Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

<p>Abstract</p> <p>Background</p> <p>The complete and accurate human reference genome is important for functional genomics researches. Therefore, the incomplete reference genome and individual specific sequences have significant effects on various studies.</p> <p>Results</p> <p>we used two RNA-Seq datasets from human brain tissues and 10 mixed cell lines to investigate the completeness of human reference genome. First, we demonstrated that in previously identified ~5 Mb Asian and ~5 Mb African novel sequences that are absent from the human reference genome of NCBI build 36, ~211 kb and ~201 kb of them could be transcribed, respectively. Our results suggest that many of those transcribed regions are not specific to Asian and African, but also present in Caucasian. Then, we found that the expressions of 104 RefSeq genes that are unalignable to NCBI build 37 in brain and cell lines are higher than 0.1 RPKM. 55 of them are conserved across human, chimpanzee and macaque, suggesting that there are still a significant number of functional human genes absent from the human reference genome. Moreover, we identified hundreds of novel transcript contigs that cannot be aligned to NCBI build 37, RefSeq genes and EST sequences. Some of those novel transcript contigs are also conserved among human, chimpanzee and macaque. By positioning those contigs onto the human genome, we identified several large deletions in the reference genome. Several conserved novel transcript contigs were further validated by RT-PCR.</p> <p>Conclusion</p> <p>Our findings demonstrate that a significant number of genes are still absent from the incomplete human reference genome, highlighting the importance of further refining the human reference genome and curating those missing genes. Our study also shows the importance of <it>de novo </it>transcriptome assembly. The comparative approach between reference genome and other related human genomes based on the transcriptome provides an alternative way to refine the human reference genome.</p

WO-GRID METHOD FOR BURGERS’ EQUATION BY A NEW MIXED FINITE ELEMENT SCHEME

In this article, we present two-grid stable mixed finite element method for the 2D Burgers’ equation approximated by the -P1 pair which satisfies the inf–sup condition. This method consists in dealing with the nonlinear system on a coarse mesh with width H and the linear system on a fine mesh with width h << H by using Crank–Nicolson time-discretization scheme. Our results show that if we choose H2 = h this method can achieve asymptotically optimal approximation. Error estimates are derived in detail. Finally, numerical experiments show the efficiency of our proposed method and justify the theoretical results

Synthesis and Characterization of a Poly (styrene-block-methylacrylate-random-octadecylacrylate-block-styrene) Shape Memory ABA Triblock Copolymer

A new shape memory polymer (SMP) was prepared from an ABA triblock copolymer with polystyrene (PS) end blocks and a random copolymer midblock of poly(methylacrylate-random-octadecylacrylate) (PMA-r-PODA). The self-assembly of the triblock copolymer generates a three-dimensional, physically cross-linked network by the bridging of the midblocks across the glassy PS domains, which is used as the permanent network in the SMP. A second reversible network is generated by the side-chain crystallization of the PODA side-chains. Shape memory testing by uniaxial deformation and recovery of molded tensile bars demonstrated that shape fixities greater than 96% and shape recoveries greater than 98% were obtained for extensional strains up to 300%. Although some loss of properties was observed with cycling, the entirely physically cross-linked nature of the polymer allowed erasing of the sample history and recovery of the initial properties by annealing the sample at elevated temperature