Where pathways meet sun radiation

Global warming is due to sun’s radiation - NOT carbon emissions! • Forest Monitor

where pathways meet sun radiation

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One of the most prominent targets of solar UV-radiation is cellular DNA, which absorbs UV-B radiation and causes adverse effects on living systems such as bacteria [ 1516 ], cyanobacteria [ 17 ], phytoplankton [ 18 ], macroalgae [ 19 ], plants [ 20 ], animals, and humans [ 21 — 23 ]. Certain UV-absorbing pigments are produced by a number of organisms as a first line of defense; however, they are unable to avoid UV-radiation completely from reaching DNA in superficial tissue [ 28 — 32 ].

However, as a second line of defense several organisms have developed a number of specific and highly conserved repair mechanisms such as photoreactivation, excision repair, mismatch repair MMRdouble strand break DSB repair and certain other mechanisms like damage tolerance dimer bypassSOS save our soul response, checkpoint activation, and programmed cell death PCD or apoptosis Figure 1 that efficiently remove DNA lesions ensuring the genomic integrity [ 22 ]. Plants are unique in the obligatory nature of their exposure to UVR; it is also conceivable that they may also have evolved certain efficient repair mechanisms for the elimination of UV-induced DNA damage.

However, a number of questions concerning the basic phenomena of the DNA repair in plants remain to be elucidated. In the following, we discuss the molecular mechanisms of UV-induced DNA damage and repair mechanism s operative in various organisms. DNA damage and maintenance. Genomic lesions produced by various DNA damaging agents trigger several specific repair machinery to conserve the genomic integrity.

Sometimes the potentiality of lesions in the genome is mitigated by a phenomenon known as damage tolerance, during which DNA lesions are recognized by certain repair machinery, allowing the cells to undergo normal replication and gene expression. A number of endogenous factors such as free radicals [ 34 ] generated during metabolic processes as well as exogenous factors such as UV or ionizing radiations [ 35 ] are known to interfere with genome integrity.

DNA damage results in i misincorporation of bases during replication process, ii hydrolytic damage, which results in deamination of bases, depurination, and depyrimidination [ 36 ], iii oxidative damage, caused by direct interaction of ionizing radiations IR with the DNA molecules, as well as mediated by UV radiation-induced free radicals or reactive oxygen species [ 3738 ], and iv alkylating agents that may result in modified bases [ 3639 ]. The hydrolytic deamination loss of an amino group can directly convert one base to another; for example, deamination of cytosine results in uracil and at much lower frequency adenine to hypoxanthine.

Among different types of damages, DNA double strand breaks DSBs are the most deleterious, since they affect both strands of DNA and can lead to the loss of genetic material. At high concentrations oxygen-free radicals or, more frequently, reactive oxygen species ROS can induce damage to cell structure, lipids, proteins as well as DNA and results in oxidative stress which has been implicated in a number of human diseases [ 40 ].

UV-Induced Pyrimidine Photoproducts UV-B radiation is one of the most important energetic solar components that may lead to the formation of three major classes of DNA lesions, such as cyclobutane pyrimidine dimers CPDspyrimidine pyrimidone photoproducts PPsand their Dewar isomers Figure 2 [ 5222341 — 43 ]. The diastereoisomers of pyrimidine dimers Figure 4 can be observed in free solution that differ in the orientation of the two pyrimidine rings relative to the cyclobutane ring, and on the relative orientations of the C5—C6 bonds in each pyrimidine base [ 44 ].

It has been demonstrated that the main photoproducts are cis-syn-configured CPD lesions, while trans-syn-configured CPD lesions are formed in much less quantity [ 47 ]. In double stranded B-DNA, where the dimer entails two adjoining pyrimidine bases on the same DNA strand, only the syn isomers can be generated, whereas the cis isomer is preferred over the trans isomer to a great extent [ 42 ].

The incidence of trans-syn isomer in single-stranded or denatured DNA is more common because of the increased flexibility of the DNA backbone. A few CPD lesions i. In most cellular environments, there is no much significance of this photoproduct, since it requires anhydrous conditions for its formation [ 49 ].

Possible diastereoisomers of pyrimidine dimer. CPDs are formed at higher quantity by cycloaddition reaction between two pyrimidine bases [ 47 ] in single-stranded DNA ssDNA and at the flexible ends of poly dA - dT tracts, but not at their rigid centre [ 5051 ]. Thus the heterogeneous distribution of the UV-induced photolesions in the DNA depends on the sequences that facilitate DNA bending as well as the chromatin modulation through the binding of specific protein [ 55 ].

