Another explanation for the low allergy rate in the rural Alpine foothills

Background

IL4/IL4RA pathway plays an important role in atopy and asthma. Different polymorphisms in IL4 and IL4RA genes have been described. Particularly, -33C>TIL4 and 576Q>RIL4RA SNPs have been independently associated to atopy and asthma. The purpose of this study was to analyse these polymorphisms in a population of patients with a well-characterized asthma phenotype.

Methods

A total of 212 unrelated Caucasian individuals, 133 patients with asthma and 79 healthy subjects without symptoms or history of asthma or atopy and with negative skin prick tests were recruited. Lung function was measured by spirometry and asthma was specialist physician-diagnosed according to the ATS (American Thoracic Society) criteria and classified following the GINA (Global Initiative for Asthma) guidelines. Skin prick tests were performed according to EAACI recommendations. -33C>TIL4 was studied with TaqMan assay and 576Q>RIL4RA by PCR-RFLP technique. Hardy-Weinberg equilibrium was analysed in all groups. Dichotomous variables were analysed using χ², Fisher exact test, Monte Carlo simulation test and odds ratio test. To model the effects of multiple covariates logistic regression was used.

Results

No statistically significant differences between the group of patients with asthma and the controls were found when the allele and genotype distribution of -33C>TIL4 and 576Q>RIL4RA polymorphisms were compared. However, the T allele of the -33C>TIL4 SNP was more frequent in patients with persistent asthma. Multivariate analysis adjusted for age and sex confirmed that carriers of allele T had an increased risk of persistent asthma (OR:2.77, 95%CI:1.18–6.49; p = 0.019). Analysis of combination of polymorphisms showed that patients carrying both the T allele of -33C>TIL4 and the A allele of 576Q>RIL4RA had an increased risk of asthma. This association was particularly observed in persistent asthma [Fisher's p value = 0.0021, Monte Carlo p value (after 10⁴ simulations) = 0.0016, OR:3.39; 95% CI:1.50–7.66].

Conclusion

Our results show a trend of association between the genetic combination of the T allele of -33C>TIL4 and the A allele of 576Q>RIL4RA with asthma. This genetic variant was more frequently observed in patients with persistent asthma. As long as this study was performed in a small population, further studies in other populations are needed to confirm these results.     

Femtochemistry in enzyme catalysis: DNA photolyase

Photolyase uses light energy to split UV-induced cyclobutane pyrimidine dimers in damaged DNA. This photoenzyme encompasses a series of elementary dynamical processes during repair function from early photoinitiation by a photoantenna molecule to enhance repair efficiency, to in vitro photoreduction through aromatic residues to reconvert the cofactor to the active form, and to final photorepair to fix damaged DNA. The corresponding series of dynamics include resonance energy transfer, intraprotein electron transfer, and intermolecular electron transfer, bond breaking-making rearrangements and back electron return, respectively. We review here our recent direct studies of these dynamical processes in real time, which showed that all these elementary reactions in the enzyme occur within subnanosecond timescale. Active-site solvation was observed to play a critical role in the continuous modulation of catalytic reactions. As a model system for enzyme catalysis, we isolated the enzyme–substrate complex in the transition-state region and mapped out the entire evolution of unmasked catalytic reactions of DNA repair. These observed synergistic motions in the active site reveal a perfect correlation of structural integrity and dynamical locality to ensure maximum repair efficiency on the ultrafast time scale.     

Distribution of Proteus (Amphibia: Urodela: Proteidae) and its possible explanation

Approximately 250 localities of the nominal species Proteus anguinus Laurenti 1768 have been evaluated and listed. The species is limited to the Dinaric Karst; it ranges from the Isonzo-Soĉa River in southeastern Venezia Giulia, Italy, through the southern half of Slovenia, southern Croatia, and parts of Bosnia and Hercegovina, to the Trebišnica River in eastern Hercegovina. In some regions, populations have been extinguished or endangered by pollution or human-induced hydrographical changes. The distribution of Proteus is compared with those of some cave Crustacea: Troglocaris (Crustacea: Decapoda), Monolistra , and Titanethes (Crustacea: Isopoda). The similarity of distribution patterns within this ecologically diverse assemblage supports their paleogeographic rather than ecological foundation. The paleogeographical and paleoclimatological data, in combination with the physiological requirements of Proteus, strongly suggest that these animals invaded the caves, at least in the NW parts of their ranges, only after the last glaciations, within the last 10,000 years. It is suggested that the high heterozygosity of populations can best be explained by fusion of some locally restricted immigration waves. The close morpho- logical similarity of nearly all populations of Proteus is probably due to the convergent evolution of previously differentiated populations (or even species) after their withdrawal underground.     

