Department of Bioscience & Bioengineering

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IIT Jodhpur

Many microorganisms carry genes that have the potential to code for specific functions but remain inactive during the normal lifetime of the organism. Such genes have been termed cryptic genes and their activation usually requires a mutational event. They are different from pseudogenes which arise as a result of duplication of a functional gene but remain inactivated because of the accumulation of multiple mutations. This review is an attempt to examine some of the well-characterized cryptic genetic systems in Escherichia coli in an effort to understand their functional and evolutionary significance.

World University root node

Journal of Genetics

Cryptic genes: Evolutionary puzzles

In brain sections stained with monoclonal antibody SMI-32, which recognizes non-phosphorylated neurofilament protein, we distinguished separate caudal, intermediate, and rostral subdivisions of gigantocellular precentral cortex (areas 4c, 4i, and 4r) in macaque monkeys. The divisions form bands extending mediolaterally across the major body-region representations of the primary motor cortex (M1). These observations provide additional evidence that primary motor cortex is not a single, structurally homogeneous cortical area.

Brain Research

Multiple divisions of macaque precentral motor cortex identified with neurofilament antibody SMI-32

We consider 2D lattices which are disordered by an external field, in this case by a dense, random distribution of attractive pinning centers of an underlying substrate. The preferred configuration of the 2D system with screened-Coulomb two-body interactions and a fixed number of particles is a triangular lattice configuration. The pinning centers strongly affect the triangular lattice configuration. By keeping the location and the density of the pinning centers fixed, we study the effects of pinning strength on the structural properties of the lattice. We find that the strongly disordered lattice prefers to form irregular domains of size s which are composed entirely of topological defects. The distribution of sizes of these domains, D(s) suggest that s-τ for sufficiently large s. Our results are consistent with τ ≥ 2 in the solid phase and τ &lt; 2 in the liquid phase. We present a general argument in support of our findings and suggest that the physics which dictates the structure of 2D lattices on substrates with randomly distributed pinning centers is the same as that for a broad range of problems in which an external field strongly influences the behavior of an interacting physical system.

Materials Research Society Symposium - Proceedings

2D lattices on substrates with randomly distributed pinning centers: a possible scaling law for domain sizes

Transection of a sensory nerve in adults results in profound abnormalities in sensory perception, even if the severed nerve is surgically repaired to facilitate accurate nerve regeneration. In marked contrast, fewer perceptual errors follow nerve transection and surgical repair in children. The basis for this superior recovery in children was unknown. Here we show that there is little or no topographic order in the median nerve to the hand after median nerve section and surgical repair in immature macaque monkeys. Remarkably, however, in the same animals the representation of the reinnervated hand in primary somatosensory cortex (area 3b) is quite orderly. This indicates that there are mechanisms in the developing brain that can create cortical topography, despite disordered sensory inputs. Presumably the superior recovery of perceptual abilities after peripheral nerve transection in children depends on this restoration of somatotopy in the central sensory maps.

Nature

Central reorganization of sensory pathways following peripheral nerve regeneration in fetal monkeys

Most of the existing dynamical studies in one dimension on magnetic insulators have considered the simplest spin models with nearest-neighbor interactions. In real systems, however, it is possible that longer range interactions are not entirely negligible. It is expected that the inclusion of next-nearest-neighbor interactions between spins in one-dimensional spin models will introduce a multitude of new frequencies in addition to the ones already present in the dynamics that arises due to nearest-neighbor interactions. We first present an exact solution for the dynamical xx-spin-pair correlations in an Ising chain with both nearest- and next-nearest-neighbor interactions to confirm our expectation. We next show, via an approximate analytical calculation, that the dynamical zz-spin-pair correlations in the next-nearest-neighbor transverse Ising chain when plotted as a function of time is noticeably different with respect to the exactly solvable nearest-neighbor transverse Ising chain at T→∞ when the next-nearest-neighbor interaction is ≳1/2 of the magnitude of the nearest-neighbor interaction. The effects could be fairly subtle in the time domain representation and in the spectral function when these additional interactions are weak (i.e., <1/2 of the nearest-neighbor interaction magnitude). The general conclusions reached in this work are expected to be valid for other simple quantum spin models such as the XY and XXZ models in one dimension. © 1996 The American Physical Society.

