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91.
Hoare S Zou Y Purohit V Krishnasamy R Skorvaga M Van Houten B Geacintov NE Basu AK 《Biochemistry》2000,39(40):12252-12261
The UvrABC nuclease system from Escherichia coli removes DNA damages induced by a wide range of chemical carcinogens with variable efficiencies. The interactions with UvrABC proteins of the following three lesions site-specifically positioned in DNA, and of known conformations, were investigated: (i) adducts derived from the binding of the (-)-(7S,8R,9R,10S) enantiomer of 7,8-dihydroxy-9, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(-)-anti-BPDE] by cis-covalent addition to N(2)-2'-deoxyguanosine [(-)-cis-anti-BP-N(2)-dG], (ii) an adduct derived from the binding of the (+)-(1R,2S,3S,4R) enantiomer of 1,2-dihydroxy-3,4-epoxy-1,2,3, 4-tetrahydro-5-methylchrysene [(+)-anti-5-MeCDE] by trans addition to N(2)-2'-deoxyguanosine [(+)-trans-anti-MC-N(2)-dG], and (iii) a C8-2'-deoxyguanosine adduct (C8-AP-dG) formed by reductively activated 1-nitropyrene (1-NP). The influence of these three different adducts on UvrA binding affinities, formation of UvrB-DNA complexes by quantitative gel mobility shift analyses, and the rates of UvrABC incision were investigated. The binding affinities of UvrA varied among the three adducts. UvrA bound to the DNA adduct (+)-trans-anti-MC-N(2)-dG with the highest affinity (K(d) = 17 +/- 2 nM) and to the DNA containing C8-AP-dG with the least affinity (K(d) = 28 +/- 1 nM). The extent of complex formation with UvrB was also the lowest with the C8-AP-dG adduct. 5' Incisions occurred at the eighth phosphate from the modified guanine. The major 3' incision site corresponded to the fifth phosphodiester bond for all three adducts. However, additional 3' incisions were observed at the fourth and sixth phosphates in the case of the C8-AP-dG adduct, whereas in the case of the (-)-cis-anti-BP-N(2)-dG and (+)-trans-anti-MC-N(2)-dG lesions additional 3' cleavage occurred at the sixth and seventh phosphodiester bonds. Both the initial rate and the extent of 5' and 3' incisions revealed that C8-AP-dG was repaired less efficiently in comparison to the (-)-cis-anti-BP-N(2)-dG and (+)-trans-anti-MC-N(2)-dG containing DNA adducts. Our study showed that UvrA recognizes conformational changes induced by structurally different lesions and that in certain cases the binding affinities of UvrA and UvrB can be correlated with the incision rates. The size of the bubble formed around the damaged site with mismatched bases also appears to influence the incision rates. A particularly noteworthy finding in this study is that UvrABC repair of a substrate with no base opposite C8-AP-dG was quite inefficient as compared to the same adduct with a C opposite it. These findings are discussed in terms of the available NMR solution structures. 相似文献
92.
IMpRH server: an RH mapping server available on the Web 总被引:9,自引:0,他引:9
Milan D Hawken R Cabau C Leroux S Genet C Lahbib Y Tosser G Robic A Hatey F Alexander L Beattie C Schook L Yerle M Gellin J 《Bioinformatics (Oxford, England)》2000,16(6):558-559
SUMMARY: The INRA-Minnesota Porcine Radiation Hybrid (IMpRH) Server provides both a mapping tool (IMpRH mapping tool) and a database (IMpRH database) of officially submitted results. The mapping tool permits the mapping of a new marker relatively to markers previously mapped on the IMpRH panel. The IMpRH database is the official database for submission of new results and queries. The database not only permits the sharing of public data but also semi-private and private data. 相似文献
93.
