Principles of resilient coding for plant ecophysiologists

Plant ecophysiology is founded on a rich body of physical and chemical theory, but it is challenging to connect theory with data in unambiguous, analytically rigorous and reproducible ways. Custom scripts written in computer programming languages (coding) enable plant ecophysiologists to model plant processes and fit models to data reproducibly using advanced statistical techniques. Since many ecophysiologists lack formal programming education, we have yet to adopt a unified set of coding principles and standards that could make coding easier to learn, use and modify. We identify eight principles to help in plant ecophysiologists without much programming experience to write resilient code: (i) standardized nomenclature, (ii) consistency in style, (iii) increased modularity/extensibility for easier editing and understanding, (iv) code scalability for application to large data sets, (v) documented contingencies for code maintenance, (vi) documentation to facilitate user understanding; (vii) extensive tutorials and (viii) unit testing and benchmarking. We illustrate these principles using a new R package, {photosynthesis}, which provides a set of analytical and simulation tools for plant ecophysiology. Our goal with these principles is to advance scientific discovery in plant ecophysiology by making it easier to use code for simulation and data analysis, reproduce results and rapidly incorporate new biological understanding and analytical tools.

Is desiccation tolerance and avoidance reflected in xylem and phloem anatomy of two coexisting arid-zone coniferous trees?

Plants close their stomata during drought to avoid excessive water loss, but species differ in respect to the drought severity at which stomata close. The stomatal closure point is related to xylem anatomy and vulnerability to embolism, but it also has implications for phloem transport and possibly phloem anatomy to allow sugar transport at low water potentials. Desiccation-tolerant plants that close their stomata at severe drought should have smaller xylem conduits and/or fewer and smaller interconduit pits to reduce vulnerability to embolism but more phloem tissue and larger phloem conduits compared with plants that avoid desiccation. These anatomical differences could be expected to increase in response to long-term reduction in precipitation. To test these hypotheses, we used tridimensional synchroton X-ray microtomograph and light microscope imaging of combined xylem and phloem tissues of 2 coniferous species: one-seed juniper (Juniperus monosperma) and piñon pine (Pinus edulis) subjected to precipitation manipulation treatments. These species show different xylem vulnerability to embolism, contrasting desiccation tolerance, and stomatal closure points. Our results support the hypothesis that desiccation tolerant plants require higher phloem transport capacity than desiccation avoiding plants, but this can be gained through various anatomical adaptations in addition to changing conduit or tissue size.

Impacts of long-term precipitation manipulation on hydraulic architecture and xylem anatomy of piñon and juniper in Southwest USA

Hydraulic architecture imposes a fundamental control on water transport, underpinning plant productivity, and survival. The extent to which hydraulic architecture of mature trees acclimates to chronic drought is poorly understood, limiting accuracy in predictions of forest responses to future droughts. We measured seasonal shoot hydraulic performance for multiple years to assess xylem acclimation in mature piñon (Pinus edulis) and juniper (Juniperus monosperma) after 3+ years of precipitation manipulation. Our treatments consisted of water addition (+20% ambient precipitation), partial precipitation-exclusion (-45% ambient precipitation), and exclusion-structure control. Supplemental watering elevated leaf water potential, sapwood-area specific hydraulic conductivity, and leaf-area specific hydraulic conductivity relative to precipitation exclusion. Shifts in allocation of leaf area to sapwood area enhanced differences between irrigated and droughted K_L in piñon but not juniper. Piñon and juniper achieved similar K_L under ambient conditions, but juniper matched or outperformed piñon in all physiological measurements under both increased and decreased precipitation treatments. Embolism vulnerability and xylem anatomy were unaffected by treatments in either species. Absence of significant acclimation combined with inferior performance for both hydraulic transport and safety suggests piñon has greater risk of local extirpation if aridity increases as predicted in the southwestern USA.

Tree water dynamics in a drying and warming world

Disentangling the relative impacts of precipitation reduction and vapour pressure deficit (VPD) on plant water dynamics and determining whether acclimation may influence these patterns in the future is an important challenge. Here, we report sap flux density (F_D ), stomatal conductance (G_s ), hydraulic conductivity (K_L ) and xylem anatomy in piñon pine (Pinus edulis) and juniper (Juniperus monosperma) trees subjected to five years of precipitation reduction, atmospheric warming (elevated VPD) and their combined effects. No acclimation occurred under precipitation reduction: lower G_s and F_D were found for both species compared to ambient conditions. Warming reduced the sensibility of stomata to VPD for both species but resulted in the maintenance of G_s and F_D to ambient levels only for piñon. For juniper, reduced soil moisture under warming negated benefits of stomatal adjustments and resulted in reduced F_D , G_s and K_L . Although reduced stomatal sensitivity to VPD also occurred under combined stresses, reductions in G_s , F_D and K_L took place to similar levels as under single stresses for both species. Our results show that stomatal conductance adjustments to high VPD could minimize but not entirely prevent additive effects of warming and drying on water use and carbon acquisition of trees in semi-arid regions.

Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation

Relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.

Social living mitigates the costs of a chronic illness in a cooperative carnivore

Infection risk is assumed to increase with social group size, and thus be a cost of group living. We assess infection risk and costs with respect to group size using data from an epidemic of sarcoptic mange (Sarcoptes scabiei) among grey wolves (Canis lupus). We demonstrate that group size does not predict infection risk and that individual costs of infection, in terms of reduced survival, can be entirely offset by having sufficient numbers of pack-mates. Infected individuals experience increased mortality hazards with increasing proportions of infected pack-mates, but healthy individuals remain unaffected. The social support of group hunting and territory defence are two possible mechanisms mediating infection costs. This is likely a common phenomenon among other social species and chronic infections, but difficult to detect in systems where infection status cannot be measured continuously over time.

Prolonged experimental drought reduces plant hydraulic conductance and transpiration and increases mortality in a piñon-juniper woodland

Plant hydraulic conductance (k_s) is a critical control on whole-plant water use and carbon uptake and, during drought, influences whether plants survive or die. To assess long-term physiological and hydraulic responses of mature trees to water availability, we manipulated ecosystem-scale water availability from 2007 to 2013 in a piñon pine (Pinus edulis) and juniper (Juniperus monosperma) woodland. We examined the relationship between k_s and subsequent mortality using more than 5 years of physiological observations, and the subsequent impact of reduced hydraulic function and mortality on total woody canopy transpiration (E_C) and conductance (G_C). For both species, we observed significant reductions in plant transpiration (E) and k_s under experimentally imposed drought. Conversely, supplemental water additions increased E and k_s in both species. Interestingly, both species exhibited similar declines in k_s under the imposed drought conditions, despite their differing stomatal responses and mortality patterns during drought. Reduced whole-plant k_s also reduced carbon assimilation in both species, as leaf-level stomatal conductance (g_s) and net photosynthesis (A_n) declined strongly with decreasing k_s. Finally, we observed that chronically low whole-plant k_s was associated with greater canopy dieback and mortality for both piñon and juniper and that subsequent reductions in woody canopy biomass due to mortality had a significant impact on both daily and annual canopy E_C and G_C. Our data indicate that significant reductions in k_s precede drought-related tree mortality events in this system, and the consequence is a significant reduction in canopy gas exchange and carbon fixation. Our results suggest that reductions in productivity and woody plant cover in piñon–juniper woodlands can be expected due to reduced plant hydraulic conductance and increased mortality of both piñon pine and juniper under anticipated future conditions of more frequent and persistent regional drought in the southwestern United States.

