858 research outputs found
Genome-wide sequence information reveals recurrent hybridization among diploid wheat wild relatives
Compartmentation of phosphoglycerate kinase in Trypanosoma brucei plays a critical role in parasite energy metabolism
QUANTIZATION OF A CLASS OF PIECEWISE AFFINE TRANSFORMATIONS ON THE TORUS
We present a unified framework for the quantization of a family of discrete
dynamical systems of varying degrees of "chaoticity". The systems to be
quantized are piecewise affine maps on the two-torus, viewed as phase space,
and include the automorphisms, translations and skew translations. We then
treat some discontinuous transformations such as the Baker map and the
sawtooth-like maps. Our approach extends some ideas from geometric quantization
and it is both conceptually and calculationally simple.Comment: no. 28 pages in AMSTE
HIV subtype and drug resistance patterns among drug naĂŻve persons in Jos, Nigeria
To determine HIV-1 subtypes and antiretroviral drug resistance mutations for 16 infected, pregnant women in Jos, Nigeria, part of pol (1040 bp) was amplified from patient PBMC DNA, sequenced andanalyzed. Eight of the samples were subtype G, three were CRF02_AG and 2 were unique recombinant forms (URF) between G and CRF02_AG. The remaining consisted of 3 different strains: one was subtypeC, and the other 2 were unrelated URF. Nearly full-length genome sequences were completed for 6 of the strains: 4 subtype G and 2 CRF02_AG. In the 14 drug-naĂŻve subjects, no primary resistance-associated mutations were found, but secondary mutations were identified in 7 different codons of the gene coding for protease: PR K20I, M36I, L63A/P/V, V82I, L10M/I and I93L. In addition, the K238R mutation was identified in the reverse transcriptase gene of 3 viruses. The PR K20I and M36I mutations occurred in all of the strains, and the L10M and V82I mutations occurred only in subtype G. The mutation, I93L, was carried by subtype C viruses. Two of the women that had prior niverapine treatment, had primary resistance-associated mutations, RT M184V and K103N, archived in their proviral DNA several months after treatment cessation. The study reports a predominance of clade G and CRF02_AG, and provides many more examples of nearly full-length genome sequences for subtype G viruses from Nigeria. The ubiquitous presence of PI secondary resistance-associated mutations, as well as primary resistanceassociatedmutations in 2 previously treated women, underscores the need to ensure adherence compliance to treatment
Classification of simple linearly compact n-Lie superalgebras
We classify simple linearly compact n-Lie superalgebras with n>2 over a field
F of characteristic 0. The classification is based on a bijective
correspondence between non-abelian n-Lie superalgebras and transitive Z-graded
Lie superalgebras of the form L=\oplus_{j=-1}^{n-1} L_j, such that L_{-1}=g,
where dim L_{n-1}=1, L_{-1} and L_{n-1} generate L, and [L_j, L_{n-j-1}] =0 for
all j, thereby reducing it to the known classification of simple linearly
compact Lie superalgebras and their Z-gradings. The list consists of four
examples, one of them being the n+1-dimensional vector product n-Lie algebra,
and the remaining three infinite-dimensional n-Lie algebras.Comment: Final version to appear in Communications in Mathematical Physic
Global organization of metabolic fluxes in the bacterium, Escherichia coli
Cellular metabolism, the integrated interconversion of thousands of metabolic
substrates through enzyme-catalyzed biochemical reactions, is the most
investigated complex intercellular web of molecular interactions. While the
topological organization of individual reactions into metabolic networks is
increasingly well understood, the principles governing their global functional
utilization under different growth conditions pose many open questions. We
implement a flux balance analysis of the E. coli MG1655 metabolism, finding
that the network utilization is highly uneven: while most metabolic reactions
have small fluxes, the metabolism's activity is dominated by several reactions
with very high fluxes. E. coli responds to changes in growth conditions by
reorganizing the rates of selected fluxes predominantly within this high flux
backbone. The identified behavior likely represents a universal feature of
metabolic activity in all cells, with potential implications to metabolic
engineering.Comment: 15 pages 4 figure
Competitiveness and the export performance of the euro area
Chapter 1 provides an overview and assessment of the price competitiveness and export performance of the euro area and the larger euro area countries, as well as an evaluation of how standard equations have been able to explain actual export developments. Chapter 2 carries out a constant market share analysis for the euro area and thereby sheds light on the reasons for movements in aggregate export market shares by looking at the sectoral and geographical composition of euro area exports. Chapter 3 looks at the evolution of the technological competitiveness of the euro area and major competitors â proxied by patenting activity and R&D expenditure â and analyses some structural indicators of competitiveness using survey data. Chapter 4 then looks at the impact of FDI on competitiveness and export performance. Finally, Chapter 5 summarises the main findings of the report, but also critically evaluates their importance and implications.
Promoter analysis by saturation mutagenesis
Gene expression and regulation are mediated by DNA sequences, in most instances, directly upstream to the coding sequences by recruiting transcription factors, regulators, and a RNA polymerase in a spatially defined fashion. Few nucleotides within a promoter make contact with the bound proteins. The minimal set of nucleotides that can recruit a protein factor is called a cis-acting element. This article addresses a powerful mutagenesis strategy that can be employed to define cis-acting elements at a molecular level. Technical details including primer design, saturation mutagenesis, construction of promoter libraries, phenotypic analysis, data analysis, and interpretation are discussed
Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus
The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus , displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus . The Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. became allotetraploid after the split from the clade âŒ29 Ma. A. St.-Hil. (179 Mbp), a close relative of , proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus a with an intermediate 1C value (400â800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral
Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors
We investigate the application of hierarchical classification schemes to the
annotation of gene function based on several characteristics of protein
sequences including phylogenic descriptors, sequence based attributes, and
predicted secondary structure. We discuss three Bayesian models and compare
their performance in terms of predictive accuracy. These models are the
ordinary multinomial logit (MNL) model, a hierarchical model based on a set of
nested MNL models, and a MNL model with a prior that introduces correlations
between the parameters for classes that are nearby in the hierarchy. We also
provide a new scheme for combining different sources of information. We use
these models to predict the functional class of Open Reading Frames (ORFs) from
the E. coli genome. The results from all three models show substantial
improvement over previous methods, which were based on the C5 algorithm. The
MNL model using a prior based on the hierarchy outperforms both the
non-hierarchical MNL model and the nested MNL model. In contrast to previous
attempts at combining these sources of information, our approach results in a
higher accuracy rate when compared to models that use each data source alone.
Together, these results show that gene function can be predicted with higher
accuracy than previously achieved, using Bayesian models that incorporate
suitable prior information
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