Extraction of Soluble Proteins from Leaves

Protein biochemistry can provide valuable answers to better understand plant performance and responses to the surrounding environment. In this chapter, we describe the process of extracting proteins from plant leaf samples. We highlight the key aspects to take into consideration to preserve protein integrity, from sample collection to extraction and preparation or storage for subsequent analysis of protein abundance and/or enzymatic activities.

Purification of Rubisco from Leaves

Rubisco fixes CO2 through the carboxylation of ribulose 1,5-bisphosphate (RuBP) during photosynthesis, enabling the synthesis of organic compounds. The natural diversity of Rubisco properties represents an opportunity to improve its performance and there is considerable research effort focusing on better understanding the properties and regulation of the enzyme. This chapter describes a method for large-scale purification of Rubisco from leaves. After the extraction of Rubisco from plant leaves, the enzyme is separated from other proteins by fractional precipitation with polyethylene glycol followed by ion-exchange chromatography. This method enables the isolation of Rubisco in large quantities for a wide range of biochemical applications.

Frailty Assessment in Vascular OUtpatients Review (FAVOUR) protocol: single-centre prospective cohort study comparing feasibility and prognostic value of commonly used frailty assessment tools

INTRODUCTION

Frailty has consistently demonstrated associations with poorer healthcare outcomes. Vascular guidelines have recognised the importance of frailty assessment. However, an abundance of frailty tools and a lack of prospective studies confirming suitability of routine frailty assessment in clinical practice has delayed the uptake of these guidelines. The Frailty Assessment in Vascular OUtpatients Review study speaks to this evidence gap. The primary aim is to assess feasibility of implementing routine frailty assessment in a reproducible outpatient setting. Secondary objectives include comparing prognostic values and interuser agreement across five frailty assessment tools.

METHODS AND ANALYSIS

This single-centre prospective cohort study of feasibility is conducted in a rapid-referral vascular surgery clinic, serving a population of 2 million. Adults with capacity (>18 years), attending a clinic for any reason, are eligible for inclusion. Five assessments are completed by patient (Rockwood Clinical Frailty Scale (CFS) and Frail NonDisabled Questionnaire), clinician (CFS, Healthcare Improvement Scotland FRAIL tool and 'Initial Clinical Evaluation') and researcher (11-item modified Frailty Index). Consistent with feasibility objectives, outcome measures include recruitment rates, frailty assessment completion rates, time-to-complete assessments and interuser variability. Electronic follow-up at 30 days and 1 year will assess home-time and mortality as prognostic indicators. Patients treated surgically/endovascularly will undergo additional 30-day and 1-year postoperative follow-up, outcome measures include: surgical procedure, mortality, complications (according to Clavien-Dindo Classification), length of stay, readmission rates, non-home discharge, home-time, higher social care requirements on discharge and amputation-free survival. Prognostic value will be compared by area under receiver operating characteristic curves. Continuous outcome variables will be analysed using Spearman's rank correlation coefficient. Interuser agreement will be compared by percentage agreement in Cohen's kappa coefficient.  ETHICS AND DISSEMINATION: The study is sponsored by National Health Service Greater Glasgow and Clyde (R&IUGN23CE014). London-Riverside REC (23/PR/0062) granted ethical approval. Results will be disseminated through publication in peer-reviewed vascular surgery and geriatric medicine themed journals and presentation at similar scientific conferences.

TRIALS REGISTRATION NUMBER

NCT06040658. Stage of study: pre-results.

A systematic review of frailty assessment tools used in vascular surgery research

OBJECTIVE

Frailty is common in vascular patients and is recognized for its prognostic value. In the absence of consensus, a multitude of frailty assessment tools exist. This systematic review aimed to quantify the variety in these tools and describe their content and application to inform future research and clinical practice.

METHODS

Multiple cross-disciplinary electronic literature databases were searched from inception to August 2022. Studies describing frailty assessment in a vascular surgical population were eligible. Data extraction to a validated template included patient demographics, tool content, and analysis methods. A secondary systematic search for papers describing the psychometric properties of commonly used frailty tools was then performed.

RESULTS

Screening 5358 records identified 111 eligible studies, with an aggregate population of 5,418,236 patients. Forty-three differing frailty assessment tools were identified. One-third of these failed to assess frailty as a multidomain deficit and there was a reliance on assessing function and presence of comorbidity. Substantial methodological variability in data analysis and lack of methodological description was also identified. Published psychometric assessment was available for only 4 of the 10 most commonly used frailty tools. The Clinical Frailty Scale was the most studied and demonstrates good psychometric properties within a surgical population.

CONCLUSIONS

Substantial heterogeneity in frailty assessment is demonstrated, precluding meaningful comparisons of services and data pooling. A uniform approach to assessment is required to guide future frailty research. Based on the literature, we make the following recommendations: frailty should be considered a continuous construct and the reporting of frailty tools' application needs standardized. In the absence of consensus, the Clinical Frailty Scale is a validated tool with good psychometric properties that demonstrates usefulness in vascular surgery.

