Analysis of T cell activation requirements with the use of alloantigens or an anti-clonotypic monoclonal antibody

H-2Kb-specific alloreactive cytotoxic T lymphocyte (CTL) clones, which secrete macrophage-activating factor (MAF) in response to antigen, were used to study the antigenic and physiologic parameters for T cell-antigen receptor (Ti)-mediated activation. When H-2Kb was presented on untreated, formaldehyde (FOR)-fixed cells, or liposomes, optimal stimulation in the absence of co-factors was obtained only with the untreated cells. FOR cells, which were efficient inhibitors of CTL-target cell interactions for the CTL clones studied, had a greatly reduced activating capacity. Phorbol myristic acetate (PMA), which alone had no activating effect on the CTL clones, acted in synergy with FOR cells, restoring an unimpaired H-2Kb-dependent activation for some CTL clones. H-2Kb-liposomes were not stimulatory even in the presence of PMA and/or splenic feeder cells. For one H-2Kb-specific CTL clone (KB5-C20), activation was studied with the use of an anti-clonotypic (anti-Ti) monoclonal antibody (mAb), Désiré-1. By using this immunoglobulin (Ig) G2a mAb or its F(ab')2 or Fab fragments, it was observed that the association constant of the IgG2a (4.7 X 10(9) M-1) for KB5-C20 was 30-fold higher than that of the Fab fragment, whereas the molar concentration of mAb required to inhibit 50% of the H-2Kb-specific CTL activity of clone KB5-C20 was 70-fold to 90-fold higher for the Fab fragment than for the IgG2a (1 to 5 X 10(-10) M). It was also observed that activation as measured by MAF secretion of clone KB5-C20 was obtained by using the divalent IgG2a mAb or its F(ab')2 fragment at 10(-9) M to 10(-8) M in the absence of any added co-factor or feeder cells, whereas a 500-fold higher molar concentration of the Fab fragment only induced very low levels of MAF secretion. Also, in the presence of PMA, the mAb-mediated activation of MAF secretion by clone KB5-C20 was increased, but Fab-induced activation never resulted in high titers of MAF. We conclude that the intrinsic "affinity" of the H-2Kb-Ti interaction is probably so low for the Ti of clone KB5-C20 that efficient activation by H-2Kb is obtained only when multivalency is achieved on H-2Kb-expressing cells, and possibly when molecules on the T cells such as Lyt-2 and LFA-1 stabilize the interactions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Conditions of anti-Lyt-2-mediated inhibition of TcR/CD3-induced IFN-gamma secretion by a CTL clone

The relationship between the T cell receptor (TcR) for antigen (Ag) and the Lyt-2/3 molecule during T cell activation was studied using the T cell clone KB5.C20, which is dependent upon Lyt-2 for target cell killing. This cytolytic T cell clone can be activated to secrete IFN-gamma by stimulation with H-2Kb expressing cells or with monoclonal antibodies directed against a clonotypic structure of the TcR or against associated CD3 molecules. IFN-gamma production induced by H-2Kb can be inhibited by anti-Lyt-2mAb. In addition, TcR-mediated activation using the anticlonotypic mAb Désiré-1 in soluble form can be inhibited by anti-Lyt-2 mAb in soluble form either as a divalent IgG or as its monovalent Fab fragment. Anti-Lyt-2 mAb immobilized on plastic wells was also inhibitory. Stimulation induced by the anti-TcR mAb or by anti-CD3 mAb immobilized on plastic can be inhibited only with plastic immobilized and not with soluble anti-Lyt-2mAb, however. These results are discussed in terms of local interactions between TcR and Lyt-2 molecules.     

Expression vectors for the introduction of highly diverged sequences into the six complementarity-determining regions of an antibody

We prepared three kinds of phagemid vector that permit the simultaneous introduction of highly diverged sequences into six complementarity-determining regions (CDRs) of an antibody (Ab) by the polymerase chain reaction (PCR) with degenerate oligodeoxynucleotide (oligo) primers. The phages expressed either the Fv, single-chain Fv (sc Fv) or Fab form of an Ab fused with a half-molecule of cpIII on the surface of M13 phage. A phage-display library, composed of 2 × 10⁸ independent clones, was constructed; the phages that were specific for hen egg-white lysozyme (HEL) were selected by three rounds of panning; and 20 clones were isolated. The isolated clones consisted of 17 different clones. Among them, 16 clones expressed proteins that were able to bind to HEL. The association constants for binding of the encoded proteins to HEL ranged from 1.48 × 10⁶ to 7.71 × 10⁶/M. These vectors allowed us to prepare many libraries of artificial Ab in which the sequences of six CDRs were very different and reflected the artificial sequences that had been designed for the degenerate oligo that we used as primers for PCR. The libraries should be also useful for the analysis of relationships between the sequences of the CDRs and antigen (Ag) specificity.     