Regulation and acclimation of leaf gas exchange in a piñon-juniper woodland exposed to three different precipitation regimes

Leaf gas-exchange regulation plays a central role in the ability of trees to survive drought, but forecasting the future response of gas exchange to prolonged drought is hampered by our lack of knowledge regarding potential acclimation. To investigate whether leaf gas-exchange rates and sensitivity to drought acclimate to precipitation regimes, we measured the seasonal variations of leaf gas exchange in a mature piñon-juniper Pinus edulis-Juniperus monosperma woodland after 3 years of precipitation manipulation. We compared trees receiving ambient precipitation with those in an irrigated treatment (+30% of ambient precipitation) and a partial rainfall exclusion (-45%). Treatments significantly affected leaf water potential, stomatal conductance and photosynthesis for both isohydric piñon and anisohydric juniper. Leaf gas exchange acclimated to the precipitation regimes in both species. Maximum gas-exchange rates under well-watered conditions, leaf-specific hydraulic conductance and leaf water potential at zero photosynthetic assimilation all decreased with decreasing precipitation. Despite their distinct drought resistance and stomatal regulation strategies, both species experienced hydraulic limitation on leaf gas exchange when precipitation decreased, leading to an intraspecific trade-off between maximum photosynthetic assimilation and resistance of photosynthesis to drought. This response will be most detrimental to the carbon balance of piñon under predicted increases in aridity in the southwestern USA.

Increased susceptibility to drought-induced mortality in Sequoia sempervirens (Cupressaceae) trees under Cenozoic atmospheric carbon dioxide starvation

PREMISE OF THE STUDY

Climate-induced forest retreat has profound ecological and biogeochemical impacts, but the physiological mechanisms underlying past tree mortality are poorly understood, limiting prediction of vegetation shifts with climate variation. Climate, drought, fire, and grazing represent agents of tree mortality during the late Cenozoic, but the interaction between drought and declining atmospheric carbon dioxide ([CO2]a) from high to near-starvation levels ∼34 million years (Ma) ago has been overlooked. Here, this interaction frames our investigation of sapling mortality through the interdependence of hydraulic function, carbon limitation, and defense metabolism. •

METHODS

We recreated a changing Cenozoic [CO2]a regime by growing Sequoia sempervirens trees within climate-controlled growth chambers at 1500, 500, or 200 ppm [CO2]a, capturing the decline toward minimum concentrations from 34 Ma. After 7 months, we imposed drought conditions and measured key physiological components linking carbon utilization, hydraulics, and defense metabolism as hypothesized interdependent mechanisms of tree mortality. •

KEY RESULTS

Catastrophic failure of hydraulic conductivity, carbohydrate starvation, and tree death occurred at 200 ppm, but not 500 or 1500 ppm [CO2]a. Furthermore, declining [CO2]a reduced investment in carbon-rich foliar defense compounds that would diminish resistance to biotic attack, likely exacerbating mortality. •

CONCLUSIONS

Low-[CO2]a-driven tree mortality under drought is consistent with Pleistocene pollen records charting repeated Californian Sequoia forest contraction during glacial periods (180-200 ppm [CO2]a) and may even have contributed to forest retreat as grasslands expanded on multiple continents under low [CO2]a over the past 10 Ma. In this way, geologic intervals of low [CO2]a coupled with drought could impose a demographic bottleneck in tree recruitment, driving vegetation shifts through forest mortality.

Early vessel evolution and the diverisification of wood function: Insights from Malagasy Canellales

Xylem vessels have long been proposed as a key innovation for the ecological diversification of angiosperms by providing a breakthrough in hydraulic efficiency to support high rates of photosynthesis and growth. However, recent studies demonstrated that angiosperm woods with structurally "primitive" vessels did not have greater whole stem hydraulic capacities as compared to vesselless angiosperms. As an alternative to the hydraulic superiority hypothesis, the heteroxylly hypothesis proposes that subtle hydraulic efficiencies of primitive vessels over tracheids enabled new directions of functional specialization in the wood. However, the functional properties of early heteroxyllous wood remain unknown. We selected the two species of Canellales from Madagascar to test the heteroxylly hypothesis because Canellaceae (represented by Cinnamosma madagascariensis) produces wood with vessels of an ancestral form, while Winteraceae, the sister clade (represented by Takhtajania perrieri) is vesselless. We found that heteroxylly correlated with increased wood functional diversity related predominantly to biomechanical specialization. However, vessels were not associated with greater stem hydraulic efficiency or increased shoot hydraulic capacity. Our results support the heteroxylly hypothesis and highlight the importance integrating a broader ecological context to understand the evolution of vessels.

Bacteriophage library construction and selection of recombinant antibodies

This unit describes the use of E. coli and bacteriophages to display a diverse library of antibody fragments equivalent in complexity to the mammalian immune repertoire, and subsequent screening of the library for antibody fragments with specific binding affinities. The methods are also used for affinity enhancement (maturation), through the display and selection of improved affinity mutants derived from a single parent antibody. This unit discusses the following key components needed in library construction technology: a repertoire of antibody genes, typically amplified by polymerase chain reaction (PCR) technology; construction of scFv genes by PCR assembly; a method for producing a stable library, using bacteriophage that can both display individual antibodies on the viral surface and carry the gene encoding the antibody; a method of growing phage for selection; a method of selecting the highest-affinity antibody from the phage library; a method for monitoring progress of phage selection; an affinity-enhancement strategy for improving and manipulating the selected antibody; and expression of affinity-enhanced antibodies.

Parasite co-infection and interaction as drivers of host heterogeneity

We examined the hypothesis that the interaction between concomitant infecting parasites modifies host susceptibility, parasite intensity and the pattern of parasite distribution within the host population. We used a 26 year time series of three common parasites in a natural population of rabbits: two gastrointestinal nematodes (Trichostrongylus retortaeformis and Graphidium strigosum) and the immunosuppressive myxoma virus. The frequency distribution of nematodes in the host population and the relationship between host age and nematode intensity were explored in rabbits with either single or dual nematode infections and rabbits infected with the nematodes and myxoma virus. The aggregation of T. retortaeformis and G. strigosum among the rabbits varied with the nature of the co-infection both in male and female hosts. The two nematodes exhibited different age-intensity profiles: G. strigosum intensity increased exponentially with host age while T. retortaeformis intensity exhibited a convex shape. The presence of a secondary infection did not change the age-intensity profile for G. strigosum but for T. retortaeformis co-infection (either both nematodes or myxoma-nematodes) resulted in significantly greater intensities in adult hosts. Results suggest that multi-species infections contributed to aggregation of parasites in the host population and to seasonal variation in intensity, but also enhanced differences in parasitism between sexes. This effect was apparent for T. retortaeformis, which appears to elicit a strong acquired immune response but not for G. strigosum which does not produce any evident immune reaction. We concluded that concomitant infections mediated by host immunity are important in modifying host susceptibility and influencing heterogeneity amongst individual hosts.

