The cell wall and secretory proteome of a tobacco cell line synthesising secondary wall

The utility of plant secondary cell wall biomass for industrial and biofuel purposes depends upon improving cellulose amount, availability and extractability. The possibility of engineering such biomass requires much more knowledge of the genes and proteins involved in the synthesis, modification and assembly of cellulose, lignin and xylans. Proteomic data are essential to aid gene annotation and understanding of polymer biosynthesis. Comparative proteomes were determined for secondary walls of stem xylem and transgenic xylogenic cells of tobacco and detected peroxidase, cellulase, chitinase, pectinesterase and a number of defence/cell death related proteins, but not marker proteins of primary walls such as xyloglucan endotransglycosidase and expansins. Only the corresponding detergent soluble proteome of secretory microsomes from the xylogenic cultured cells, subjected to ion-exchange chromatography, could be determined accurately since, xylem-specific membrane yields were of poor quality from stem tissue. Among the 109 proteins analysed, many of the protein markers of the ER such as BiP, HSP70, calreticulin and calnexin were identified, together with some of the biosynthetic enzymes and associated polypeptides involved in polymer synthesis. However 53% of these endomembrane proteins failed identification despite the use of two different MS methods, leaving considerable possibilities for future identification of novel proteins involved in secondary wall polymer synthesis once full genomic data are available.

UV irradiance as a major influence on growth, development and secondary products of commercial importance in Lollo Rosso lettuce 'Revolution' grown under polyethylene films

The growth and production of anthocyanin, flavonoid and phenolic compounds were evaluated in Lollo Rosso lettuce 'Revolution' grown continuously under films varying in their ability to transmit LTV radiation (completely transparent to IN, transparent above 320, 350, 370 and 3 80 nm and completely opaque to LTV radiation). Plants were grown from seed under UV transparent and UV blocking films and destructively harvested 3-4 weeks after transplanting. Plants under a complete UV blocking film (UV400) produced up to 2.2 times more total above ground dry weight than plants under the UV transparent film. In contrast, anthocyanin content in plants under the UV blocking film was approximately eight times lower than in plants under a UV transparent film. Furthermore, there was a curvilinear relationship between the anthocyanin content and LTV wavelength cutoff such that above 370 run there was no further reduction in anthocyanin content. Fluorescence measurements indicated that photosynthetic performance index was 15% higher under the presence of UVB and UVA (UV280) than under the presence of UVA (UV320) and 53% higher than in the absence of UV radiation suggesting protection of the photosynthetic apparatus possibly by phenolic compounds. These findings are of particular importance as the potential of UV transmitting films to increase secondary compounds may offer the opportunity to produce plants commercially with increased health benefits compared to those grown under conventional films.

An evaluation of the costs of making specific secondary metabolites: does the yield penalty incurred by host plant resistance to insects due to competition for resources?

The presumption that the synthesis of 'defence' compounds in plants must incur some 'trade-off' or penalty in terms of annual crop yields has been used to explain observed inverse correlations between resistance to herbivores and rates of growth or photosynthesis. An analysis of the cost of making secondary compounds suggests that this accounts for only a small part of the overall carbon budget of annual crop plants. Even the highest reported amounts of secondary metabolites found in different crop species (flavonoids, allylisothiocyanates, hydroxamic acids, 2-tridecanone) represent a carbon demand that can be satisfied by less than an hour's photosynthesis. Similar considerations apply to secondary compounds containing nitrogen or sulphur, which are unlikely to represent a major investment compared to the cost of making proteins, the major demand for these elements. Decreases in growth and photosynthesis in response to stress are more likely the result of programmed down-regulation. Observed correlations between yield and low contents of unpalatable or toxic compounds may be the result of parallel selection during the refinement of crop species by humans.