Early responses of resistant and susceptible potato roots during invasion by the potato cyst nematode Globodera rostochiensis

Signals from roots of resistant (cv. Maris Piper) and susceptible (cv. Désirée) potato cultivars during invasion by second stage juveniles (J2s) of the potato cyst nematode, Globodera rostochiensis, were investigated. Novel experimental chambers enabled the recording of electrophysiological responses from roots during nematode invasion. The root cell membrane potentials were maintained throughout the 3 d required to assess invasion and feeding site development. The steady-state resting membrane potentials of Désirée were more negative than those of Maris Piper on day 1, but the reverse on day 3. After 5 d there was no difference between the two cultivars. Intracellular microelectrodes detected marked spike activity in roots after the application of J2s and there were distinct and reproducible differences between the two cultivars, with the response from Désirée being much greater than that from Maris Piper. The responses to mechanical stimulation of roots by blunt micropipettes and sharp electrodes were consistent and similar in both cultivars to the responses in Maris Piper obtained after nematode invasion, but could not account for the marked response found in Désirée. Exogenous application of exoenzymes, used to mimic nematode chemical secretions, resulted in a distinct depolarization pattern that, although similar in both cultivars, was different from patterns obtained during nematode invasion or mechanical stimulation. The pH of homogenates prepared from roots of both cultivars was measured and a Ca2+ channel blocker was used to assess the role of Ca2+ in nematode invasion. The results indicated a role for Ca2+ in the signalling events that occur during nematode invasion.     

Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.)

The effects of genotype, plant growth and experimental factors (soil and year) on potato-associated bacterial communities were studied. Cultivars Achirana Inta, Désirée, Merkur and transgenic Désirée line DL12 (containing T4 lysozyme gene) were assessed in two field experiments. Cross-comparisons between both experiments were made using Désirée plants. Culture-dependent and -independent approaches were used to demonstrate effects on total bacterial, actinobacterial and Pseudomonas communities in bulk and rhizosphere soils and endospheres. PCR-denaturing gradient gel electrophoresis fingerprints prepared with group-specific primers were analyzed using multivariate analyses and revealed that bacterial communities in Achirana Inta plants differed most from those of Désirée and Merkur. No significant effects were found between Désirée and DL12 lines. Plant growth stage strongly affected different plant-associated communities in both experiments. To investigate the effect of plant-associated communities on plant health, 800 isolates from rhizospheres and endospheres at the flowering stage were tested for suppression of Ralstonia solanacearum biovar 2 and/or Rhizoctonia solani AG3. A group of isolates closely resembling Lysobacter sp. dominated in young plants. Its prevalence was affected by plant growth stage and experiment rather than by plant genotype. It was concluded that plant growth stage overwhelmed any effect of plant genotype on the bacterial communities associated with potato.     

The effects of deep cultivation and oxamyl on control of potato cyst-nematode, Globodera rostochiensis

Soil compaction associated with frequent cultivation of potatoes was partly removed with a deep winged-tine coulter. This increased the yield of tubers of cv. Cara in 1987 and 1988 and of cv. Désirée in 1987 in soil which was heavily infested with potato cyst-nematode, Globodera rostochiensis (Woll.), and which was treated with oxamyl at 5.6 kg ha^-1. In 1988, in soil not treated with oxamyl, deep cultivation significantly decreased the yield of cv. Cara. In both years, oxamyl decreased numbers of G. rostochiensis eggs in the soil following cv. Désirée potatoes but not following cv. Cara which were resistant to the nematode.     

Structural effects of framework mutations on a humanized anti-lysozyme antibody.

A humanized version of the mouse anti-lysozyme Ab D1.3 was previously constructed as an Fv fragment and its structure was crystallographically determined in the free form and in complex with lysozyme. Here we report five new crystal structures of single-amino acid substitution mutants of the humanized Fv fragment, four of which were determined as Fv-lysozyme complexes. The crystals were isomorphous with the parent forms, and were refined to free R values of 28-31% at resolutions of 2.7-2.9 A. Residue 27 in other Abs has been implicated in stabilizing the conformation of the first complementarity-determining region (CDR) of the H chain, residues 31-35. We find that a Phe-to-Ser mutation at 27 alters the conformation of immediately adjacent residues, but this change is only weakly transmitted to Ag binding residues in the nearby CDR. Residue 71 of the H chain has been proposed to control the relative disposition of H chain CDRs 1 and 2, based on the bulk of its side chain. However, in structures we determined with Val, Ala, or Arg substituted in place of Lys at position 71, no significant change in the conformation of CDRs 1 and 2 was observed.     