Climate disruption and parasite-host dynamics: patterns and processes associated with warming and the frequency of extreme climatic events

Levels of parasitism and the dynamics of helminth systems is subject to the impact of environmental conditions such that we may expect long term increases in temperature will increase the force of infection and the parasite's basic reproduction number, R0. We postulate that an increase in the force of infection will only lead to an increase in mean intensity of adults when adult parasite mortality is not determined by acquired immunity. Preliminary examination of long term trends of parasites of rabbits and grouse confirm these predictions. Parasite development rate increases with temperature and while laboratory studies indicate this is linear some recent studies indicate that this may be non-linear and would have an important impact on R0. Warming would also reduce the selective pressure for the development of arrestment and this would increase R0 so that in systems like the grouse and Trichostrongylus tenuis this would increase the instability and lead to larger disease outbreaks. Extreme climatic events that act across populations appear important in synchronizing transmission and disease outbreaks, so it is speculated that climate disruption will lead to increased frequency and intensity of disease outbreaks in parasite populations not regulated by acquired immunity.

Faecal egg counts provide a reliable measure of Trichostrongylus tenuis intensities in free-living red grouse Lagopus lagopus scoticus

The reliability of different egg counting methods for estimating the intensity of Trichostrongylus tenuis infections in red grouse, Lagopus lagopus scoticus, was investigated in the autumn, when grouse may harbour high parasite intensities. Possible limitations to the use of these methods were also examined. Faecal egg counts were found to accurately estimate T. tenuis worm intensities, at least up to an observed maximum of c. 8000 worms. Two egg counting methods (smear and McMaster) gave consistent results, although the exact relationship with worm intensity differed according to the method used. Faecal egg counts significantly decreased with increasing length of sample storage time, but egg counts were reliable for estimating worm intensity for three weeks. The concentration of eggs in the caecum was also found to reliably estimate worm intensity. However, egg counts from frozen gut samples cannot be used to estimate worm intensities. These results conclude that, despite some limitations, faecal and caecum egg counts provide useful and reliable ways of measuring T. tenuis intensities in red grouse.

The role of sex in parasite dynamics: model simulations on transmission of Heligmosomoides polygyrus in populations of yellow-necked mice, Apodemus flavicollis

We investigated possible mechanisms that could cause sex-biased parasite transmission of the helminth Heligmosomoides polygyrus in its rodent host, Apodemus flavicollis, using a modelling approach. Two, not mutually exclusive, hypotheses were examined: that sex-biased parasite transmission is caused by differences in immunity that influence the success of free-living stages and/or is caused by sex differences in host behaviour and the dissemination of infective stages. Model simulations were compared with results from a field manipulation experiment of H. polygyrus in replicated populations of A. flavicollis. Simulations predicted the experimental field results, and both hypotheses explained the pattern observed. Transmission is male-biased if a male immune response increases fertility, hatching or survival of free-living stages. Alternatively, transmission is male-biased if their behavioural characteristics allow them to spread infective larvae in areas more frequently used by females. These results highlight that host sex is not only responsible for differences in parasite susceptibility, but may profoundly influence host-parasite interactions, resulting in a sex bias in parasite transmission.

Protein microarrays in clinical microbiology

Clinical microbiology laboratories have, in the past, broadly adopted new molecular biology techniques and automation. In the near future, the adoption of protein microarray technology has the potential to revolutionise the field in a manner similar to that of polymerase chain reaction (PCR). With the advantages of far greater sensitivity, parallel experimentation, reduced sample consumption and cost-per-test, the development of protein microarrays has come about through the realisation that mRNA levels do not necessarily correlate with protein expression.

Hantavirus and arenavirus antibody prevalence in rodents and humans in Trentino, Northern Italy

The spatial and temporal distribution of hantavirus and arenavirus antibody-positive wild rodents in Trentino, Italy, was studied using immunofluorescence assays (IFA) in two long-term sites trapped in 2000-2003, and six other sites trapped in 2002. The overall hantavirus seroprevalence in the bank voles, Clethrionomys glareolus (n=229) screened for Puumala virus (PUUV) antibodies was 0.4%, and that for Apodemus flavicollis mice (n=1416) screened for Dobrava virus (DOBV) antibodies was 0.2%. Antibodies against lymphocytic choriomeningitis virus (LCMV) were found in 82 (5.6%) of the 1472 tested rodents; the seroprevalence being 6.1% in A. flavicollis (n=1181), 3.3% in C. glareolus (n=276), and 14.3% in Microtus arvalis (n=7). Of the serum samples of 488 forestry workers studied by IFA, 12 were LCMV-IgG positive (2.5%) and one DOBV-IgG positive (0.2%), however, the latter could not be confirmed DOBV-specific with a neutralization assay. Our results show a widespread distribution but low prevalence of DOBV in Trentino, and demonstrate that the arenavirus antibodies are a common finding in several other rodent species besides the house mouse.

The effect of single and concomitant pathogen infections on condition and fecundity of the wild rabbit (Oryctolagus cuniculus)

We assessed the effect of two pathogens (myxoma virus and Eimeria stiedae) and five macroparasites (gastrointestinal helminth species) of the wild rabbit (Oryctolagus cuniculus) upon total host body mass and abdominal fat level. Additionally, we assessed the effects of these organisms on the number of foetuses in adult females during the peak breeding period. Both mass of abdominal fat and total body mass of the rabbit were negatively associated with myxoma virus infection and increasing helminth species richness. Total body mass was also negatively associated with the protozoan parasite E. steidae. No relationship was found between any of the parasites/pathogens and the number of foetuses in adult females, although only relatively small sample sizes were available for this section of the analysis. Increasing host body mass was positively associated with number of foetuses and we propose that mass reduction caused by the pathogen and parasite species could also have the consequence of reducing foetal number.

Peak shift and epidemiology in a seasonal host-nematode system

Insight into the dynamics of parasite-host relationships of higher vertebrates requires an understanding of two important features: the nature of transmission and the development of acquired immunity in the host. A dominant hypothesis proposes that acquired immunity develops with the cumulative exposure to infection, and consequently predicts a negative relationship between peak intensity of infection and host age at this peak. Although previous studies have found evidence to support this hypothesis through between-population comparisons, these results are confounded by spatial effects. In this study, we examined the dynamics of infection of the nematode Trichostrongylus retortaeformis within a natural population of rabbits sampled monthly for 26 years. The rabbit age structure was reconstructed using body mass as a proxy for age, and the host age-parasite intensity relationship was examined for each rabbit cohort born from February to August. The age-intensity curves exhibited a typical concave shape, and a significant negative relationship was found between peak intensity of infection and host age at this peak. Adult females showed a distinct periparturient rise in T. retortaeformis infection, with higher intensities in breeding adult females than adult males and non-breeding females. These findings are consistent with the hypothesis of an acquired immune response of the host to a parasite infection, supporting the principle that acquired immunity can be modelled using the cumulative exposure to infection. These findings also show that seasonality can be an important driver of host-parasite interactions.

