Targeting age‐specific changes in CD4+ T cell metabolism ameliorates alloimmune responses and prolongs graft survival

Age impacts alloimmunity. Effects of aging on T‐cell metabolism and the potential to interfere with immunosuppressants have not been explored yet. Here, we dissected metabolic pathways of CD4⁺ and CD8⁺ T cells in aging and offer novel immunosuppressive targets. Upon activation, CD4⁺ T cells from old mice failed to exhibit adequate metabolic reprogramming resulting into compromised metabolic pathways, including oxidative phosphorylation (OXPHOS) and glycolysis. Comparable results were also observed in elderly human patients. Although glutaminolysis remained the dominant and age‐independent source of mitochondria for activated CD4⁺ T cells, old but not young CD4⁺ T cells relied heavily on glutaminolysis. Treating young and old murine and human CD4⁺ T cells with 6‐diazo‐5‐oxo‐l‐norleucine (DON), a glutaminolysis inhibitor resulted in significantly reduced IFN‐γ production and compromised proliferative capacities specifically of old CD4⁺ T cells. Of translational relevance, old and young mice that had been transplanted with fully mismatched skin grafts and treated with DON demonstrated dampened Th1‐ and Th17‐driven alloimmune responses. Moreover, DON diminished cytokine production and proliferation of old CD4⁺ T cells in vivo leading to a significantly prolonged allograft survival specifically in old recipients. Graft prolongation in young animals, in contrast, was only achieved when DON was applied in combination with an inhibition of glycolysis (2‐deoxy‐d‐glucose, 2‐DG) and OXPHOS (metformin), two alternative metabolic pathways. Notably, metabolic treatment had not been linked to toxicities. Remarkably, immunosuppressive capacities of DON were specific to CD4⁺ T cells as adoptively transferred young CD4⁺ T cells prevented immunosuppressive capacities of DON on allograft survival in old recipients. Depletion of CD8⁺ T cells did not alter transplant outcomes in either young or old recipients. Taken together, our data introduce an age‐specific metabolic reprogramming of CD4⁺ T cells. Targeting those pathways offers novel and age‐specific approaches for immunosuppression.     

A genetic and spatial Bayesian analysis of mastitis resistance

A nationwide health card recording system for dairy cattle was introduced in Norway in 1975 (the Norwegian Cattle Health Services). The data base holds information on mastitis occurrences on an individual cow basis. A reduction in mastitis frequency across the population is desired, and for this purpose risk factors are investigated. In this paper a Bayesian proportional hazards model is used for modelling the time to first veterinary treatment of clinical mastitis, including both genetic and environmental covariates. Sire effects were modelled as shared random components, and veterinary district was included as an environmental effect with prior spatial smoothing. A non-informative smoothing prior was assumed for the baseline hazard, and Markov chain Monte Carlo methods (MCMC) were used for inference. We propose a new measure of quality for sires, in terms of their posterior probability of being among the, say 10% best sires. The probability is an easily interpretable measure that can be directly used to rank sires. Estimating these complex probabilities is straightforward in an MCMC setting. The results indicate considerable differences between sires with regards to their daughters disease resistance. A regional effect was also discovered with the lowest risk of disease in the south-eastern parts of Norway.     

Conformationally altered aortic myosin light chains

Aorta smooth myosin contains two types of light chain, LC20 and LC17, which fold together with the N-terminal region of each heavy chain to form the globular head region of myosin. We demonstrate an altered conformation of LC20 after its separation from heavy chain by high concentrations of urea, on the basis of the following evidende: 1) A polyclonal antibody against LC20 was not able to recognize this conformationally altered form; 2) Myosin reconstituted from heavy chains and urea-dissociated light chains exhibited extremely low ATPase activity. Circular dichroism unfolding profiles showed that light chains dissociated from heavy chains by SDS appeared to be more stable than those generated by urea dissociation.     

A multistate Markov chain model for evaluating a sterilization policy

"A multistate Markov chain model corresponding to varying fertility and mortality rates at different levels of surviving children of a couple was developed. Asymptotic probabilities of having a fixed number of children have been worked out." The implied geographical focus is on India.     

