709 research outputs found
Conspiracy in bacterial genomes
The rank ordered distribution of the codon usage frequencies for 123
bacteriae is best fitted by a three parameters function that is the sum of a
constant, an exponential and a linear term in the rank n. The parameters depend
(two parabolically) from the total GC content. The rank ordered distribution of
the amino acids is fitted by a straight line. The Shannon entropy computed over
all the codons is well fitted by a parabola in the GC content, while the
partial entropies computed over subsets of the codons show peculiar different
behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of
the codon usage frequencies over particular sets, e.g. with C and A
(respectively G and U) as i-th nucleotide, shows a clear linear dependence from
the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references
added, figures added, some tables remove
The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007
In special coordinates (codon position--specific nucleotide frequencies)
bacterial genomes form two straight lines in 9-dimensional space: one line for
eubacterial genomes, another for archaeal genomes. All the 348 distinct
bacterial genomes available in Genbank in April 2007, belong to these lines
with high accuracy. The main challenge now is to explain the observed high
accuracy. The new phenomenon of complementary symmetry for codon
position--specific nucleotide frequencies is observed. The results of analysis
of several codon usage models are presented. We demonstrate that the
mean--field approximation, which is also known as context--free, or complete
independence model, or Segre variety, can serve as a reasonable approximation
to the real codon usage. The first two principal components of codon usage
correlate strongly with genomic G+C content and the optimal growth temperature
respectively. The variation of codon usage along the third component is related
to the curvature of the mean-field approximation. First three eigenvalues in
codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and
archaeal genomes codon usage is clearly distributed along two third order
curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct
bacterial genomes available in Genbank in April 200
A Gibbs approach to Chargaff's second parity rule
Chargaff's second parity rule (CSPR) asserts that the frequencies of short
polynucleotide chains are the same as those of the complementary reversed
chains. Up to now, this hypothesis has only been observed empirically and there
is currently no explanation for its presence in DNA strands. Here we argue that
CSPR is a probabilistic consequence of the reverse complementarity between
paired strands, because the Gibbs distribution associated with the chemical
energy between the bonds satisfies CSPR. We develop a statistical test to study
the validity of CSPR under the Gibbsian assumption and we apply it to a large
set of bacterial genomes taken from the GenBank repository.Comment: 16 page
Electron and positron scattering from 1,1-C₂H₂F₂
1,1-difluoroethylene (1,1-C₂H₂F₂) molecules have been studied for the first time experimentally and theoretically by electron and positron impact. 0.4-1000 eV electron and 0.2-1000 eV positron impact total cross sections (TCSs) were measured using a retarding potential time-of-flight apparatus. In order to probe the resonances observed in the electron TCSs, a crossed-beam method was used to investigate vibrational excitation cross sections over the energy range of 1.3-49 eV and scattering angles 90 degrees and 120 degrees for the two loss energies 0.115 and 0.381 eV corresponding to the dominant C-H (ν₂ and ν₉) stretching and the combined C-F (ν₃) stretching and CH₂ (ν₁₁) rocking vibrations, respectively. Electron impact elastic integral cross sections are also reported for calculations carried out using the Schwinger multichannel method with pseudopotentials for the energy range from 0.5 to 50 eV in the static-exchange approximation and from 0.5 to 20 eV in the static-exchange plus polarization approximation. Resonance peaks observed centered at about 2.3, 6.5, and 16 eV in the TCSs have been shown to be mainly due to the vibrational and elastic channels, and assigned to the B₂, B₁, and A₁ symmetries, respectively. The pi* resonance peak at 1.8 eV in C₂H₄ is observed shifted to 2.3 eV in 1,1-C₂H₂F₂ and to 2.5 eV in C₂F₄; a phenomenon attributed to the decreasing C=C bond length from C₂H₄ to C₂F₄. For positron impact a conspicuous peak is observed below the positronium formation threshold at about 1 eV, and other less pronounced ones centered at about 5 and 20 eV.The work was supported in part by a Grant-in-Aid, the
Ministry of Education, Science, Technology, Sport and Culture,
Japan, the Japan Society for the Promotion of Science
JSPS, and the Japan Atomic Energy Research Institute
JAERI. One of the authors C.M. is also grateful to the
JSPS for financial support under Grant No. P04064. Another
author H.T. acknowledges Dr. T. Ozeki of the JAERI for
his encouragement and support during this work. This work
was also done under the International Atomic Energy Agency
IAEA project for three of the authors C.M., M.H., and
H.T.. Two of the authors M.H.F.B. and M.A.P.L. acknowledge
support from the Brazilian agency Conselho Nacional
de Desenvolvimento Científico e Tecnológico CNPq.