Population biology of Trichostrongylus tenuis, a parasite of economic importance for red grouse management

The caecal nematode, Trichostrongylus tenuis, is associated with dramatic decreases in the density of red grouse (Lagopus lagopus scoticus) resulting in a significant loss of sporting income to many upland estates in the UK. In this article Peter Hudson and Andrew Dobson describe the dynamics of the grouse-T. tenuis system, show that the parasites can cause population crashes and present preliminary findings from the development of new control methods.

Aggregation of Argulus coregoni (Crustacea: Branchiura) on rainbow trout (Oncorhynchus mykiss): a consequence of host susceptibility or exposure?

By sampling individual rainbow trout, Oncorhynchus mykiss, at a fish farm we showed that Argulus coregoni were aggregated within their host population. The relative significance of susceptibility and exposure generating the observed pattern was tested using experimental infections. We examined, whether rainbow trout developed protective resistance mechanisms against the louse following a challenge infection and if there was variation between individual trout in their susceptibility to A. coregoni metanauplii. Fish were exposed to 20 A. coregoni for 5, 25, 50, 85 or 120 min and the numbers attaching recorded. Three weeks later, developing argulids were removed and the experiment repeated with a standardized exposure of 20 metanauplii. Prior exposure of fish with A. coregoni did not reduce the total infection intensity compared to naïve fish, but fish gained infection more rapidly. We suggest that there is no protective acquired resistance of pre-exposed rainbow trout to subsequent Argulus exposure. The possibility that an immunosuppressive mechanism by argulids was acting enabling the higher attachment rate could be refuted since control individuals, not previously exposed to lice, gained the infection at a similar rate as the fish challenged twice. Our results do not indicate clear differences in susceptibility among individual fish but the transmission of metanauplii on fish seemed to be opportunistic and non-selective. Our results support the view that variation in exposure time, rather than differences in susceptibility of individual hosts, might be the key factor in generating the aggregated distribution of Argulus on their hosts.

Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor

The Ig new antigen receptors (IgNARs) are single-domain antibodies found in the serum of sharks. Here, we report 2.2- and 2.8-A structures of the type 2 IgNAR variable domains 12Y-1 and 12Y-2. Structural features include, first, an Ig superfamily topology transitional between cell adhesion molecules, antibodies, and T cell receptors; and, second, a vestigial complementarity-determining region 2 at the "bottom" of the molecule, apparently discontinuous from the antigen-binding paratope and similar to that observed in cell adhesion molecules. Thus, we suggest that IgNARs originated as cell-surface adhesion molecules coopted to the immune repertoire and represent an evolutionary lineage independent of variable heavy chain/variable light chain type antibodies. Additionally, both 12Y-1 and 12Y-2 form unique crystallographic dimers, predominantly mediated by main-chain framework interactions, which represent a possible model for primordial cell-based interactions. Unusually, the 12Y-2 complementarity-determining region 3 also adopts an extended beta-hairpin structure, suggesting a distinct selective advantage in accessing cryptic antigenic epitopes.

Epidemiology of rabbit haemorrhagic disease virus in the United Kingdom: evidence for seasonal transmission by both virulent and avirulent modes of infection

Rabbit haemorrhagic disease virus (RHDV) has killed many millions of wild rabbits in Europe and Australia, but has had little impact in the United Kingdom, despite outbreaks having occurred since 1994. High seroprevalence detected in the absence of associated mortality had suggested the presence of an endemic non-pathogenic strain which may be 'protecting' UK populations. Following the first detailed field study of RHDV epidemiology in the United Kingdom, using mark-recapture with serum sampling, we report that RHDV caused highly prevalent persistent infection in seropositive rabbits in the absence of associated mortality. Furthermore the virus strains responsible could not be distinguished phylogenetically from known pathogenic isolates, and were clearly very different from the only previously identified non-pathogenic strain of RHDV. These findings suggest that many--perhaps most--strains of RHDV may be propagated through both 'pathogenic' and 'non-pathogenic' modes of behaviour. Transmission occurred predominantly during and just after the breeding season.

Patterns of cercarial production fromDiplostomum spathaceum: terminal investment or bet hedging?

In the production of the infective cercariae of trematodes, the terminal investment hypothesis of life-history theory predicts that the rate of host exploitation and cercarial production should increase during the period of cercarial shedding since the reproductive value of the parasite decreases during this period. In contrast, a bet hedging hypothesis that focuses on the success of transmission when host contact rate is variable predicts that cercarial production should decrease in an attempt to keep the host alive for longer and thus would increase the probability of successful transmission. We examined these two hypotheses under laboratory conditions and recorded the production ofDiplostomum spathaceumcercariae from naturally infected snail hosts,Lymnaea stagnalis. The average number of cercariae produced per day decreased as the snail host approached death counter to the terminal investment hypothesis. The finding supports the prediction of the bet hedging hypothesis and implies that the pattern of cercarial production may be explained by reduced virulence of the parasite within the snails to ensure extended total production time of cercariae. Nevertheless, survival of infected snails was still lower than uninfected snails suggesting that ultimately the infection still increased snail mortality rate. Cercarial production varied between days but was not cyclic, probably because of the physiology of the sporocysts within snails. Fewer cercariae were released at night, which may increase transmission efficiency to diurnally-active fish hosts. The mechanisms associated with daily cercarial production are discussed.

Large shifts in pathogen virulence relate to host population structure

Theory on the evolution of virulence generally predicts selection for an optimal level of virulence determined by trade-offs with transmission and/or recovery. Here we consider the evolution of pathogen virulence in hosts who acquire long-lived immunity and live in a spatially structured population. We show theoretically that large shifts in virulence may occur in pathogen populations as a result of a bistability in evolutionary dynamics caused by the local contact or social population structure of the host. This model provides an explanation for the rapid emergence of the highly virulent strains of rabbit hemorrhagic disease virus.

Rising burden of immature sheep ticks (Ixodes ricinus) on red grouse (Lagopus lagopus scoticus) chicks in the Scottish uplands

The sheep tick Ixodes ricinus (L.) (Acari: Ixodidae) is an ectoparasite of major economic and pathogenic importance in Scotland. Its distribution in the Scottish uplands is assumed to be governed by the abundance and distribution of its definitive hosts (deer and sheep) and climatic variables such as temperature and rainfall. As the numbers of its major host in Scotland, red deer, have increased dramatically and climatic conditions have become more favourable, the level of parasitism could have been expected to rise. We use data gathered from tick counts on over 4000 red grouse chicks Lagopus lagopus scoticus Latham (Galliformes: Tetraonidae) in various experiments over the past 19 years to ascertain whether the intensity and prevalence of parasitism has been increasing. From 1985 to 2003 the average tick burden of a parasitized red grouse chick has grown from 2.60 +/- 1.12 ticks per chick to 12.71 +/- 1.44. Over this period the percentage of chicks of a given brood parasitized has also increased from 4 +/- 2% to 92 +/- 3%. The possible implications of this increase in parasitism for red grouse production are discussed.

