Cloning,sequence and variability analysis of expressed immunoglobulin light chain genes from yellowtail Seriola quinqueradiata

The cDNA clones encoding immunoglobulin (Ig) light (L) chain variable (V) region associated with constant (C) region were isolated from yellowtail (Seriola quinqueradiata) kidney by expressed sequence tag analysis (accession numbers: AB062619-AB062668, AB064322). The sequences of both VL and CL region contain well-conserved cysteine residues important for intra- and inter-domain interaction in mammals. Comparisons of the amino acid sequence of the CL domain with those of other species showed a high degree of similarity, with 88.3%, 59.8%, and 60.6% to those of wolf fish (Anarhichas lupus), rainbow trout IgL I isotype (Oncorhynchus mykiss) and channel catfish G isotype (Ictalurus punctatus), respectively. Multiple sequence alignments of the CL domain with those of higher vertebrates, however, did not readily allow it to be classified as kappa or lambda isotypes. Furthermore, the pI, hydrophobicity and variability of yellowtail VL regions were studied in 65 cDNA clones and the diversity was observed in CDR1, CDR2 and CDR3 regions.     

Codon usage tabulated from international DNA sequence databases: status for the year 2000

The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon usage of genes and the sum of the codons used by each organism can be obtained through the web site http://www.kazusa.or.jp/codon/ . The present study also reports recent developments on the WWW site. The new web interface provides data in the CodonFrequency-compatible format as well as in the traditional table format. The use of the database is facilitated by keyword based search analysis and the availability of codon usage tables for selected genes from each species. These new tools will provide users with the ability to further analyze for variations in codon usage among different genomes.     

A novel bioinformatics strategy for searching industrially useful genome resources from metagenomic sequence libraries

Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it is usually difficult to know whether a single genome harbors the entire gene set or whether different genomes have individual genes. By modifying Self-Organizing Map (SOM), we previously developed BLSOM for oligonucleotide composition, which allowed classification (self-organization) of sequence fragments according to genomes. Because BLSOM could reassociate genomic fragments according to genomes, BLSOM may ameliorate the abovementioned weakness of metagenome analyses. Here, we have developed a strategy for clustering of metagenomic sequences according to phylotypes and genomes, by testing a gene set contributing to environment preservation.     

Impaired AMPA signaling and cytoskeletal alterations induce early synaptic dysfunction in a mouse model of Alzheimer's disease

Alzheimer's disease (AD) is a devastating neurodegenerative disorder that impairs memory and causes cognitive and psychiatric deficits. New evidences indicate that AD is conceptualized as a disease of synaptic failure, although the molecular and cellular mechanisms underlying these defects remain to be elucidated. Determining the timing and nature of the early synaptic deficits is critical for understanding the progression of the disease and for identifying effective targets for therapeutic intervention. Using single‐synapse functional and morphological analyses, we find that AMPA signaling, which mediates fast glutamatergic synaptic transmission in the central nervous system (CNS), is compromised early in the disease course in an AD mouse model. The decline in AMPA signaling is associated with changes in actin cytoskeleton integrity, which alters the number and the structure of dendritic spines. AMPA dysfunction and spine alteration correlate with the presence of soluble but not insoluble Aβ and tau species. In particular, we demonstrate that these synaptic impairments can be mitigated by Aβ immunotherapy. Together, our data suggest that alterations in AMPA signaling and cytoskeletal processes occur early in AD. Most important, these deficits are prevented by Aβ immunotherapy, suggesting that existing therapies, if administered earlier, could confer functional benefits.     

Giant G+C% mosaic structures of the human genome found by arrangement of GenBank human DNA sequences according to genetic positions

To determine the overall variation in the G+C% distribution over long ranges of the human genome, DNA sequences of human genes, which were closely linked genetically or physically, were surveyed from the GenBank Data Bank. A total of 72 sequences longer than 2 kb, which were mutually linked within 500 kb, were identified. The sequences belonged to 17 linkage groups and were ordered in each group according to their genetic positions. Analyses of the G+C% distribution along the ordered sequences showed that sequences within each group almost always had similar G+C% levels, but those belonging to different groups often had different levels. Similar analyses of more distantly linked sequences (e.g., greater than 10 Mb) showed mosaic structures of G+C% distribution. These findings are consistent with predictions made from the "isochore" structures found by CsCl equilibrium centrifugation, in that the structures having homogeneous base compositions stretched over at least several hundred kilobases. A possible boundary of the giant G+C% mosaic structures was identified between X-linked G6PD and F8C.     

Neutralization of activity of two different heat-stable enterotoxins (STh and STp) of enterotoxigenic Escherichia coli by homologous and heterologous antisera

Abstract Two distinct heat-stable enterotoxins (ST) produced by enterotoxigenic Escherichia coli , ST_p and ST_h, were purified and antisera against the purified ST_p and ST_h were prepared by immunizing rabbits with the purified ST's coupled with bovine serum albumin. Neutralizing activity of each antiserum was examined and it was found that both antisera neutralized not only homologous ST but also heterologous St. These data indicate that the two anti-ST antisera are raised against the region of common amino acid sequence of the two ST's.