Timing vocal behaviour: experimental evidence for song overlap avoidance in Eurasian wrens.

Timing during vocal interactions can play a significant role in terms of audibility as signal overlap may lead to masking of acoustic details for both of the interacting animals as well as for third-party eavesdroppers. Here we investigated timing aspects experimentally in Eurasian wrens (Troglodytes troglodytes) using non-interactive playback. We applied a randomized overlay method incorporating the temporal pattern of singing by the focal bird to establish a null model and to test observed patterns of overlap against this null model. We used different stimulus song rates but temporal response patterns always resulted in significantly lower levels of overlap than expected by chance. The male wrens avoided overlapping by timing their song starts predominately right after the end of stimulus songs, but they did not avoid being overlapped by the stimulus songs. The territorial males typically raised their song rates during and after playback with a tendency to shorten between-song intervals while keeping song durations unchanged. Higher song rates of the playback stimuli increased the extent to which responders were being overlapped by the stimulus songs. Our data provide experimental evidence for a timing ability in Eurasian wrens by which they reduce mutual interference during vocal interactions.

Sphingobacterium hotanense sp. nov., isolated from soil of a Populus euphratica forest, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense.

A novel Gram-staining-negative bacterial strain, designated XH4(T), was isolated from soil of a Populus euphratica forest in the Hotan River valley, Xinjiang Uyghur autonomous region, PR China. The cells were strictly aerobic, non-motile, short rods. The isolate grew optimally at 37 °C and at pH 7.0-8.0. Based on 16S rRNA gene sequence analysis, strain XH4(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium mizutaii ATCC 33299(T) (96.1 % sequence similarity). The DNA G+C content was 41.2 mol%. The major polar lipid of strain XH4(T) was phosphatidylethanolamine, and several unidentified polar lipids were also present. Strain XH4(T) showed the typical chemotaxonomic features of the genus Sphingobacterium, with the presence of ceramide phosphorylethanolamine 2 (CerPE-2) as the major ceramide. The major cellular fatty acids of strain XH4(T) were iso-C15 : 0 (34.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.7 %) and iso-C17 : 0 3-OH (14.7 %). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic data and phylogenetic inference, strain XH4(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium hotanense sp. nov. is proposed. The type strain is XH4(T) ( = NRRL B-59204(T)  = CCTCC AB 209007(T)). Emended descriptions of Sphingobacterium daejeonense and Sphingobacterium shayense are also given.

Expression trend of selected ribosomal protein genes in nasopharyngeal carcinoma.

BACKGROUND: Ribosomal proteins are traditionally associated with protein biosynthesis until recent studies that implicated their extraribosomal functions in human diseases and cancers. Our previous studies using GeneFishing™ DEG method and microarray revealed underexpression of three ribosomal protein genes, RPS26, RPS27, and RPL32 in cancer of the nasopharynx. Herein, we investigated the expression pattern and nucleotide sequence integrity of these genes in nasopharyngeal carcinoma to further delineate their involvement in tumourigenesis. The relationship of expression level with clinicopathologic factors was also statistically studied. METHODS: Quantitative Polymerase Chain Reaction was performed on nasopharyngeal carcinoma and their paired normal tissues. Expression and sequence of these three genes were analysed. RESULTS: All three ribosomal protein genes showed no significant difference in transcript expressions and no association could be established with clinicopathologic factors studied. No nucleotide aberrancy was detected in the coding regions of these genes. CONCLUSION: There is no early evidence to substantiate possible involvement of RPS26, RPS27, and RPL32 genes in NPC tumourigenesis.

[Bias of base composition and codon usage in pseudorabies virus genes].

The complete sequence of the Pseudorabies Virus (PRV) genomic DNA has not yet been determined, primarily because of the high content of G + C nucleotides of about 74%. We examined the base composition and codon usage of the 68 known PRV genes. As a result, we found a strong bias towards GC-rich codons especially NNC or NNG (N represents any one of four nucleotides) in PRV genes. This demonstrated that the usage bias of synonymous codon and amino acid is the main cause of the high G + C content of PRV. The results showed that the genome regions adjacent UL48, UL40, UL14, IE180 genes where the G + C content occurs as pronounced waves are corresponding to the replication origins. It was also found that the codon usage patterns of regulatory genes are apparently different from other PRV genes. A corresponding analysis of amino acid compositions indicated that the bias of codon usage could be related to the differences of gene function.

DNAskew: statistical analysis of base compositional asymmetry and prediction of replication boundaries in the genome sequences.

Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.