Different protein tyrosine phosphatase superfamilies resulting from different gene reading frames

Protein tyrosine phosphatases (PTPs) are comprised of two superfamilies, the phosphatase I superfamily containing a single low-molecular-weight PTP (lmwPTP) family and the phosphatase II superfamily including both the higher-molecular-weight PTP (hmwPTP) and the dual-specificity phosphatase (DSP) families. The phosphatase I and H superfamilies are often considered to be the result of convergent evolution. The PTP sequence and structure analyses indicate that lmwPTPs, hmwPTPs, and DSPs share similar structures, functions, and a common signature motif, although they have low sequence identities and a different order of active sites in sequence or a circular permutation. The results of this work suggest that lmwPTPs and hmwPTPs/DSPs are remotely related in evolution. The earliest ancestral gene of PTPs could be from a short fragment containing about 90similar to120 nucleotides or 30similar to40 residues; however, a probable full PTP ancestral gene contained one transcript unit with two lmwPTP genes. All three PTP families may have resulted from a common ancestral gene by a series of duplications, fusions, and circular permutations. The circular permutation in PTPs is caused by a reading frame difference, which is similar to that in DNA methyltransferases. Nevertheless, the evolutionary mechanism of circular permutation in PTP genes seems to be more complicated than that in DNA methyltransferase genes. Both mechanisms in PTPs and DNA methyltransferases can be used to explain how some protein families and superfamilies came to be formed by circular permutations during molecular evolution.

A 1,000 Frames/s Programmable Vision Chip with Variable Resolution and Row-Pixel-Mixed Parallel Image Processors

A programmable vision chip with variable resolution and row-pixel-mixed parallel image processors is presented. The chip consists of a CMOS sensor array, with row-parallel 6-bit Algorithmic ADCs, row-parallel gray-scale image processors, pixel-parallel SIMD Processing Element (PE) array, and instruction controller. The resolution of the image in the chip is variable: high resolution for a focused area and low resolution for general view. It implements gray-scale and binary mathematical morphology algorithms in series to carry out low-level and mid-level image processing and sends out features of the image for various applications. It can perform image processing at over 1,000 frames/s (fps). A prototype chip with 64 x 64 pixels resolution and 6-bit gray-scale image is fabricated in 0.18 mu m Standard CMOS process. The area size of chip is 1.5 mm x 3.5 mm. Each pixel size is 9.5 mu m x 9.5 mu m and each processing element size is 23 mu m x 29 mu m. The experiment results demonstrate that the chip can perform low-level and mid-level image processing and it can be applied in the real-time vision applications, such as high speed target tracking.

Adaptive image sequence coding based on global and local compensability analysis

Our study of a novel technique for adaptive image sequence coding is reported. The number of reference frames and the intervals between them are adjusted to improve the temporal compensability of the input video. The bits are distributed more efficiently on different frame types according to temporal and spatial complexity of the image scene. Experimental results show that this dynamic group-of-picture (GOP) structure coding scheme is not only feasible but also better than the conventional fixed GOP method in terms of perceptual quality and SNR. (C) 1996 Society of Photo-Optical Instrumentation Engineers.

Spatiotemporal segmentation based on two-dimensional spatiotemporal entropic thresholding

A novel spatiotemporal segmentation technique is further developed for extracting uncovered background and moving objects from the image sequences, then the following motion estimation is performed only on the regions corresponding to moving objects. The frame difference contrast (FCON) and local variance contrast (LCON), which are related to the temporal and spatial homogeneity of the image sequence, are selected to form the 2-D spatiotemporal entropy. Then the spatial segmentation threshold is determined by maximizing the 2-D spatiotemporal entropy, and the temporal segmentation point is selected to minimize the complexity measure for image sequence coding. Since both temporal and spatial correlation of an image sequence are exploited, this proposed spatiotemporal segmentation technique can further be used to determine the positions of reference frames adaptively, hence resulting in a low bit rate. Experimental results show that this segmentation-based coding scheme is more efficient than usual fixed-size coding algorithms. (C) 1997 Society of Photo-Optical Instrumentation Engineers.