Long-term survival of New Zealand rabbit haemorrhagic disease virus RNA in wild rabbits, revealed by RT-PCR and phylogenetic analysis

Because Rabbit haemorrhagic disease virus (RHDV) is highly pathogenic for rabbits, farmers illegally introduced it as a bio-control agent onto New Zealand farms in 1997. The virus was dispersed rapidly, initially causing high fatality rates in rabbits. Nevertheless, many survived and these surviving rabbits have been investigated for evidence of infection by RHDV. Livers from healthy rabbits contained RHDV-specific RNA, as shown by nested RT-PCR sequencing. The sequences of the viral capsids were related closely to the released Czech strain of RHDV, although the sequence from one rabbit was related most closely to a Spanish strain of RHDV. Phylogenetic analysis of the capsid sequences of 38 samples implied that there have been at least two introductions of the Czech virus into New Zealand, probably corresponding firstly to the original illegal introduction by farmers and secondly to the introduction of the same virus under governmental control. Genomic length sequence of two samples was obtained, suggesting that they may have retained the potential to be infectious, although this has not yet been demonstrated. The detection of genomic-length RNA in the liver of healthy rabbits suggests that even though a highly virulent virus was introduced into New Zealand, it rapidly established persistent or latent infections in a proportion of rabbits. This might account for their ability to survive in the face of virulent released virus. Moreover, the co-circulation of other strains of RHDV in the same rabbit population, such as the Spanish strain, might also impact on their susceptibility to the bio-control agent.

Transmission, infectivity and survival of Diplostomum spathaceum cercariae

The transmission dynamics of the cercariae of Diplostomum spathaceum were investigated under laboratory conditions using cercariae collected from naturally infected Lymnaea stagnalis. Cercariae were kept in a constant temperature of 20 degrees C and the survival and infectivity to naïve young rainbow trout recorded at 3-h intervals until few cercariae were alive. Mortality initially remained constant but increased rapidly after 20 h. While a model of constant mortality fitted the survival data, an age-dependent model provided a better fit and implied that cercariae tended to carry similar quantities of resources and once these were exhausted the cercariae died. Cercarial infectivity also showed an age-dependent pattern although infectivity tended (P = 0.09) to increase with age over the first 6 h of life and then fall. The per capita transmission rate of cercariae was investigated by experimentally infecting rainbow trout under standardized conditions, first with an increasing cercarial density and second, by keeping density constant but increasing numbers of cercariae. The per capita transmission rate was frequency dependent and averaged 0.341/h (+/- 0.036).

The effect of aggressiveness on the population dynamics of a territorial bird

A central issue in ecology lies in identifying the importance of resources, natural enemies and behaviour in the regulation of animal populations. Much of the debate on this subject has focused on animals that show cyclic fluctuations in abundance. However, there is still disagreement about the role of extrinsic (food, parasites or predators) and intrinsic (behaviour) factors in causing cycles. Recent studies have examined the impact of natural enemies, although spatial patterns resulting from restricted dispersal or recruitment are increasingly recognized as having the potential to influence unstable population dynamics. We tested the hypothesis that population cycles in a territorial bird, red grouse Lagopus lagopus scoticus, are caused by delayed density-dependent changes in the aggressiveness and spacing behaviour of males. Here we show that increasing aggressiveness experimentally for a short period in autumn reduced recruitment and subsequent breeding density by 50%, and changed population trajectories from increasing to declining. Intrinsic processes can therefore have fundamental effects on population dynamics.

Stochasticity accelerates nematode egg development

Day-degrees models of nematode development assume that temperature stochasticity has no effect on the development rate of infective stages as long as the mean temperature is held constant. This assumption was tested in this study. Unembryonated Heterakis gallinarum eggs were subjected to nocturnal and diurnal daily temperature cycles at 12 and 17 C. respectively, and embryonation was compared with eggs subjected to similar stochastic daily cycles, in which random normal variations in the temperature were added to the 2 temperatures. The prediction that there is no effect of stochasticity was refuted. Embryonation of eggs subjected to variable daily cycles occurred significantly earlier than that of eggs subjected to deterministic daily cycles, suggesting that stochastic variation in temperature accelerated embryonation even though mean temperatures were the same. These findings show that the development time of H. gallnarum eggs is decreased by stochastic variation in temperature, which may have important implications for the effects of climate change on parasite availability.

Epidemiological consequences of a pathogen having both virulent and avirulent modes of transmission: the case of rabbit haemorrhagic disease virus

A number of pathogens cause chronic infection in survivors of acute disease and this is believed to be a common means of persistence, including for highly virulent agents. We present a model in which transmission from chronically infected hosts causes chronic infection in naive individuals, without causing acute disease--indeed 'protecting' against it. Thus the pathogen obtains the benefit of virulence (high transmission rate), but mitigates against the cost (high host mortality). Recent findings suggest that rabbit haemorrhagic disease virus (RHDV), a highly contagious and virulent pathogen, may also utilize this alternative, 'avirulent', mode of transmission. The model may resolve the paradox of how RHDV can be highly prevalent in some populations, in the absence of mortality. Differences in host demography determine whether avirulent transmission prevents large-scale mortality (as in most UK populations) or not. Other pathogens may exhibit similar behaviour and the implications for emerging diseases in general are discussed.

Molecular epidemiology of Rabbit haemorrhagic disease virus

Millions of domestic and wild European rabbits (Oryctolagus cuniculus) have died in Europe, Asia, Australia and New Zealand during the past 17 years following infection by Rabbit haemorrhagic disease virus (RHDV). This highly contagious and deadly disease was first identified in China in 1984. Epidemics of RHDV then radiated across Europe until the virus apparently appeared in Britain in 1992. However, this concept of radiation of a new and virulent virus from China is not entirely consistent with serological and molecular evidence. This study shows, using RT-PCR and nucleotide sequencing of RNA obtained from the serum of healthy rabbits stored at 4 degrees C for nearly 50 years, that, contrary to previous opinions, RHDV circulated as an apparently avirulent virus throughout Britain more than 50 years ago and more than 30 years before the disease itself was identified. Based on molecular phylogenetic analysis of British and European RHDV sequences, it is concluded that RHDV has almost certainly circulated harmlessly in Britain and Europe for centuries rather than decades. Moreover, analysis of partial capsid sequences did not reveal significant differences between RHDV isolates that came from either healthy rabbits or animals that had died with typical haemorrhagic disease. The high stability of RHDV RNA is also demonstrated by showing that it can be amplified and sequenced from rabbit bone marrow samples collected at least 7 weeks after the animal has died.

