Indicators of UV Exposure in Corals and Their Relevance to Global Climate Change and Coral Bleaching

A compelling aspect of the deterioration of coral reefs is the phenomenon of coral bleaching. Through interactions with other factors such as sedimentation, pollution, and bacterial infection, bleaching can impact large areas of a reef with limited recovery, and it might be induced by a variety of stressors including temperature and salinity extremes, and ultraviolet light. Under conditions of ocean warming, often associated with calm and stratified waters, photobleaching of UV-absorb-ing chromophoric dissolved organic matter (CDOM) is increased, and penetration of both UV-B and UV-A is greatly enhanced. Indices of UV-specific effects in coral tissue are needed to test whether UV increases, associated with global climate change, are harmful to corals. To address this challenge, we have evaluated UV-specific effects in corals and have characterized factors that alter penetration of UV radiation over coral reefs. An immunoblotting assay was developed to examine UV-specific lesions (thymine dimers) in coral and zooxanthellae DNA. We observed dose-dependent increases of thymine dimers in coral (Porites porites var porites) exposed to artificial solar irradiance in a solar simulator, although effects were not strictly proportional. UV measurements were made in July 1999 at Eastern Sambo reef and nearby sites, including profiling along transects from reef to shore. Results of these analyses indicate that the coral at Eastern Sambo reef (at 3-4 meters) were receiving UV-B radiation that was equivalent to 25 to 30% of surface UV irradiance. However, the water just inside the reef in Hawk Channel (located closer to land) was considerably more opaque to UV. This water photobleached with loss of UV absorbance and fluorescence when it was exposed to simulated solar radiation. These results indicate that photobleaching of the DOM and transport of near-shore water out over the reefs might play a key role in controlling UV penetration to the reef surface.     

Unique oligomeric intermediates of bovine liver catalase

Catalases, although synthesized from single genes and built up from only one type of subunit, exist in heterogeneous form with respect to their conformations and association states in biological systems. This heterogeneity is not of genetic origin, but rather reflects the instability of this oligomeric heme enzyme. To understand better the factors that stabilize the various association states of catalase, we performed studies on the multimeric intermediates that are stabilized during guanidine-hydrochloride- and urea-induced unfolding of bovine liver catalase (BLC). For the first time, we have observed an enzymatically active, folded dimer of native BLC. This dimer has slightly higher enzymatic activity and altered structural properties compared to the native tetramer. Comparative studies of the effect of NaCl, GdmCl, and urea on BLC show that cation binding to negatively charged groups present in amino acid side chains of the enzyme leads to stabilization of an enzymatically active, folded dimer of BLC. Besides the folded dimer, an enzymatically active expanded tetramer and a partially unfolded, enzymatically inactive dimer of BLC were also observed. A complete recovery of native enzyme was observed on refolding of expanded tetramers and folded dimers; however, a very low recovery (maximum of approximately 5%) of native enzyme was observed on refolding of partially unfolded dimers and fully unfolded monomers.     

Metabolism of the lignin model compounds veratrylglycerol-β-guaiacyl ether and 4-ethoxy-3-methoxyphenylglycerol-β-guaiacyl ether by Phanerochaete chrysosporium

The white rot fungus Phanerochaete chrysosporium metabolized the lignin model compounds veratylglycerol--guaiacyl ether I and 4-ethoxy-3-methoxy-phenylglycerol--guaiacyl ether V in stationary culture under an atmosphere of 100% oxygen and under nitrogen limiting conditions. 2-(o-methoxyphenoxy)-ethanol VII was identified as a product of the metabolism of both substrates. Veratryl alcohol and 4-ethoxy-3-methoxybenzyl alcohol IV were identified as metabolites of I and V respectively. Metabolites were identified after comparison with chemically synthesized standards by mass spectrometry. These results indicate the existence of an enzyme system capable of directly cleaving the etherated dimers I and V at the , bond. The additional identification of 2-(o-methoxyphenoxy)-1,3 propanediol IX as a metabolic product indicates that cleavage of the alkyl-phenyl bond of these dimers or their metabolites also occurs.Abbreviations GLC Gas liquid chromatography - TMSi trimethylsilyl - TLC Thin layer chromatography     

Recognition in action: flipping pyrimidine dimers

DNA bases are normally sheltered within a double helix, but enzymes that modify and repair DNA gain access by flipping individual bases out of the double helix.     

Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly’ s composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a ‘monomer world’ towards polymer-based living entities.We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a ‘scaffold’ for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer ‘take-over’ – the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.     

