Abstract. The Master Chemical Mechanism has been updated from MCMv3 to MCMv3.1 in order to take into account recent improvements in the understanding of aromatic photo-oxidation. Newly available kinetic and product data from the literature have been incorporated into the mechanism. In particular, the degradation mechanisms for hydroxyarenes have been revised following the observation of high yields of ring-retained products, and product studies of aromatic oxidation under relatively low NO x conditions have provided new information on the branching ratios to first generation products. Experiments have been carried out at the European Photoreactor (EUPHORE) to investigate key subsets of the toluene system. These results have been used to test our understanding of toluene oxidation, and, where possible, refine the degradation mechanisms. The evaluation of MCMv3 and MCMv3.1 using data on benzene, toluene, p-xylene and 1,3,5-trimethylbenzene photosmog systems is described in a companion paper, and significant model shortcomings are identified. Ideas for additional modifications to the mechanisms, and for future experiments to further our knowledge of the details of aromatic photo-oxidation are discussed.

Abstract. Kinetic and mechanistic data relevant to the tropospheric degradation of aromatic volatile organic compounds (VOC) have been used to define a mechanism development protocol, which has been used to construct degradation schemes for 18 aromatic VOC as part of version 3 of the Master Chemical Mechanism (MCM v3). This is complementary to the treatment of 107 non-aromatic VOC, presented in a companion paper. The protocol is divided into a series of subsections describing initiation reactions, the degradation chemistry to first generation products via a number of competitive routes, and the further degradation of first and subsequent generation products. Emphasis is placed on describing where the treatment differs from that applied to the non-aromatic VOC. The protocol is based on work available in the open literature up to the beginning of 2001, and some other studies known by the authors which were under review at the time. Photochemical Ozone Creation Potentials (POCP) have been calculated for the 18 aromatic VOC in MCM v3 for idealised conditions appropriate to north-west Europe, using a photochemical trajectory model. The POCP values provide a measure of the relative ozone forming abilities of the VOC. These show distinct differences from POCP values calculated previously for the aromatics, using earlier versions of the MCM, and reasons for these differences are discussed.

Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.cytoskeleton | calcium-signaling | carbohydrate-active enzymes | stress tolerance | vitamin B 12T he red algae are one of the founding groups of photosynthetic eukaryotes (Archaeplastida) and among the few multicellular lineages within Eukarya. A red algal plastid, acquired through secondary endosymbiosis, supports carbon fixation, fatty acid synthesis, and other metabolic needs in many other algal groups in ways that are consequential. For example, diatoms and haptophytes have strong biogeochemical effects; apicomplexans cause human disease (e.g., malaria); and dinoflagellates include both coral symbionts and toxin-producing "red tides" (1). The evolutionary processes that produced the Archaeplastida and secondary algal lineages remain under investigation (2-5), but it is clear that both nuclear and plastid genes from the ancestral red algae have contributed dramatically to broader eukaryotic evolution and diversity. Consequently, the imprint of red algal metabolism on the Earth's climate system, aquatic foodwebs, and

Flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. To further understand the molecular organization of the eyespot apparatus and the phototactic movement that is controlled by light and the circadian clock, a detailed understanding of all components of the eyespot apparatus is needed. We developed a procedure to purify the eyespot apparatus from the green model alga Chlamydomonas reinhardtii. Its proteomic analysis resulted in the identification of 202 different proteins with at least two different peptides (984 in total). These data provide new insights into structural components of the eyespot apparatus, photoreceptors, retina(l)-related proteins, members of putative signaling pathways for phototaxis and chemotaxis, and metabolic pathways within an algal visual system. In addition, we have performed a functional analysis of one of the identified putative components of the phototactic signaling pathway, casein kinase 1 (CK1). CK1 is also present in the flagella and thus is a promising candidate for controlling behavioral responses to light. We demonstrate that silencing CK1 by RNA interference reduces its level in both flagella and eyespot. In addition, we show that silencing of CK1 results in severe disturbances in hatching, flagellum formation, and circadian control of phototaxis.