Strategies for nematode transmission: selective migration of Trichostrongylus tenuis infective larvae

Successful transmission of macroparasites is dependent on exposure of susceptible hosts to free-living infective stages. When these hosts are herbivores that feed mostly on a single food plant then natural selection should favour those infective larvae that selectively ascend this main food plant. Red grouse feed predominantly on heather, Calluna vulgaris, so we predict that the infective larvae (L3) of the caecal nematode Trichostrongylus tenuis selectively locate and ascend heather plants. To determine whether the presence of heather influences the horizontal dispersal of T. tenuis L3 across soil, the movement of L3 across trays of soil with and without heather was investigated in the laboratory. More T. tenuis L3 were recovered from soil when heather was present, implying that larval migration may be influenced by chemical cues produced by heather plants. This was investigated in a second experiment, in which the horizontal dispersal of T. tenuis larvae was examined in the presence of heather and grass vegetation. This trial was repeated with larvae of a second species, Haemonchus contortus, a nematode whose hosts feed on a wide range of grass and shrub species. Significantly more larvae of both nematode species were recovered in the region of the heather than the grass or controls. This implies that T. tenuis and H. contortus L3 exhibit selective migration towards heather, perhaps reflecting a general response to plant cues which may be stronger for heather than for grass.

Patterns of parasite aggregation in the wild European rabbit (Oryctolagus cuniculus)

Understanding the factors controlling the distribution of parasites within their host population is fundamental to the wider understanding of parasite epidemiology and ecology. To explore changes in parasite aggregation, Taylor's power law was used to examine the distributions of five gut helminths of the wild rabbit. Aggregation was found to be a dynamic process that varied with year, season, host sex, age class, and myxomatosis. Yearly and seasonal changes are thought, in the main, to be the result of variations in weather conditions acting upon infectious stages (or intermediate hosts). Evidence in support of this was the comparatively low degree of fluctuation in the aggregation of the pinworm, Passalurus ambiguus, as the infectious stage of this parasite is likely to be less susceptible to environmental variation. Host age had a marked effect on the level of aggregation of all parasites, but this effect varied between parasite species. P. ambiguus, Trichostrongylus retortaeformis and Cittotaenia denticulata aggregation were lower in adult than juvenile rabbits whilst Graphidium strigosum and Mosgovoyia pectinata aggregation tended to increase with age. Host immunity is thought to be responsible for these differences. Differences in aggregation for different parasites were also seen when the rabbit population was split into males and females. Myxomatosis had a marked effect on helminth distribution with substantially less aggregation in rabbits showing clinical signs of the disease.

Dimeric and trimeric antibodies: high avidity scFvs for cancer targeting

Recombinant antibody fragments can be engineered to assemble into stable multimeric oligomers of high binding avidity and specificity to a wide range of target antigens and haptens. This review describes the design and expression of diabodies (dimers), triabodies (trimers) and tetrabodies (tetramers). In particular we discuss the role of linker length between V-domains and the orientation of the V-domains to direct the formation of either diabodies (60 kDa), triabodies (90 kDa) or tetrabodies (120 kDa), and how the size, flexibility and valency of each molecules is suited to different applications for in vivo imaging and therapy. Single chain Fv antibody fragments joined by polypeptide linkers of at least 12 residues irrespective of V-domains orientation predominantly form monomers with varying amounts of dimer and higher molecular mass oligomers in equilibrium. A scFv molecule with a linker of 3-12 residues cannot fold into a functional Fv domain and instead associates with a second scFv molecule to form a bivalent dimer (diabody, approximately 60 kDa). Reducing the linker length below three residues can force scFv association into trimers (triabodies, approximately 90 kDa) or tetramers ( approximately 120 kDa) depending on linker length, composition and V-domain orientation. A particular advantage for tumour targeting is that molecules of 60-100 kDa have increased tumour penetration and fast clearance rates compared with the parent Ig (150 kDa). We highlight a number of cancer-targeting scFv diabodies that have undergone successful pre-clinical trials for in vivo stability and efficacy. We also briefly review the design of multi-specific Fv modules suited to cross-link two or more different target antigens. Bi-specific diabodies formed by association of different scFv molecules have been designed as cross-linking reagents for T-cell recruitment into tumours (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics). The more challenging trispecific multimers (triabodies) remain to be described.

Tick-borne encephalitis virus in northern Italy: molecular analysis, relationships with density and seasonal dynamics of Ixodes ricinus

Ixodes ricinus ticks were collected from dragging vegetation and from shot roe deer in the province of Trento and Belluno in northern Italy. Ticks were pooled for analyses and from 1060 pools of ticks collected in the province of Belluno and 12390 tick samples collected in Trentino, four proved positive by immunofluorescence microscopy using a tick-borne encephalitis (TBE)-specific antiserum. The identity of the virus isolates was determined by RT-PCR cycle sequencing and they were all found to be closely similar (> 98% nucleotide identity) to typical western European TBE complex viruses as found in Austria. The isolates from Trentino differed from the Neudorfl strain of western European TBE virus at eight nucleotide positions but as these nucleotide substitutions were all synonymous, there were no amino acid changes. These results imply that the virus isolates in Trentino have changed slightly from the typical European strains isolated in nearby Austria. The abundance of questing ticks and ticks feeding on roe deer was greater in TBE positive hunting districts than in hunting districts where TBE complex viruses were only probable or believed to be absent. In TBE positive and probable districts synchrony in the seasonal dynamics of larvae and nymphs of L. ricinus was observed. This study provides evidence to suggest that roe deer may have an important role to play in the maintenance of tick density and in the persistence of TBE virus.

Recombinant antibodies for cancer diagnosis and therapy

Recombinant antibodies now represent over 30% of biopharmaceuticals in clinical trials, highlighted by the recent approvals for cancer immunotherapy from the FDA which has awoken the biotechnology industry. Sales of these antibodies are increasing very rapidly to a predicted US$ 3 billion per annum worldwide by 2002. Since the development of new therapeutic reagent into commercial product takes 10 years, the recent FDA-approved antibodies are based on early antibody designs which are now considered primitive. Emerging technologies have created a vast range of novel, recombinant, antibody-based reagents which specifically target clinical biomarkers of disease. In the past year, radiolabelling of antibodies has increased their potential for cancer imaging and targeting. Recombinant antibodies have also been reduced in size and rebuilt into multivalent molecules for higher affinity. In addition, antibodies have been fused with many molecules including toxins, enzymes and viruses for prodrug therapy, cancer treatment and gene delivery. Recombinant antibody technology has enabled clever manipulations in the construction of complex antibody library repertoires for the selection of high-affinity reagents against refractory targets. Although phage display remains the most extensively used method, this year high affinity reagents have been isolated using alternative display and selection systems such as ribosome display and yeast display confirming the emergence of new display methods. Furthermore, innovative affinity maturation strategies have been developed to obtain high affinity reagents. This review focuses on developments in the last 12 months and describes the latest developments in the design, production and clinical use of recombinant antibodies for cancer diagnosis and therapy.

Isolation of the new antigen receptor from wobbegong sharks, and use as a scaffold for the display of protein loop libraries

The new antigen receptor (NAR) from nurse sharks consists of an immunoglobulin variable domain attached to five constant domains, and is hypothesised to function as an antigen-binding antibody-like molecule. To determine whether the NAR is present in other species we have isolated a number of new antigen receptor variable domains from the spotted wobbegong shark (Orectolobus maculatus) and compared their structure to that of the nurse shark protein. To determine whether these wNARs can function as antigen-binding proteins, we have used them as scaffolds for the construction of protein libraries in which the CDR3 loop was randomised, and displayed the resulting recombinant domains on the surface of fd bacteriophages. On selection against several protein antigens, the highest affinity wNAR proteins were generated against the Gingipain K protease from Porphyromonas gingivalis. One wNAR protein bound Gingipain K specifically by ELISA and BIAcore analysis and, when expressed in E. coli and purified by affinity chromatography, eluted from an FPLC column as a single peak consistent with folding into a monomeric protein. Naturally occurring nurse shark and wobbegong NAR variable domains exhibit conserved cysteine residues within the CDR1 and CDR3 loops which potentially form disulphide linkages and enhance protein stability; proteins isolated from the in vitro NAR wobbegong library showed similar selection for such paired cysteine residues. Thus, the New Antigen Receptor represents a protein scaffold with possible stability advantages over conventional antibodies when used in in vitro molecular libraries.

