Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron-5 of the Sheep SCF Gene: A Novel Splice Variant

Stem cell factor (SCF) is a growth factor, essential for haemopoiesis, mast cell development and melanogenesis. In the hematopoietic microenvironment (HM), SCF is produced either as a membrane-bound (−) or soluble (+) forms. Skin expression of SCF stimulates melanocyte migration, proliferation, differentiation, and survival. We report for the first time, a novel mRNA splice variant of SCF from the skin of white merino sheep via cloning and sequencing. Reverse transcriptase (RT)-PCR and molecular prediction revealed two different cDNA products of SCF. Full-length cDNA libraries were enriched by the method of rapid amplification of cDNA ends (RACE-PCR). Nucleotide sequencing and molecular prediction revealed that the primary 1519 base pair (bp) cDNA encodes a precursor protein of 274 amino acids (aa), commonly known as ‘soluble’ isoform. In contrast, the shorter (835 and/or 725 bp) cDNA was found to be a ‘novel’ mRNA splice variant. It contains an open reading frame (ORF) corresponding to a truncated protein of 181 aa (vs 245 aa) with an unique C-terminus lacking the primary proteolytic segment (28 aa) right after the D175G site which is necessary to produce ‘soluble’ form of SCF. This alternative splice (AS) variant was explained by the complete nucleotide sequencing of splice junction covering exon 5-intron (5)-exon 6 (948 bp) with a premature termination codon (PTC) whereby exons 6 to 9/10 are skipped (Cassette Exon, CE 6–9/10). We also demonstrated that the Northern blot analysis at transcript level is mediated via an intron-5 splicing event. Our data refine the structure of SCF gene; clarify the presence (+) and/or absence (−) of primary proteolytic-cleavage site specific SCF splice variants. This work provides a basis for understanding the functional role and regulation of SCF in hair follicle melanogenesis in sheep beyond what was known in mice, humans and other mammals

Iterative Substructuring Methods for Spectral Element Discretizations of Elliptic Systems. I: Compressible Linear Elasticity

An iterative substructuring method for the system of linear elasticity in three dimensions is introduced and analyzed. The pure displacement formulation for compressible materials is discretized with the spectral element method. The resulting stiffness matrix is symmetric and positive definite. The proposed method provides a domain decomposition preconditioner constructed from local solvers for the interior of each element and for each face of the elements and a coarse, global solver related to the wire basket of the elements. As in the scalar case, the condition number of the preconditioned operator is independent of the number of spectral elements and grows as the square of the logarithm of the spectral degree

BDDC DELUXE ALGORITHMS FOR TWO-DIMENSIONAL H(curl ) ISOGEOMETRIC ANALYSIS

Isogeometric analysis has been introduced as an alternative to finite elements to simplify the integration of computer-aided design and the discretization of variational problems of continuum mechanics. In contrast to finite elements, the basis functions of isogeometric analysis, B-splines and nonuniform rational basis splines, are typically not nodal which makes the interface between subdomains fat with several layers of knots and which creates new issues in the design and analysis of iterative solvers based on domain decomposition methods. The resulting systems of algebraic equations also tend to be much more ill-conditioned than those derived from finite elements. The deluxe variant of adaptive balancing domain decomposition by constraints algorithms have proven successful, and in this study, it is applied to two-dimensional problems formulated in \bfH (curl). Numerical results show very good performance even for high degrees of the underlying B-splines, and fast convergence has been found for p \leq 7 using no more than 2(p2 + p - 1) global (primal) variables per subdomain, where p is the degree of the B-splines. All our results are focused on the most difficult case with the maximum degree of continuity of the B-splines