Dynamics of Rubisco regulation by sugar phosphate derivatives and their phosphatases

Regulating the central CO2-fixing enzyme Rubisco is as complex as its ancient reaction mechanism and involves interaction with a series of cofactors and auxiliary proteins that activate catalytic sites and maintain activity. A key component among the regulatory mechanisms is the binding of sugar phosphate derivatives that inhibit activity. Removal of inhibitors via the action of Rubisco activase is required to restore catalytic competency. In addition, specific phosphatases dephosphorylate newly released inhibitors, rendering them incapable of binding to Rubisco catalytic sites. The best studied inhibitor is 2-carboxy-d-arabinitol 1-phosphate (CA1P), a naturally occurring nocturnal inhibitor that accumulates in most species during darkness and low light, progressively binding to Rubisco. As light increases, Rubisco activase removes CA1P from Rubisco, and the specific phosphatase CA1Pase dephosphorylates CA1P to CA, which cannot bind Rubisco. Misfire products of Rubisco's complex reaction chemistry can also act as inhibitors. One example is xylulose-1,5-bisphosphate (XuBP), which is dephosphorylated by XuBPase. Here we revisit key findings related to sugar phosphate derivatives and their specific phosphatases, highlighting outstanding questions and how further consideration of these inhibitors and their role is important for better understanding the regulation of carbon assimilation.

Structural plasticity enables evolution and innovation of RuBisCO assemblies

Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.

Rubiscosome gene expression is balanced across the hexaploid wheat genome

Functional and active Rubisco is essential for CO₂ fixation and is a primary target for engineering approaches to increasing crop yields. However, the assembly and maintenance of active Rubisco are dependent on the coordinated biosynthesis of at least 11 nuclear-encoded proteins, termed the 'Rubiscosome'. Using publicly available gene expression data for wheat (Triticum aestivum L.), we show that the expression of Rubiscosome genes is balanced across the three closely related subgenomes that form the allohexaploid genome. Each subgenome contains a near complete set of homoeologous genes and contributes equally to overall expression, both under optimal and under heat stress conditions. The expression of the wheat thermo-tolerant Rubisco activase isoform 1β increases under heat stress and remains balanced across the subgenomes, albeit with a slight shift towards greater contribution from the D subgenome. The findings show that the gene copies in all three subgenomes need to be accounted for when designing strategies for crop improvement.

A procedure to introduce point mutations into the Rubisco large subunit gene in wild-type plants

Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Rubisco is a key target for improvement as it plays a central role in carbon fixation during photosynthesis and is remarkably inefficient. Introduction of mutations to the chloroplast-encoded Rubisco large subunit rbcL is of particular interest for improving the catalytic activity and efficiency of the enzyme. However, manipulation of rbcL is hampered by its location in the plastome, with many species recalcitrant to plastome transformation, and by the plastid's efficient repair system, which can prevent effective maintenance of mutations introduced with homologous recombination. Here we present a system where the introduction of a number of silent mutations into rbcL within the model plant Nicotiana tabacum facilitates simplified screening via additional restriction enzyme sites. This system was used to successfully generate a range of transplastomic lines from wild-type N. tabacum with stable point mutations within rbcL in 40% of the transformants, allowing assessment of the effect of these mutations on Rubisco assembly and activity. With further optimization the approach offers a viable way forward for mutagenic testing of Rubisco function in planta within tobacco and modification of rbcL in other crops where chloroplast transformation is feasible. The transformation strategy could also be applied to introduce point mutations in other chloroplast-encoded genes.

Heat-induced changes in the abundance of wheat Rubisco activase isoforms

The Triticum aestivum (wheat) genome encodes three isoforms of Rubisco activase (Rca) differing in thermostability, which could be exploited to improve the resilience of this crop to global warming. We hypothesized that elevated temperatures would cause an increase in the relative abundance of heat-stable Rca1β. Wheat plants were grown at 25° C : 18°C (day : night) and exposed to heat stress (38° C : 22°C) for up to 5 d at pre-anthesis. Carbon (C) assimilation, Rubisco activity, CA1Pase activity, transcripts of Rca1β, Rca2β, and Rca2α, and the quantities of the corresponding protein products were measured during and after heat stress. The transcript of Rca1β increased 40-fold in 4 h at elevated temperatures and returned to the original level after 4 h upon return of plants to control temperatures. Rca1β comprised up to 2% of the total Rca protein in unstressed leaves but increased three-fold in leaves exposed to elevated temperatures for 5 d and remained high at 4 h after heat stress. These results show that elevated temperatures cause rapid changes in Rca gene expression and adaptive changes in Rca isoform abundance. The improved understanding of the regulation of C assimilation under heat stress will inform efforts to improve wheat productivity and climate resilience.

CRISPR-Cas9-Mediated Mutagenesis of the Rubisco Small Subunit Family in Nicotiana tabacum

Engineering the small subunit of the key CO2-fixing enzyme Rubisco (SSU, encoded by rbcS) in plants currently poses a significant challenge, as many plants have polyploid genomes and SSUs are encoded by large multigene families. Here, we used CRISPR-Cas9-mediated genome editing approach to simultaneously knock-out multiple rbcS homologs in the model tetraploid crop tobacco (Nicotiana tabacum cv. Petit Havana). The three rbcS homologs rbcS_S1a, rbcS_S1b and rbcS_T1 account for at least 80% of total rbcS expression in tobacco. In this study, two multiplexing guide RNAs (gRNAs) were designed to target homologous regions in these three genes. We generated tobacco mutant lines with indel mutations in all three genes, including one line with a 670 bp deletion in rbcS-T1. The Rubisco content of three selected mutant lines in the T1 generation was reduced by ca. 93% and mutant plants accumulated only 10% of the total biomass of wild-type plants. As a second goal, we developed a proof-of-principle approach to simultaneously introduce a non-native rbcS gene while generating the triple SSU knockout by co-transformation into a wild-type tobacco background. Our results show that CRISPR-Cas9 is a viable tool for the targeted mutagenesis of rbcS families in polyploid species and will contribute to efforts aimed at improving photosynthetic efficiency through expression of superior non-native Rubisco enzymes in plants.

