PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

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.

Analysis of expressed sequence tags of a marine red alga, Gracilaria lemaneiformis

The expressed sequence tags (EST) has been proved to be a useful tool for discovering and identifying functional genes, especially in some species whose genetic information is unavailable. A total of 180 ESTs have been generated from a cDNA library of gametophytic Gracilaria lemaneiformis in this study. These clones are clustered into 151 groups, among which 8 groups are highly homologous to chloroplast genes and are abundant in the library. After searching for matches in the EST database of red alga, 22 groups are found to match with the registered ESTs of Rhadophyta and 6 with Gracilaria. Searching in the protein database reveal that 73 non-redundant clones have significant similarity to some known sequences, the majority of which are involved in photosynthesis, DNA transcription or translation, and 6, 4 and 3 clones are associated with growth or development, signal transduction and stress or defense response, respectively.

An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Characters of variation of LURR during the earthquake sequence of Xinjiang

The theory of the loading/unloading response ratio (LURR) was applied to the Jiashi earthquake sequence which occurred at the beginning of 1997 in Xinjiang, and found that, before the earthquakes with relatively high magnitudes In the sequence, the ratio showed anomalies of high values. That is to say, the LURR theory can be applied to the short-term earthquake prediction in some cases, especially in the early period after a strong earthquake, such as the forecasts for some strong earthquakes in the Jiashi sequence.

Assessment of bursting detection methods with LES database of turbulent channel flows

Validated by comparison with DNS, numerical database of turbulent channel flows is yielded by Large Eddy Simulation (LES). Three conventional techniques: uv quadrant 2, VITA and mu-level techniques for detecting turbulent bursts are applied to the identification of turbulent bursts. With a grouping parameter introduced by Bogard & Tiedemann (1986) or Luchik & Tiederman (1987), multiple ejections detected by these techniques which originate from a single burst can be grouped into a single-burst event. The results are compared with experimental results, showing that all techniques yield reasonable average burst period. However, uv quadrant 2 and mu-level are found to be superior to VITA in having large threshold-independent range.

Asymmetry of the photoionization rate of H atoms by a sequence of one-cycle laser pulses

Using an unperturbed scattering theory, the characteristics of H atom photoionization are studied respectively by a linearly- and by a circularly- polarized one-cycle laser pulse sequence. The asymmetry for photoelectrons in two directions opposite to each other is investigated. It is found that the asymmetry degree varies with the carrier-envelope (CE) phase, laser intensity, as well as the kinetic energy of photoelectrons. For the linear polarization, the maximal ionization rate varies with the CE phase, and the asymmetry degree varies with the CE phase in a sine-like pattern. For the circular polarization, the maximal ionization rate keeps constant for various CE phases, but the variation of asymmetry degree is still in a sine-like pattern.

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.