Identification and characterization of novel reptile cathelicidins from elapid snakes

Three cDNA sequences coding for elapid cathelicidins were cloned from constructed venom gland cDNA libraries of Naja atra, Bungarus fasciatus and Ophiophagus hannah. The open reading frames of the cloned elapid cathelicidins were all composed of 576 bp an

Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization

Organisms living in water are inevitably exposed to periods of hypoxia. Environmental hypoxia has been an important stressor having manifold effects on aquatic life. Many fish species have evolved behavioral, physiological, biochemical and molecular adaptations that enable them to cope with hypoxia. However, the molecular mechanisms of hypoxia tolerance in fish, remain unknown. in this study, we used suppression subtractive hybridization to examine the differential gene expression in CAB cells (Carassius auratus blastulae embryonic cells) exposed to hypoxia for 24 h. We isolated 2100 clones and identified 211 differentially expressed genes (e-value <= 5e-3; Identity > 45%). Among the genes whose expression is modified in cells, a vast majority involved in metabolism, signal transduction, cell defense, angiogenesis, cell growth and proliferation. Twelve genes encoding for ERO1-L, p53, CPO, HO-1, MKP2, PFK-2, cystatin B, GLUT1, BTG1, TGF beta 1, PGAM1, hypothetical protein F1508, were selected and identified to be hypoxia-induced using semi-quantitive RT-PCR and real-time PCR. Among the identified genes, two open reading frames (ORFs) encoding for CaBTG1 and Cacystatin B were obtained. The deduced amino acid sequence of CaBTG1 had 94.1%, 72.8%, 72.8%, 72.8%, 68.6% identity with that of DrBTG1, HsBTG1, BtBTG1, MmBTG1 and XIBTG1. Comparison of Cacystatin B with known cystatin B, the molecules exhibited 49.5 to 76.0% identity overall. These results may provide significant information for further understanding of the adaptive mechanism by which C. auratus responds to hypoxia. (c) 2008 Elsevier Inc. All rights reserved.

Characterization of complete genome sequence of the spring viremia of carp virus isolated from common carp (Cyprinus carpio) in China

The complete genome of spring viraemia of carp virus (SVCV) strain A-1 isolated from cultured common carp (Cyprinus carpio) in China was sequenced and characterized. Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed and the DNA was sequenced. It showed that the entire genome of SVCV A-1 consists of 11,100 nucleotide base pairs, the predicted size of the viral RNA of rhabdoviruses. However, the additional insertions in bp 4633-4676 and bp 4684-4724 of SVCV A-1 were different from the other two published SVCV complete genomes. Five open reading frames (ORFs) of SVCV A-1 were identified and further confirmed by RT-PCR and DNA sequencing of their respective RT-PCR products. The 5 structural proteins encoded by the viral RNA were ordered 3'-N-P-M-G-L-5'. This is the first report of a complete genome sequence of SVCV isolated from cultured carp in China. Phylogenetic analysis indicates that SVCV A-1 is closely related to the members of the genus Vesiculovirus, family Rhabdoviridae.

Complete genome sequence of lymphocystis disease virus isolated from China

Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.

A programmable SIMD vision chip for real-time vision applications

A programmable vision chip for real-time vision applications is presented. The chip architecture is a combination of a SIMD processing element array and row-parallel processors, which can perform pixel-parallel and row-parallel operations at high speed. It implements the mathematical morphology method to carry out low-level and mid-level image processing and sends out image features for high-level image processing without I/O bottleneck. The chip can perform many algorithms through software control. The simulated maximum frequency of the vision chip is 300 MHz with 16 x 16 pixels resolution. It achieves the rate of 1000 frames per second in real-time vision. A prototype chip with a 16 x 16 PE array is fabricated by the 0.18 mu m standard CMOS process. It has a pixel size of 30 mu m x 40 mu m and 8.72 mW power consumption with a 1.8 V power supply. Experiments including the mathematical morphology method and target tracking application demonstrated that the chip is fully functional and can be applied in real-time vision applications.

A novel vision chip for high-speed target tracking

This paper presents a novel vision chip for high-speed target tracking. Two concise algorithms for high-speed target tracking are developed. The algorithms include some basic operations that can be used to process the real-time image information during target tracking. The vision chip is implemented that is based on the algorithms and a row-parallel architecture. A prototype chip has 64 x 64 pixels is fabricated by 0.35 pm complementary metal-oxide-semiconductor transistor (CMOS) process with 4.5 x 2.5 mm(2) area. It operates at a rate of 1000 frames per second with 10 MHz chip main clock. The experiment results demonstrate that a high-speed target can be tracked in complex static background and a high-speed target among other high-speed objects can be tracked in clean background.