Purification of Escherichia coli DNA photolyase

Escherichia coli photolyase is a DNA repair enzyme which monomerizes pyrimidine dimers, the major UV photoproducts in DNA, to pyrimidines in a light-dependent reaction. We recently described the construction of a tac-phr plasmid that greatly overproduces the enzyme (Sancar, G. B., Smith, F. W., and Sancar, A. (1983) Nucleic Acids Res. 11, 6667-6678). Using a strain carrying the overproducing plasmid as the starting material, we have developed a purification procedure that yields several milligrams of apparently homogeneous enzyme. The purified protein is a single polypeptide that has an apparent Mr of 49,000 under both denaturing and nondenaturing conditions. The enzyme has no requirement for divalent cations and it restores the biological activity of irradiated DNA only in the presence of photoreactivating light. The purified photolyase has a turnover number of 2.4 dimers/molecule/min; this value agrees well with the in vivo rate of photoreactivation in E. coli.     

Assay of DNA photolyase activity in spinach leaves in relation to cell compartmentation-evidence for lack of DNA photolyase in chloroplasts

Spinach cyclobutane pyrimidine dimer (CPD)-specific DNA photolyase was successfully detected in leaf extracts by an assay system for plant photolyase using an improved enzyme-linked immunosorbent assay (ELISA) which was newly introduced by novel horseradish peroxidase (HRP)-linked CPD specific monoclonal antibodies. The assay system includes two main steps: a photorepair reaction of CPD introduced in substrate DNA and measurement of CPD remained after the photorepair by the improved ELISA. When CPD- induced salmon sperm DNA was used as a substrate, high CPD-photolyase activities were observed in the enzyme fraction prepared from whole spinach leaf extracts, but not from chloroplast extracts. This strongly suggests that spinach CPD-specific photolyases are localized in cell compartments other than chloroplasts.     

Binding of Escherichia coli DNA photolyase to UV-irradiated DNA

Escherichia coli DNA photolyase is a flavoprotein which catalyzes the photomonomerization of pyrimidine dimers produced in DNA by UV irradiation. In vivo, the enzyme acts by a two-step mechanism: it binds to dimer-containing DNA in a light-independent reaction and upon exposure to 300-500-nm light breaks the cyclobutane ring and dissociates from the substrate. Using photolyase purified to homogeneity, we have investigated in vitro the first step of the reaction, DNA binding; enzyme-DNA complex formation was quantitated by the nitrocellulose filter binding assay. We find that the enzyme binds specifically to UV-irradiated DNA regardless of whether the DNA is in the superhelical, open circular, or linear form or whether the DNA is single or double stranded. The binding reaction is optimum at a NaCl concentration of 125 mM and at pH 7.5. Although photolyase is retained by the nitrocellulose filters with near 100% efficiency, the binding efficiency of a single enzyme-substrate complex is about 0.34. The complexes can be dissociated by exposing them to photoreactivating light either in solution or on the filter.     

Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA

Class II photolyases ubiquitously occur in plants, animals, prokaryotes and some viruses. Like the distantly related microbial class I photolyases, these enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light. Methanosarcina mazei Mm0852 is a class II photolyase of the archaeal order of Methanosarcinales, and is closely related to plant and metazoan counterparts. Mm0852 catalyses light-driven DNA repair and photoreduction, but in contrast to class I enzymes lacks a high degree of binding discrimination between UV-damaged and intact duplex DNA. We solved crystal structures of Mm0852, the first one for a class II photolyase, alone and in complex with CPD lesion-containing duplex DNA. The lesion-binding mode differs from other photolyases by a larger DNA-binding site, and an unrepaired CPD lesion is found flipped into the active site and recognized by a cluster of five water molecules next to the bound 3'-thymine base. Different from other members of the photolyase-cryptochrome family, class II photolyases appear to utilize an unusual, conserved tryptophane dyad as electron transfer pathway to the catalytic FAD cofactor.     