Panning and selection of proteins using ribosome display

Eukaryotic ribosome complexes can be used as a means to display a library of proteins, and isolate specific binding reagents by screening against target molecules. Here we present, as an example, a method for the display of a library of immunoglobulin variable-like domains (VLDs) for the production of stable mRNA/ribosome/protein complexes. These complexes are produced by the addition of specific in vitro transcriptional promoter elements and translation control sequences to the template DNA. Furthermore, an appropriate spacer (anchor) domain is included for efficient folding of the nascent translated protein, which remains attached to the ribosome complex. Ribosome complexes are panned against hen egg lysozyme-conjugated magnetic beads and genes encoding specific, binding, V-like domains are recovered by RT-PCR and cloned into an Escherichia coli expression vector.

The emergence of rabbit haemorrhagic disease virus: will a non-pathogenic strain protect the UK?

Rabbit haemorrhagic disease virus emerged in China in 1984, and has killed hundreds of millions of wild rabbits in Australia and Europe. In the UK there appears to be an endemic non-pathogenic strain, with high levels of seroprevalence being recorded, in the absence of associated mortality. Using a seasonal, age-structured model we examine the hypothesis that differences in rabbit population demography differentially affect the basic reproductive rates (R(0)) of the pathogenic and non-pathogenic strains, leading to each dominating in some populations and not others. The strain with the higher R(0) excluded the other, with the dynamics depending upon the ratio of the two R(0) values. When the non-pathogenic strain dominated, the pathogenic strain caused only transient mortality, although this could be significant when the two R(0) values were similar. When the pathogenic strain dominated, repeated epidemics led to host eradication. Seroprevalence data suggest that the non-pathogenic strain may be protecting some, but not all UK populations, with half being 'at risk' from invasion by the pathogenic strain and a fifth prone to significant transient mortality. We identify key questions for empirical research to test this prediction.

Protein affinity maturation in vivo using E. coli mutator cells

This protocol provides a simple in vivo strategy for introducing random mutations to a target DNA sequences using E. coli mutator cells. The method has been used in our laboratory for affinity maturation of proteins encoded by target DNA sequences. Selection conditions can be modified for antibody fragments with increased production levels. Growth conditions in E. coli mutator cells can be adjusted to introduce a single random point mutation per kilobase of DNA, approximately equivalent to one codon change per scFv fragment.

Ligand-binding characteristics of recombinant amino- and carboxyl-terminal fragments of human insulin-like growth factor-binding protein-3

Insulin-like growth factor-binding protein-3 (IGFBP-3) is a member of a family of structurally conserved proteins (IGFBP-1 to -6) which act as carriers and regulators of the mitogenic peptide hormones IGF-I and IGF-II. Members of the IGFBP family share conserved cysteine-rich amino- and carboxyl-terminal regions. The amino-terminal domain of these proteins is recognised to contain an IGF-binding determinant, but evidence to support a binding site in the carboxyl-terminal region of the protein is less rigorous. To further investigate this, we have synthesised both the amino-terminal (residues 1-88; N-88) and carboxyl-terminal (residues 165-264; C-165) domains of human IGFBP-3 in bacteria, as fusion proteins with a carboxyl-terminal FLAG peptide. Although only C-165 showed binding to IGF-I and -II by solution-binding assays, both N-88 and C-165 demonstrated binding to IGF-I and -II by biosensor analysis albeit with reduced affinities compared with full-length IGFBP-3. Only the carboxyl-terminal fragment (C-165) was able to form hetero-trimeric complexes with IGF-I and the acid-labile subunit (ALS). We conclude that the carboxyl-terminal domain of IGFBP-3 contains an IGF-binding determinant and can form ternary complexes with ALS.

Biodistribution properties of (111)indium-labeled C-functionalized trans-cyclohexyl diethylenetriaminepentaacetic acid humanized 3S193 diabody and F(ab')(2) constructs in a breast carcinoma xenograft model

The humanized complementarity determining region-grafted anti-Lewis Y (Le(y)) monoclonal antibody [humanized 3S193 (hu3S193)] was developed for targeting Le(y)-expressing epithelial tumors such as breast, colon, lung, prostate, and ovarian carcinoma. We are exploring the potential use of smaller molecular size, bivalent analogues of hu3S193, because the faster blood clearance of M(r) approximately 54,000 diabody and M(r) approximately 110,000 F(ab')(2) molecules may be advantageous in achieving optimal and rapid tumor uptake for diagnostic and potential therapeutic applications. The single-chain variable fragment-5 residue linker construct (diabody) was expressed using the bacterial secretion vector pPOW3, and soluble product was purified without refolding processes. The F(ab')(2) fragment was obtained by pepsin digest of parental hu3S193. To facilitate evaluations, the radiometal (111)In was used to label C-functionalized trans-cyclohexyl diethylenetriaminepentaacetic acid chelated diabody and F(ab')(2). The immunoreactivity of the radiolabeled constructs was 41.3 and 58.6%, and the K(a) was 1.68 x 10(6) M(-1) and 5.33 x 10(6) M(-1) for the diabody and F(ab')(2), respectively. Radioconjugates were injected into mice bearing Le(y)-positive MCF-7 tumors, and biodistribution properties were determined at various time points after injection. The uptake of radiolabeled diabody in xenografts was maximal at 1 h after injection (4.7 +/- 0.6% injected dose/g), whereas the F(ab')(2) peaked at 8 h after injection (14.2 +/- 2.4% injected dose/g). The tumor:blood ratio at 4 h for the diabody and F(ab')(2) was 5:1 and 2:1, which increased to 20:1 and 5:1, respectively, at 8 h and increased further to 40:1 and 130:1, respectively, at 48 h. These results demonstrate that the diabody construct may have applications as a diagnostic imaging reagent, whereas F(ab')(2) displayed effective tumor targeting and may have potential as a therapeutic molecule in patients with Le(y)-expressing tumors.

