Biomedical subjects

T B Kepler

Publications and source records attributed to T B Kepler.

30 records · Page 2Linked to original sources

PubMed1998

Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection.

The germinal centre reaction (GCR) is a fundamental component of the immune response to T-dependent antigens, during which the immunoglobulin (Ig) genes of B cells experience somatic hypermutation and selection. A maximum-likelihood method on DNA sequence data from 16 individual germinal centres was used to infer that the waiting time for position 33 key (high-affinity) mutations in the anti-(4-hydroxy-3-nitrophenyl) acetyl (NP) response is 8.3 days. This is in marked contrast to the prediction of a key mutant each generation (waiting time about 1/3 day) obtained from a simple model and parameters available in the literature. This disagreement is resolved in part by the finding that the targeted base occurs in a cold spot for hypermutation, raising the predicted waiting time to 2.3 days, although this value remains significantly lower than that inferred from the sequence data. It is proposed that the remaining disparity is attributable to some further stochastic process in the GCR: many early key mutations arise but fail to 'take root' within the GC, either due to emigration or failure of cognate T cell/B cell interaction. Furthermore, it is argued that the frequency with which position 33 mutations are found in secondary responses to NP indicates the presence of selection after the GCR.

Animals↗

PubMed1998

The distribution of variation in regulatory gene segments, as present in MHC class II promoters.

Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and mouse using extensive collections of published sequences together with unpublished sequences recently deposited by us in the EMBL gene bank using the Shannon entropy to quantify diversity. For comparison, we also apply our analysis to distantly related MHC class II promoters, as well as to class I promoters and to class II coding regions. We observe a high level of intraspecies variability, which in mouse but not in man is localized to a significant extent near the binding sites of transcription factors-sites that are conserved over longer evolutionary distances. This localization may both indicate and enhance heterozygote advantage, as the presence of two functionally different promoters would be expected to confer flexibility in the immune response.

Animals↗

PubMed1997

Codon bias and plasticity in immunoglobulins.

Immunoglobulin genes experience Darwinian evolution twice. In addition to the germline evolution all genes experience, immunoglobulins are subjected, upon exposure to antigen, to somatic hypermutation. This is accompanied by selection for high affinity to the eliciting antigen and frequently results in a significant increase in the specificity of the responding population. The hypermutation mechanism displays a strong sequence specificity. Thus arises the opportunity to manipulate codon bias in a site-specific manner so as to direct hypermutation to those parts of the gene that encode the antigen-binding portions of the molecule and away from those that encode the structurally conserved regions. This segregation of mutability would clearly be advantageous; it would enhance the generation of potentially useful variants while keeping mutational loss to acceptably low levels. But it is not clear that the advantage gained would be large enough to produce a measurable effect within the background stochasticity of the evolutionary process. I have performed a pair of statistical tests to determine whether site-specific codon bias in human immunoglobulin genes is correlated with the sequence specificity of the somatic mutation mechanism. The sequence specificity of the mutator was determined by analysis of a database of published immunoglobulin intron sequences that had experienced somatic mutation but not selection. The site-specific codon bias was determined by analysis of published sequences of human germline immunoglobulin V genes. Both tests strongly suggest that evolution has acted to enhance the plasticity of immunoglobulin genes under somatic hypermutation.

Amino Acids↗

PubMed1996

Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement.

Diversity in the Ag binding receptors of B and T cells is achieved through a process of genomic rearrangement involving selection of recombination sites and, in adult mice, addition of nontemplated (N) nucleotides. We have analyzed 543 Ig heavy chain nonproductive rearrangements, involving a single variable region gene segment, from adult and perinatal mice. We infer several fundamental and novel features of the recombination mechanism. N regions are formed predominantly from the DNA plus strand or from the DNA minus strand polymerizations, rather than as a concatenation of the two. Homologous overlaps of as few as one nucleotide between gene segments cause significant skewing of recombination sites. The V(H) recombination site spectrum differs in perinatal and adult mice, with sites representing overlap between V(H) and D over-represented in the perinatal mice, and sites representing overlaps between V(H) and the N strand polymerized onto the D segment over-represented in the adult mice. Thus, in V(D)J joining, N nucleotide addition and recombination site choice are highly interdependent events.

Animals↗

PubMed1995

Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

B-Lymphocytes↗

PubMed1995

Cellular interaction in germinal centers. Roles of CD40 ligand and B7-2 in established germinal centers.