Theis K Skorvaga M Machius M Nakagawa N Van Houten B Kisker C 《Mutation research》2000,460(3-4):277-300
Nucleotide excision repair (NER) is a universal DNA repair mechanism found in all three kingdoms of life. Its ability to repair a broad range of DNA lesions sets NER apart from other repair mechanisms. NER systems recognize the damaged DNA strand and cleave it 3', then 5' to the lesion. After the oligonucleotide containing the lesion is removed, repair synthesis fills the resulting gap. UvrB is the central component of bacterial NER. It is directly involved in distinguishing damaged from undamaged DNA and guides the DNA from recognition to repair synthesis. Recently solved structures of UvrB from different organisms represent the first high-resolution view into bacterial NER. The structures provide detailed insight into the domain architecture of UvrB and, through comparison, suggest possible domain movements. The structure of UvrB consists of five domains. Domains 1a and 3 bind ATP at the inter-domain interface and share high structural similarity to helicases of superfamilies I and II. Not related to helicase structures, domains 2 and 4 are involved in interactions with either UvrA or UvrC, whereas domain 1b was implicated for DNA binding. The structures indicate that ATP binding and hydrolysis is associated with domain motions. UvrB's ATPase activity, however, is not coupled to the separation of long DNA duplexes as in helicases, but rather leads to the formation of the preincision complex with the damaged DNA substrate. The location of conserved residues and structural comparisons with helicase-DNA structures suggest how UvrB might bind to DNA. A model of the UvrB-DNA interaction in which a beta-hairpin of UvrB inserts between the DNA double strand has been proposed recently. This padlock model is developed further to suggest two distinct consequences of domain motion: in the UvrA(2)B-DNA complex, domain motions lead to translocation along the DNA, whereas in the tight UvrB-DNA pre-incision complex, they lead to distortion of the 3' incision site. 相似文献
94.
Despite abundant library resources for many organisms, physical mapping of these organisms has been seriously limited due to lack of efficient library screening techniques. We have developed a highly efficient strategy for large-scale screening of genomic libraries based on multiplex oligonucleotide hybridization on high-density genomic filters. We have applied this strategy to generate a bacterial artificial chromosome (BAC) anchored map of mouse chromosome 11. Using the MIT mouse SSLP data, 320 pairs of oligonucleotide probes were designed with an “overgo” computer program that selects new primer sequences that avoid the microsatellite repeat. BACs identified by these probes are automatically anchored to the chromosome. Ninety-two percent of the probes identified positive clones from a 5.9-fold coverage mouse BAC library with an average of 7 positive clones per marker. An average of 4.2 clones was confirmed for 204 markers by PCR. Our data show that a large number of clones can be efficiently isolated from a large genomic library using this strategy with minimal effort. This strategy will have wide application for large-scale mapping and sequencing of human and other large genomes. 相似文献
95.
Potential replacement vegetation: an approach to vegetation mapping of cultural landscapes 总被引:1,自引:0,他引:1
Milan Chytrý 《应用植被学》1998,1(2):177-188
Abstract. The concept of mapping potential replacement vegetation (PRV) is proposed as a parallel to potential natural vegetation (PNV). Potential replacement vegetation (PRV) is an abstract and hypothetical vegetation which is in balance with climatic and soil factors currently affecting a given habitat, with environmental factors influencing the habitat from outside such as air pollution, and with an abstract anthropogenic influence (management) of given type, frequency and intensity. For every habitat, there is a series of possible PRV-types corresponding to the different anthropogenic influences, e.g. grazing, mowing, trampling or growing cereals. The PRV-concept is especially useful in large-scale mapping (scales > 1 : 25 000) of small areas where replacement vegetation is the focus of attention for managers and land-use planners, for example in nature reserves where the aim is conservation of replacement vegetation managed in a traditional way, or in restoration ecology where the concept may be used for defining restoration goals and evaluating the success of restoration efforts. At smaller scales, PRV-mapping may be useful for revealing the biogeographical patterns of larger areas which may be different from the corresponding PNV patterns, because replacement vegetation and natural vegetation may respond to environmental gradients at different scales. An example of medium-scale PRV-mapping through the coincidence of diagnostic species of vegetation types, based on species distribution grid data, is presented. In cultural landscapes, the advantage of using the PRV-concept instead of PNV is its direct relationship to the replacement vegetation. In the habitat mapping with respect to the replacement vegetation, the PRV concept yields more valuable results than the mapping of actual vegetation, as the latter is strongly affected by spatially variable anthropogenic influences which may be largely independent from climatic and soil factors. 相似文献
96.
