1,572 research outputs found
Evolution of gene fusions: horizontal transfer versus independent events
BACKGROUND: Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution. RESULTS: The evolutionary history of gene fusions was studied by phylogenetic analysis of the domains in the fused proteins and the orthologous domains that form stand-alone proteins. Clustering of fusion components from phylogenetically distant species was construed as evidence of dissemination of the fused genes by horizontal transfer. Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms. On many occasions, the evolutionary scenario also involves one or more secondary fissions of the fusion gene. For approximately half of the fusions, stand-alone forms of the fusion components are encoded by juxtaposed genes, which are known or predicted to belong to the same operon in some of the prokaryotic genomes. This indicates that evolution of gene fusions often, if not always, involves an intermediate stage, during which the future fusion components exist as juxtaposed and co-regulated, but still distinct, genes within operons. CONCLUSION: These findings suggest a major role for horizontal transfer of gene fusions in the evolution of protein-domain architectures, but also indicate that independent fusions of the same pair of domains in distant species is not uncommon, which suggests positive selection for the multidomain architectures
Correct quantum chemistry in a minimal basis from effective Hamiltonians
We describe how to create ab-initio effective Hamiltonians that qualitatively
describe correct chemistry even when used with a minimal basis. The
Hamiltonians are obtained by folding correlation down from a large parent basis
into a small, or minimal, target basis, using the machinery of canonical
transformations. We demonstrate the quality of these effective Hamiltonians to
correctly capture a wide range of excited states in water, nitrogen, and
ethylene, and to describe ground and excited state bond-breaking in nitrogen
and the chromium dimer, all in small or minimal basis sets
Semantic distillation: a method for clustering objects by their contextual specificity
Techniques for data-mining, latent semantic analysis, contextual search of
databases, etc. have long ago been developed by computer scientists working on
information retrieval (IR). Experimental scientists, from all disciplines,
having to analyse large collections of raw experimental data (astronomical,
physical, biological, etc.) have developed powerful methods for their
statistical analysis and for clustering, categorising, and classifying objects.
Finally, physicists have developed a theory of quantum measurement, unifying
the logical, algebraic, and probabilistic aspects of queries into a single
formalism. The purpose of this paper is twofold: first to show that when
formulated at an abstract level, problems from IR, from statistical data
analysis, and from physical measurement theories are very similar and hence can
profitably be cross-fertilised, and, secondly, to propose a novel method of
fuzzy hierarchical clustering, termed \textit{semantic distillation} --
strongly inspired from the theory of quantum measurement --, we developed to
analyse raw data coming from various types of experiments on DNA arrays. We
illustrate the method by analysing DNA arrays experiments and clustering the
genes of the array according to their specificity.Comment: Accepted for publication in Studies in Computational Intelligence,
Springer-Verla
Synapse efficiency diverges due to synaptic pruning following over-growth
In the development of the brain, it is known that synapses are pruned
following over-growth. This pruning following over-growth seems to be a
universal phenomenon that occurs in almost all areas -- visual cortex, motor
area, association area, and so on. It has been shown numerically that the
synapse efficiency is increased by systematic deletion. We discuss the synapse
efficiency to evaluate the effect of pruning following over-growth, and
analytically show that the synapse efficiency diverges as O(log c) at the limit
where connecting rate c is extremely small. Under a fixed synapse number
criterion, the optimal connecting rate, which maximize memory performance,
exists.Comment: 15 pages, 16 figure
Mammalian Genes Preferentially Co-Retained in Radiation Hybrid Panels Tend to Avoid Coexpression
Coexpression has been frequently used to explore modules of functionally related genes in eukaryotic genomes. However, we found that genetically interacting mammalian genes identified through radiation hybrid (RH) genotypes tend not to be coexpressed across tissues. This pattern remained unchanged after controlling for potential confounding factors, including chromosomal linkage, chromosomal distance, and gene duplication. Because >99.9% of the genetically interacting genes were identified according to the higher co-retention frequencies, our observation implies that coexpression is not necessarily an indication of the need for the co-presence of two genes in the genome, which is a prerequisite for cofunctionality of their coding proteins in the cell. Therefore, coexpression information must be applied cautiously to the exploration of the functional relatedness of genes in a genome
Leaf-applied sodium chloride promotes cadmium accumulation in durum wheat grain
Cadmium (Cd) accumulation in durum wheat grain is a growing concern. Among the factors affecting Cd accumulation in plants, soil chloride (Cl) concentration plays a critical role. The effect of leaf NaCl application on grain Cd was studied in greenhouse-grown durum wheat (Triticum turgidum L. durum, cv. Balcali-2000) by immersing (10 s) intact flag leaves into Cd and/or NaCl-containing solutions for 14 times during heading and dough stages. Immersing flag leaves in solutions containing increasing amount of Cd resulted in substantial increases in grain Cd concentration. Adding NaCl alone or in combination with the Cd-containing immersion solution promoted accumulation of Cd in the grains, by up to 41%. In contrast, Zn concentrations of grains were not affected or even decreased by the NaCl treatments. This is likely due to the effect of Cl complexing Cd and reducing positive charge on the metal ion, an effect that is much smaller for Zn. Charge reduction or removal (CdCl2 0 species) would increase the diffusivity/lipophilicity of Cd and enhance its capability to penetrate the leaf epidermis and across membranes. Of even more significance to human health was the ability of Cl alone to penetrate leaf tissue and mobilize and enhance shoot Cd transfer to grains, yet reducing or not affecting Zn transfer
MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation
MADNESS (multiresolution adaptive numerical environment for scientific
simulation) is a high-level software environment for solving integral and
differential equations in many dimensions that uses adaptive and fast harmonic
analysis methods with guaranteed precision based on multiresolution analysis
and separated representations. Underpinning the numerical capabilities is a
powerful petascale parallel programming environment that aims to increase both
programmer productivity and code scalability. This paper describes the features
and capabilities of MADNESS and briefly discusses some current applications in
chemistry and several areas of physics
Investigation of crystallization process in isotropic rare-earth-rich (Nd or Pr)–Fe–B films
In this paper, the relationship between the initial crystalline behavior and annealing conditions in pulsed laser deposition (PLD)-made Nd-Fe-B and Pr-Fe-B films with rare-earth-rich composition is discussed. The films with rare-earth-rich compositions are prepared via PLD. An annealing process is necessary to obtain the crystalline 2-14-1 phase of hard magnetic properties because all the as-deposited films have an amorphous structure. In conventional annealing, the initial crystallization of the Pr2Fe14B phase occurred at lower temperatures compared with that of the Nd2Fe14B phase, indicating that the annealing temperature of the initial crystallization of the Pr2Fe14B phase was lower than that of the Nd2Fe14B phase. Considering the same crystallization temperature in both the phases, the melting points of both rare-earth elements, Nd and Pr, are considered to relate to the initial crystallization behavior. We also confirmed that the annealing time for Pr2Fe14B phase formation was shorter than that for Nd2Fe14B phase formation
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