Physical Review B - Condensed Matter and Materials Physics

Relaxation in S=1/2 quantum spin chains: The role of second neighbor interactions

We present a careful simulational study of the onset of instabilities in a toy model grain pile as it is tilted through a threshold angle. Our simulations on a system of 1196 grains reveal qualitative differences in the number of grains undergoing translation over extended length scales below and at the threshold angle. The results are consistent with available experimental data and with the mean field treatments of self-organized critical behavior.

Physica A: Statistical Mechanics and its Applications

Metastability and instability in model grain piles: Scaling below and at the threshold

We present a detailed simulational study of the vertical propagation of weak and strong impulses in deep gravitationally compacted granular columns [see R. S. Sinkovits and S. Sen, Phys. Rev. Lett. 74, 2686 (1995)]. The intergrain potential is assumed to be [Formula Presented], [Formula Presented], where [Formula Presented] is the overlap between the grains. Due to gravitational compaction, the magnitude of the overlap between the grains increases progressively with increasing depth. Therefore the sound velocity increases as an impulse travels vertically downward into a granular column. For weak impulses, our large scale simulational studies show that the sound velocity [Formula Presented], where [Formula Presented] is the depth at which [Formula Presented] is measured. This result, which has been obtained from particle dynamical studies, is in perfect agreement with the predictions based upon elasticity theory. We then extend our analysis to show that (i) for columns with small void fractions, [Formula Presented], [Formula Presented] and (ii) for large amplitude impulses, the velocity of the perturbation [Formula Presented] behaves very differently compared to [Formula Presented] at shallow depths with [Formula Presented] as [Formula Presented]. We also present a detailed numerical study of the velocity power spectra of the individual grains as a function of depth [Formula Presented]. We close with a discussion of the effects of both light and heavy impurities on the vertical sound and shock propagation. © 1996 The American Physical Society.

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

Sound propagation in impure granular columns

Using extensive numerical and some exact asymptotic analyses, we argue that the canonical ensemble relaxation of a classical particle in an anharmonic multi-well potential landscape with leading quartic anharmonicity exhibits a 1/t decay to equilibrium. In addition, we provide numerical evidence of algebraic decay of form 1/tθ, 0 &lt; θ &lt; 1, for stronger leading anharmonicities. Our results have important consequences for relaxation studies in several problems of considerable interest in condensed matter physics such as in the Krumhansl-Schrieffer model of displacive structural phase transitions, and in various complex systems.

Relaxation of classical particles in anharmonic multi-well potentials

Relaxation phenomena in a class of nondissipative systems with two highly disparate time scales (i.e., Brownian systems) have unique commonalities quantifiable via two scalars. It is shown that the exactly solvable problem of the dynamics of a weakly linked impurity spin in a s=1/2 XY chain belongs to this dynamical universality class and so does that of a heavy mass in an infinite harmonic oscillator chain and a spinless quasi two-dimensional attractive Fermi gas in the long-wavelength limit. The case of the strongly linked impurity in the XY chain is also discussed along with the corresponding limits in the harmonic oscillator chain and the electron-gas problems. © 1996 The American Physical Society.

Dynamical universality class of Brownian motion and exact results for a single-impurity s=1/2 XY chain

1. To better understand the limits and extents of plasticity in sensory systems of adult mammals, we unilaterally sectioned the dorsal funiculus at thoracic levels in nine adult rats to deactivate ascending afferents from the hindpaw and lower body. After postsurgical recovery periods of 3 h to 3 mo, the region of primary somatosensory cortex (S1) representing the limbs and trunk was extensively mapped with microelectrodes. 2. Recording sites were later identified as being within the hindlimb representation and other parts of S1 by relating locations of microlesions to the cytochrome oxidase pattern in sections of cortex cut tangential to the pial surface. The extent and effectiveness of spinal cord lesions were evaluated by injecting cholera toxin B subunit conjugated with horseradish peroxidase (B-HRP) at various sites in the deafferented hindpaw. 3. In five animals with complete section of the dorsal funiculus, we failed to detect any response to cutaneous stimulation of any part of the body in the deafferented hindlimb cortex. In four other animals with incomplete lesions, neurons in some penetrations could be activated by hindlimb stimulation, but not by stimulating other body parts. In those cases without activation of hindlimb cortex, B-HRP was detected in the spinal cord only caudal to the lesion, and it was not transported to the nucleus gracilis. Limited transport past the lesion to nucleus gracilis was detected in cases with incomplete lesions. 4. The results indicate that forelimb inputs do not substitute for missing hindlimb inputs in primary somatosensory cortex in rats and that the potential for somatotopic reorganization is more limited than previously thought.