Physical parameters affecting the rate and completion of RNA driven hybridization of DNA: new measurements relevant to quantitation based on kinetics.

Differences in the RNA-driven hybridization kinetics of genomic DNA and cDNA probes led us to examine physical parameters affecting these reactions. Cloned cDNA complementary to serum albumin (SA) mRNA hybridized in accordance with single component kinetics, whereas cloned SA genomic DNA hybridized more slowly and with multiple component kinetics. This difference is largely attributable to the relatively short and variable lengths of the mRNA complementary regions in the cloned genomic DNA. The rate of mRNA driven hybridization is affected to about half the extent observed for DNA renaturation as Na+ is increased or decreased from 0.18M. In the annealing of nucleic acids of high sequence complexity, after approximately 70% of reaction has been reached, the rate of the reaction is slowed and completion is not reached under "static" conditions. In practical terms, this is not the case for systems of low sequence complexity. This problem can be largely overcome by continuous or frequent mixing of the reactants, so that complex cDNA probes are hybridized essentially to completion, and kinetics can therefore be more readily compared to simple complexity standards.     

Capreomycin is active against non-replicating M. tuberculosis

Background

Eradication of Helicobacter pylori is an important objective in overcoming gastric diseases. Many regimens are currently available but none of them could achieve 100% success in eradication. Eugenol and cinnamaldehyde that are commonly used in various food preparations are known to possess antimicrobial activity against a wide spectrum of bacteria.

Aim

The present study was performed to assess the in vitro effects of eugenol and cinnamaldehyde against indigenous and standard H. pylori strains, their minimum inhibitory concentrations (MICs) and time course lethal effects at various pH.

Methods

A total of 31 strains (29 indigenous and one standard strain of H. pylori ATCC 26695, one strain of E. coli NCIM 2089) were screened. Agar dilution method was used for the determination of drug sensitivity patterns of isolates to the commonly used antibiotics and broth dilution method for the test compounds.

Results

Eugenol and cinnamaldehyde inhibited the growth of all the 30 H. pylori strains tested, at a concentration of 2 μg/ml, in the 9th and 12th hours of incubation respectively. At acidic pH, increased activity was observed for both the compounds. Furthermore, the organism did not develop any resistance towards these compounds even after 10 passages grown at sub-inhibitory concentrations.

Conclusion

These results indicate that the two bioactive compounds we tested may prevent H. pylori growth in vitro, without acquiring any resistance.     

Chlorophyll fluorescence performance of sweet almond [Prunus dulcis (Miller) D. Webb] in response to salinity stress induced by NaCl

One-year old sweet almond (Prunus dulcis) seedlings were submitted to four levels of salt stress induced by NaCl, namely 0.3, 0.5, 0.7, and 1.0 S m⁻¹. Effects of salt stress on a range of chlorophyll (Chl) fluorescence parameters (Chl FPs) and Chl contents were investigated in order to establish an eco-physiological characterization of P. dulcis to salinity. Salt stress promoted an increase in F₀, F_s, and F₀/F_m and a decrease in F_m, F′_m, F_v/F_m, q_P, ΔF/F′_m, F_v/F₀, and UQF_(rel), in almost all Chl fluorescence yields (FY) and FPs due to its adverse effect on activity of photosystem 2. No significant changes were observed for quenchings q_N, NPQ, and q_N(rel). The contents of Chl a and b and their ratio were also significantly reduced at increased salt stress. In general, adverse salinity effects became significant when the electric conductivity of the nutrient solution (EC_n) exceeded 0.3 S m⁻¹. The most sensitive salt stress indicators were F_v/F₀ and Chl a content, and they are thus best used for early salt detection in P. dulcis. Monitoring of a simple Chl FY, such as F₀, also gave a good indication of induced salt stress due to the significant correlations observed between the different Chl FYs and FPs. Even essential Chl FYs, like F₀, F_m, F′_m, and F_s, and mutually independent Chl FPs, like F_v/F₀ and q_P, were strongly correlated with each other.     

Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird

In human-modified environments, ecological traps may result from a preference for low-quality habitat where survival or reproductive success is lower than in high-quality habitat. It has often been shown that low reproductive success for birds in preferred habitat types was due to higher nest predator abundance. However, between-habitat differences in nest predation may only weakly correlate with differences in nest predator abundance. An ecological trap is at work in a farmland bird (Lanius collurio) that recently expanded its breeding habitat into open areas in plantation forests. This passerine bird shows a strong preference for forest habitat, but it has a higher nest success in farmland. We tested whether higher abundance of nest predators in the preferred habitat or, alternatively, a decoupling of nest predator abundance and nest predation explained this observed pattern of maladaptive habitat selection. More than 90% of brood failures were attributed to nest predation. Nest predator abundance was more than 50% higher in farmland, but nest predation was 17% higher in forest. Differences between nest predation on actual shrike nests and on artificial nests suggested that parent shrikes may facilitate nest disclosure for predators in forest more than they do in farmland. The level of caution by parent shrikes when visiting their nest during a simulated nest predator intrusion was the same in the two habitats, but nest concealment was considerably lower in forest, which contributes to explaining the higher nest predation in this habitat. We conclude that a decoupling of nest predator abundance and nest predation may create ecological traps in human-modified environments.     

Restriction generated oligonucleotides utilizing the two base recognition endonuclease CviJI*.

The conversion of an anonymous DNA sample into numerous oligonucleotides is enzymatically feasible using an unusual restriction endonuclease, CviJI. Depending on reaction conditions, CviJI is capable of digesting DNA at a two or three base recognition sequence. CviJI normally cleaves RGCY sites between the G and C to leave blunt ends. Under 'relaxed' conditions CviJI* cleaves RGCY, and RGCR/YGCY, but not YGCR sites. In theory, CviJI* restriction of pUC19 (2686 bp) should produce 157 fragments, 75% of which are smaller than 20 bp. Instead, 96% of the CviJI* fragments were 18-56 bp long and none of the fragments were smaller than 18 bp. Thermal denaturation of these fragments generates sequence specific oligonucleotides homologous for the cognate template. The enzymatic conversion of anonymous DNA into sequence specific oligomers has implications for several conventional and novel molecular biology procedures.     

Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping

Marker-assisted selection (MAS) uses genetic marker genotypes to predict an animal's production potential and will provide additional selection information for progeny testing. With the discovery of highly polymorphic microsatellite markers, the tools now exist to begin the search for economic trait loci (ETL), which is the first step toward MAS. The objective of this study was to identify ETL for somatic cell score in an existing Holstein population. Using the granddaughter design, sons from seven grandsire families were genotyped with 20 autosomal microsatellites from five chromosomes (4, 8, 13, 17, 23), with an emphasis on chromosome 23, which is the location of the bovine major histocompatibility complex (BoLA). Selective genotyping was used to reduce the number of genotypes required, in which the 10 highest and 10 lowest sons from the phenotypic distribution curve were tested (140 sons in seven families). One marker (513), located near BoLA, showed evidence of an ETL in three of five polymorphic families. Additional sons were genotyped from the five families to estimate the effect and to compare selective and ‘complete’ genotyping. Both methods detected an ETL at marker 513, but in different families. This study provides evidence of the usefulness of microsatellite markers and the granddaughter design in the detection of ETL; however, additional markers need to be evaluated to determine the usefulness of selective genotyping. Based on the results from the 20 studied markers, the most likely position of a somatic cell score ETL lies near marker 513, located on chromosome 23.     

Factors inhibiting IFN activity

Several factors may inhibit the activity of IFNs. Some of these occur naturally, others are therapy-induced or artificial. Naturally occurring antibodies appear to have a much broader reactivity than therapy-induced antibodies. Naturally induced antibodies are reported in patients suffering from chronic graft-versus-host disease after bone marrow transplantation. Differences in the reported immunogenicity between interferons may not be due to the minor variation in amino acid sequence. The clinical significance of therapy-induced antibodies has been unclear. In patients treated for chronic hepatitis C, antibody formation is closely related to relapse. In animal studies the efficacy of treatments targeting the IFN receptor interaction has been shown. Soluble IFN- receptor inhibits the development of autoimmune diseases in mice. Monoclonal antibodies to the IFN- receptor protects against allograft rejections in monkeys. Two naturally occurring inhibitors of IFN action were reported. The clinical significance and structure of these inhibitors remain elusive.