During photosynthetic induction, biochemical and stomatal limitations differ between Brassica crops

Interventions to increase crop radiation use efficiency rely on understanding of how biochemical and stomatal limitations affect photosynthesis. When leaves transition from shade to high light, slow increases in maximum Rubisco carboxylation rate and stomatal conductance limit net CO₂ assimilation for several minutes. However, as stomata open intercellular [CO₂ ] increases, so electron transport rate could also become limiting. Photosynthetic limitations were evaluated in three important Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. Measurements of induction after a period of shade showed that net CO₂ assimilation by B. rapa and B. napus saturated by 10 min. A new method of analyzing limitations to induction by varying intercellular [CO₂ ] showed this was due to co-limitation by Rubisco and electron transport. By contrast, in B. oleracea persistent Rubisco limitation meant that CO₂ assimilation was still recovering 15 min after induction. Correspondingly, B. oleracea had the lowest Rubisco total activity. The methodology developed, and its application here, shows a means to identify the basis of variation in photosynthetic efficiency in fluctuating light, which could be exploited in breeding and bioengineering to improve crop productivity.

Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis

The primary CO2-fixing enzyme Rubisco limits the productivity of plants. The small subunit of Rubisco (SSU) can influence overall Rubisco levels and catalytic efficiency, and is now receiving increasing attention as a potential engineering target to improve the performance of Rubisco. However, SSUs are encoded by a family of nuclear rbcS genes in plants, which makes them challenging to engineer and study. Here we have used CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] and T-DNA insertion lines to generate a suite of single and multiple gene knockout mutants for the four members of the rbcS family in Arabidopsis, including two novel mutants 2b3b and 1a2b3b. 1a2b3b contained very low levels of Rubisco (~3% relative to the wild-type) and is the first example of a mutant with a homogenous Rubisco pool consisting of a single SSU isoform (1B). Growth under near-outdoor levels of light demonstrated Rubisco-limited growth phenotypes for several SSU mutants and the importance of the 1A and 3B isoforms. We also identified 1a1b as a likely lethal mutation, suggesting a key contributory role for the least expressed 1B isoform during early development. The successful use of CRISPR/Cas here suggests that this is a viable approach for exploring the functional roles of SSU isoforms in plants.

Novel bacterial clade reveals origin of form I Rubisco

Rubisco sustains the biosphere through the fixation of CO₂ into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.

Rubisco and carbon-concentrating mechanism co-evolution across chlorophyte and streptophyte green algae

Green algae expressing a carbon-concentrating mechanism (CCM) are usually associated with a Rubisco-containing micro-compartment, the pyrenoid. A link between the small subunit (SSU) of Rubisco and pyrenoid formation in Chlamydomonas reinhardtii has previously suggested that specific RbcS residues could explain pyrenoid occurrence in green algae. A phylogeny of RbcS was used to compare the protein sequence and CCM distribution across the green algae and positive selection in RbcS was estimated. For six streptophyte algae, Rubisco catalytic properties, affinity for CO₂ uptake (K_0.5 ), carbon isotope discrimination (δ¹³ C) and pyrenoid morphology were compared. The length of the βA-βB loop in RbcS provided a phylogenetic marker discriminating chlorophyte from streptophyte green algae. Rubisco kinetic properties in streptophyte algae have responded to the extent of inducible CCM activity, as indicated by changes in inorganic carbon uptake affinity, δ¹³ C and pyrenoid ultrastructure between high and low CO₂ conditions for growth. We conclude that the Rubisco catalytic properties found in streptophyte algae have coevolved and reflect the strength of any CCM or degree of pyrenoid leakiness, and limitations to inorganic carbon in the aquatic habitat, whereas Rubisco in extant land plants reflects more recent selective pressures associated with improved diffusive supply of the terrestrial environment.

Photosynthesis across African cassava germplasm is limited by Rubisco and mesophyll conductance at steady state, but by stomatal conductance in fluctuating light

Sub-Saharan Africa is projected to see a 55% increase in food demand by 2035, where cassava (Manihot esculenta) is the most widely planted crop and a major calorie source. Yet, cassava yield in this region has not increased significantly for 13 yr. Improvement of genetic yield potential, the basis of the first Green Revolution, could be realized by improving photosynthetic efficiency. First, the factors limiting photosynthesis and their genetic variability within extant germplasm must be understood. Biochemical and diffusive limitations to leaf photosynthetic CO2 uptake under steady state and fluctuating light in 13 farm-preferred and high-yielding African cultivars were analyzed. A cassava leaf metabolic model was developed to quantify the value of overcoming limitations to leaf photosynthesis. At steady state, in vivo Rubisco activity and mesophyll conductance accounted for 84% of the limitation. Under nonsteady-state conditions of shade to sun transition, stomatal conductance was the major limitation, resulting in an estimated 13% and 5% losses in CO2 uptake and water use efficiency, across a diurnal period. Triose phosphate utilization, although sufficient to support observed rates, would limit improvement in leaf photosynthesis to 33%, unless improved itself. The variation of carbon assimilation among cultivars was three times greater under nonsteady state compared to steady state, pinpointing important overlooked breeding targets for improved photosynthetic efficiency in cassava.