Elicitation of Ethylene by Verticillium albo-atrum Phytotoxins in Potato

Petioles from a susceptible cultivar (Désirèe) of Solanum tuberosum treated with a low‐molecular mass toxin, separated from culture fluid of Verticillium albo‐atrum, produced greater quantities of ethylene than did petioles of a tolerant cultivar (Home Guard). Pretreatment of leaflets from cv. Désirèe with silver thiosulphite, which inhibits perception of ethylene, prevented the chlorosis and necrosis normally associated with exposure to the toxin. Similarly, application of aminoethoxyvinylglycine (AVG) an inhibitor of aminocyclopropane‐1‐carboxylic acid (ACC) synthase, to petioles of cv. Désirèe reduced toxin‐induced ethylene synthesis and symptom development. The data indicate that, in part, Verticillium‐toxin acts through induction of ethylene biosynthesis in the host tissues, and different responses of susceptible and tolerant potato cultivars to V. albo‐atrum are the result of differential production of ethylene.     

Effects of rotation length and oxamyl on potato yield and the potato cyst-nematode, Globodera rostochiensis, in a sandy loam soil

In sandy loam infested with golden potato cyst-nematode, Globodera rostochiensis, oxamyl at 5.6 kg a.i. ha^-1 incorporated in the top 15 cm of the soil just before planting potatoes greatly reduced nematode population increase on susceptible cv. Désirée grown six, seven or eight years after the last susceptible potato crop, but did not significantly increase tuber yields. In four-course and two-course rotations, oxamyl also controlled increase of G. rostochiensis and greatly increased yields of both cv. Désirée and resistant cv. Maris Piper. Oxamyl maintained tuber yields in a four-course rotation at the same level as in a six to eight-course rotation. Decline of G. rostochiensis in the soil was much faster under barley in some two-course rotations than under barley in four-course rotations.     

The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.

The crystal structure of a mouse T-cell antigen receptor (TCR) Fv fragment complexed to the Fab fragment of a specific anti-clonotypic antibody has been determined to 2.6 A resolution. The polypeptide backbone of the TCR V alpha domain is very similar to those of other crystallographically determined V alphas, whereas the V beta structure is so far unique among TCR V beta domains in that it displays a switch of the c" strand from the inner to the outer beta-sheet. The beta chain variable region of this TCR antigen-binding site is characterized by a rather elongated third complementarity-determining region (CDR3beta) that packs tightly against the CDR3 loop of the alpha chain, without leaving any intervening hydrophobic pocket. Thus, the conformation of the CDR loops with the highest potential diversity distinguishes the structure of this TCR antigen-binding site from those for which crystallographic data are available. On the basis of all these results, we infer that a significant conformational change of the CDR3beta loop found in our TCR is required for binding to its cognate peptide-MHC ligand.     

A human antibody fragment with high affinity for biodegradable polymer film

Antibodies with high affinity for the surface of a solid material would be advantageous in biomaterial science as a protein device. A human antibody fragment that binds to poly(hydroxybutyrate) (PHB), a biodegradable polymer matter, was generated by a phage display system. Clone PH7-3d3 was isolated after several rounds of selection and prepared as a fragment of immunoglobulin variable regions (Fv). The quartz crystal microbalance technique showed that PH7-3d3 Fv completely inhibited PHB enzymatic degradation by competing with PHB depolymerase. Kinetic analysis based on surface plasmon resonance demonstrated that PH7-3d3 Fv bound to the PHB film with an equilibrium dissociation constant of 14 nM. The three-dimensional structure of PH7-3d3 Fv was resolved to 1.7 A, revealing that the complementarity determining regions (CDRs) in the Fv fragment form a relatively flat surface on which uncharged polar and aromatic amino acids are distributed in clusters. The structure of PH7-3d3 Fv was similar to that of PHB depolymerase in the orientation of aromatic residues in the binding sites. Alanine scanning mutagenesis demonstrated that these aromatic residues, especially tryptophan residues in CDRs, were critical in the interaction between PH7-3d3 Fv and PHB. Our results suggest the possible selection of an antibody fragment that binds a material surface in a manner similar to protein-ligand interaction.     

