Dimerization of short RNA fragments from avian leukosis virus as revealed with 2-aminopurine fluorescence

The dimerization of genomic retroviral RNA is well studied for several groups of viruses, the dimerization of human immunodeficiency (HIV) RNA being investigated in more detail. Regions of dimerization apparently involve the short sequences RNA which are directly responsible for the formation of two type dimers: kissing loop-loop (KD) and linear (LD). The 5'-end sequences from RNA avian viruses, where the dimers are basically formed, considerably differ from those of HIV. However, as it was described earlier, the mechanism of dimerization of RNA from human immunodeficiency and from avian leukosis viruses are identical. The fluorescence of adenine analogue 2-aminopurine (2-AP) incorporated into loop sequence of short fragments RNA ALV was used for analysis of dimers formation. Using the temperature dependence of fluorescence intensity 2-AP we have determined RNA melting temperature under various conditions for KD RNA ALV formed by two strands. Effects of magnesium and aminoglycoside antibiotic paromomycin on stabilization of kissing loop-loop dimer RNA have been studied. Under the experimental conditions KD RNA ALV was found to have the stability at the magnesium concentration higher than 1 mM and at paromomycin concentration higher than 2.5 mkM.     

Multidrug resistance-associated protein-1 (MRP1) genetic variants,MRP1 protein levels and severity of COPD

Background

Multidrug resistance-associated protein-1 (MRP1) protects against oxidative stress and toxic compounds generated by cigarette smoking, which is the main risk factor for chronic obstructive pulmonary disease (COPD). We have previously shown that single nucleotide polymorphisms (SNPs) in MRP1 significantly associate with level of FEV₁ in two independent population based cohorts. The aim of our study was to assess the associations of MRP1 SNPs with FEV₁ level, MRP1 protein levels and inflammatory markers in bronchial biopsies and sputum of COPD patients.

Methods

Five SNPs (rs212093, rs4148382, rs504348, rs4781699, rs35621) in MRP1 were genotyped in 110 COPD patients. The effects of MRP1 SNPs were analyzed using linear regression models.

Results

One SNP, rs212093 was significantly associated with a higher FEV₁ level and less airway wall inflammation. Another SNP, rs4148382 was significantly associated with a lower FEV₁ level, higher number of inflammatory cells in induced sputum and with a higher MRP1 protein level in bronchial biopsies.

Conclusions

This is the first study linking MRP1 SNPs with lung function and inflammatory markers in COPD patients, suggesting a role of MRP1 SNPs in the severity of COPD in addition to their association with MRP1 protein level in bronchial biopsies.     

Smoking status and anti-inflammatory macrophages in bronchoalveolar lavage and induced sputum in COPD

Background

Macrophages have been implicated in the pathogenesis of COPD. M1 and M2 macrophages constitute subpopulations displaying pro- and anti-inflammatory properties. We hypothesized that smoking cessation affects macrophage heterogeneity in the lung of patients with COPD. Our aim was to study macrophage heterogeneity using the M2-marker CD163 and selected pro- and anti-inflammatory mediators in bronchoalveolar lavage (BAL) fluid and induced sputum from current smokers and ex-smokers with COPD.

Methods

114 COPD patients (72 current smokers; 42 ex-smokers, median smoking cessation 3.5 years) were studied cross-sectionally and underwent sputum induction (M/F 99/15, age 62 ± 8 [mean ± SD] years, 42 (31-55) [median (range)] packyears, post-bronchodilator FEV₁ 63 ± 9% predicted, no steroids past 6 months). BAL was collected from 71 patients. CD163⁺ macrophages were quantified in BAL and sputum cytospins. Pro- and anti-inflammatory mediators were measured in BAL and sputum supernatants.

Results

Ex-smokers with COPD had a higher percentage, but lower number of CD163⁺ macrophages in BAL than current smokers (83.5% and 68.0%, p = 0.04; 5.6 and 20.1 ×10⁴/ml, p = 0.001 respectively). The percentage CD163⁺ M2 macrophages was higher in BAL compared to sputum (74.0% and 30.3%, p < 0.001). BAL M-CSF levels were higher in smokers than ex-smokers (571 pg/ml and 150 pg/ml, p = 0.001) and correlated with the number of CD163⁺ BAL macrophages (Rs = 0.38, p = 0.003). No significant differences were found between smokers and ex-smokers in the levels of pro-inflammatory (IL-6 and IL-8), and anti-inflammatory (elafin, and Secretory Leukocyte Protease Inhibitor [SLPI]) mediators in BAL and sputum.