Hybrid Cyanobacterial-Tobacco Rubisco Supports Autotrophic Growth and Procarboxysomal Aggregation

Much of the research aimed at improving photosynthesis and crop productivity attempts to overcome shortcomings of the primary CO2-fixing enzyme Rubisco. Cyanobacteria utilize a CO2-concentrating mechanism (CCM), which encapsulates Rubisco with poor specificity but a relatively fast catalytic rate within a carboxysome microcompartment. Alongside the active transport of bicarbonate into the cell and localization of carbonic anhydrase within the carboxysome shell with Rubisco, cyanobacteria are able to overcome the limitations of Rubisco via localization within a high-CO2 environment. As part of ongoing efforts to engineer a β-cyanobacterial CCM into land plants, we investigated the potential for Rubisco large subunits (LSU) from the β-cyanobacterium Synechococcus elongatus (Se) to form aggregated Rubisco complexes with the carboxysome linker protein CcmM35 within tobacco (Nicotiana tabacum) chloroplasts. Transplastomic plants were produced that lacked cognate Se Rubisco small subunits (SSU) and expressed the Se LSU in place of tobacco LSU, with and without CcmM35. Plants were able to form a hybrid enzyme utilizing tobacco SSU and the Se LSU, allowing slow autotrophic growth in high CO2 CcmM35 was able to form large Rubisco aggregates with the Se LSU, and these incorporated small amounts of native tobacco SSU. Plants lacking the Se SSU showed delayed growth, poor photosynthetic capacity, and significantly reduced Rubisco activity compared with both wild-type tobacco and lines expressing the Se SSU. These results demonstrate the ability of the Se LSU and CcmM35 to form large aggregates without the cognate Se SSU in planta, harboring active Rubisco that enables plant growth, albeit at a much slower pace than plants expressing the cognate Se SSU.

Overexpression of ca1pase Decreases Rubisco Abundance and Grain Yield in Wheat

Rubisco catalyzes the fixation of CO2 into organic compounds that are used for plant growth and the production of agricultural products, and specific sugar-phosphate derivatives bind tightly to the active sites of Rubisco, locking the enzyme in a catalytically inactive conformation. 2-carboxy-d-arabinitol-1-phosphate phosphatase (CA1Pase) dephosphorylates such tight-binding inhibitors, contributing to the maintenance of Rubisco activity. Here, we investigated the hypothesis that overexpressing ca1pase would decrease the abundance of Rubisco inhibitors, thereby increasing the activity of Rubisco and enhancing photosynthetic performance and productivity in wheat (Triticum aestivum). Plants of four independent wheat transgenic lines overexpressing ca1pase showed up to 30-fold increases in ca1pase expression compared to the wild type. Plants overexpressing ca1pase had lower numbers of Rubisco tight-binding inhibitors and higher Rubisco activation state than the wild type; however, there were 17% to 60% fewer Rubisco active sites in the four transgenic lines than in the wild type. The lower Rubisco content in plants overexpressing ca1pase resulted in lower initial and total carboxylating activities measured in flag leaves at the end of the vegetative stage and lower aboveground biomass and grain yield measured in fully mature plants. Hence, contrary to what would be expected, ca1pase overexpression decreased Rubisco content and compromised wheat grain yields. These results support a possible role for Rubisco inhibitors in protecting the enzyme and maintaining an adequate number of Rubisco active sites to support carboxylation rates in planta.

Extraction of RuBisCO to Determine Catalytic Constants

RuBisCO enables net carbon fixation through the carboxylation of RuBP during photosynthesis. Its complex biochemistry and catalytic diversity found among different plants make characterization of RuBisCO properties useful for investigations aimed at improving photosynthetic performance. This chapter reports methods for rapid extraction of soluble proteins to examine RuBisCO catalytic properties, and for large-scale purification of RuBisCO from leaves to measure the specificity of the enzyme toward its gaseous substrates.

Engineering photosynthesis: progress and perspectives

Photosynthesis is the basis of primary productivity on the planet. Crop breeding has sustained steady improvements in yield to keep pace with population growth increases. Yet these advances have not resulted from improving the photosynthetic process per se but rather of altering the way carbon is partitioned within the plant. Mounting evidence suggests that the rate at which crop yields can be boosted by traditional plant breeding approaches is wavering, and they may reach a “yield ceiling” in the foreseeable future. Further increases in yield will likely depend on the targeted manipulation of plant metabolism. Improving photosynthesis poses one such route, with simulations indicating it could have a significant transformative influence on enhancing crop productivity. Here, we summarize recent advances of alternative approaches for the manipulation and enhancement of photosynthesis and their possible application for crop improvement.