The occurrence of 5-methylcytosine-containing photoproducts in UV-irradiated DNA is still controversial. However, Su et al. There is little information concerning the formation of cytosine hydrates in UV-irradiated DNA due to instability of the resulting photoproduct [ 63 ]. The oxidation product of pyrimidine bases such as pyrimidine glycols is also formed by means of hydration reaction [ 42 ]. Formation of cytosine photohydrate 6-hydroxy-5,6-dihydrocytosine as a result of photohydration reaction.

These comprise the photoproducts that involve, at least, one adenine residue that undergoes photocycloaddition reactions with contiguous adenine or thymine Figure 6 upon exposure to UV-B radiation [ 6566 ]. The extent of adenine-containing photoproduct A-T is very low in native DNA but these lesions may contribute to the biological effects of UV radiation in view of the fact that the A-T adduct has been shown to be mutagenic [ 6768 ].

Conversion of both these photoproducts into 4,6-diaminoguanidinopyrimidine DGPY and 8- 5-aminoimidazolyl adenine 8-AIArespectively, can be detected from individual acid hydrolysates of UV-irradiated polynucleotides and DNA [ 71 ]. Moreover, photoreactivity of adjoining adenine bases in DNA is strongly suppressed by the complementary base pairing [ 5072 ].

Molecular Mechanisms of Ultraviolet Radiation-Induced DNA Damage and Repair

A number of oxidation products of purine bases such as 8-oxo-7,8-dihydroguanyl 8-oxoGua8-oxo-Ade, 2,6-diaminohydroxyformamidoguanine FapyGuaFapyAde, and oxazolone have been reported to form upon exposure of DNA to UV radiation [ 447374 ]. Structure of purinic photoproduct, that is, adenine dimer, porschke photoproduct and thymine-adenine photoadduct. Overall, it has been concluded that UV-induced DNA lesions such as CPDs, PPs, abasic site, strand breaks, and oxidative product are the predominant and most persistent lesions and if not repaired may cause severe structural distortions in the DNA molecule, thereby affecting the important cellular processes such as DNA replication and transcription, compromising cellular viability and functional integrity and ultimately leading to mutagenesis, tumorigenesis, and cell death [ 3036 ].

It has been well established that the comparative orientation of damaged residues is unusual from that observed in unmodified DNA duplexes [ 75 ]. Nuclear overhauser enhancement NOE study of interactions among the photoadduct H6 and methyl CH3 groups has established that the cis-syn CPD changes the cyclobutane conformation from a left-handed twist observed in the isolated dimer to a right-handed twist in DNA duplex [ 46 ] Figure 7. Moreover, in contrast to the cis-syn CPD, the duplex spectra of the trans-syn lesion illustrated no abnormally shifted 31P or imino proton signal, signifying the absence of major distortions in the conformation of the sugar-phosphate backbone [ 75 ].

It has been reported that the preexisting CPDs in the DNA molecule can influence its rotational setting on the histone surface during nucleosome formation [ 81 ]. Recently, Rumora et al. The one- and two-dimensional NMR data on the -adduct-containing DNA duplex decamer was analyzed in H2O and D2O solutions to elicit the base pairing and unusual conformation in the vicinity of the lesion [ 768384 ].

Dotted arrows elucidate the strongest nuclear overhauser enhancement NOE interaction in both cases Adopted from Lukin and de los Santos [ 75 ].

Journal of Nucleic Acids

The main conformational perturbations caused by the adduct and Dewar product are concerned with their effects on global DNA curvature. Both duplex decamers are significantly bent at the lesion sites.

In contrast to the PPs, the 5,6-dihydrohydroxythymine base is the most perturbed part of the Dewar lesion. Even though there are no hydrogen bonds between 5,6-dihydrohydroxythymine and its partner adenine residue, this lesion produces minor distortions in comparison to the PP.

The glycosyl bond torsion angle at the T5 residue of the lesion and the Dewar lesion prevails in the anti and high-anti conformation, respectively, and thus both the lesions exhibit considerable differential effects on DNA backbone conformation.

It has been observed that the large structural distortion induced by the lesion may ensure a favorable recognition by the repair enzyme, which may possibly elucidate the correlation with the elevated repair rate of the T-T adduct than of the T-T Dewar product and the T-T cis-syn dimer [ 76 ]. A significantly low amount of DSBs was found in the cell where replication was inhibited.