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Simulating the formation of secondary organic aerosol from the photooxidation of aromatic hydrocarbons

The formation and composition of secondary organic aerosol (SOA) from the photooxidation of benzene, p-xylene, and 1,3,5-trimethylbenzene has been simulated using the Master Chemical Mechanism version 3.1 (MCM v3.1) coupled to a representation of the transfer of organic material from the gas to particle phase. The combined mechanism was tested against data obtained from a series of experiments conducted at the European Photoreactor (EUPHORE) outdoor smog chamber in Valencia, Spain. Simulated aerosol mass concentrations compared reasonably well with the measured SOA data only after absorptive partitioning coefficients were increased by a factor of between 5 and 30. The requirement of such scaling was interpreted in terms of the occurrence of unaccounted-for association reactions in the condensed organic phase leading to the production of relatively more nonvolatile species. Comparisons were made between the relative aerosol forming efficiencies of benzene, toluene, p-xylene, and 1,3,5-trimethylbenzene, and differences in the OH-initiated degradation mechanisms of these aromatic hydrocarbons. A strong, nonlinear relationship was observed between measured (reference) yields of SOA and (proportional) yields of unsaturated dicarbonyl aldehyde species resulting from ring-fragmenting pathways. This observation, and the results of the simulations, is strongly suggestive of the involvement of reactive aldehyde species in association reactions occurring in the aerosol phase, thus promoting SOA formation and growth. The effect of NO, concentrations on SOA formation efficiencies (and formation mechanisms) is discussed.

Simulating the detailed chemical composition of secondary organic aerosol formed on a regional scale during the TORCH 2003 campaign in the southern UK

Following on from the companion study (Johnson et al., 2006), a photochemical trajectory model (PTM) has been used to simulate the chemical composition of organic aerosol for selected events during the 2003 TORCH (Tropospheric Organic Chemistry Experiment) field campaign. The PTM incorporates the speciated emissions of 124 nonmethane anthropogenic volatile organic compounds (VOC) and three representative biogenic VOC, a highly-detailed representation of the atmospheric degradation of these VOC, the emission of primary organic aerosol (POA) material and the formation of secondary organic aerosol (SOA) material. SOA formation was represented by the transfer of semi and non-volatile oxidation products from the gas-phase to a condensed organic aerosol-phase, according to estimated thermodynamic equilibrium phase-partitioning characteristics for around 2000 reaction products. After significantly scaling all phase-partitioning coefficients, and assuming a persistent background organic aerosol (both required in order to match the observed organic aerosol loadings), the detailed chemical composition of the simulated SOA has been investigated in terms of intermediate oxygenated species in the Master Chemical Mechanism, version 3.1 ( MCM v3.1). For the various case studies considered, 90% of the simulated SOA mass comprises between ca. 70 and 100 multifunctional oxygenated species derived, in varying amounts, from the photooxidation of VOC of anthropogenic and biogenic origin. The anthropogenic contribution is dominated by aromatic hydrocarbons and the biogenic contribution by alpha-and beta-pinene (which also constitute surrogates for other emitted monoterpene species). Sensitivity in the simulated mass of SOA to changes in the emission rates of anthropogenic and biogenic VOC has also been investigated for 11 case study events, and the results have been compared to the detailed chemical composition data. The role of accretion chemistry in SOA formation, and its implications for the results of the present investigation, is discussed.

Simulating regional scale secondary organic aerosol formation during the TORCH 2003 campaign in the southern UK

A photochemical trajectory model has been used to simulate the chemical evolution of air masses arriving at the TORCH field campaign site in the southern UK during late July and August 2003, a period which included a widespread and prolonged photochemical pollution episode. The model incorporates speciated emissions of 124 nonmethane anthropogenic VOC and three representative biogenic VOC, coupled with a comprehensive description of the chemistry of their degradation. A representation of the gas/aerosol absorptive partitioning of ca. 2000 oxygenated organic species generated in the Master Chemical Mechanism (MCM v3.1) has been implemented, allowing simulation of the contribution to organic aerosol (OA) made by semi- and non-volatile products of VOC oxidation; emissions of primary organic aerosol (POA) and elemental carbon (EC) are also represented. Simulations of total OA mass concentrations in nine case study events (optimised by comparison with observed hourly-mean mass loadings derived from aerosol mass spectrometry measurements) imply that the OA can be ascribed to three general sources: (i) POA emissions; (ii) a '' ubiquitous '' background concentration of 0.7 mu g m(-3); and (iii) gas-to-aerosol transfer of lower volatility products of VOC oxidation generated by the regional scale processing of emitted VOC, but with all partitioning coefficients increased by a species-independent factor of 500. The requirement to scale the partitioning coefficients, and the implied background concentration, are both indicative of the occurrence of chemical processes within the aerosol which allow the oxidised organic species to react by association and/or accretion reactions which generate even lower volatility products, leading to a persistent, non-volatile secondary organic aerosol (SOA). The contribution of secondary organic material to the simulated OA results in significant elevations in the simulated ratio of organic carbon (OC) to EC, compared with the ratio of 1.1 assigned to the emitted components. For the selected case study events, [OC]/[EC] is calculated to lie in the range 2.7-9.8, values which are comparable with the high end of the range reported in the literature.