Uncertainty in measurements of the photorespiratory CO2 compensation point and its impact on models of leaf photosynthesis

Rates of carbon dioxide assimilation through photosynthesis are readily modeled using the Farquhar, von Caemmerer, and Berry (FvCB) model based on the biochemistry of the initial Rubisco-catalyzed reaction of net C3 photosynthesis. As models of CO2 assimilation rate are used more broadly for simulating photosynthesis among species and across scales, it is increasingly important that their temperature dependencies are accurately parameterized. A vital component of the FvCB model, the photorespiratory CO2 compensation point (Γ *), combines the biochemistry of Rubisco with the stoichiometry of photorespiratory release of CO2. This report details a comparison of the temperature response of Γ * measured using different techniques in three important model and crop species (Nicotiana tabacum, Triticum aestivum, and Glycine max). We determined that the different Γ * determination methods produce different temperature responses in the same species that are large enough to impact higher-scale leaf models of CO2 assimilation rate. These differences are largest in N. tabacum and could be the result of temperature-dependent increases in the amount of CO2 lost from photorespiration per Rubisco oxygenation reaction.

Rubisco small subunits from the unicellular green alga Chlamydomonas complement Rubisco-deficient mutants of Arabidopsis

Introducing components of algal carbon concentrating mechanisms (CCMs) into higher plant chloroplasts could increase photosynthetic productivity. A key component is the Rubisco-containing pyrenoid that is needed to minimise CO₂ retro-diffusion for CCM operating efficiency. Rubisco in Arabidopsis was re-engineered to incorporate sequence elements that are thought to be essential for recruitment of Rubisco to the pyrenoid, namely the algal Rubisco small subunit (SSU, encoded by rbcS) or only the surface-exposed algal SSU α-helices. Leaves of Arabidopsis rbcs mutants expressing 'pyrenoid-competent' chimeric Arabidopsis SSUs containing the SSU α-helices from Chlamydomonas reinhardtii can form hybrid Rubisco complexes with catalytic properties similar to those of native Rubisco, suggesting that the α-helices are catalytically neutral. The growth and photosynthetic performance of complemented Arabidopsis rbcs mutants producing near wild-type levels of the hybrid Rubisco were similar to those of wild-type controls. Arabidopsis rbcs mutants expressing a Chlamydomonas SSU differed from wild-type plants with respect to Rubisco catalysis, photosynthesis and growth. This confirms a role for the SSU in influencing Rubisco catalytic properties.

Surveying Rubisco Diversity and Temperature Response to Improve Crop Photosynthetic Efficiency

The threat to global food security of stagnating yields and population growth makes increasing crop productivity a critical goal over the coming decades. One key target for improving crop productivity and yields is increasing the efficiency of photosynthesis. Central to photosynthesis is Rubisco, which is a critical but often rate-limiting component. Here, we present full Rubisco catalytic properties measured at three temperatures for 75 plants species representing both crops and undomesticated plants from diverse climates. Some newly characterized Rubiscos were naturally "better" compared to crop enzymes and have the potential to improve crop photosynthetic efficiency. The temperature response of the various catalytic parameters was largely consistent across the diverse range of species, though absolute values showed significant variation in Rubisco catalysis, even between closely related species. An analysis of residue differences among the species characterized identified a number of candidate amino acid substitutions that will aid in advancing engineering of improved Rubisco in crop systems. This study provides new insights on the range of Rubisco catalysis and temperature response present in nature, and provides new information to include in models from leaf to canopy and ecosystem scale.

Rubisco catalytic properties of wild and domesticated relatives provide scope for improving wheat photosynthesis

Rubisco is a major target for improving crop photosynthesis and yield, yet natural diversity in catalytic properties of this enzyme is poorly understood. Rubisco from 25 genotypes of the Triticeae tribe, including wild relatives of bread wheat (Triticum aestivum), were surveyed to identify superior enzymes for improving photosynthesis in this crop. In vitro Rubisco carboxylation velocity (V c), Michaelis-Menten constants for CO2 (K c) and O2 (K o) and specificity factor (S c/o) were measured at 25 and 35 °C. V c and K c correlated positively, while V c and S c/o were inversely related. Rubisco large subunit genes (rbcL) were sequenced, and predicted corresponding amino acid differences analysed in relation to the corresponding catalytic properties. The effect of replacing native wheat Rubisco with counterparts from closely related species was analysed by modelling the response of photosynthesis to varying CO2 concentrations. The model predicted that two Rubisco enzymes would increase photosynthetic performance at 25 °C while only one of these also increased photosynthesis at 35 °C. Thus, under otherwise identical conditions, catalytic variation in the Rubiscos analysed is predicted to improve photosynthetic rates at physiological CO2 concentrations. Naturally occurring Rubiscos with superior properties amongst the Triticeae tribe can be exploited to improve wheat photosynthesis and crop productivity.

Socioeconomic deprivation does not affect prescribing of secondary prevention in patients with peripheral arterial disease

AIM

Aim of the study was to assess the effect of socioeconomic deprivation on prescribing of cardiovascular secondary prevention medications in patients referred with peripheral arterial disease (PAD).

METHODS

A retrospective review of vascular clinic referrals was performed. All patients referred from primary care with suspected PAD over a two month period were included. The deprivation score, prescription of cardiovascular secondary prevention medications, smoking status and the presence of cardiovascular co-morbidities (coronary artery or cerebrovascular disease--CAD/CVD) were assessed. Comparison was made between socioeconomic groups using the Carstairs Deprivation (DepCat) Score and between patients with and without a history of currently existing cardiovascular co-morbidities.