Abstract. A phenological map has been prepared for the Podyjí/Thayatal National Park, located on the border between the Czech Republic and Austria. The area is characterized by V-shaped river valleys deeply incised into a gently undulating landscape. Five stages of phenological development were defined, based upon phenological spectra of plant communities in late April; 96 sites, more or less regularly spaced over the area, were assigned to one of these stages using field observations of these spectra. Potential direct solar irradiation was calculated from a digital elevation model for a 25 m x 25 m grid extending over the study area. A method was developed for interpolation of phenological observations by weighted regression of phenology on the irradiation model. This interpolation enables the prediction of the local stage of phenological development across the study area without levelling out phenological patterns dependent upon small-scale topographic variation. Spring phenological events appear to be more advanced in the valleys (except for steep north-facing slopes) than in the adjacent landscape. Possible climatic processes underlying this pattern are discussed with emphasis on temperature inversions in the river valleys. Cold-air-drainage inversions reported from the valleys are probably too infrequent and of too short duration to delay plant phenology. The combined effects of advanced phenology and the increased risk of spring frost injury due to these inversions in the valleys may be an explanation for local distributional patterns of flora and vegetation. 相似文献
97.
Passannante Anthony N.; Hazucha Milan J.; Bromberg Philip A.; Seal Elston; Folinsbee Larry; Koch Gary 《Journal of applied physiology》1998,85(5):1863-1870
We have previously suggested that ozone(O3)-induced pain-relatedsymptoms and inhibition of maximal inspiration are due to stimulationof airway C fibers (M. J. Hazucha, D. V. Bates, and P. A. Bromberg.J. Appl.Physiol. 67: 1535-1541, 1989). If this were so,pain suppression or inhibition by opioid-receptor agonists shouldpartially or fully reverseO3-induced symptomatic and lung functional responses. The objectives of this study were to determine whether O3-induced pain limitsmaximal inspiration and whether endogenous opioids contribute tomodulation of the effects of inhaledO3 on lung function. Theparticipants in this double-blind crossover study were healthyvolunteers (18-59 yr) known to be "weak" (WR;n = 20) and "strong"O3 responders (SR;n = 42). They underwent either two 2-hexposures to air or two 2-h exposures to 0.42 parts/millionO3 with moderate intermittentexercise. Immediately afterpost-O3 spirometry, the WR wererandomly given either naloxone (0.15 mg/kg iv) or saline, whereas SRrandomly received either sufentanil (0.2 µg/kg iv) or saline.O3 exposure significantly(P < 0.001) impaired lung function.In SR, sufentanil rapidly, although not completely, reversed both thechest pain and spirometric effects (forced expiratory volume in 1 s;P < 0.0001) compared with saline.Immediate postexposure administration of saline or naloxone had nosignificant effect on WR. Plasma -endorphin levels were not relatedto an individual's O3responsiveness. Cutaneous pain variables showed a nonsignificantweak association with O3responsiveness. These observations demonstrate that nociceptive mechanisms play a key role in modulatingO3-induced inhibition ofinspiration but not in causing lack of spirometric response toO3 exposure in WR. 相似文献
98.
