Induction of broadly neutralizing antibodies in Germinal Centre simulations

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Bursa of Fabricius as Site of Origin of Germinal Centre Cells

GERMINAL centres consist of proliferating lymphoid blast cells arising in follicular areas of lymphoid tissue in response to antigen injection¹. These centres have been implicated as sites of origin of memory cells for the secondary immune response^2–4 with specificity for the antigen which induced their formation⁵.     

Germinal center-independent affinity maturation in tumor necrosis factor receptor 1-deficient mice

Germinal centers (GCs) have been identified as site at which the somatic mutation of immunoglobulins occurs.However, somatic mutations in immunoglobulins have also been observed in animals that normally do not harbor germinal centers. This clearly indicates that somatic mutations can occur in the absence of germinal centers.We therefore attempted to determine whether or not GCs exist in TNFR1-deficient mice, and are essential for the somatic mutation of immunoglobulins, using (4-hydroxy-3-nitropheny)acetyl-ovalbumin (NP-OVA). Both wild-type and TNFR1-deficient mice were immunized with NPOVA, and then examined with regard to the existence of GCs. No typical B-cell follicles were detected in the TNFR1-deficient mice. Cell proliferation was detected throughout all splenic tissue types, and no in vivo immunecomplex retention was observed in the TNFR1-deficient mice. All of these data strongly suggest that no GCs were formed in the TNFR1-deficient mice. Although TNFR1-deficient mice are unable to form GCs, serological analyses indicated that affinity maturation had been achieved in both the wild-type and TNFR1-deficient mice. We therefore isolated and sequenced several DNA clones from wild-type and the TNFR1-deficient mice. Eight out of 12 wild-type clones, and 11 out of 14 clones of the TNFR-1-deficient mice contained mutations at the CDR1 site. Thus, the wild-type and TNFR1-deficient mice were not extremely different with regard to types and rates of somatic mutation. Also, high-affinity antibodies were detected in both types of mice. Collectively, our data appear to show that affinity maturation may occur in TNFR1-deficient mice, which completely lack GCs.     

From databases to modelling of functional pathways

This short review comments on current informatics resources and methodologies in the study of functional pathways in cell biology. It highlights recent achievements in unveiling the structural design of protein and gene networks and discusses current approaches to model and simulate the dynamics of regulatory pathways in the cell.     

From continuum Fokker-Planck models to discrete kinetic models

Two theoretical formalisms are widely used in modeling mechanochemical systems such as protein motors: continuum Fokker-Planck models and discrete kinetic models. Both have advantages and disadvantages. Here we present a "finite volume" procedure to solve Fokker-Planck equations. The procedure relates the continuum equations to a discrete mechanochemical kinetic model while retaining many of the features of the continuum formulation. The resulting numerical algorithm is a generalization of the algorithm developed previously by Fricks, Wang, and Elston through relaxing the local linearization approximation of the potential functions, and a more accurate treatment of chemical transitions. The new algorithm dramatically reduces the number of numerical cells required for a prescribed accuracy. The kinetic models constructed in this fashion retain some features of the continuum potentials, so that the algorithm provides a systematic and consistent treatment of mechanical-chemical responses such as load-velocity relations, which are difficult to capture with a priori kinetic models. Several numerical examples are given to illustrate the performance of the method.     

Web-based kinetic modelling using JWS Online

JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet. It is implemented using a client-server strategy where the clients, in the form of web browser based Java applets, act as a graphical interface to the model servers, which perform the required numerical computations. AVAILABILITY: The JWS Online website is publicly accessible at http://jjj.biochem.sun.ac.za/ with mirrors at http://www.jjj.bio.vu.nl/ and http://jjj.vbi.vt.edu/     

tRNA selection and kinetic proofreading in translation

Using single-molecule methods we observed the stepwise movement of aminoacyl-tRNA (aa-tRNA) into the ribosome during selection and kinetic proofreading using single-molecule fluorescence resonance energy transfer (smFRET). Intermediate states in the pathway of tRNA delivery were observed using antibiotics and nonhydrolyzable GTP analogs. We identified three unambiguous FRET states corresponding to initial codon recognition, GTPase-activated and fully accommodated states. The antibiotic tetracycline blocks progression of aa-tRNA from the initial codon recognition state, whereas cleavage of the sarcin-ricin loop impedes progression from the GTPase-activated state. Our data support a model in which ribosomal recognition of correct codon-anticodon pairs drives rotational movement of the incoming complex of EF-Tu-GTP-aa-tRNA toward peptidyl-tRNA during selection on the ribosome. We propose a mechanistic model of initial selection and proofreading.     