RESULTS

The study included 391 patients. Almost two thirds of patients (253) were from the most deprived socioeconomic groups and were significantly younger at presentation (median age DepCat 7: 63 yrs, DepCat 1-2: 74.5 yrs, P<0.0001). The majority of patients with a prior history of CAD/CVD were prescribed secondary preventative medications at the time of referral with suspected PAD whereas those with no prior history of CAD/CVD, (212 patients, 54%) were significantly less likely to be prescribed antiplatelets (47% vs. 83%), statins (45% vs. 86%) or ACEi/ARBs (29% vs. 68%) (all P<0.05). Secondary prevention prescribing did not differ between socioeconomic groups.

CONCLUSION

Secondary prevention prescribing is inadequate in patients with suspected PAD regardless of socioeconomic group and is significantly lower in those without previously diagnosed CAD/CVD. There remains a lack of appreciation of the high cardiovascular risk associated with PAD.

Occupational injuries in foreign-national workers presenting to St James's Hospital Plastic Surgery service

This study was undertaken to investigate our impression that migrant foreign-national workers were more at risk of sustaining work place injuries requiring referral to our Plastic Surgery service than their indigenous Irish counterparts. Data were collected prospectively from August 2006 to February 2007 on all work-related injuries presenting to the Plastic Surgery service in St James's Hospital, Dublin. 201 work-related injuries were recorded during the six month study period. 40% (n = 81) of the study group were foreign-national workers. Foreign-national workers account for only nine percent of the total Irish workforce. 31% (n = 25) of the study group required a translator. Over half (55%) of all the foreign-national workers in the current study had been in their present job for less than six months at the time of injury compared to only nine percent of Irish workers. This study highlights that foreign-national workers in Ireland are at a disproportionately high risk of occupational injury when compared to their Irish colleagues and emphasises the need for targeted occupational health and safety measures in this vulnerable group.

The Use of Clopidogrel in Carotid Endarterectomy: An Audit of Current Practice

Clopidogrel is commonly encountered in patients presenting for carotid endarterectomy (CEA). Its use around this time is controversial and there is no randomized control trial data to determine best practice. Questionnaires were posted to all members of the Vascular Society investigating clopidogrel use at the time of CEA. 52% discontinue clopidogrel preoperatively, with 51% of those using no alternative and 49% replacing it with aspirin. Clopidogrel use is not related to the number of endarterectomies performed by each surgeon. There is no consensus on clopidogrel use during CEA. This highlights the need for quality prospective data on this subject.

Neutralising IL-12 activity as a strategy for prolonging allograft survival and preventing graft-versus-host disease

Interleukin-12 (IL-12) is a key immunoregulatory cytokine which promotes the development of Thl-dependent, cell-mediated immune responses. Acute allograft rejection after organ transplantation and acute graft-versus-host disease (GVHD) after bone-marrow transplantation are generally attributed to cell-mediated immune mechanisms and, therefore, potentially susceptible to immunological intervention at the level of IL-12. Recent data from murine models of transplantation have highlighted the potential of IL-12 as a selective target for immunotherapy. Neutralising endogenous IL-12 for a brief period at the time of transplant promotes long-term deviation from a Th1 to a polarised Th2 alloimmune response. This confers lasting protection from GVHD but is less effective at preventing acute rejection, possibly because Th2-dependent immune responses are also capable of effecting graft rejection.

Skin allograft rejection in mice lacking inducible nitric oxide synthase

BACKGROUND

During allograft rejection, up-regulation of cytokine-inducible nitric oxide synthase (iNOS) leads to the production of large amounts of nitric oxide (NO). The net effect of NO on the alloimmune response is, however, difficult to predict because of its diverse biological effects, which include potentially opposing roles as an effector and immunoregulatory molecule.

METHODS

In this study, the role of iNOS on the in vitro and in vivo alloimmune response was defined using mutant mice that lack a functional iNOS gene. The ability of spleen cells obtained from iNOS-deficient mutants to proliferate and to produce cytokines in response to irradiated BALB/c stimulator cells was determined, and the rate at which iNOS-deficient mice were able to reject BALB/c skin allografts was observed.

RESULTS

Spleen cells from homozygous iNOS-deficient (129xMF1)F1 mice, when compared with cells from heterozygous control mice, showed an increased in vitro proliferative response and produced substantially higher levels of interferon-gamma, and also more interleukin-2 and interleukin-12, in response to allogeneic stimulation. The kinetics of BALB/c skin graft rejection were comparable in heterozygous control animals and iNOS-deficient mice. Moreover, no net effect of iNOS on skin allograft rejection was apparent in mice treated with depleting monoclonal antibodies (mAb) to CD4 or CD8 T cells, either alone or in combination, or in mice treated with both anti-CD8 mAb and a neutralizing anti-tumor necrosis factor mAb.

CONCLUSIONS

These results show that iNOS has an immunomodulatory effect on the in vitro alloimmune response but lack of iNOS has no net influence on the kinetics of murine skin allograft rejection in either unmodified recipients or recipients in which the early contribution of T-cell subsets and tumor necrosis factor-alpha to graft rejection has been abrogated.