Abstract.A high quality dataset on the photo-oxidation of benzene, toluene, p-xylene and 1,3,5-trimethylbenzene has been obtained from experiments in the European Photoreactor (EUPHORE), a large outdoor environmental reaction chamber. The experiments were designed to test sensitive features of detailed aromatic mechanisms, and the dataset has been used to evaluate the performance of the Master Chemical Mechanism Version 3 (MCMv3). An updated version (MCMv3.1) was constructed based on recent experimental data, and details of its development are described in a companion paper. The MCMv3.1 aromatic mechanisms have also been evaluated using the EUPHORE dataset. Significant deficiencies have been identified in the mechanisms, in particular: 1) an over-estimation of the ozone concentration, 2) an under-estimation of the NO oxidation rate, 3) an under-estimation of OH. The use of MCMv3.1 improves the model-measurement agreement in some areas but significant discrepancies remain.

Abstract. Toluene photooxidation is chosen as an example to examine how simulations of smog-chamber experiments can be used to unravel shortcomings in detailed mechanisms and to provide information on complex reaction systems that will be crucial for the design of future validation experiments. The mechanism used in this study is extracted from the Master Chemical Mechanism Version 3 (MCM v3) and has been updated with new modules for cresol and γ -dicarbonyl chemistry. Model simulations are carried out for a toluene-NO x experiment undertaken at the European Photoreactor (EUPHORE). The comparison of the simulation with the experimental data reveals two fundamental shortcomings in the mechanism: OH production is too low by about 44%, and the ozone concentration at the end of the experiment is over-predicted by 55%. The radical budget was analysed to identify the key intermediates governing the radical transformation in the toluene system. Ring-opening products, particularly conjugated γ -dicarbonyls, were identified as dominant radical sources in the early stages of the experiment. The analysis of the time evolution of radical production points to a missing OH source that peaks when the system reaches highest reactivity. First generation products are also of major importance for the ozone production in the system. The analysis of the radical budget suggests two options to explain the concurrent under-prediction of OH and overprediction of ozone in the model: (1) missing oxidation processes that produce or regenerate OH without or with little NO to NO 2 conversion or (2) NO 3 chemistry that sequesters reactive nitrogen oxides into stable nitrogen compounds and at the same time produces peroxy radicals. Sensitivity analyCorrespondence to: M. J. Pilling (M.J.Pilling@chem.leeds.ac.uk sis was employed to identify significant contributors to ozone production and it is shown how this technique, in combination with ozone isopleth plots, can be used for the design of validation experiments.

[1] On the basis of a data set collected during the Indian Ocean Experiment (INDOEX) campaign 1999, we investigated the formaldehyde (CH 2 O) budget in the southern Indian Ocean (SIO). With a photochemical box model we simulated the contribution of methane and nonmethane volatile organic compounds to the CH 2 O budget. To identify the reactions and model constraints that introduce the largest uncertainties in the modeled CH 2 O concentration, we carried out a local sensitivity analysis. Furthermore, a Monte Carlo method was used to assess the global error of the model predictions. According to this analysis the 2s uncertainty in the modeled CH 2 O concentration is 49%. The deviation between observed (200 ± 70 parts per trillion by volume (pptv) (2s)) and modeled (224 ± 110 pptv (2s)) daily mean CH 2 O concentration is 12%. However, the combined errors of model and measurement are such that deviations as large as 65% are not significant at the 2s level. Beyond the ''standard'' photochemistry we analyzed the impact of halogen and aerosol chemistry on the CH 2 O concentration and investigated the vertical distribution of CH 2 O in the marine boundary layer (MBL). Calculations with the Model of Chemistry Considering Aerosols indicate that, based on the current understanding, halogen chemistry and aerosol chemistry have no significant impact on the CH 2 O concentration under conditions encountered in the SIO. However, a detailed investigation including meteorological effects such as precipitation scavenging and convection reveals an uncertainty in state-of-the-art model predictions for CH 2 O in the MBL that is too large for a meaningful test of the current understanding of CH 4 photooxidation.

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