Specificity of binding of regulatory proteins with DNA: possible explanation in terms of point interactions

On the basis of the previously obtained data on the specificity of the interactions between amino acids and nucleotide bases an attempt is undertaken to explain the origin of the specificity of binding of repressors and cro proteins to corresponding operator DNA sequences in phages lambda and P22. The rules describing the interactions between amino acids and bases are supposed to be the same for the binding of different proteins to DNA. The suggested consideration, based on the known crystallographic data as well, allows to describe the specific binding of studied regulatory proteins to operators, the absence of their binding to other DNA sequences and the decrease of their affinity to the operator sites due to the mutations.     

Insect cells and their potential as stabilization barriers for DNA of multiple and single nucleopolyhedroviruses against ultraviolet-B-simulated sunlight inactivation

A cell line from Trichoplusia ni (TN-CL1) infected with the Autographa californica multiple nucleopolyhedrovirus (AcMNPV-HPP) and a cell line from Helicoverpa zea (BCIRL-HZ-AM1) infected with the Helicoverpa zea single nucleopolyhedrovirus (HzSNPV/BrCL2) were subjected to ultraviolet-B (UV-B) irradiation at a predetermined level of exposure that would inactivate greater than 95% of the virus suspended in the liquid. The working hypothesis was that the homologous insect cells would utilize their inherent deoxyribonucleic acid (DNA) repair mechanism(s) to prevent, repair, or at least mitigate the damaging effects of UV-B light on viral DNA synthesis. We attempted to determine this by using infected cells that were subjected to UV-B irradiation at different postinoculation periods under two experimental conditions of exposure: (1) shielded, and (2) nonshielded. Of the two cell lines infected with their respective homologous viruses, the virus from TN-CL1 cells was the least sensitive to UV-B light because the extracellular virus (ECV) and occlusion body (OB) levels of virus-infected TN-CL1 cells were higher than those of the virus-infected BCIRL-HZ-AM1 cells. Production of ECV and OB from both cell lines was lower in the exposed, nonshielded treatment than in the exposed, shielded treatment. However, AcMNPV-HPP was produced in enough quantity to indicate that TN-CL1 might impart a level of protection to the virus against UV light.     

Efficacy of selected adjuvants for protecting Spodoptera litura nucleopolyhedrovirus from sunlight inactivation

Efficacy of selected adjuvants for protecting Spodoptera litura nucleopolyhedrovirus (SpltNPV) from sunlight inactivation was tested in direct sunlight exposure bioassays and in the field on virus-treated Brassica chinensis var parachinensis plants. All adjuvants, except palm oil, gave significant protection to the virus after 16 h of sunlight exposure, as shown by the larval mortalities. Cumulative mortalities after 14 days show that the virus + Tinopal treatment and the virus not to sunlight treatment attained 100% mortality, while the virus in riboflavin treatment and the crude brown sugar treatment caused mortality of less than 30%. However, the LT₅₀ value of virus + Tinopal was 1.2 times lower than the unexposed virus. All virus-treated plants in the field trials had higher yields and lower damage indices than the control plants. Unlike the results from direct sunlight exposure bioassays, adjuvants, including virus + Tinopal LPW, did not significantly enhance efficacy of the virus against early instars of S. litura in the field. The unformulated virus was as effective as virus + Tinopal LPW and Nurelle-D in protecting the plants from infestation. Thus, in a well-planned pest management program, SpltNPV, without any adjuvant, can be used effectively for controlling S. litura on B. chinensis var parachinensis.     

DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer

Photolyase is an enzyme that catalyses photorepair of thymine dimers in UV damaged DNA by electron transfer reaction. The structure of the photolyase/DNA complex is unknown at present. Using crystal structure coordinates of the substrate-free enzyme from E. coli, we have recently built a computer molecular model of a thymine dimer docked to photolyase catalytic site and studied molecular dynamics of the system. In this paper, we present analysis of the electronic coupling and electron transfer pathway between the catalytic cofactor FADH(-) and the pyrimidine dimer by the method of interatomic tunneling currents. Electronic structure is treated in the extended Hückel approximation. The root mean square transfer matrix element is about 6 cm(-1), which is consistent with the experimentally determined rate of transfer. We find that electron transfer mechanism responsible for the repair utilizes an unusual folded conformation of FADH(-) in photolyases, in which the isoalloxazine ring of the flavin and the adenine are in close proximity, and the peculiar features of the docked orientation of the dimer. The tunneling currents show explicitly that despite of the close proximity between the donor and acceptor complexes, the electron transfer mechanism between the flavin and the thymine bases is not direct, but indirect, with the adenine acting as an intermediate. These calculations confirm the previously made conclusion based on an indirect evidence for such mechanism.     

