Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics

Apomixis: an enigma with potential applications

Apomixis has been the focus of research in plant sciences in recent years with lot of scope for crop improvement. It results in clonal progeny without fertilization, having maternal genetic constitution. The impact of introducing apomixis in crop plants could be significant mainly for its use in fixation of hybrid vigour. Because of epigenetic barriers, introgression of apomixis from a close relative to a sexual crop plant by conventional plant breeding methods could not generate expected results. Recent developments in plant molecular biology and biotechnology can help in developing potential strategies. This article summarizes various aspects of apomixis research that are being followed in India and abroad

Inelastic X-ray scattering in correlated (Mott) insulators

We calculate the inelastic light scattering from X-rays, which allows the photon to transfer both energy and momentum to the strongly correlated charge excitations. We find that the charge transfer peak and the low energy peak both broaden and disperse through the Brillouin zone similar to what is seen in experiments in materials like Ca_2 Cu O_2 Cl_2.Comment: 5 pages Revtex4, 6 figure

Convergence rates and source conditions for Tikhonov regularization with sparsity constraints

This paper addresses the regularization by sparsity constraints by means of weighted $\ell^p$ penalties for $0\leq p\leq 2$. For $1\leq p\leq 2$ special attention is payed to convergence rates in norm and to source conditions. As main result it is proven that one gets a convergence rate in norm of $\sqrt{\delta}$ for $1\leq p\leq 2$ as soon as the unknown solution is sparse. The case $p=1$ needs a special technique where not only Bregman distances but also a so-called Bregman-Taylor distance has to be employed. For $p<1$ only preliminary results are shown. These results indicate that, different from $p\geq 1$, the regularizing properties depend on the interplay of the operator and the basis of sparsity. A counterexample for $p=0$ shows that regularization need not to happen

Black Hole Mergers and Unstable Circular Orbits

We describe recent numerical simulations of the merger of a class of equal mass, non-spinning, eccentric binary black hole systems in general relativity. We show that with appropriate fine-tuning of the initial conditions to a region of parameter space we denote the threshold of immediate merger, the binary enters a phase of close interaction in a near-circular orbit, stays there for an amount of time proportional to logarithmic distance from the threshold in parameter space, then either separates or merges to form a single Kerr black hole. To gain a better understanding of this phenomena we study an analogous problem in the evolution of equatorial geodesics about a central Kerr black hole. A similar threshold of capture exists for appropriate classes of initial conditions, and tuning to threshold the geodesics approach one of the unstable circular geodesics of the Kerr spacetime. Remarkably, with a natural mapping of the parameters of the geodesic to that of the equal mass system, the scaling exponent describing the whirl phase of each system turns out to be quite similar. Armed with this lone piece of evidence that an approximate correspondence might exist between near-threshold evolution of geodesics and generic binary mergers, we illustrate how this information can be used to estimate the cross section and energy emitted in the ultra relativistic black hole scattering problem. This could eventually be of use in providing estimates for the related problem of parton collisions at the Large Hadron Collider in extra dimension scenarios where black holes are produced.Comment: 16 pages, 12 figures; updated to coincide with journal versio

Crystal structure of monomeric human β-2- microglobulin reveals clues to its amyloidogenic properties

Dissociation of human β-2-microglobulin (β(2)m) from the heavy chain of the class I HLA complex is a critical first step in the formation of amyloid fibrils from this protein. As a consequence of renal failure, the concentration of circulating monomeric β(2)m increases, ultimately leading to deposition of the protein into amyloid fibrils and development of the disorder, dialysis-related amyloidosis. Here we present the crystal structure of a monomeric form of human β(2)m determined at 1.8-Å resolution that reveals remarkable structural changes relative to the HLA-bound protein. These involve the restructuring of a β bulge that separates two short β strands to form a new six-residue β strand at one edge of this β sandwich protein. These structural changes remove key features proposed to have evolved to protect β sheet proteins from aggregation [Richardson, J.&Richardson, D. (2002) Proc. Natl. Acad. Sci. USA 99, 2754–2759] and replaces them with an aggregationcompetent surface. In combination with solution studies using (1)H NMR, we show that the crystal structure presented here represents a rare species in solution that could provide important clues about the mechanism of amyloid formation from the normally highly soluble native protein