Design and application of diabodies, triabodies and tetrabodies for cancer targeting

Multivalent recombinant antibody fragments provide high binding avidity and unique specificity to a wide range of target antigens and haptens. This review describes the design and expression of diabodies, triabodies and tetrabodies using examples of scFv molecules that target viruses (influenza neuraminidase) and cancer (Ep-CAM; epithelial cell adhesion molecule). We discuss the preferred choice of linker length between V-domains to direct the formation of either diabodies (60 kDa), triabodies (90 kDa) or tetrabodies (120 kDa), each with size, flexibility and valency suited to different applications for in vivo imaging and therapy. The increased binding valency of these scFv multimers results in high avidity (low off-rates). A particular advantage for tumour targeting is that molecules of 60-100 kDa have increased tumour penetration and fast clearance rates compared to the parent Ig (150 kDa). We highlight a number of cancer-targeting scFv multimers that have recently successfully undergone pre-clinical trials for in vivo stability and efficacy. We also review the design of multi-specific Fv modules suited to cross-link two or more different target antigens. These bi- and tri-specific multimers can be formed by association of different scFv molecules and, in the first examples, have been designed as cross-linking reagents for T-cell recruitment into tumours (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics).

Ribosome display and affinity maturation: from antibodies to single V-domains and steps towards cancer therapeutics

Protein affinity maturation using molecular evolution techniques to produce high-affinity binding proteins is an important step in the generation of reagents for cancer diagnosis and treatment. Currently, the most commonly used molecular evolution processes involve mutation of a single gene into complex gene repertoires followed by selection from a display library. Fd-bacteriophage are the most popular display vectors, but are limited in their capacity for library presentation, speed of processing and mutation frequency. Recently, the potential of ribosome display for directed molecular evolution was recognised and developed into a rapid and simple affinity selection strategy using ribosome complexes to display antibody fragments (scFv). Ribosome display and selection has the potential to generate and display large libraries more representative of the theoretical optima for naïve repertoires (10(14)). Even more important is the application of ribosome display for the affinity maturation of individual proteins by rapid mutation and selection cycles. These display strategies can apply to other members of the immunoglobulin superfamily; for example single V-domains which have an important application in providing specific targeting to either novel or refractory cancer markers. We discuss the application of ribosome display and selection in conjunction with variable domain (CTLA-4) libraries as the first step towards this objective and review affinity maturation strategies for in vitro ribosome display systems.

Differential impact of a shared nematode parasite on two gamebird hosts: implications for apparent competition

If the deleterious effects of non-specific parasites are greater on vulnerable host species than on reservoir host species then exclusion of the vulnerable host through apparent competition is more likely. Evidence suggests that such a mechanism occurs in interactions between the ring-necked pheasant (Phasianus colchicus), the grey partridge (Perdix perdix), and their shared caecal nematode Heterakis gallinarum. Modelling of the system predicts that the reduced parasite impact on the pheasant compared to the partridge results in the force of infection transmitted from pheasants to partridges being sufficient to cause partridge exclusion. Since the parasite impacts are currently estimated from correlational work, controlled infections were conducted to experimentally compare the impact of H. gallinarum on the two hosts and verify cause and effect. While challenged partridges showed reduced mass gain, decreased food consumption, and impaired caecal activity, in comparison to controls, the only detectable effect of parasite challenge on the pheasant was impaired caecal activity. The impact of H. gallinarum on challenged partridges conforms with previous correlational data, supporting the prediction that parasite-mediated apparent competition with the ring-necked pheasant may result in grey partridge exclusion. However, the observed decrease in the caecal activity of challenged pheasants could imply that H. gallinarum may also have an impact on the fecundity and survival of pheasants in the wild, particularly if food is limiting. If this is the case, the associated decrease in the force of infection to which the partridge is exposed may be sufficient to change the model prediction from partridge exclusion to pheasant and partridge coexistence.

The role of oxygen availability in the embryonation of Heterakis gallinarum eggs

The importance of oxygen availability in the embryonation of the infective egg stages of the gastrointestinal nematode parasite Heterakis gallinarum was studied in the laboratory. Unembryonated H. gallinarum eggs were kept under either aerobic conditions by gassing with oxygen, or anaerobic conditions by gassing with the inert gas nitrogen, under a range of constant temperatures. Oxygenated eggs embryonated at a rate influenced by temperature. Conversely, eggs treated with nitrogen showed no embryonation although when these eggs were transferred from nitrogen to oxygen gas after 60 days of treatment, embryonation occurred. This demonstrated that oxygen is an essential requirement for H. gallinarum egg development, although undeveloped eggs remain viable, even after 60 days in low oxygen conditions. The effects of climate on the biology of free-living stages studied under constant laboratory conditions cannot be applied directly to the field where climatic factors exhibit daily cycles. The effect of fluctuating temperature on development was investigated by including an additional temperature group in which H. gallinarum eggs were kept under daily temperature cycles between 12 and 22 degrees C. Cycles caused eggs to develop significantly earlier than those in the constant mean cycle temperature, 17 degrees C, but significantly slower than those in constant 22 degrees C suggesting that daily temperature cycles had an accelerating effect on H. gallinarum egg embryonation but did not accelerate to the higher temperature. These results suggest that daily fluctuations in temperature influence development of the free-living stages and so development cannot be accurately predicted on the basis of constant temperature culture.

Expression and purification of antigenically active soluble derivatives of the heterodimeric and homodimeric forms of the mouse CD8 lymphocyte membrane glycoprotein

The T lymphocyte membrane glycoprotein CD8 enhances antigen recognition by class I-restricted T cells. There are two naturally occurring forms of CD8, an alphabeta heterodimer expressed by the majority of CD8(+) T cells, and a less abundant alphaalpha homodimer found on specialised T cell subsets. An expression strategy was developed for production of soluble CD8alphaalpha and CD8alphabeta extracellular domains for use in ligand binding studies. Mouse CD8alpha was expressed autonomously as a homodimer at 10 mg/l in mammalian fibroblasts, but CD8beta was not expressed at significant levels in the absence of CD8alpha. Co-expression with CD8alpha led to significant enhancement in the level of CD8beta expression, which was secreted as a non-covalent heterodimer at 3 mg/l with CD8alpha. Despite the marked increase of CD8beta expression in the presence of CD8alpha, an excess of soluble CD8alphaalpha homodimer was also present in the supernatant of co-expressing cell clones. In order to resolve the CD8alphaalpha homodimer from the CD8alphabeta heterodimer, affinity chromatographic techniques specific for the CD8beta subunit were employed. Purification procedures requiring elution from affinity matrices at low pH led to substantial losses in the total antigenic activity and partial subunit dissociation of the soluble CD8alphabeta heterodimer. The inclusion of a hexahistidine tag at the C-terminus of CD8beta enabled affinity purification of soluble CD8alphabeta (and sCD8alphaalpha) under neutral conditions, yielding recombinant protein with the correct stoichiometry and full antigenic activity. This method may prove useful for production of other soluble recombinant heterodimeric receptor proteins whose antigenicity is affected by denaturation during immunoaffinity purification.

Immunoglobulin VH domains and beyond: design and selection of single-domain binding and targeting reagents

Identification of the smallest antibody fragment still capable of binding to antigen has progressed from full antibody molecules to Fab and recombinant single chain Fv fragments. Now, a further reduction to single domain binding proteins based upon immunoglobulin VH and VH-like domains offers exciting prospects in the development of novel immunotherapeutics and immunodiagnostics. Minimisation of the antigen-binding fragment to such small single-domain proteins offers the advantages of enhanced stability, and possibly access to a class of antigenic epitopes not generally recognised by conventional antibodies.