Characterization of the low temperature thermoluminescence band Zv in leaf: an explanation for its variable nature

Out of the six thermoluminescence bands reported for a mature leaf, one band (Zv) appearing at the lowest temperatures is dependent on the temperature of illumination. The characteristics of this band in fresh leaf are compared with those is a leaf heated to 60 degrees C for 5 min. It is concluded here that this band, following illumination at temperatures lower than 173 K, is part of Arnold and Azzi's Z band (Arnold, W. and Azzi, J.R. (1971) Photochem. Photobiol. 14, 233--240). However, it is part of peak I when observed subsequent to illumination beyond 173 K. An explanation for the appearance of this band at different temperatures is proposed.     

Purification and properties of Methanobacterium thermoautotrophicum DNA photolyase

We have purified DNA photolyase from the autotrophic anaerobic archaebacterium Methanobacterium thermoautotrophicum to near homogeneity by a two-column affinity chromatography. The purified enzyme has an Mr = 60,000 and shows near UV absorption peak at 440 nm and a fluorescence emission maximum at 462 nm indicating that it contains 8-hydroxy-5-deazaflavin (coenzyme F420) as an intrinsic chromophore. The photolyase binds with high specificity to thymine dimer in DNA with an equilibrium binding constant, KA = 1.4 x 10(9) M-1, and a dissociation rate constant, koff = 1.4 x 10(-4) s-1 (t1/2 = 43 min). Despite 6-fold higher affinity compared to the folate-containing Escherichia coli photolyase the two enzymes apparently contact the same phosphates around the thymine dimer: the phosphate immediately 5' and the three phosphates immediately 3' to the dimer on the damaged strand and the phosphate across from the dimer in the minor groove on the complementary strand. The absolute action spectrum of the Methanobacterium photolyase in the 400-500-nm region closely matches the absorption of the enzyme-bound F420. The quantum yield (phi) over this region is constant and is approximately 0.2. The value is measurably smaller than the quantum yields reported for other DNA photolyases.     

A possible explanation for the refractoriness of uterine prostaglandin production

Arachidonic acid increased the outputs of prostaglandin (PG) F-2 alpha, PGE-2 and 6-keto-PGF-1 alpha from the Day-7 and Day-15 guinea-pig uterus superfused in vitro. Similar increases in PG output were observed when the arachidonic acid treatment was repeated after an interval of 1, 3 or 5 h. Phospholipase (PL) A-2 increased the outputs of PGF-2 alpha, PGE-2 and 6-keto-PGF-1 alpha from the Day-7 guinea-pig uterus, but repeating the PLA-2 treatment 1 h later failed to stimulate PG output. The increase in outputs of PGF-2 alpha and PGE-2 caused by PLA-2 were partly restored after 3 h and were fully restored after 5 h, whereas the increase in 6-keto-PGF-1 alpha output produced by PLA-2 was only partly restored after 3 and 5 h. PLA-2 had little or no effect on PGF-2 alpha and PGE-2 outputs from the Day-15 guinea-pig uterus initially, and when repeated after 1, 3 and 5 h. This was probably due to the output of these two PGs, particularly of PGF-2 alpha, being stimulated in vivo before removal of the uterus. PLA-2 increased 6-keto-PGF-1 alpha output from the Day-15 uterus initially, but failed to cause a response when administered again 1 h later. After 3 and 5 h, the increase in 6-keto-PGF-1 alpha output from the Day-15 uterus caused by PLA-2 was partly restored. A23187 and PLC increased the outputs of PGF-2 alpha, PGE-2 and 6-keto-PGF-1 alpha from the Day-7 and Day-15 guinea-pig uterus. These responses to A23187 and PLC were reduced (but not abolished) when the two compounds were administered again 1 h later. After 3 and 5 h, the increases in output of PGF-2 alpha and PGE-2 produced by A23187 and PLC had returned to the initial values. The increases in output of 6-keto-PGF-1 alpha from the Day-7 and Day-15 guinea-pig uterus produced by A23187 and PLC were partly restored after 3 and 5 h, except for the response to PLC on Day 7 which was fully restored after 5 h. The results show that there is no failure with time in the mechanism which converts arachidonic acid into PGF-2 alpha in the guinea-pig uterus.(ABSTRACT TRUNCATED AT 400 WORDS)