Transformation of potato via Agrobacterium coated microparticle bombardment

The transformation of potato (Solanum tuberosum L. cv. Désirée) was extended by the Agrobacterium-mediated biolistic method. Using this approach transgenic shoots could be obtained at a similar frequency to that achieved through conventional biolistics. Leaves from shoot cultures were bombarded with gold particles coated in Agrobacterium tumefaciens cells harboring a binary plasmid encoding three genes of interest in the T-DNA. Nine shoots were obtained from 20 shots, with selection of transgenic shoots on a series of media containing progressively increasing concentrations of hygromycin from 5 to 20 mg dm⁻³.     

Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528

To investigate the role of Vernier zone residues, which are comprised in the framework regions and underlie the complementarity-determining regions (CDRs) of antibodies, in the specific, high affinity interactions of antibodies with their targets, we focused on the variable domain fragment of murine anti-human epidermal growth factor receptor antibody 528 (m528Fv). Grafting of the CDRs of m528Fv onto a selected framework region of human antibodies, referred to as humanization, reduced the antibody's affinity for its target by a factor of 1/40. The reduction in affinity was due to a substantial reduction in the negative enthalpy change associated with binding. Crystal structures of the ligand-free antibody fragments showed no noteworthy conformational changes due to humanization, and the loop structures of the CDRs of the humanized antibodies were identical to those of the parent antibodies. Several mutants of the CDR-grafted (humanized) variable domain fragment (h528Fv), in which some of the Vernier zone residues in the heavy chain were replaced with the parental murine residues, were constructed and prepared using a bacterial expression system. Thermodynamic analyses of the interactions between the mutants and the soluble extracellular domain of epidermal growth factor receptor showed that several single mutations and a double mutation increased the negative enthalpy and heat capacity changes. Combination of these mutations, however, led to somewhat reduced negative enthalpy and heat capacity changes. The affinity of each mutant for the target was within the range for the wild-type h528Fv, and this similarity was due to enthalpy-entropy compensation. These results suggest that Vernier zone residues make enthalpic contributions to antigen binding and that the regulation of conformational entropy changes upon humanization of murine antibodies must be carefully considered and optimized.     

Crystal Structure and Computational Modeling of the Fab Fragment from a Protective Anti-Ricin Monoclonal Antibody

Background

Many antibody crystal structures have been solved. Structural modeling programs have been developed that utilize this information to predict 3-D structures of an antibody based upon its sequence. Because of the problem of self-reference, the accuracy and utility of these predictions can only be tested when a new structure has not yet been deposited in the Protein Data Bank.

Methods

We have solved the crystal structure of the Fab fragment of RAC18, a protective anti-ricin mAb, to 1.9 Å resolution. We have also modeled the Fv structure of RAC18 using publicly available Ab modeling tools Prediction of Immunoglobulin Structures (PIGS), RosettaAntibody, and Web Antibody Modeling (WAM). The model structures underwent energy minimization. We compared results to the crystal structure on the basis of root-mean-square deviation (RMSD), template modeling score (TM-score), Z-score, and MolProbity analysis.

Findings

The crystal structure showed a pocket formed mainly by AA residues in each of the heavy chain complementarity determining regions (CDRs). There were differences between the crystal structure and structures predicted by the modeling tools, particularly in the CDRs. There were also differences among the predicted models, although the differences were small and within experimental error. No one modeling program was clearly superior to the others. In some cases, choosing structures based only on sequence homology to the crystallized Ab yielded RMSDs comparable to the models.

Conclusions

Molecular modeling programs accurately predict the structure of most regions of antibody variable domains of RAC18. The hypervariable CDRs proved most difficult to model, particularly H chain CDR3. Because CDR3 is most often involved in contact with antigen, this defect must be considered when using models to identify potential contacts between antibody and antigen. Because this study represents only a single case, the results cannot be generalized. Rather they highlight the utility and limitations of modeling programs.     