Costimulatory interactions between T and B lymphocytes are crucial for T cell activation and B cell proliferation and differentiation. We have compared the roles of CD40L and B7-2 in the initiation and maturation of humoral immunity by administering anti-CD40 ligand (L) or anti-B7-2 Ab during the early (days -1 to 3) or late (days 6-10) phases of primary responses to thymus-dependent (Td) and -independent (Ti) Ags. Germinal center (GC) formation in response to a Td Ag was inhibited completely by the early administration of anti-CD40L or anti-B7-2 Abs. Later in the response, established GCs remained sensitive to anti-CD40L but were resistant to treatment with anti-B7-2. However, Ig hypermutation was reduced dramatically in GCs of anti-B7-2-treated mice and humoral memory was impaired. Early administration of anti-CD40L reduced serum Ab levels to approximately 10% of controls, whereas early treatment with anti-B7-2 reduced Ab production by only 50%. Later treatments with either Ab had no effect on Ab production. Response to a type II Ti Ag was more resistant than Td responses to interruption of costimulatory interactions. Our findings suggest that the costimulatory roles of CD40:CD40L and B7-2:CD28/CTLA-4 differ in the GC; administration of anti-CD40L abrogates an established GC reaction, whereas Ab to B7-2 suppresses Ig hypermutation and entry into the B cell memory compartment. Once B cells have entered the differentiation pathway to Ab production, neither CD40L nor B7-2 is necessary for their continued differentiation and persistence.

Animals↗

PubMed1993

Somatic hypermutation in B cells: an optimal control treatment.

The vertebrate immune system generates high-affinity antibodies to external antigens through a process of somatic hypermutation that takes place in germinal centers formed in the secondary lymphoid tissues. B cells proliferating in these germinal centers experience random mutations in the genes encoding the variable region of their immunoglobulin molecules and are subsequently selected for high-affinity binding to antigen. These germinal center reactions last for only about 2 weeks, yet in that time typically produce multiple point mutations resulting in affinity increases of factors of ten to a hundred or more. We have attempted to understand this extraordinary effectiveness by causing the problem of affinity maturation as an optimization problem in which a quantity that we call the total affinity is maximized as a functional of mu(t), the mutation rate as a function of time. We have developed a single-compartment model for the process and an optimization algorithm based on the Pontryagin maximum principle. Our results show that the optimum mutation schedule is one with brief bursts of high mutation rates interspersed between periods of mutation-free growth. Though this result at first seems highly non-physiological, we show that, in fact, it provides a framework within which the anatomy and kinetics of the germinal center reaction can be understood.

Animals↗

PubMed1993

Spike initiation and propagation on axons with slow inward currents.

We investigate spike initiation and propagation in a model axon that has a slow regenerative conductance as well as the usual Hodgkin-Huxley type sodium and potassium conductances. We study the role of slow conductance in producing repetitive firing, compute the dispersion relation for an axon with an additional slow conductance, and show that under appropriate conditions such an axon can produce a traveling zone of secondary spike initiation. This study illustrates some of the complex dynamics shown by excitable membranes with fast and slow conductances.

Action Potentials↗

PubMed1993

Cyclic re-entry of germinal center B cells and the efficiency of affinity maturation.

Affinity maturation of the humoral immune response by somatic hypermutation is marked by a rapid and dramatic increase in affinity for the eliciting antigen. We suggest that the optimal mutation schedule is one in which periods of rapid mutation alternate with periods of mutation-free growth. The multicompartmental structure of the germinal center, together with re-entry of positively selected B cells back into the germinal center, will naturally implement such a schedule, thereby providing an anatomical basis for the efficiency of the germinal center reaction.

B-Lymphocytes↗

PubMed1992

Reduction of conductance-based neuron models.

We present a scheme for systematically reducing the number of differential equations required for biophysically realistic neuron models. The techniques are general, are designed to be applicable to a large set of such models and retain in the reduced system as high a degree of fidelity to the original system as possible. As examples, we provide reductions of the Hodgkin-Huxley system and the A-current model of Connor et al. (1977).

Mathematics↗

PubMed1991

Geometric phase shifts in chemical oscillators.

One of the most remarkable developments in quantum mechanics in recent years has been the discovery that when a system is moved adiabatically around a closed loop in parameter space there occurs, besides the familiar dynamical phase shift, an additional phase shift (sometimes referred to as 'Berry's phase') that is purely geometric in nature. The dynamical phase shift, which results from the variation of the period of the oscillatory system with the change in parameters, is relatively easily understood and is proportional to the time over which the parameter change occurs. The geometric phase shift, on the other hand, is less intuitive and depends on the curvature of the surface in parameter space bounded by the closed path, but is independent of the time taken to traverse the circuit. Here we present evidence for time-independent geometric phase shifts in numerical solutions for a model of an oscillating chemical reaction. The conditions for the occurrence of such shifts seem to be sufficiently general that geometric phase effects should be experimentally observable in essentially all chemical oscillators as well as in biological networks such as the brain and the central nervous system, where phase control is of vital importance.

Brain↗

PubMed1990

The effect of electrical coupling on the frequency of model neuronal oscillators.

Neurons with oscillatory properties are a common feature of the nervous system, but little is known about how neural oscillators shape the behavior of neuronal networks or how network interactions influence the properties of neural oscillators. Mathematical models are used to examine the effect of electrically coupling an oscillatory neuron to a second neuron that is either silent or tonically firing. Models of oscillatory neurons with varying degrees of complexity show that this coupling can either increase or decrease the frequency of an oscillator, depending on its membrane potential wave form, the state of the neuron to which it is coupled, and the strength of the coupling. Thus, electrical coupling provides a flexible mechanism for modifying the behavior of an oscillatory neural network.

Action Potentials↗