) gene, the alternative major virulence gene known to be absent in pandemic strains. All 5 strains gave positive Kanagawa phenomenon reaction with characteristic beta-haemolysis on Wagatsuma agar medium. Southern blot analysis of the HindIII-digested chromosomal DNA demonstrated, in all 5 strains, the presence of 2 tdh genes common to strains positive for Kanagawa phenomenon. However, the 5 strains were found to belong to 3 different serotypes (O3:K29, O4:K37, and O3:K6). The 2 with pandemic serotype O3:K6 gave positive results in group-specific PCR and ORF8 PCR assays, characteristics unique to the pandemic clone. Clonal variations among the 5 isolates were analyzed by comparing RAPD and ribotyping patterns. Results showed different patterns for the 3 serotypes, but the pattern was identical among the O3:K6 strains. This is the first report on the isolation of pandemic O3:K6 strains of V. parahaemolyticus from the aquatic environment of Bangladesh.