Schematic representation showing different pathways of DSBs. A number of pathways have been considered for the formation of DSBs at a stalled replication fork. It was shown that when the DNA replication machinery encounters a replication-blocking lesion, DNA polymerase DP enzyme is stalled at the blocked site resulting in the formation of a Y-shaped DNA structure, which may be recognized by a specific endonuclease, that successively makes a nick in the template strand resulting in the induction of a DSB close to the replication-blocking lesion [ ].

Recently, Harper et al. In spite of the above possible facts regarding the formation of DSBs, more experimental evidences are still needed. An alkaline gel method for quantitating single-strand breaks SSBs in nanogram quantities of nonradioactive DNA was developed by Freeman et al. V before analyzing on sequencing gels. However, it has been experienced that TUNEL assay is not able to distinguish various types of cell death; hence, an alternate method based on flow cytometry FCM has been developed for the detection of apoptosis [ ].

The changes in DNA organization in the individual cells can be determined by halo assay [ ].

where pathways meet sun radiation

SSBs at the single cell level can be assessed by alkaline-halo assay AHAwhere cells are embedded in melted agarose and spread on the microscope slide and then incubated in a high-salt alkaline lysis solution followed by another incubation in a hypotonic alkaline solution and, finally, stained with ethidium bromide EtBr.

Under these conditions, single-stranded DNA fragments diffuse radically from the nuclear cage [ ]. Numerical aberrations in chromosome can be detected efficiently by fluorescence in situ hybridization FISH method [ ]. Recently, immuno-dot-blot assay is used extensively to detect UV-induced photoproducts in various organisms such as mammals, cyanobacteria, phytoplankton, macroalgae, and liverwort [ 1759, ].

This technique is based on use of thymine-dimer specific antibodies followed by blotting and chemiluminescence method. Certain photoproducts such as 5-Methylcytosine and adenine can be detected by high-performance liquid chromatography and mass spectrometry [ 61 ]. Recently, Kumari et al.

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Various strategies for the detection of damaged DNA. DNA Repair The idea about the ability of living beings to overcome the lethal effects of UV-radiation emerged as early as the mid s [ ], but the existence of repair mechanisms was observed by Kelner [ ] and Dulbecco [ ] independently. The determination of a particular repair pathway within the cell mainly depends on the types and location of lesions in the genome [ ].

The biochemical and molecular studies on repair pathways have been extensively investigated in some model organisms such as E. The absorption of every blue-light photon may split approximately one dimer [ ]. CPD photolyases have been reported in diverse groups such as archaea, bacteria, fungi, virus, plants, invertebrates, and many vertebrates including aplacental mammals Table 2. On the other hand, photolyases have been identified in certain organisms like Drosophila, silkworm, Xenopus laevis, and rattle snakes [ 22 ].

Photolyases seem to be absent or nonfunctional in placental mammals like human [, ]. However, Sutherland [ ], Sutherland and Bennett [ ], and Harm [ ] have demonstrated photolyase activity in cells and tissues, including white blood cells WBCs of several placental mammals, such as humans, ox, cat, and mouse.

Photolyase enzymes in four different kingdoms. DNA photolyases 45—66 kDa having — amino acid residues [ ] are monomeric flavin-dependent repair enzymes, consisting of two known cofactors, a catalytic cofactor and a light-harvesting cofactor. In comparison to other eukaryotic systems, reports on the repair of UV-induced DNA damage in plants are still very limited. To avoid the deleterious effects of UVR, plants have acquired two main protective strategies; shielding by flavonoids and phenolic compounds [] and DNA repair by photoreactivation.

Photoreactivation mediated by the enzyme photolyases is thought to be the major DNA repair pathway in several higher plants such as rice, Arabidopsis, wheat, and maize [ — ]. Studies on Arabidopsis seedling, rice, and alfalfa indicate that photoreactivation greatly enhances the rate of removal of dimers, although, in the absence of photoreactivating blue light, dimers are slowly eliminated from bulk DNA and PPs are generally observed to be repaired more quickly than CPDs [].

Plants grown in the presence of photoreactivating radiation can eliminate the majority of both products and CPD lesion within hours, or in some cases minutes, of their induction [ 30 ].

The structural information about the interaction between CPD lesions and photolyases became clear with the help of X-ray crystallography [ ] and nuclear magnetic resonance NMR spectroscopy [ ]. The splitting of CPD lesion proceeds rapidly within 0. The back-transfer of electrons from the CPD lesion to the FADH radical is efficiently avoided by the enzyme before completion of cleavage of the cyclobutane ring [ ].

