Transient establishment of imprinted DNA methylation of transgenic human IC1 sequence in mouse during the pre-implantation period

Monoallelic gene expression at the Igf2/H19 locus is controlled by paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) that is established during spermatogenesis. We demonstrated that the H19 ICR fragment in transgenic mice acquires allele-specific methylation only after fertilization, which is essential for maintaining its allelic methylation during early embryogenesis. We identified a DNA element required for establishing post-fertilization methylation within a 118 bp (m118) region. A previously generated knock-in mouse whose endogenous H19 ICR was substituted with the human H19 ICR (hIC1; 4.8 kb) sequence revealed that the hIC1 sequence was partially methylated in sperm, although this methylation was lost by the blastocyst stage, which we assume is due to a lack of an m118-equivalent sequence in the hIC1 transgene. To identify a cis sequence involved in post-fertilization methylation within the hIC1 region, we generated three transgenic mouse lines (TgM): one carrying an 8.8 kb hIC1 sequence joined to m118 (hIC1+m118), one with the 8.8 kb hIC1, and one with the 5.8 kb hIC1 sequence joined to m118 (hIC1–3′+m118). We found that the hIC1–3′ region was resistant to de novo DNA methylation throughout development. In contrast, the 5′ portion of the hIC1 (hIC1–5′) in both hIC1+m118 and hIC1 TgM were preferentially methylated on the paternal allele only during preimplantation. As DNA methylation levels were higher in hIC1+m118, the m118 sequence could also induce imprinted methylation of the human sequence. Most importantly, the hIC1–5′ sequence appears to possess an activity equivalent to that of m118.

Scalar Multiplication via Elliptic Net using Generalized Equivalent Sequences

Chord and tangent is a classical method to calculate the elliptic curve scalar multiplication. Alternatively, the scalar multiplication can be calculated by dividing polynomials over certain finite fields and the first elliptic net scalar multiplication was implemented on a short Weierstrass curve. The net was originated from non-linear recurrence sequences, namely as elliptic divisibility sequence. It is well known that the linear recurrence sequences have been applied in the cryptosystem as a cipher in the encryption and decryption process. From the perspective of cryptographic application, the elliptic divisibility sequence is used generally for integer factorization, solving elliptic curve discrete logarithm problem and computation of pairing or scalar multiplication. But there is a lack of contribution of these non-linear recurrence sequences in scalar multiplication. Therefore, this paper aims to discuss a generalization of the equivalent sequence of elliptic divisibility for computing scalar multiplication. The experimental results of scalar multiplication via the net and its coding in computer programming are presented. The future direction of scalar multiplication via the elliptic net is also discussed.

Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery

Motivation Protein function is intrinsically linked to native dynamics, but the systematic characterization of functionally relevant dynamics remains elusive besides specific examples. Here we exhaustively characterize three types of dynamical couplings between protein residues: co-directionality (moving along collinear directions), coordination (small fluctuations of the interatomic distance) and deformation (the extent by which perturbations applied at one residue modify the local structure of the other one), which we analytically compute through the torsional network model. Results We find that ligand binding sites are characterized by large within-site coordination and co-directionality, much larger than expected for generic sets of residues with equivalent sequence distances. In addition, catalytic sites are characterized by high coordination couplings with other residues in the protein, supporting the view that the overall protein structure facilitates the catalytic dynamics. The binding sites of allosteric effectors are characterized by comparably smaller coordination and higher within-site deformation than other ligands, which supports their dynamic nature. Allosteric inhibitors are coupled to the active site more frequently through deformation than through coordination, while the contrary holds for activators. We characterize the dynamical couplings of the sodium-dependent Leucine transporter protein (LeuT). The couplings between and within sites progress consistently along the transport cycle, providing a mechanistic description of the coupling between the uptake and release of ions and substrate, and they highlight qualitative differences between the wild-type and a mutant for which chloride is necessary for transport. Availability and implementation The program tnm is freely available at https://github.com/ugobas/tnm Supplementary information Supplementary data are available at Bioinformatics online.

Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

An ideal is a family of subsets of positive integers which is closed under taking finite unions and subsets of its elements. In this paper, we introduce a new definition of asymptotically ideal -statistical equivalent sequence in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

The Enantiocontrolled Synthesis of a Highly Functionalized Cyclohexenone Related to the A-Ring of the Furanosteroid Viridin

A seven-step reaction sequence has been used to convert the enantiomerically pure cis-1,2-dihydrocatechol 10 into the cyclohexenone 17a. A near equivalent sequence involving the same starting material has allowed for the synthesis of the regioisomeric system 17b. Compound 17a is related to the A-ring of ent-viridin (ent-1), the non-natural enantiomer of the furanosteroid viridin (1).

The insulin enhancer binding site 2 (IEB2; FAR) box of the insulin gene regulatory region binds at least three factors that can be distinguished by their DNA binding characteristics

Located at approximately 230 bp upstream from the transcription start site, the insulin enhancer binding site 2 (IEB2) or FAR region of the insulin gene is one of several important sequences involved in regulating transcription of the gene. The present study was undertaken to characterize the transcription factors binding at the IEB2/FAR region of the rat insulin II gene and to compare these with factors known to bind to the equivalent sequence in the rat I and human insulin genes. An endocrine-enriched factor, EFD3, was identified, which bound to the sequence CAGGAG. A second factor (D4) was identified as the widely expressed factor USF (upstream stimulating factor), while a third factor (D5) remained largely uncharacterized. The binding affinities of these three factors differed in the three genes, suggesting that the role of the IEB2/FAR sequence may vary subtly between the rat insulin II, rat insulin I and human insulin genes.

Significance of a molluscan fauna to the physiographic history of the Calgary area, Alberta

A newly discovered molluscan fauna provides an approximate age for a previously undated gravel sequence capping Nose Hill, a relict plateau adjacent to the Bow River in Calgary, Alberta, and constrains the age of the physiographic relief in the area. The fauna consists of a mixed terrestrial–aquatic assemblage whose composition indicates a paleoclimatic regime similar to that of the area today. The fossiliferous sediment, interpreted as a pond deposit, is a pebbly mud within a thick braid-plain gravel sequence. Isoleucine epimerization in the molluscs is not inconsistent with an Early Pleistocene or older age for the deposit. The Nose Hill gravels and an equivalent sequence capping another outlier (Broadcast Hill) located on the other side of the Bow River define an originally extensive paleo-plains surface. Fluvial dissection of the surface, including 175 m of incision by the Bow River and resultant separation of the two outliers, occurred within the last one to two million years.

The Role of Acetate in Denitrification and Biological Phosphate Removal in Modified Bardenpho Systems

The importance of easily biodegradable organic substances such as acetate and propionate in biological phosphate removal has been recognised by many researchers. Laboratory-scale studies on the performance of three-stage modified Bardenpho nutrient removal systems, fed with settled sewage supplemented with 0, 50, 100 and 200 mg/l sodium acetate respectively are described. Particular attention is given to the effects of these additions on biological phosphate release and uptake and also to the fate of parameters such as pH, calcium, potassium, ammonia and nitrate. Additional phosphate of 10 mg/l (as P) was initially introduced into the feed in order to burden the experimental systems beyond their normal phosphate removal capacity. This was increased to 20 mg/l and eventually to 40 mg/l of phosphate (as P). Increasing concentrations of sodium acetate resulted in distinct increases in pH values, increase in phosphate release in the anaerobic zones and significantly improved overall phosphate removal in the experimental units. The correlation of phosphate removal on acetate concentration was found to be 0.9886. In some instances the unit receiving 200 mg/l acetate removed up to an average of 30 mg/l of phosphate (as P), constituting an improvement of up to 200% compared with the unit receiving no acetate. The alternating release and uptake of phosphate was accompanied by an equivalent sequence for potassium and magnesium. The high pH value plus the disappearance of phosphate, ammonia and magnesium places doubt on a purely biological phosphate removal but could point at the crystallization of ammonium magnesium phosphate.