We conducted minisatellite-associated sequence amplification (MASA) with an oligo (5' CACCTCTCCACCTGCC 3') based on consensus of 33.15 repeat loci using cDNA from the testis, ovary, spleen, kidney, heart, liver, and lung of water buffalo Bubalus bubalis and uncovered 25 amplicons of six different sizes (1,263, 846/847, 602, 576, 487, and 324 base pairs). These fragments, cloned and sequenced, were found to represent several functional, regulatory, and structural genes. Blast search of all the 25 amplicons showed homologies with 43 transcribing genes across the species. Of these, the 846/847-bp fragment, having homology with the adenylate kinase gene, showed nucleotide changes at six identical places in the ovary and testis. The 1,263; 324; and 487-bp fragments showed homology with the secreted modular calcium binding protein (SMOC-1), leucine-rich repeat neuronal 6A (LRRN6A) mRNA, and human TTTY5 mRNA, respectively. Real-time PCR showed maximum expression of AKL, LRRN6A, and T-cell receptor gamma (TCR-gamma)-like genes in the testis, SMOC-1 in the liver, and the T-cell receptor-like (TCRL) gene in the spleen compared to those used as endogenous control. We construe that these genes have evolved from a common progenitor and conformed to various biological functions during the course of evolution. MASA approach coupled with real-time PCR has potentials to uncover accurate expression of a large number of genes within and across the species circumventing the screening of cDNA library.

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This paper generalizes a previously-conceived, continuation-based optimization technique for scalar objective functions on constraint manifolds to cases of periodic and quasiperiodic solutions of delay-differential equations. A Lagrange formalism is used to construct adjoint conditions that are linear and homogenous in the unknown Lagrange multipliers. As a consequence, it is shown how critical points on the constraint manifold can be found through several stages of continuation along a sequence of connected one-dimensional manifolds of solutions to increasing subsets of the necessary optimality conditions. Due to the presence of delayed and advanced arguments in the original and adjoint differential equations, care must be taken to determine the degree of smoothness of the Lagrange multipliers with respect to time. Such considerations naturally lead to a formulation in terms of multi-segment boundary-value problems (BVPs), including the possibility that the number of segments may change, or that their order may permute, during continuation. The methodology is illustrated using the software package COCO on periodic orbits of both linear and nonlinear delaydifferential equations, keeping in mind that closed-form solutions are not typically available even in the linear case. Finally, we demonstrate optimization on a family of quasiperiodic invariant tori in an example unfolding of a Hopf bifurcation with delay and parametric forcing. The quasiperiodic case is a further original contribution to the literature on optimization constrained by partial differential BVPs.

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In this exposition we consider the wave dynamics of a one-dimensional periodic granular dimer (diatomic) chain mounted on a damped and an undamped linear elastic foundation (otherwise called the on-site potential). It is very well known that periodic granular dimers support solitary wave propagation (similar to that in the homogeneous granular chains) for a specific discrete set of mass ratios. In this work we present the analytical investigation of the evolution of solitary waves and primary pulses in granular dimers when they are mounted on on-site potential with and without velocity proportional foundation damping. We invoke a methodology based on the multiple time-scale asymptotic analysis and partition the dynamics of the perturbed dimer chain into slow and fast components. The dynamics of the dimer chain in the limit of large mass mismatch (auxiliary chain) mounted on on-site potential and foundation damping is used as the basis for the analysis. A systematic analytical procedure is then developed for the slowly varying response of the beads and in estimating primary pulse amplitude evolution resulting in a nonlinear map relating the relative displacement amplitudes of two adjacent beads. The methodology is applicable for arbitrary mass ratios between the beads. We present several examples to demonstrate the efficacy of the proposed method. It is observed that the amplitude evolution predicted by the described methodology is in good agreement with the numerical simulation of the original system. This work forms a basis for further application of the considered methodology to weakly coupled granular dimers which finds practical relevance in designing shock mitigating granular layers.