With the help of ultrafast femtosecond laser spectroscopy, MacFarlane and Stanley [ ] have suggested that photolyase enzyme is indeed left in the semiquinonid state after accomplishment of repair of the CPD lesion.

However, Kavakli and Sancar [ ] have analyzed the role of intraprotein electron transfer in photoreactivation by DNA photolyase and found that photoreduction process is not a regular part of the photolyase photocycle under physiological conditions, because the enzyme may undergo at least 25 repair cycles before loosing its activity. After completion of DNA repair, a thymine pair is flipped back into the duplex DNA to form a hydrogen bond with their complementary adenine base.

In the absence of photoreactivating light, the enzyme binds to and stimulates the removal of UV damage by stimulating the NER system in vivo or in vitro and defense against DNA damage even in the absence of light [ ]. Excision Repair Unlike photoreactivation, excision repair is a multistep, dark repair pathway, where an abnormal or damaged base is removed by two major subpathways: Base Excision Repair BER BER is the predominant DNA repair pathway against base lesions arising from hydrolytic deamination, strong alkylating agents, ionizing radiation IRor by different intracellular metabolites and, indirectly, also by UV radiation via generation of ROS [ — ] and proceeds through a series of repair complexes that act at the site of DNA damage [].

The efficiency and specificity of the repair pathway are determined by several forms of DNA glycosylase which removes different types of modified bases Table 3 by cleaving the N-glycosidic bond between the abnormal base and deoxyribose creating either an abasic site or an SSB [ ]. Recently, Parsons et al. These fluctuations average around 0. However, the variations can also fluctuate — depending on wavelength, because the sun shines in numerous different bands of the spectrum.

The ultraviolet radiation mentioned above, for example, which is particularly relevant with regard to the climate, varies by several tens of percents in the short wavelengths. By way of its energy input, the sun can directly influence the climate of our planet. However, the atmosphere only allows radiation to pass through in specific wavelengths, predominantly in visible light; the remainder is, in a manner of speaking, absorbed by molecules.

Only part of the radiation therefore reaches Earth's surface and can heat it up. The irradiated surface, in turn, emits infra-red light, which is then held back by clouds or aerosols. This effect, without which the Earth would be around 32 degrees Celsius colder, warms the atmosphere.

These processes resemble the conditions in a greenhouse. This illustration shows variations within the eleven-year solar cycle as well as short-term variations caused by individual sunspot groups and solar flares. The average total brightness is represented by the grey curve. The different colours depict measurements with different instruments.

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PMOD This is where the ultraviolet radiation plays its part. It is involved in a range of different chemical reactions — whereby UV is not just UV! For example, radiation at wavelengths less than nanometres promotes the formation of ozone, longer wavelength UV, in contrast, destroys the same molecule. And together with the radiation at different wavelengths, different amounts of energy enter the troposphere, the lowest layer of the atmosphere, extending to around 15 kilometres above the ground.

The sun, however, not only emits radiation, but also a permanent flow of electrically charged particles, the aforementioned solar. If these particles penetrate the upper layers of Earth's atmosphere, they eject electrons from nitrogen or oxygen atoms, that is, they ionize them.

This process influences atmospheric chemistry — whether, and if so, how this impacts the climate, is currently a matter of debate. To investigate the influence of the sun on the climate, researchers look to the past. Here, they focus on the star's magnetic activity, from which the radiation intensity can be reconstructed. It is then apparent that the sun produces more intense radiation during active periods — apparent thanks to numerous spots and flares — than during its quiescent phases.

The sun had just such a break in activity during the second half of the 17th century, for example: And even the summer was substantially cooler in some regions during this "Little Ice Age.

When looking back at the past the scientists work with both old records of observational sunspot data beginning in and using the C14 method, which can be particularly well applied to wood, as Carbon input at the ground trees is not constant, but also changes with solar activity.

This radioactive isotope is created when what are known as cosmic rays meet an air molecule in the upper layers of Earth's atmosphere.

where pathways meet sun radiation

Factoring in the human influence: Models can only reproduce the observational data if anthropogenic influences are included in the calculations. IPCC Report 5 The solar magnetic field extends throughout the entire solar system and partially screens off cosmic rays. If the magnetic field fluctuates, so does C14 production. In this manner, the deviation between tree ring age and C14 age represents a measure of magnetic activity and consequently for the radiant power of the sun.

So, how strongly does the sun currently influence the climate?