We consider the logical system of boolean expressions built on the single connector of implication and on positive literals. Assuming all expressions of a given size to be equally likely, we prove that we can define a probability distribution on the set of boolean functions expressible in this system. We then show how to approximate the probability of a function f when the number of variables g...

Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies. Non-long terminal repeat (non-LTR) retrotransposons are a class of MGEs that have been found in most eukaryotic genomes, sometimes in extremely high numbers. In this article, we present a computational tool, MGEScan-non-LT...

Transcriptional gene silencing (TGS) can be achieved by small RNAs targeted to upstream promoter regions. Previously we characterized siRNAs targeted to the HIV-1 long terminal repeat (LTR) promoter at site 247, and found that a 21-base antisense strand of siRNA-247 (LTR-247as) suppressed LTR-mediated expression. To characterize the specificity of LTR-247as, vectors expressing antisense RNAs ta...

Long terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constra...

Marek’s disease (MD), a lymphoproliferative disorder of chickens caused by the MD virus (MDV), is economically significant. The resistance/susceptibility to MD is controlled by host genetics. The host response to different virus strains varies. The pathogenicity of REV-LTR deleted GX0101∆LTR MDV has been previously reported. However, the precise molecular mechanism of the response of chickens t...

In the present study, effect of nano additives in different ratios added to melamine formaldehyde adhesives on properties particleboards was investigated. this respect, two nanoclays [organo-modified (OMC) and unmodified (NC)] graphene nanoplatelet (GNP) were adhesive at rate 1%, 2% 4%. Along with physical (thickness swelling water absorption), mechanical (modulus rupture, modulus elasticity in...

In this study, the torsional stability analysis is presented for thin cylindrical with the functionally graded (FG) middle layer resting on the Winker elastic foundation. The mechanical properties of functionally graded material (FGM) are assumed to be graded in the thickness direction according to a simple power law and exponential distributions in terms of volume fractions of the constituents...

In this paper, we investigate to what extent high resolution transmission electron microscopy images can be used to measure the mass, in terms of thickness, and surface profile, corresponding to the defocus offset, of an object at the atomic scale. Therefore, we derive an expression for the statistical precision with which these object parameters can be estimated in a quantitative analysis. Eva...

Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long termi...

In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual ele...