Alu Clusters Research Articles

Implementation of FPGA based MRPMA for high performance applications

In the last few decay, Network on Chip’s (NoC) are the powerful chips for high speed communications pertaining to 802.11 Ethernet protocol which is a need to be reconfigurable for successful data frame transmission. The existing architectures like coarse grained reconfigurable, ALU cluster and expression grain reconfigurable architecture and look-up-table used in fine grained reconfigurable devices requires a lot of storage memory, hardware resources such as slices, cell area and cell delay. To tackle these issues, Multigrained Reconfiguration and Parallel Mapping Architecture (MRPMA) is proposed and their performance analysis parameters are calculated. The MRPMA uses the four contributions to optimize Processing Elements (PE’s) operations: 1) Fast Fourier Transformation (FFT) to perform fixed point numbers to the configuration words, 2) Discrete Cosine Transformation (DCT) to analyze the data in the frequency domain, 3) Finite Impulse Response (FIR) for parallel mapping the data and 4) Channel encoder and decoder to encode the data and to calculate the shortest route from source to destination switch.

A 64-bit stream processor architecture for scientific applications

Stream architecture is a novel microprocessor architecture with wide application potential. But as for whether it can be used efficiently in scientific computing, many issues await further study. This paper first gives the design and implementation of a 64-bit stream processor, FT64 (Fei Teng 64), for scientific computing. The carrying out of 64-bit extension design and scientific computing oriented optimization are described in such aspects as instruction set architecture, stream controller, micro controller, ALU cluster, memory hierarchy and interconnection interface here. Second, two kinds of communications as message passing and stream communications are put forward. An interconnection based on the communications is designed for FT64-based high performance computers. Third, a novel stream programming language, SF95 (Stream FORTRAN95), and its compiler, SF95Compiler (Stream FORTRAN95 Compiler), are developed to facilitate the development of scientific applications. Finally, nine typical scientific application kernels are tested and the results show the efficiency of stream architecture for scientific computing.

Duplication, coclustering, and selection of human Alu retrotransposons.

Alu and L1 are families of non-LTR retrotransposons representing approximately equal 30% of the human genome. Genomic distributions of young Alu and L1 elements are quite similar, but over time, Alu densities in GC-rich DNA increase in comparison with L1 densities. Here we analyze two processes that may contribute to this phenomenon. First, DNA duplications in the human genome occur more frequently in Alu- and GC-rich than in AT-rich chromosomal regions. Second, most Alu elements tend to be coclustered with each other, but recently retroposed elements are likely to be inserted outside the existing clusters. These "stand-alone" elements appear to be rapidly eliminated from the genome. We also report that over time, the densities of recently retroposed Alu families on chromosome Y decline rapidly, whereas Alu densities on chromosome X increase relative to autosomal densities. We propose that these changes in the chromosomal proportions of Alu densities and the elimination of stand-alone Alus represent the same process of paternal Alu selection. We also propose that long-term Alu accumulation in GC-rich DNA is associated with DNA duplication initiated by elevated recombinogenic activities in Alu clusters.

Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex.

The human genome is composed of long-range G+C% (GC%) mosaic structures thought to be related to chromosome bands. We previously reported a boundary of megabase-sized GC% mosaic domains at the junction area between major histocompatibility complex (MHC) classes II and III, proposing it as a possible chromosome band boundary. DNA replication timing during the S phase is known to be correlated cytogenetically with chromosome band zones, and thus the band boundaries have been predicted to contain a switch point for DNA replication timing. In this study, to identify to the nucleotide sequence level the replication switch point during the S phase, we determined the precise DNA replication timing for MHC classes II and III, focusing on the junction area. To do this, we used PCR-based quantitation of nascent DNA obtained from synchronized human myeloid leukemia HL60 cells. The replication timing changed precisely in the boundary region with a 2-h difference between the two sides, supporting the prediction that this region may be a chromosome band boundary. We supposed that replication fork movement terminates (pauses) or significantly slows in the switch region, which contains dense Alu clusters; polypurine/polypyrimidine tracts; di-, tri-, or tetranucleotide repeats; and medium-reiteration-frequency sequences. Because the nascent DNA in the switch region was recovered at low efficiency, we investigated whether this region is associated with the nuclear scaffold and found three scaffold-associated regions in and around the switch region.

A boundary of long-range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary

The human genome is composed of long-range G+C% (GC%) mosaic structures related to chromosome bands. We found the human MHC locus to be an example of megabase-level GC% mosaic structures and predicted a possible boundary of the megabase-level domains within an undercharacterized 450-kb region harboring the junction of MHC classes II and III. Chromosome walking of the 450-kb region and base-compositional analysis precisely located the boundary of the mosaic domains, disclosing a sharp GC% transition. Near the transition point there was a 20-kb dense Alu cluster, a 30-kb dense LINE-1 cluster, and a sequence highly homologous with the pseudoautosomal boundary of the short arms of human sex chromosomes (PAB1X and PAB1Y); PAB1X and PAB1Y are the interface between sex-specific and pseudoautosomal regions. Many PAB1XY-like sequences (PABLs) were detected by hybridization against genomic DNA, and the new sequences defined the complete form of PABLs to be about 650 nt.

Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment.

We have conducted a detailed structural analysis of 90 kilobases (kb) of the HLA Class III region from the Bat2 gene at the centromeric end to 23 kb beyond TNF. A single contig of 80 kb was sequenced entirely with a group of four smaller contigs covering 10 kb being only partly sequenced. This region contains four known genes and a novel telomeric potential coding region. The genes are bracketed by long, dense clusters of Alu repeats belonging to all the major families. At least six new families of MER repeats and one pseudogene are intercalated within and between the Alu clusters. The most telomeric 3.8 kb contains three potential exons, one of which bears strong homology to the ankyrin domain of the DNA binding factors NF kappa B and I kappa B.

Sequence of human glucose-6-phosphate dehydrogenase cloned in plasmids and a yeast artificial chromosome

The sequence of 20,114 bp of DNA including the human glucose-6-phosphate dehydrogenase (G6PD) gene was determined. The region included a prominent CpG island, starting about 680 nucleotides upstream of the transcription start site, extending about 1050 nucleotides downstream of the start site, and ending just at the start of the first intron. The transcribed region from the start site to the poly (A) addition site covers 15,860 bp. The sequence of the 13 exons agreed with published cDNA sequence and for the 11 exons tested, with the corresponding sequence in a yeast artificial chromosome (YAC). The latter confirms YAC cloning fidelity at the DNA sequence level. Sixteen Alu sequences constitute 24% of the total sequence tract. Four were outside the borders of the mRNA transcript of the gene; all the others were found in a large (9858 bp) intron between exons 2 and 3. Two Alu clusters each contain Alus lying between the monomers of another.

Polymorphism and evolution of Alu sequences in the human low density lipoprotein receptor gene.

Two clusters of Alu sequences in the human low density lipoprotein (LDL) receptor gene have been analyzed in detail. One Alu cluster is present within the intron separating exons 15 and 16 of the gene and contains a polymorphic Pvu II site. The presence or absence of this site gives rise to two allelic fragments of 14 and 16.5 kilobases, respectively, in genomic Southern blots using cloned cDNA probes. This DNA polymorphic site is caused by a single adenine to guanine transition within an Alu repetitive element. The second cluster of Alu sequences is located in exon 18 of the LDL receptor gene. Southern blotting of primate DNAs suggests that this cluster became associated with the gene about 30 million years ago. Comparison of bovine DNA sequences, which lack this Alu cluster, with those of the human indicates that the Alu sequences inserted in exon 18 in two independent events.