We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4–5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post-speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).

A genome-wide comparison of recent chimpanzee and human segmental duplications RID E-6420-2011

The concept of boson realization (or mapping) of Lie algebras appeared first in nuclear physics in 1962 as the idea of expanding bilinear forms in fermion creation and annihilation operators in Taylor series of boson operators, with the object of converting the study of nuclear vibrational motion into a problem of coupled oscillators. The physical situations of interest are quite diverse, depending, for instance, on whether excitations for fixed- or variable-particle number are being studied, on how total angular momentum is decomposed into orbital and spin parts, and on whether isotopic spin and other intrinsic degrees of freedom enter. As a consequence, all of the semisimple algebras other than the exceptional ones have proved to be of interest at one time or another, and all are studied in this review. Though the salient historical facts are presented in the introduction, in the body of the review the progression is (generally) from the simplest algebras to the more complex ones. With a sufficiently broad view of the physics requirements, the mathematical problem is the realization of an arbitrary representation of a Lie algebra in a subspace of a suitably chosen Hilbert space of bosons (Heisenberg-Weyl algebra). Indeed, if one includes the study of odd nuclei, one is forced to consider the mappings to spaces that are direct-product spaces of bosons and (quasi)fermions. Though all the methods that have been used for these problems are reviewed, emphasis is placed on a relatively new algebraic method that has emerged over the past decade. Many of the classic results are rederived, and some new results are obtained for odd systems. The major application of these ideas is to the derivation, starting from the shell model, of the phenomenological models of nuclear collective motion, in particular, the geometric model of Bohr and Mottelson and the more recently developed interacting boson model of Arima and Iachello. A critical discussion of those applications is interwoven with the theoretical developments on which they are based; many other applications are included, some of practical interest, some simply to illustrate the concepts, and some to suggest new lines of inquiry.

Boson realizations of Lie algebras with applications to nuclear physics

A new simple four-dimensional equilibrium-free autonomous ODE system is described. The system has seven terms, two quadratic nonlinearities, and only two parameters. Its Jacobian matrix everywhere has rank less than 4. It is hyperchaotic in some regions of parameter space, while in other regions it has an attracting torus that coexists with either a symmetric pair of strange attractors or with a symmetric pair of limit cycles whose basin boundaries have an intricate fractal structure. In other regions of parameter space, it has three coexisting limit cycles and Arnold tongues. Since there are no equilibria, all the attractors are hidden. This combination of features has not been previously reported in any other system, especially one as simple as this.

Coexisting Hidden Attractors in a 4-D Simplified Lorenz System

Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.

Satellite DNA: An Evolving Topic.

Development and applications of the IGISOL technique

Coupling of a three-particle (hole) valence-shell cluster to quadrupole vibrations (Alaga model): the Z = 50 region: odd Ag and I isotopes and the Z = 28 region: odd Mn and Ga isotopes

A parabolic rule for the energy dependence on x = I( I + 1) for proton-neutron multiplets in odd-odd nuclei

SU(6) quadrupole phonon model for even and odd nuclei and the SU(3) limit

We introduce the SU(6) model IBOM/OTQM for odd-odd nuclei and discuss the bands in O(6) limit. Bands are characterized by a particular type of phase correlations in the wave functions and exhibit splitting of the SU(3) analogs of Gallagher-Moszkowski bands.

Vladimir Paar

Papers

Coupling of a three-particle (hole) valence-shell cluster to quadrupole vibrations (Alaga model): the Z = 50 region: odd Ag and I isotopes and the Z = 28 region: odd Mn and Ga isotopes

A parabolic rule for the energy dependence on x = I( I + 1) for proton-neutron multiplets in odd-odd nuclei

SU(6) quadrupole phonon model for even and odd nuclei and the SU(3) limit

SU(6) model for odd-odd nuclei (OTQM/IBOM) and boson-aligned phase diagram inO(6) limit

“Decoupled” and “strongly coupled” band patterns in the particle-vibration coupling model