Separation of monoclonal antibody alemtuzumab monomer and dimers using ultrafiltration

This article examines the feasibility of using ultrafiltration to separate the monomer of the monoclonal antibody alemtuzumab (Campath or Campath-1H) from a mixture of dimer and higher-order oligomers (collectively called "dimers" here). Using parameter scanning ultrafiltration, we initially assessed the suitability of the following membranes: 100 kDa and 300 kDa polyethersulfone (PES) membranes, and a 100 kDa polyvinylidene fluoride (PVDF) membrane. A detailed study was then carried out to examine the effects of operating conditions (such as solution pH, ionic strength, stirring speed, and permeate flux) on the separation of the monomer from the dimers using 300 kDa PES and 100 kDa PVDF membranes. Results of the experiments carried out in the carrier phase ultrafiltration (CPUF) mode indicate that the size-based protein-protein separation critically depends on the membrane used as well as the system hydrodynamics. The separation of the monoclonal antibody monomer and dimers using 100 kDa PVDF membranes in the diafiltration mode was also examined. Experimental results demonstrate that under suitable conditions, it is feasible to obtain the alemtuzumab monomer with a purity of more than 93% and a yield of more than 85% (from a mixture of 75% monomer and 25% dimers, which is the typical composition obtained after affinity chromatography). Simulation study indicates that this could be further improved to a purity of more than 96% and a monomer yield of more than 96% by increasing the selectivity of separation or by employing a two-stage diafiltration process.     

Sensitivity of Laminariales zoospores from Helgoland (North Sea) to ultraviolet and photosynthetically active radiation: implications for depth distribution and seasonal reproduction

Depth distribution of kelp species in Helgoland (North Sea) is characterized by occurrence of Laminaria digitata in the upper sublittoral, whereas L. saccharina and L. hyperborea dominate the mid and lower sublittoral region. Laminaria digitata is fertile in summer whereas both other species are fertile in autumn/winter. To determine the light sensitivity of the propagules, zoospores of L. digitata, L. saccharina and L. hyperborea were exposed in the laboratory to different exposure times of photosynthetically active radiation (PAR; 400–700 nm), PAR + UVA radiation (UVAR; 320–400 nm) and PAR + UVAR + UVB radiation (UVBR; 280–320 nm). Optimum quantum yield of PSII and DNA damage were measured after exposure. Subsequently, recovery of photosynthetic efficiency and DNA damage repair, as well as germination rate were measured after 2 and 3 d cultivation in dim white light. Photosynthetic efficiency of all species was photoinhibited already at 20 µmol photons m⁻² s⁻¹ PAR, whereas UV radiation (UVR) had a significant additional effect on photoinhibition. Recovery of the PSII function was observed in all species but not in spores exposed to irradiation longer than 4 h of PAR + UVA + UVB and 8 h of PAR + UVA. The amount of UVB-induced DNA damage measured as cyclobutane–pyrimidine dimers (CPDs) increased with exposure time and highest damage was detected in the spores of lower subtidal L. hyperborea relative to the other two species. Significant removal of CPDs indicating repair of DNA damage was observed in all species after 2 d in low white light especially in the spores of upper subtidal L. digitata. Therefore, efficient DNA damage repair and recovery of PSII damage contributed to the germination success but not in spores exposed to 16 h of UVBR. UV absorption of zoospore suspension in L. digitata is based both on the absorption by the zoospores itself as well as by exudates in the medium. In contrast, the absorption of the zoospore suspension in L. saccharina and L. hyperborea is based predominantly on the absorption by the exudates in the medium. This study indicates that UVR sensitivity of zoospores is related to the seasonal zoospore production as well as the vertical distribution pattern of the large sporophytes.     

Should I stay or should I go: VCP/p97-mediated chromatin extraction in the DNA damage response

The ordered assembly of DNA repair factors on chromatin has been studied in great detail, whereas we are only beginning to realize that selective extraction of proteins from chromatin plays a central role in the DNA damage response. Interestingly, the protein modifier ubiquitin not only regulates the well-documented recruitment of repair proteins, but also governs the temporally and spatially controlled extraction of proteins from DNA lesions. The facilitator of protein extraction is the ubiquitin-dependent ATPase valosin-containing protein (VCP)/p97 complex, which, through its segregase activity, directly extracts ubiquitylated proteins from chromatin. In this review, we summarize recent studies that uncovered this important role of VCP/p97 in the cellular response to genomic insults and discuss how ubiquitin regulates two intuitively counteracting activities at sites of DNA damage.