Proposed scheme for parallel 10Gb/s VSR system and its Verilog HDL realization

This paper proposes a novel and innovative scheme for 10Gb/s parallel Very Short Reach (VSR) optical communication system. The optimized scheme properly manages the SDH/SONET redundant bytes and adjusts the position of error detecting bytes and error correction bytes. Compared with the OIF-VSR4-01.0 proposal, the scheme has a coding process module. The SDH/SONET frames in transmission direction are disposed as follows: (1) The Framer-Serdes Interface (FSI) gets 16x622.08Mb/s STM-64 frame. (2) The STM-64 frame is byte-wise stripped across 12 channels, all channels are data channels. During this process, the parity bytes and CRC bytes are generated in the similar way as OIF-VSR4-01.0 and stored in the code process module. (3) The code process module will regularly convey the additional parity bytes and CRC bytes to all 12 data channels. (4) After the 8B/10B coding, the 12 channels is transmitted to the parallel VCSEL array. The receive process approximately in reverse order of transmission process. By applying this scheme to 10Gb/s VSR system, the frame size in VSR system is reduced from 15552x12 bytes to 14040x12 bytes, the system redundancy is reduced obviously.

Picosecond ultra-wideband short pulse radiated by antenna arrays

This report presents the experiments to study the characteristics of the picosecond ultra-wideband pulses coherent radiation. The testing involves bow-tie horn antennas for both the transninting and receiving antenna. Sixteen channels of electrical pulses with 290 ps duration and jitter < 30 ps have been used. The antenna arrays with various frames of 4 x 1, 4 x 2, 4 x 3, 4 x 4 are employed to radiate the pulses. The receiving antenna measures the electrical field in different distance front the transmitting antennas arrant The results show that if the pulses are in coherent condition, the peak power pulse of output by antennas array with N elements are N-2 of that of the single element antenna. (c) 2007 Wiley Periodicals, Inc.

Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation. Conclusions/Significance: Of the,27,000 predicted open reading frames, transcripts homologous to only,5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

SYNTHESIS AND PROPERTIES OF ALPHA-MOLYBDOTUNGSTONIOBIC DIPHOSPHATES

Four kinds of new molybdotungstoniobic diphosphates with the Dawson structure, formulated as alpha-P2W15Mo2Nb62(7-), are prepared and characterized by IR, UV spectra, polarography and W-183 NMR which show that the same ''polar'' W atoms in the Dawson frames-are substituted. The mean value of W-183 chemical shifts of the ''polar'' group varies linearly with the number of substituted atoms in the opposite polar group.

Molecular identification of 16 Porphyra lines using sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) is a novel molecular marker technique designed to amplify open reading frames (ORFs). The SRAP analytic system was set up and applied to Porphyra germplasm identification in this study for the first time. Sixteen Porphyra lines were screened by SRAP technique with 30 primer combinations. In the analysis, 14 primer combinations produced stable and reproducible amplification patterns in three repetitive experiments. Among the total 533 amplified fragments, 522 (98%) were polymorphic, with an average of 38 fragments for each primer combination, ranging in size from 50 to 500 bp. The 533 fragments were visually scored one by one and then used to develop a dendrogram with Unweighted Pair-Group Method Arithmetic Average (UPGMA), and the 16 Porphyra lines were divided into two major groups at the 0.68 similarity level. From the total 533 fragments, I I amplified by two primer combinations, ME1/EM1 and ME4/EM6, were used to develop the DNA fingerprints of the 16 Porphyra lines. The DNA fingerprints were then converted into binary codes, with I and 0 representing presence and absence of the corresponding amplified fragment, respectively. In the DNA fingerprints, each of the 16 Porphyra lines has its unique binary code and can be easily distinguished from the others. This is the first report on the development of SRAP technique and its utilization in germplasm identification of seaweeds. The results demonstrated that SRAP is a simple, stable, polymorphic and reproducible molecular marker technique for the classification and identification of Porphyra lines. (c) 2007 Elsevier B.V. All rights reserved.