MHFB also acknowledges support from the Paraná state
agency Fundação Araucária and from FINEP ( under Project
No. CT-Infra 1)
Recommended from our members
Calculation of Doppler Coefficient and Other Safety Parameters for a Large Fast Oxide Reactor
Several safety parameters are calculated for a large, fast, Na-cooled, oxide-fueled reactor. The Doppler coefficient is studied as regards its effect on the reactivity during a power excursion, and its dependence on the neutron spectrum, on the concentrations of U/sup 238/, Pu /sup 239/ , a nd Pu/sup 240/, on spatial temperature and power distributions, and on temperature. Other parameters studied include the Na temperature coefficient of reactivity, and the reactivity insertion caused by total Na loss; reactivity coefficients caused by thermal expansion of fuel and steel cladding; the excess operating reactivity; and the reactivity caused by a fuel slump. The effects of a Be reflector on neutron lifetimes are determined. The safety aspects are balanced against economic considerations. (T.F.H.
Contact-Induced Nonlinearity in Oscillating Belts and Webs
This study is motivated by issues in belt dynamics and paper forming where the oscillatory motion of the contact point between the belt and pulley or the web and roll is important. The objective is to evaluate the influence of the nonlinear contact boundary conditions on the dynamics of the belt or web. To accomplish this objective, two models are analyzed using perturbation methods. The first model represents a string on an elastic foundation (an approximation of the paper forming process) and the second model represents a tensioned beam (accessory drive belt). The first correction to the fundamental natural frequency and the dynamic belt/web length are determined as a function of the governing parameters. For both models, the change in belt length is found to be proportional to the radius of the pulley/roll and the initial belt/web energy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69021/2/10.1177_107754639500100404.pd
Does codon bias have an evolutionary origin?
<p>Abstract</p> <p>Background</p> <p>There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.</p> <p>Results</p> <p>Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 ± 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.</p> <p>Conclusion</p> <p>The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.</p
An observation of spin-valve effects in a semiconductor field effect transistor: a novel spintronic device
We present the first spintronic semiconductor field effect transistor.
The injector and collector contacts of this device were made from magnetic
permalloy thin films with different coercive fields so that they could be
magnetized either parallel or antiparallel to each other in different applied
magnetic fields. The conducting medium was a two dimensional electron gas
(2DEG) formed in an AlSb/InAs quantum well.
Data from this device suggest that its resistance is controlled by two
different types of spin-valve effect: the first occurring at the
ferromagnet-2DEG interfaces; and the second occuring in direct propagation
between contacts.Comment: 4 pages, 2 figure
Pressures in Archaeal Protein Coding Genes: A Comparative Study
Our studies on the bases of codons from 11 completely sequenced archaeal genomes
show that, as we move from GC-rich to AT-rich protein-coding gene-containing
species, the differences between G and C and between A and T, the purine load (AG
content), and also the overall persistence (i.e. the tendency of a base to be followed
by the same base) within codons, all increase almost simultaneously, although the
extent of increase is different over the three positions within codons. These findings
suggest that the deviations from the second parity rule (through the increasing
differences between complementary base contents) and the increasing purine load
hinder the chance of formation of the intra-strand Watson–Crick base-paired
secondary structures in mRNAs (synonymous with the protein-coding genes we dealt
with), thereby increasing the translational efficiency. We hypothesize that the ATrich
protein-coding gene-containing archaeal species might have better translational
efficiency than their GC-rich counterparts
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