Some kinetic aspects and modelling of biotransformation of D-glucose to keto-D-gluconates

The bacterial oxidation of D-glucose to D-gluconic and keto-D-gluconic acids has been studied. Different approaches to pH-control have been checked. It is demonstrated, that the microbial growth is independent on pH-control. However, the rate of keto-gluconate production is too sensitive to the strategy of pH-maintenance and particularly to the neutralizing agent. The general opinion for the essential importance of addition of calcium ions for keto-gluconate formation is confirmed. The interpretation of the obtained experimental data by means of a simple mathematical model shows that the apparent lag-phase in keto-gluconate production is probably due to the necessity of accumulation of biomass as a biocatalyst and gluconic acids as a substrate.     

Application of modelling techniques to the planning of in vitro arsenic kinetic studies

A kinetic model describing the hepatic methylation of arsenite [As(III)] was developed on the basis of limited data from in vitro mechanistic studies. The model structure is as follows: sequential enzymic methylation of arsenite to its monomethylated (MMA) and dimethylated (DMA) products by first-order and Michaelis-Menten kinetics, respectively; uncompetitive inhibition of the formation of DMA by As(III); and first-order reversible binding of As(III), MMA and DMA to cytosolic proteins. Numerical sensitivity analysis was used to evaluate systematically the impact of changes in input parameters on model responses. Sensitivity analysis was used to investigate the possibility of designing experiments for robust testing of the uncompetitive inhibition hypothesis, and for further refining the model. Based on the sensitivity analysis, the MMA concentration is the most important response on which to focus. The parameters V(max) and k(i) can be reliably estimated by using the same concentration time-course data at intermediate initial arsenite concentrations of 1--5microM at 30 +/- 5 minutes. K(m) must be estimated independently of V(max), since the two parameters are highly correlated at all times, and the optimal experimental conditions would include lower initial concentrations of arsenite (0.1--0.5microM) and earlier time-points (about 8--18 minutes). The use of initial arsenite concentrations much above 5microM would not yield additional useful information, because the sensitivity coefficients for MMA, protein-bound MMA, DMA and protein-bound DMA tend to become extremely small or exhibit erratic trends. Overall trends in the sensitivity analysis indicated the desirability of performing measurements at times shorter than 60 minutes. This work demonstrates that physiological modelling and sensitivity analysis can be efficient tools for experimental planning and hypothesis testing when applied in the earliest phases of kinetic model development, thus allowing more-efficient and more-directed experimentation, and minimising the use of laboratory animals.     

Analyzing a kinetic titration series using affinity biosensors

The classical method of measuring binding constants with affinity-based biosensors involves testing several analyte concentrations over the same ligand surface and regenerating the surface between binding cycles. Here we describe an alternative approach to collecting kinetic binding data, which we call "kinetic titration." This method involves sequentially injecting an analyte concentration series without any regeneration steps. Through a combination of simulation and experimentation, we show that this method can be as robust as the classical method of analysis. In addition, kinetic titrations can be more efficient than the conventional data collection method and allow us to fully characterize analyte binding to ligand surfaces that are difficult to regenerate.     

Combinatorial selection of high affinity RNA ligands to live African trypanosomes

African trypanosomiasis is a parasitic disease caused by a specific class of protozoan organisms. The best-studied representative of that group is Trypanosoma brucei which is transmitted by tsetse flies and multiplies in the blood of many mammals. Trypanosomes evade the immune system by altering their surface structure which is dominated by a layer of a variant surface glycoprotein (VSG). Although invariant surface proteins exist, they are inaccessible to the humoral immune response. Using a combinatorial selection method in conjunction with live trypanosomes as the binding target, we show that short RNA ligands (aptamers) for constant surface components can be isolated. We describe the selection of three classes of RNA aptamers that crosslink to a single 42 kDa protein located within the flagellar pocket of the parasite. The RNAs associate rapidly and with high affinity. They do not discriminate between two different trypanosome VSG variant strains and, furthermore, are able to bind to other trypanosome strains not used in the selection protocol. Thus, the aptamers have the potential to function as markers on the surface of the extracellular parasite and as such they might be modified to function as novel drugs against African trypanosomiasis.     