Craniofrontonasal dysplasia

A series of 10 patients with craniofrontonasal dysplasia presenting to the Oxford Craniofacial Unit since 1983 is presented. In addition to the well-described combination of coronal synostosis and frontonasal dysplasia, 9 patients had very characteristic dry, curly or frizzy hair. All the patients were female. Recognition of the syndrome is important for genetic counselling, although the precise mode of genetic transmission is unclear with females predominating and males being less severely affected. Surgical correction was in two stages: early frontal advancement followed by correction of hypertelorism when the child became aware of the deformity. Four patients had their craniosynostosis treated in the Oxford Craniofacial Unit. Three patients had previously had frontal remodelling elsewhere. Nine patients had surgery for hypertelorism. The preferred technique for hypertelorism correction was facial bipartition. Following hypertelorism correction, the excess skin was allowed to redrape and subsequently dealt with by medial canthoplasties, thus avoiding a midline scar. Careful attention to the primary frontal advancement procedure is important to avoid complications following difficult dissection of the frontal bone flap at the time of hypertelorism correction.

Follicular carcinoma of thyroid presenting as back pain leading to a delay in diagnosis

The case is described of a 53-year-old man presenting with right-sided low back and thigh pain. Non-urgent investigations showed a metastatic lesion in his right hemipelvis arising from a thyroid primary.

Home traction in the management of femoral fractures in children

Fracture of the femur in children is a common problem which can be managed in a variety of ways. We treated such fractures in children up to the age of 13 by immobilization in a Thomas splint, after reduction, if necessary, and traction in hospital. After a short period, traction was continued at home using a mobile frame with the Thomas splint. The results of such home traction were assessed in terms of both healing of the fracture and any complications and of the parental attitudes to treatment at home. It was found that traction at home was an acceptable method for the management of such fractures. Results were comparable to other methods of treatment and parental satisfaction was very high, providing there was adequate surveillance by the district nurse and immediate access to advice. The cost-savings of such a treatment are significant.

Management of malignant melanoma of the head and neck

A total of 91 patients with melanoma of the head and neck treated between 1973 and 1991 were studied prospectively with regard to prognostic features, treatment and outcome. Other than Breslow thickness, the only important prognostic feature was the less aggressive nature of lentigo maligna melanoma. A policy of selective excision margins, 1 cm for impalpable and 2 cm for palpable lesions, was found to be safe, although preliminary biopsy should be used if there is diagnostic uncertainty or where the expected extent of surgery entails a mutilating procedure. Local recurrence rates were not affected by the method of wound closure, which should be determined by the best functional and cosmetic outcome. These results support the trend against prophylactic neck dissection. Such dissection, when indicated for lesions of the face, pinna, anterior scalp and parotid area, should routinely include superficial parotidectomy. Uncontrolled symptomatic loco-regional recurrence is an uncommon complication that may occur despite radical primary surgery. The role of preoperative radiotherapy for high-risk melanoma in this situation warrants investigation.

Safe margins in the excision of primary cutaneous melanoma

A group of 434 patients treated for primary cutaneous melanoma over an 18-year period by a policy of selective excision margins based on clinical estimation of tumour thickness was studied prospectively. Clinical assessments of tumour as impalpable, palpable but not overtly nodular, and nodular correspond to thicknesses of < or = 0.75, 0.76-1.49 and > or = 1.50 mm respectively. From 1971 to 1987, 330 patients were treated with excision margins of 1, 2 and 3-5 cm based on these respective ranges. During 1988 and 1989, 104 patients were treated after reduction of the maximum width of excision to 2 cm. The overall local recurrence rate was 11 of 434 patients (2.5 per cent), with no recurrence in melanoma < or = 0.75 mm thick and no increase in the local recurrence rate after reduction of the maximum margin from 3 to 2 cm. A policy of 2-cm clearance for palpable and nodular melanoma and 1 cm for impalpable lesions is recommended. Any further reduction must be tested prospectively.

Fibroblast stimulation of breast cancer cell growth in a serum-free system

Conditioned media from 14 short term fibroblast cell lines were mitogenic for human breast cancer cells with different steroid receptor profiles in serum-free culture. Fibroblast-conditioned medium stimulated tritiated thymidine incorporation in short term culture and growth in a longer proliferation study as measured by the MTT colorimetric assay. Conditioned media from benign and malignant epithelial cells were non-stimulatory for breast cancer cells but that derived from endothelial cells showed similar stimulation to fibroblasts. Partial purification of fibroblast-conditioned medium identified a peptide with a molecular weight of approximately 8 kDa that showed no affinity for heparin and was mitogenic for MCF-7 breast cancer cells.

The response of primary cultured adult mouse sensory neurons to ethanol, propanol, acetaldehyde and acrolein treatments

Primary cultures of adult mouse sensory neurons maintained for 8 days in vitro (8 div), in both the presence of non-neuronal cell (NNC) outgrowth and in NNC-reduced cultures, were exposed to doses of ethanol, propanol, acetaldehyde and acrolein. The effects on cell viability were monitored: LD50's of 600 microM acrolein and 100 mM propanol were obtained after 24 h exposures and after 48 h with 1 mM acetaldehyde and 500 mM ethanol. Morphological effects were evident by scanning electron microscopy with sub-acute doses for each agent, using both lower concentrations and shorter exposures. Membrane pitting of the perikaryon and a reduction in the proportion of neurons bearing neurites were common signs of toxic insult. The neurites of treated cells were thicker and more irregular than those of untreated cells; this proved a good indicator of specific neurotoxicity rather than merely a cytotoxic response. Fetal calf serum in the medium lessened the response of neurons to ethanol treatments. Comparison with other in vitro studies suggests these primary cultures are a more sensitive system than established cell lines of neuronal origin for use in neurotoxicity testing.