Mechanisms for the formation of secondary organic aerosol components from the gas-phase ozonolysis of alpha-pinene

Gas-phase ozonolysis of alpha-pinene was studied in static chamber experiments under 'OH-free' conditions. A range of multifunctional products-in particular low-volatility carboxylic acids-were identified in the condensed phase using gas chromatography coupled to mass spectrometry after derivatisation. The dependence of product yields on reaction conditions (humidity, choice of OH radical scavengers, added Criegee intermediate scavengers, NO2 etc.) was investigated to probe the mechanisms of formation of these products; additional information was obtained by studying the ozonolysis of an enal and an enone derived from alpha-pinene. On the basis of experimental findings, previously suggested mechanisms were evaluated and detailed gas-phase mechanisms were developed to explain the observed product formation. Atmospheric implications of this work are discussed.

Truancy in secondary pupils: prevalance, trajectories and pupil perspectives

School absenteeism and particularly unauthorized absenteeism or truancy has been the focus of a number of, so far largely unsuccessful, recent policy initiatives. The paper draws upon two sources of data, the British Household Panel Survey and detailed interviews with a group of persistent truants, to consider the extent, consequences and explanations for truancy from secondary schools. Truancy increases steadily across the years of secondary school and, especially in the later years of compulsory schooling there is evidence that patterns of truancy established in one year carry on into the next. Truancy is strongly associated with negative outcomes in terms of not staying in education post-16, GCSE results and becoming unemployed. Coming from families of low socio-economic status, parents not monitoring homework, negative attitudes towards teachers and the value of education are all associated with higher levels of truancy. However, the majority of young people in these situations do not truant and there are many truants who do not have these characteristics. A major explanation given by young people themselves for their non-attendance is poor relationships with teachers, including teachers failing to match their expectations. Other factors mentioned by young people include bullying but also a more general dislike of the atmosphere of the school, sometimes associated with a change of school. There was little evidence of negative responses to the curriculum leading to truancy. It is suggested that we can distinguish between socio-economic and attitudinal factors which make young people vulnerable to truancy and precipitating events or processes which result in truanting behaviour.

Shaping literacy in the secondary school: policy, practice and agency in the age of the national literacy strategy

This article examines the definitions of literacy in operation in secondary schools, and the relationship between official literacy policy and the practices of the agents responsible for implementing this policy. We trace the history of national policy back to the Language Across the Curriculum movement of the 1970s as it provides an illustrative point of comparison with the first five years of the National Literacy Strategy. Drawing on empirical data which illuminate the views, perceptions and practices of key agents on a number of levels, we critically review the concept of 'school literacy' promoted in government policy, defining it as 'school-centric literacy' and question its ability to facilitate participation in the practices associated with the media and technological literacies which are increasingly a feature of school life. There is evidence of some unplanned effects of the current national policy but also that levels of agency, for literacy teachers in particular, may be rapidly diminishing.

Moving on: the challenges for foreign language learning on transition from primary to secondary school

Europe's commitment to language learning has resulted in higher percentages of pupils studying foreign languages during primary education. In England, recent policy decisions to expand foreign language learning at primary level by 2010 create major implications for transition to secondary. This paper presents findings on transition issues from case studies of a DfES-funded project evaluating 19 local authority Pathfinders piloting the introduction of foreign language learning at primary level. Research on transition in other countries sets these findings in context. Finally, it investigates the challenges England faces for transition in the light of this expansion and discusses future implications.

IEPs in mainstream secondary schools: an agenda for research

Providing children with special educational needs with individual education plans (IEPs) was advocated in the 1994 code of practice for SEN, and retained in the 2000 code. Specifically as it relates to mainstream secondary schools, this has proved highly controversial: many SENCos report that the writing and implementing of IEPs is a bureaucratic encumbrance, whilst others, going about the process of writing IEPs in very different ways, report that the process is both manageable and beneficial to the children concerned. Given this contradictory evidence, there is an urgent need for research into this area. Having looked at three case-studies of schools using very different methods to write IEPs in ways with which they feel comfortable, a research agenda is set out with a view to informing policies which ensure that resources spent on SEN are used as productively as possible.