Multistage affinity cross-flow filtration: mathematical modelling and analysis

A multistage affinity cross-flow filtration (mACFF) process for protein purification is proposed. The process is mathematically modelled taking into account a case of rapid equilibrium binding of a target protein to its macroligand. The process performance, i.e., dimensionless breakthrough volume (Q _b ⁺ )and recovery yield (REC) to obtain a desired purity is analysed by computer simulations. The results indicate that Q _b ⁺ increases with the increase of stage number (n) due to the increase of affinity binding efficiency. In addition, REC also increases with the increase of n, especially for lower affinity systems, even though the feed loading is the same as the corresponding breakthrough volume that increases with n. Thus both feed loading and recovery yield can be enhanced by raising the stage number. Incompletely permeable membranes reject the target and contaminant proteins. So they delay the appearance of the breakthrough point and compromise the contaminant washing efficiency. Hence although Q _b ⁺ increases with the increase of membrane rejection coefficient (R), REC decreases when the feed loading equals that of Q _b ⁺ . However, when the feed loading is kept unchanged and equals Q _b ⁺ at R=0, REC does not decrease, but slightly increases with the increase of R. This result indicates that incompletely permeable membranes may also be employed for the mACFF process. In general, the model gives a predictive evaluation of the mACFF process successfully.     

From annotated genomes to metabolic flux models and kinetic parameter fitting

Significant advances in system-level modeling of cellular behavior can be achieved based on constraints derived from genomic information and on optimality hypotheses. For steady-state models of metabolic networks, mass conservation and reaction stoichiometry impose linear constraints on metabolic fluxes. Different objectives, such as maximization of growth rate or minimization of flux distance from a reference state, can be tested in different organisms and conditions. In particular, we have suggested that the metabolic properties of mutant bacterial strains are best described by an algorithm that performs a minimization of metabolic adjustment (MOMA) upon gene deletion. The increasing availability of many annotated genomes paves the way for a systematic application of these flux balance methods to a large variety of organisms. However, such a high throughput goal crucially depends on our capacity to build metabolic flux models in a fully automated fashion. Here we describe a pipeline for generating models from annotated genomes and discuss the current obstacles to full automation. In addition, we propose a framework for the integration of flux modeling results and high throughput proteomic data, which can potentially help in the inference of whole-cell kinetic parameters.     

Sequence-specific affinity selection of mammalian splicing complexes.

Antisense oligonucleotides made of 2'-OMe RNA are shown to bind specifically and efficiently to targeted sites on pre-mRNA substrates, allowing affinity selection of splicing complexes using streptavidin/biotin chromatography. The position of probe binding to the pre-mRNA influences which type of splicing complex can be selected. The accessibility of pre-mRNA sequences to antisense probes changes during the course of the splicing reaction. U1, U2, U4, U5 and U6 snRNAs are all detected in affinity-selected mammalian splicing complexes. However, antisense oligonucleotides targeted to snRNAs can block the binding of specific snRNPs to pre-mRNA. Quantitative affinity selection analyses show that only a small fraction of snRNPs in a HeLa nuclear splicing extract participate in spliceosome formation.     

Design and selection of ligands for affinity chromatography

Affinity chromatography is potentially the most selective method for protein purification. The technique has the purification power to eliminate steps, increase yields and thereby improve process economics. However, it suffers from problems regarding ligand stability and cost. Some of the most recent advances in this area have explored the power of rational and combinatorial approaches for designing highly selective and stable synthetic affinity ligands. Rational molecular design techniques, which are based on the ability to combine knowledge of protein structures with defined chemical synthesis and advanced computational tools, have made rational ligand design feasible and faster. Combinatorial approaches based on peptide and nucleic acid libraries have permitted the rapid synthesis of new synthetic affinity ligands of potential use in affinity chromatography. The versatility of these approaches suggests that, in the near future, they will become the dominant methods for designing and selection of novel affinity ligands with scale-up potential.     

Use of 3-D computer modelling and kinetic studies to analyse grapefruit pyrophosphate-dependent phosphofructokinase

The glycolytic reaction of grapefruit PPi-dependent phosphofructokinase (PFP) depends on the presence of Fru-2,6-P₂ (K_a=6.7 nM). This molecule was further demonstrated in grapefruit juice sac cells. Citrate, -ketoglutarate and isocitrate competitively inhibited the binding of Fru-2,6-P₂ to PFP. The affinity for Fru-6-P (K_m=159 μM) and PPi (K_m=33 μM) were not affected by the addition of these molecules. In the gluconeogenic reaction, the presence of Fru-2,6-P₂ did not affect the K_m of Fru-1,6-P₂ (61 μM) in contrast to orange fruit PFP. These results led to the building of a computer model of PFP, based on the known structure of Bacillus stearothermophilus ATP-dependent phosphofructokinase (ATP-PFK). The results show that catalysis of Fru-6-P in the chain is most unlikely, due to amino-acid substitutions and that Fru-2,6-P₂ can bind between the and β subunits.     

Germinal mosaicism in Crouzon syndrome

Summary Two sibs with classic Crouzon syndrome of the same mother but different fathers are presented as an example of germinal mosaicism in a known autosomal dominant disorder. The mother and both fathers were completely normal.