Christopher A. MacRaild Milan Zachrdla Dean Andrew Bankala Krishnarjuna Ji?í Nová?ek Luká? ?ídek Vladimír Sklená? Jack S. Richards James G. Beeson Robin F. Anders Raymond S. Norton 《PloS one》2015,10(3)
Merozoite surface protein 2 (MSP2) of Plasmodium falciparum is an abundant, intrinsically disordered protein that is GPI-anchored to the surface of the invasive blood stage of the malaria parasite. Recombinant MSP2 has been trialled as a component of a malaria vaccine, and is one of several disordered proteins that are candidates for inclusion in vaccines for malaria and other diseases. Nonetheless, little is known about the implications of protein disorder for the development of an effective antibody response. We have therefore undertaken a detailed analysis of the conformational dynamics of the two allelic forms of MSP2 (3D7 and FC27) using NMR spectroscopy. Chemical shifts and NMR relaxation data indicate that conformational and dynamic properties of the N- and C-terminal conserved regions in the two forms of MSP2 are essentially identical, but significant variation exists between and within the central variable regions. We observe a strong relationship between the conformational dynamics and the antigenicity of MSP2, as assessed with antisera to recombinant MSP2. Regions of increased conformational order in MSP2, including those in the conserved regions, are more strongly antigenic, while the most flexible regions are minimally antigenic. This suggests that modifications that increase conformational order may offer a means to tune the antigenicity of MSP2 and other disordered antigens, with implications for vaccine design. 相似文献
99.
Carabid beetles and ground-dwelling spiders inhabiting agroecosystems are beneficial organisms with a potential to control pest species. Intensification of agricultural management and reduction of areas covered by non-crop vegetation during recent decades in some areas has led to many potentially serious environmental problems including a decline in the diversity and abundance of beneficial arthropods in agricultural landscapes. This study investigated carabid beetle and spider assemblages in non-crop habitat islands of various sizes (50 to 18,000 square metres) within one large field, as well as the arable land within the field, using pitfall traps in two consecutive sampling periods (spring to early summer and peak summer). The non-crop habitat islands situated inside arable land hosted many unique ground-dwelling arthropod species that were not present within the surrounding arable land. Even the smallest non-crop habitat islands with areas of tens of square metres were inhabited by assemblages substantially different from these inhabiting arable land and thus enhanced the biodiversity of agricultural landscapes. The non-crop habitat area substantially affected the activity density, recorded species richness and recorded species composition of carabid and ground-dwelling spider assemblages; however, the effects were weakened when species specialised to non-crop habitats species were analysed separately. Interestingly, recorded species richness of spiders increased with non-crop habitat area, whereas recorded species richness of carabid beetles exhibited an opposite trend. There was substantial temporal variation in the spatial distribution of ground-dwelling arthropods, and contrasting patterns were observed for particular taxa (carabid beetles and spiders). In general, local environmental conditions (i.e., non-crop habitat island tree cover, shrub cover, grass cover and litter depth) were better determinants of arthropod assemblages than non-crop habitat island size, indicating that the creation of quite small but diversified (e.g., differing in vegetation cover) non-crop habitat islands could be the most efficient tool for the maintenance and enhancement of diversity of ground-dwelling carabids and spiders in agricultural landscapes. 相似文献
100.
Marek Rác Michal K?upka Svatopluk Binder Michaela Sedlá?ová Zuzana Matu?ková Milan Ra?ka Pavel Pospí?il 《PloS one》2015,10(3)
The exposure of human cells to oxidative stress leads to the oxidation of biomolecules such as lipids, proteins and nuclei acids. In this study, the oxidation of lipids, proteins and DNA was studied after the addition of hydrogen peroxide and Fenton reagent to cell suspension containing human leukemic monocyte lymphoma cell line U937. EPR spin-trapping data showed that the addition of hydrogen peroxide to the cell suspension formed hydroxyl radical via Fenton reaction mediated by endogenous metals. The malondialdehyde HPLC analysis showed no lipid peroxidation after the addition of hydrogen peroxide, whereas the Fenton reagent caused significant lipid peroxidation. The formation of protein carbonyls monitored by dot blot immunoassay and the DNA fragmentation measured by comet assay occurred after the addition of both hydrogen peroxide and Fenton reagent. Oxidative damage of biomolecules leads to the formation of singlet oxygen as conformed by EPR spin-trapping spectroscopy and the green fluorescence of singlet oxygen sensor green detected by confocal laser scanning microscopy. It is proposed here that singlet oxygen is formed by the decomposition of high-energy intermediates such as dioxetane or tetroxide formed by oxidative damage of biomolecules. 相似文献