Convergence to stationary distributions in two-species stochastic competition models

Two sets of sufficient conditions are given for convergence to stationary distributions, for some general models of two species competing in a randomly varying environment. The models are nonlinear stochastic difference equations which define Markov chains. One set of sufficient conditions involves strong continuity and -irreducibility of the transition probability for the chain. The second set has a much weaker irreducibility condition, but is only applicable to monotonic models. The results are applied to a stochastic two-species Ricker model, and to Chesson's lottery model with vacant space, to illustrate how the assumptions can be checked in specific models.     

A Markov approach for describing post-fire succession of vegetation

Vegetation dynamics in the coastal area of the Seto Inland Sea region in Japan, where wild fires occur frequently, were described using a stationary Markov model. In this region, vegetation types ofMiscanthus-Pleioblastus grassland,Lespedeza-Mallotus scrub,Pinus-Rhododendron forest andCrassocephalum-Erechtites community have been identified, and these show cyclic succession under the influence of fires. The model uses parameters determining fire frequency and rate of successional change to analyze the effect of variation in these parameters on the areal ratio of each vegetation type at equilibrium and on the time taken for one vegetation type to succeed another (elapsed successional time). The effect of fire frequency differs between hypothetical habitats with high and low productivity. A policy for vegetation management in areas of high and low productivity is proposed. The advantages and limitations of applying Markov models to studies of vegetation succession are also discussed.     

Antigenic mapping of a human λ light chain: Correlation with three dimensional structure

Although the amino acid sequence and three-dimensional structure of human immunoglobulin light chains have been known for more than 15 years, the location of antigenic markers characteristic of chains has not been determined. Here, we use a set of synthetic overlapping peptides to completely model the sequence of the chain Mcg and test these for the binding or rabbit and goat antisera specific for chain determinants. We assess peptide contributions to -antigenic reactivity and also to identify a portion of C-region where conformational factors contribute to the antigenicity. Specific determinants occur both in the constant and variable (first and third framework) domains of the molecule. The fourth framework of the variable region, a segment specified by the joining gene, is also recognized and cross-reacts antigenically with the homologous region of T cell receptor chains. Major specific determinants are localized in the N- and C-terminal segments, which are linear and devoid of major conformational folding. Other segments that are strongly antigenic, such as the third framework of the V region (residue 78–93) and a segment of the constant region (residues 177–192), show strong conformational dependence in antigenicity.     

Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding

Summary Sixty-four eucaryotic nuclear DNA sequences, half of them coding and half noncoding, have been examined as expressions of first-, second-, or third-order Markov chains. Standard statistical tests found that most of the sequences required at least second-order Markov chains for their representation, and some required chains of third order. For all 64 sequences the observed one-step second-order transition count matrices were effective in predicting the two-step transition count matrices, and 56 of 64 were effective in predicting the three-step transition count matrices. The departure from random expectation of the observed first- and second-order transition count matrices meant that a considerable sample of eucaryotic nuclear DNA sequences, both protein coding and noncoding, have significant local structure over subsequences of three to five contiguous bases, and that this structure occurs throughout the total length of the sequence. These results suggested that present DNA sequences may have arisen from the duplication, concatenation, and gradual modification of very early short sequences.     

DNA microenvironments and the molecular clock

Summary A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compartments, the isochores, defined by their G+C content has been proposed recently. We have found that only homologous gene pairs that are stationary, and belong to the same isochore, can be used consistently for the determination of phylogeny and base substitution rate. In particular, for the rodent-human couple, only about half of the homologous gene pairs are stationary. Stationary genes evolve at the third silent codon position with the same velocity independent of the genes and base composition. By contrast, nonstationary genes display apparent rate values (pseudovelocities) that are significantly higher. Our results cast doubt upon recent claims of a large acceleration in the rate of molecular evolution in rodents.     

A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameter estimators were marginal posterior means computed using a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage, and the parameters (allele frequency, QTL substitution effect, recombination rate, polygenic and residual variances). Several MCMC algorithms were derived for computing Bayesian tests of linkage, which consisted of the marginal posterior probability of linkage and the marginal likelihood of the QTL variance associated with the marker.