489 research outputs found
Collective Excitations and Stability of the Excitonic Phase in the Extended Falicov--Kimball Model
We consider the excitonic insulator state (often associated with electronic
ferroelectricity), which arises on the phase diagram of an extended spinless
Falicov--Kimball model (FKM) at half-filling. Within the Hartree--Fock
approach, we calculate the spectrum of low-energy collective excitations in
this state up to second order in the narrow-band hopping and/or hybridisation.
This allows to probe the mean-field stability of the excitonic insulator. The
latter is found to be unstable when the case of the pure FKM (no hybridisation
with a fully localised band) is approached. The instability is due to the
presence of another, lower-lying ground state and not to the degeneracy of the
excitonic phase in the pure FKM. The excitonic phase, however, may be
stabilised further away from the pure FKM limit. In this case, the low-energy
excitation spectrum contains new information about the properties of the
excitonic condensate (including the strongly suppressed critical temperature).Comment: 8 pages, LaTeX-Revtex, 3 PostScript figures, minor corrections. Phys.
Rev. B, in pres
Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)
.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties
RNA secondary structure prediction from multi-aligned sequences
It has been well accepted that the RNA secondary structures of most
functional non-coding RNAs (ncRNAs) are closely related to their functions and
are conserved during evolution. Hence, prediction of conserved secondary
structures from evolutionarily related sequences is one important task in RNA
bioinformatics; the methods are useful not only to further functional analyses
of ncRNAs but also to improve the accuracy of secondary structure predictions
and to find novel functional RNAs from the genome. In this review, I focus on
common secondary structure prediction from a given aligned RNA sequence, in
which one secondary structure whose length is equal to that of the input
alignment is predicted. I systematically review and classify existing tools and
algorithms for the problem, by utilizing the information employed in the tools
and by adopting a unified viewpoint based on maximum expected gain (MEG)
estimators. I believe that this classification will allow a deeper
understanding of each tool and provide users with useful information for
selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in
a chapter of the book `Methods in Molecular Biology'. Note that this version
of the manuscript may differ from the published versio
Molecular Analysis of Virulent Determinants of Enterovirus 71
Enterovirus 71 (EV71) is the most important causative agent of hand, foot and mouth disease (HFMD) in children. In most cases, it is a self-limiting illness. However some EV71 infectious cases can develop severe clinical outcomes, such as encephalitis, meningitis, poliomyelitis like paralysis, and even death. To identify the determinants of virulence, the deduced amino acid sequence of polyprotein and nucleotide sequence of 5′-NTR and 3′-NTR in 25 SC-EV71 strains (strains from severe cases) and 31 MC-EV71 strains (strains from mild cases) were analyzed. Results showed four amino acids on two positions (GlyP710/GlnP710/ArgP710 and GluP729) on the DE and EF loop of VP1, one (LysP930) on the surface of protease 2A and four nucleotides on three positions (GP272, UP488 and AP700/UP700) in the 5'-NTR region are associated with EV71 virulent phenotype. Predicted secondary structure of RNA using the consensus sequence of 5'-NTR by RNAStructure showed the mutation of nucleotide at position 488 in strain BJ08-Z004-3 (position 491 in prototype strain BrCr) can result in the discrepancy of an additional pair of nucleotides and thus change the stability of the second structure of IRES. Fragment base content analysis showed that in the region 696 to 714 bp at the 5'-NTR, where the AP700/UP700 was located, the nucleotide constitution ratios differed significantly between SC-EV71 and MC-EV71 strains. In conclusion, comparative genomic analysis showed that virulence of EV71 strains are mainly determined by the amino acids on two positions of VP1, one position of protease 2A and the nucleotides on three positions in 5'-NTR
Analysis of SNP-SNP interactions and bone quantitative ultrasound parameter in early adulthood
Background: Osteoporosis individual susceptibility is determined by the interaction of multiple genetic variants
and environmental factors. The aim of this study was to conduct SNP-SNP interaction analyses in candidate genes
influencing heel quantitative ultrasound (QUS) parameter in early adulthood to identify novel insights into the
mechanism of disease.
Methods: The study population included 575 healthy subjects (mean age 20.41; SD 2.36). To assess bone mass QUS
was performed to determine Broadband ultrasound attenuation (BUA, dB/MHz). A total of 32 SNPs mapping to loci
that have been characterized as genetic markers for QUS and/or BMD parameters were selected as genetic markers
in this study. The association of all possible SNP pairs with QUS was assessed by linear regression and a SNP-SNP
interaction was defined as a significant departure from additive effects.
Results: The pairwise SNP-SNP analysis showed multiple interactions. The interaction comprising SNPs rs9340799
and rs3736228 that map in the ESR1 and LRP5 genes respectively, revealed the lowest p value after adjusting for
confounding factors (p-value = 0.001, β (95% CI) = 14.289 (5.548, 23.029). In addition, our model reported others
such as TMEM135-WNT16 (p = 0.007, β(95%CI) = 9.101 (2.498, 15.704), ESR1-DKK1 (p = 0.012, β(95%CI) = 13.641 (2.
959, 24.322) or OPG-LRP5 (p = 0.012, β(95%CI) = 8.724 (1.936, 15.512). However, none of the detected interactions
remain significant considering the Bonferroni significance threshold for multiple testing (p<0.0001).
Conclusion: Our analysis of SNP-SNP interaction in candidate genes of QUS in Caucasian young adults reveal several
interactions, especially between ESR1 and LRP5 genes, that did not reach statistical significance. Although our results do
not support a relevant genetic contribution of SNP-SNP epistatic interactions to QUS in young adults, further studies in
larger independent populations would be necessary to support these preliminary findings.This study was supported by a grant PI-0414-2014 from Consejería de Salud
(Junta de Andalucía, Spain). Correa-Rodríguez M is a predoctoral fellow (FPU13/
00143) from the Ministerio de Educación, Cultura y Deporte (Programa de
Formación del Profesorado Universitario)
Approaches to link RNA secondary structures with splicing regulation
In higher eukaryotes, alternative splicing is usually regulated by protein
factors, which bind to the pre-mRNA and affect the recognition of splicing
signals. There is recent evidence that the secondary structure of the pre-mRNA
may also play an important role in this process, either by facilitating or by
hindering the interaction with factors and small nuclear ribonucleoproteins
(snRNPs) that regulate splicing. Moreover, the secondary structure could play a
fundamental role in the splicing of yeast species, which lack many of the
regulatory splicing factors present in metazoans. This review describes the
steps in the analysis of the secondary structure of the pre-mRNA and its
possible relation to splicing. As a working example, we use the case of yeast
and the problem of the recognition of the 3-prime splice site.Comment: 21 pages, 7 figure
Technical Design Report for the PANDA Solenoid and Dipole Spectrometer Magnets
This document is the Technical Design Report covering the two large
spectrometer magnets of the PANDA detector set-up. It shows the conceptual
design of the magnets and their anticipated performance. It precedes the tender
and procurement of the magnets and, hence, is subject to possible modifications
arising during this process.Comment: 10 pages, 14MB, accepted by FAIR STI in May 2009, editors: Inti
Lehmann (chair), Andrea Bersani, Yuri Lobanov, Jost Luehning, Jerzy Smyrski,
Technical Coordiantor: Lars Schmitt, Bernd Lewandowski (deputy),
Spokespersons: Ulrich Wiedner, Paola Gianotti (deputy
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