Conclusions

Our data suggest that smoking cessation partially changes the macrophage polarization in vivo in the periphery of the lung towards an anti-inflammatory phenotype, which is not accompanied by a decrease in inflammatory parameters.     

Dimerization of short RNA fragments of avian retroviruses as revealed using 2-aminopurine fluorescence

Dimerization of retroviral RNA is known in detail for several groups of viruses, especially the human immunodeficiency virus (HIV). The dimerization region seems to involve short RNA sequences directly responsible for the formation of dimers of two types, kissing loop-loop (KD) and linear (LD). The 5′-terminal sequences, where dimers are mostly formed, substantially differ between avian retroviruses and HIV, while the mechanisms of their RNA dimerization are the same. RNA dimerization was studied using the adenine analog 2-aminopurine (2-AP), which was incorporated into the loop sequence of short fragments of the avian leucosis virus (ALV) RNA. A temperature dependence of 2-AP fluorescence was used to study the KD formation under various conditions. Magnesium ions and the aminoglycoside antibiotic paromomycin were tested for the effect on KD stability. The highest KD stability was observed at >1 mM Mg²⁺ and >2.5 μM paromomycin.     

Sexual differences in caudal morphology and its relation to tail autotomy in lacertid lizards

We hypothesized that the presence of the forked hemipenes, and associated musculature, at the base of the tail in male lizards should constrain the capacity to autotomize the tail. Thus, this hypothesis predicts that the non-autotomous base of the tail should be longer in male than in female lizards. We tested this hypothesis in four species oflacertid lizards. Males have on average one to two non-autotomous vertebrae more than females, and the sexual difference in length of the non-autotomous tail base remains constant over the entire body size range. In addition, the first functional autotomy plane in males is usually located on, or is distal to, the vertebrae from which two hemipenial muscles take origin. These observations support the view that functional demands of the male intromittent organs impose constraints on the abilities of tail autotomy. In a natural population of Lacerta vivipara , the proportion of tail breaks that occurred at very short distances from the base was highest in females, indicating that the small sexual difference in length of the non-autotomous tail part is of functional significance. Total length of the tail was largest in males. This can be interpreted as a compensation for the decline in autotomy capacities at the tail base, such that the length of the autotomous part remains similar in both sexes.     

Study of the emission characteristics of a low-pressure discharge in crossed E × H fields by using an echelle spectrograph with compensated astigmatism

In order to prove that thermal ionization is the main mechanism for sustaining a high-current low-pressure diffuse discharge in crossed E × H fields, the ion temperature was estimated by analyzing the Doppler broadening of a spectral line. The emission spectrum from discharge plasma was recorded using a specially designed echelle spectrograph with compensated astigmatism and with a resolution of 0.02 nm.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> phylogenetic group determination and its application in the identification of the major animal source of fecal contamination

Background  

Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A₀, A₁, B1, B2₂, B2₃, D₁ and D₂), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.     

Effect of aminoglycoside antibiotics on the conformation of the unpaired loop adenine of avian leucosis virus RNA as revealed using 2-aminopurine fluorescence

The fluorescent properties of 2-aminopurine (2-AP) incorporated in an RNA sequence are used to study the structural dynamics and local changes of the retroviral RNA structure. Using 2-AP, the conformational states of the unpaired loop adenine in avian leucosis virus RNA were studied upon its interaction with aminoglycoside antibiotics. The intensity of 2-AP fluorescence in the monomeric RNA hairpin was higher than in both RNA dimers. The intensity of fluorescence in the extended dimer was significantly lower than in the kissing loop dimer. The finding was be explained by the fact that stacking contacts in the extended dimer produce a more compact loop structure than in the kissing loop dimer. When the binding of aminogycoside antibiotics with the kissing loop dimer RNA was analyzed, only tobramycin increased the intensity of 2-AP fluorescence almost threefold. The results showed that 2-AP fluorescence is suitable for detecting local changes in complexes of retroviral RNA with ligands.