6,908 research outputs found
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 penalties for . For 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
for as soon as the unknown solution is sparse.
The case needs a special technique where not only Bregman distances but
also a so-called Bregman-Taylor distance has to be employed.
For only preliminary results are shown. These results indicate that,
different from , the regularizing properties depend on the interplay
of the operator and the basis of sparsity. A counterexample for 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-Ă
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, 2754â2759] 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
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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
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