A new species of Saussurea (Asteraceae) from Tibet and its systematic position based on ITS sequence analysis

A new species of Saussurea, S. erecta S. W Liu, J. T Pan A J. Q. Liu sp. nov., is described from Tibet. It resembles S. kingii but may be distinguished by having distinct stems and glabrous achenes. Saussurea kingii was placed in sect. Pseudoeriocoryne of subgen. Eriocoryne; this section was circumscribed by acaulescence and an inflorescence with congested capitula surrounded by a rosette of leaves. The discovery of S. erecta with distinct stems, cauline leaves and corymbose capitula blurred the delimitation of sect. Pseudoeriocoryne and suggested that the section may be polyphyletic. Both the close relationship and the significant difference between S. erecta and S. kingii were confirmed by analyses of nrDNA ITS sequences. The resulting phylogenies based on ITS data further suggest that Saussurea sect. Pseudoeriocoryne, as traditionally defined, does not constitute a monophyletic group. The rapid radiation and speciation of Saussurea in the Qinghai-Tibetan Plateau, as inferred from ITS phylogeny, are discussed. (c) 2005 The Linnean Society of London.

Pelophylaxins: novel antimicrobial peptide homologs from the skin secretion of the Fukien gold-striped pond frog, Pelophylax plancyi fukienensis: identification by “shotgun” cDNA cloning and sequence analysis.

Amphibian skin secretions are rich in antimicrobial peptides that act as important components of an innate immune system. Here, we describe a novel “shotgun” skin peptide precursor cloning technique that facilitates rapid access to these genetically encoded molecules and effects their subsequent identification and structural characterization from the secretory peptidome. Adopting this approach on a skin secretion-derived library from a hitherto unstudied Chinese species of frog, we identified a family of novel antimicrobial peptide homologs, named pelophylaxins, that belong to previously identified families (ranatuerins, brevinins and temporins) found predominantly in the skin secretions from frogs of the genus Rana. These data further substantiate the scientifically robust nature of applying parallel transcriptome and peptidome analyses on frog defensive skin secretions that can be obtained in a non-invasive, non-destructive manner. In addition, the present data illustrate that rapid structural characterization of frog skin secretion peptides can be achieved from an unstudied species without prior knowledge of primary structures of endogenous peptides.

Lividins: Novel antimicrobial peptide homologs from the skin secretion of the Chinese Large Odorous frog, Rana (Odorrana) livida: Identification by “shotgun” cDNA cloning and sequence analysis.

Odorous frogs of the sub-genus Odorrana are of oriental distribution, and are so called due to the foul smell of their defensive skin secretions released from specialized skin glands following stress or predator attack. Here we report the application of a “shotgun” skin secretion cDNA library cloning technique which can rapidly expedite identification of secretion bioactive peptides. From a library constructed from the skin secretion of the Large Chinese Odorous frog, Rana (Odorrana) livida, we have identified four novel peptides whose primary structures were deduced initially from cloned precursors. Subsequently, mature peptides were located in and structurally characterized from reverse phase HPLC fractions of skin secretion. Named lividins 1–4, these were found to be structural homologs of known antimicrobial peptide families from Rana frogs. Rapid identification of novel peptides can thus be rapidly achieved using this non-invasive, non-destructive technology and the extensive similarities revealed between antimicrobial peptide precursor organization and nucleic acid sequences would lend support to the hypothesis that they have a common ancestral origin.

Sequence analysis of the 3' hypoxia-responsive element of the human erythropoietin gene in patients with erythrocytosis

Erythrocytosis arises from a variety of pathogenic mechanisms. We sequenced a 256-bp region 3' to the erythropoietin (Epo) gene which included a 24- to 50-bp minimal hypoxia-responsive element spanning HIF-1- and HNF-4-binding sites in 12 patients with erythrocytosis and 4 normal subjects. Four polymorphisms were found, none of which affected the HIF-1-binding site, although one polymorphism was present in the HNF-4 consensus region. The data indicate that none of these polymorphisms cause erythrocytosis.

Identification of a new mumps virus lineage by nucleotide sequence analysis of the SH gene of ten different strains

The SH gene and its flanking sequences have been analysed for 10 strains of mumps virus (MuV) and compared to 5 others. A new lineage has been identified among UK isolates. Changes in the transcription pattern could not be correlated with differences in the sequences of the F-SH and SH-HN intergenic regions of the genome.

AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis

Affiliation: Département de biochimie, Faculté de médecine, Université de Montréal

An Alternative Approach To Computer System Security Monitoring And Enhancement Through System Call Sequence Analysis

Modern computer systems are plagued with stability and security problems: applications lose data, web servers are hacked, and systems crash under heavy load. Many of these problems or anomalies arise from rare program behavior caused by attacks or errors. A substantial percentage of the web-based attacks are due to buffer overflows. Many methods have been devised to detect and prevent anomalous situations that arise from buffer overflows. The current state-of-art of anomaly detection systems is relatively primitive and mainly depend on static code checking to take care of buffer overflow attacks. For protection, Stack Guards and I-leap Guards are also used in wide varieties.This dissertation proposes an anomaly detection system, based on frequencies of system calls in the system call trace. System call traces represented as frequency sequences are profiled using sequence sets. A sequence set is identified by the starting sequence and frequencies of specific system calls. The deviations of the current input sequence from the corresponding normal profile in the frequency pattern of system calls is computed and expressed as an anomaly score. A simple Bayesian model is used for an accurate detection.Experimental results are reported which show that frequency of system calls represented using sequence sets, captures the normal behavior of programs under normal conditions of usage. This captured behavior allows the system to detect anomalies with a low rate of false positives. Data are presented which show that Bayesian Network on frequency variations responds effectively to induced buffer overflows. It can also help administrators to detect deviations in program flow introduced due to errors.