Production,storability, and regeneration of shoot tips of potato (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L.) encapsulated in calcium alginate hollow beads

Summary Shoot tips, of four potato cultivars (Désirée, Genet, Tigoni, and Tomensa), 3–4 mm in size, were precultured for 2 d on Murashige and Skoog (MS) solid medium, then encapsulated in calcium alginate to produce hollow bead synthetic seed capsules averaging 0.78 cm in diameter. Regeneration and ‘regrowth’ were tested on MS solid medium and on soil in the greenhouse, respectively. The encapsulated shoot tips were stored at 4 and 10°C for up to 390 d. For all cultivars, the encapsulated shoot tips stored at both temperatures for 180 d and at 4°C,for 270 d, 100% regeneration on MS solid medium was recorded. After 360 d in storage at 4°C, 70.8% (Tigoni), 66.7% (Genet), 58.3% (Désirée), and 51.5% (Tomensa) regeneration was recorded on MS medium, reducing to 15% (Tigoni), 25% (Genet), 10% (Désirée), and 0% (Tomensa) regeneration after 390 d in storage. ‘Regrowth’ of 93–100% was recorded for non-stored encapsulated shoot tips, directly transferred on soil in the greenhouse after a 2 wk preculture on MS solid medium with an added fungicide (carbendazim) in the encapsulating gel. The ‘regrown’ shoot tips produced plants showing normal development. The results presented here demonstrate that hollow bead synthetic seed capsules are an alternative propagating method for potato seed production.     

Effects of potato genotype, oxamyl and the numbers of potato cyst-nematodes, Globodera rostochiensis or G. pallida on tuber yields and nematode increase

A new technique is described for establishing different numbers of the potato cyst-nematode Globodera rostochiensis in field soil, which leaves the soil homogeneous in nutrient status. Field plots established in this way were used to compare yield losses in four potato cultivars (Maris Piper, Pentland Crown, Pentland Dell and Désirée) associated with different numbers of G. rostochiensis. Over the range of 7.4 to 148.4 eggs g^-1 soil at planting, yield losses were 18.7% (Maris Piper), 53.2% (Désirée), 55.7% (Pentland Crown) and 63.5% (Pentland Dell). Similar results were obtained in another experiment on the same field in a different year using only lightly and heavily infested plots. Treating the seedbed soil with oxamyl before planting prevented significant injury to potatoes by G. rostochiensis but increased the yield of Pentland Dell and perhaps Désirée (but not Maris Piper or Pentland Crown) more than expected from nematode control alone. Treating heavily infested soil with such a nematicide cannot therefore be recommended as part of a valid procedure for establishing lightly and heavily infested plots for comparing tolerances of attack by potato cyst-nematodes in a range of potato genotypes. In peaty loam soils moderately or heavily infested with G. pallida, oxamyl at 5.6 kg a.i. ha^-1 incorporated into the seedbed before potatoes were planted generally increased tuber yields, though the effects varied considerably with the cultivar grown. Increase of G. pallida in these soils was controlled better by growing potatoes bred for resistance to it (ZB 35 – 29, Caxton, Santé, Morag, 11233 ab 22, Fingal, A27/23, Cromwell). Increase of G. pallida on susceptible cultivars varied greatly and Romano increased G. pallida no more than the resistant Morag. G. pallida is probably controlled best in peaty loam by growing a resistant cultivar in soil treated with a granular (non-fumigant) nematicide.     

Observations on the control of potato cyst-nematodes, Globodera rostochiensis and G. pallida in 35 English potato soils in pots by oxamyl and resistant potatoes

The increase of 35 English field populations of potato cyst-nematodes (Globodera rostochiensis and/or G. pallida) was measured on Désirée, Maris Piper, Caxton (A25/11), Cromwell (A27/20) and clone 11233 ab 22 in pots of sandy, silty or peaty loam soil. Désirée was susceptible to all populations tested and, as in field soils, the final population (Pf) was inversely related to the initial population of potato cyst-nematode eggs (Pi) in the soil. Maris Piper and Cromwell were resistant to all G. rostochiensis populations, with one possible exception. Maris Piper was susceptible to all G. pallida populations. Caxton was susceptible to some and fairly resistant to other populations of G. rostochiensis, indicating the existence either of two biotypes within the one pathotype (Rol) as yet encountered in Britain, or the existence of an additional pathotype. Caxton and Cromwell were fairly resistant to G. pallida. Clone 11233 ab 22 was only moderately resistant to both species. Resistance to potato cyst-nematode increase varied considerably, especially in Caxton (to G. rostochiensis) and in 11233 ab 22 (to both species). Oxamyl greatly reduced the increase of G. rostochiensis populations on Désirée potatoes, with the notable exception of one population but it generally had much less effect on G. pallida populations, regardless of soil type. The difference in effect on the two species may be due to a longer period of hatching in G. pallida than in G. rostochiensis and also perhaps to a second generation in G. pallida.     

Structural consensus among antibodies defines the antigen binding site

The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that ~20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.