Neuronal maintenance and neurite extension of adult mouse neurones in non-neuronal cell-reduced cultures is dependent on substratum coating

Adult mouse DRG neurones have been maintained for 14 days in cultures where non-neuronal cell proliferation was inhibited by the inclusion of 5 × 10(−6) microM-cytosine arabinoside (AraC) in the medium from the onset of culture. On uncoated plastic neurone numbers significantly declined in the absence of non-neuronal cell outgrowth compared with uninhibited co-cultures. However, when neurones were maintained in the presence of AraC on certain coated surfaces this decrease in neurone numbers was not observed. Combinations of fibronectin (FN) and laminin (LAM) proved most effective for 7 and 14 days in vitro, although either was beneficial if used separately. Microexudates produced by the fibroblast line, 3T6, also significantly improved neuronal counts for 14 days in vitro. However, a microexudate derived from primary cultures of mouse hepatocytes, although advantageous for 7 days in vitro, was not effective in maintaining neurones over the 14-day culture period, reminiscent of previous observations when synthetic cationic agents were used. Electrophoretic analysis of the fibroblast exudate indicated that fibronectin was present in the substrate-attached material generated by this cell line. The reduction in non-neuronal cell growth facilitated the monitoring of neuronal structural detail by scanning electron microscopy. Examination of neurite extension, indicative of neurone differentiation, was particularly improved. FN/LAM and the fibroblast-derived exudate increased nerve fibre growth, whilst the hepatocyte exudate had little effect on neurite regeneration, and polylysine had a detrimental effect. The data demonstrate that substrata can have a significant effect on maintenance and differentiation of adult neurones in primary culture.(ABSTRACT TRUNCATED AT 250 WORDS)

The survival of adult mouse sensory neurons in vitro is enhanced by natural and synthetic substrata, particularly fibronectin

Primary cultures derived from adult mouse dorsal root ganglia have been maintained in the presence or absence of 5 X 10(-6)M cytosine arabinoside for periods of up to 4 weeks. In cultures in which cytosine arabinoside is present, the non-neuronal cell population is effectively reduced. When uncoated plastic substrata are used there is also a concurrent decrease in the number of neurons if the medium is supplemented with cytosine arabinoside. The effects on neuron survival of substrata coated with fibronectin, polyornithine, polylysine, and exudates prepared from mouse liver cells were studied. It was shown that neuronal densities similar to those with uninhibited media may be retained in the presence of cytosine arabinoside if fibronectin-coated substrata are prepared. With the other coating agents neuronal survival was also enhanced but to a lesser extent. The study offers a means therefore of producing purer cultures of dorsal root ganglia neurons than has previously been possible from adult mammalian sources.

Isolation and identification of products from alkylation of nucleic acids: ethyl- and isopropyl-purines

Ethylation and isopropylation of guanine in alkaline solution, or of adenine in formic acid, by alkyl methanesulphonates gave the following products: 1-, N2-, 3-, O6-, 7- and 9-alkylguanines; 1-, 3-, 7- and 9-alkyladenines. The products were identified from their characteristic u.v-absorption spectra, by comparison with either known ethyladenines or with the corresponding known methyladenines, and were also characterized by mass spectrometry. Their chromatographic properties on paper, t.l.c. and various columns were determined. DNA was alkylated in neutral solution with 14C-labelled alkyl methanesulphonates and the ratios of the alkylpurines formed were obtained, and compared for alkylation by methyl, ethyl and isopropyl methanesulphonates and by N-methyl-N-nitrosourea. The extents of alkylation at O-6 of guanine relative to those at N-7 of guanine varied with the reactivity of the methylating agents according to the predictions of Swain & Scott (1953) relating nucleophilicity of the groups alkylated with the substrate constants of the alkylating agents. The relative extents of alkylation at N-3 of adenine did not follow this correlation.

Reaction products from N-methyl-N-nitrosourea and deoxyribonucleic acid containing thymidine residues. Synthesis and identification of a new methylation product, O4-methylthymidine

1. DNA was treated with N-methyl-N-nitrosourea at pH7-8, 37 degrees C, degraded to yield 3- and 7-methylpurines and deoxyribonucleosides and the reaction products were separated by chromatography on ion-exchange resins. The following methods for identification and determination of products were used: with unlabelled N-methyl-N-nitrosourea, u.v. absorption; use of methyl-(14)C-labelled N-methyl-N-nitrosourea and use of [(14)C]thymine-labelled DNA. 2. The synthesis of O(4)-methylthymidine and its identification by u.v. and mass spectroscopy are reported. 3. 3-Methylthymidine and O(4)-methylthymidine were found as methylation products from N-methyl-N-nitrosourea with thymidine and with DNA, in relatively small yields. Unidentified products containing thymine were found in enzymic digests of N-methyl-N-nitrosourea-treated DNA, which may be phosphotriesters. 4. The possible role of formation of methylthymines in mutagenesis by N-methyl-N-nitrosourea is discussed.