IQGAP1 and IQGAP2 are Reciprocally Altered in Hepatocellular Carcinoma

<p>Abstract</p> <p>Background</p> <p>IQGAP1 and IQGAP2 are homologous members of the IQGAP family of scaffold proteins. Accumulating evidence implicates IQGAPs in tumorigenesis. We recently reported that IQGAP2 deficiency leads to the development of hepatocellular carcinoma (HCC) in mice. In the current study we extend these findings, and investigate IQGAP1 and IQGAP2 expression in human HCC.</p> <p>Methods</p> <p>IQGAP1 and IQGAP2 protein expression was assessed by Western blotting and immunohistochemistry. IQGAP mRNA was measured by quantitative RT-PCR. The methylation status of the <it>Iqgap2 </it>promoter was determined by pyrosequencing of bisulfite-treated genomic DNA.</p> <p>Results</p> <p>IQGAP1 and IQGAP2 expression was reciprocally altered in 6/6 liver cancer cell lines. Similarly, immunohistochemical staining of 82 HCC samples showed that IQGAP2 protein expression was reduced in 64/82 (78.0%), while IQGAP1 was present in 69/82 (84.1%). No IQGAP1 staining was detected in 23/28 (82.1%) normal livers, 4/4 (100.0%) hepatic adenomas and 23/23 (100.0%) cirrhosis cases, while IQGAP2 was increased in 22/28 (78.6%), 4/4 (100.0%) and 23/23 (100.0%), respectively. Although the <it>Iqgap2 </it>promoter was not hypermethylated in HCC at any of the 25 CpG sites studied (N = 17), IQGAP2 mRNA levels were significantly lower in HCC specimens (N = 23) than normal livers (N = 6).</p> <p>Conclusions</p> <p>We conclude that increased IQGAP1 and/or decreased IQGAP2 contribute to the pathogenesis of human HCC. Furthermore, downregulation of IQGAP2 in HCC occurs independently of hypermethylation of the <it>Iqgap2 </it>promoter. Immunostaining of IQGAP1 and IQGAP2 may aid in the diagnosis of HCC, and their pharmacologic modulation may represent a novel therapeutic strategy for the treatment of liver cancer.</p

Optimizing thermal transport in the Falicov-Kimball model: binary-alloy picture

We analyze the thermal transport properties of the Falicov-Kimball model concentrating on locating regions of parameter space where the thermoelectric figure-of-merit ZT is large. We focus on high temperature for power generation applications and low temperature for cooling applications. We constrain the static particles (ions) to have a fixed concentration, and vary the conduction electron concentration as in the binary-alloy picture of the Falicov-Kimball model. We find a large region of parameter space with ZT>1 at high temperature and we find a small region of parameter space with ZT>1 at low temperature for correlated systems, but we believe inclusion of the lattice thermal conductivity will greatly reduce the low-temperature figure-of-merit.Comment: 13 pages, 14 figures, typeset with ReVTe

Nonlinear Optical Response Functions of Mott Insulators Based on Dynamical Mean Field Approximation

We investigate the nonlinear optical susceptibilities of Mott insulators with the dynamical mean field approximation. The two-photon absorption (TPA) and the third-harmonic generation (THG) spectra are calculated, and the classification by the types of coupling to external fields shows different behavior from conventional semiconductors. The direct transition terms are predominant both in the TPA and THG spectra, and the importance of taking all types of interaction with the external field into account is illustrated in connection with the THG spectrum and dcKerr effect. The dependence of the TPA and THG spectra on the Coulomb interaction indicate a scaling relation. We apply this relation to the quantitative evaluation and obtain results comparable to those of experiments.Comment: 14 pages, 12 figure