Letter: TreeAdder: a tool to assist the optimal positioning of a new leaf into an existing phylogenetic tree

TreeAdder is a computer application that adds a leaf in all possible positions on a phylogenetic tree. The resulting set of trees represent a dataset appropriate for maximum likelihood calculation of the optimal tree. TreeAdder therefore provides a utility for what was previously a tedious and error-prone process

Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo.

Barley stripe mosaic virus (BSMV) contains three positive-sense, single-stranded genomic RNAs, designated alpha, beta, and gamma, that encode seven major proteins and one minor translational readthrough protein. Three proteins (alphaa, betaa, and gammaa) are translated directly from the genomic RNAs and the remaining proteins encoded on RNAbeta and RNAgamma are expressed via three subgenomic messenger RNAs (sgRNAs). sgRNAbeta1 directs synthesis of the triple gene block 1 (TGB1) protein. The TGB2 protein, the TGB2' minor translational readthrough protein, and the TGB3 protein are expressed from sgRNAbeta2, which is present in considerably lower abundance than sgRNAbeta1. A third sgRNA, sgRNAgamma, is required for expression of the gammab protein. We have used deletion analyses and site-specific mutations to define the boundaries of promoter regions that are critical for expression of the BSMV sgRNAs in infected protoplasts. The results reveal that the sgRNAbeta1 promoter encompasses positions -29 to -2 relative to its transcription start site and is adjacent to a cis-acting element required for RNAbeta replication that maps from -107 to -74 relative to the sgRNAbeta1 start site. The core sgRNAbeta2 promoter includes residues -32 to -17 relative to the sgRNAbeta2 transcriptional start site, although maximal activity requires an upstream hexanucleotide sequence residing from positions -64 to -59. The sgRNAgamma promoter maps from -21 to +2 relative to its transcription start site and therefore partially overlaps the gammaa gene. The sgRNAbeta1, beta2, and gamma promoters also differ substantially in sequence, but have similarities to the putative homologous promoters of other Hordeiviruses. These differences are postulated to affect competition for the viral polymerase, coordination of the temporal expression and abundance of the TGB proteins, and constitutive expression of the gammab protein

Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing

Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease

Potato virus Y (PVY) strains in Belgian seed potatoes and first molecular detection of the N-Wi strain

Potato virus Y (PVY), one of the most important agents causing potato crop losses worldwide, is transmitted by a variety of aphid species in a non-persistent manner. Several PVY strains have been differentiated, all of them causing different symptoms and symptom expression levels on numerous commercial potato cultivars. In Belgium, strains belonging to the N group have been reported as the most prevalent, but no detailed information on the relative importance of the PVY strains in Belgium have been published to date. We report here on a survey performed on Belgian seed potatoes harvested in 2010 in which 2700 individual tubers from 54 seed potato lots originating from 54 farms were screened for presence of PVY. The results revealed a high PVY incidence and substantial strain diversity in some farms. The dominance of the N group in Belgian seed potatoes was confirmed, while the 0 strain was only found in a few locations. Further characterization using multiplex PCR identified 75% of the isolates as NTN strains and 7.5% as Wilga strain (N-Wi). The presence of the N-Wi strain was confirmed and characterized for the first time in Belgian seed potato production

From DNA sequence to application: possibilities and complications

The development of sophisticated genetic tools during the past 15 years have facilitated a tremendous increase of fundamental and application-oriented knowledge of lactic acid bacteria (LAB) and their bacteriophages. This knowledge relates both to the assignments of open reading frames (ORF’s) and the function of non-coding DNA sequences. Comparison of the complete nucleotide sequences of several LAB bacteriophages has revealed that their chromosomes have a fixed, modular structure, each module having a set of genes involved in a specific phase of the bacteriophage life cycle. LAB bacteriophage genes and DNA sequences have been used for the construction of temperature-inducible gene expression systems, gene-integration systems, and bacteriophage defence systems. The function of several LAB open reading frames and transcriptional units have been identified and characterized in detail. Many of these could find practical applications, such as induced lysis of LAB to enhance cheese ripening and re-routing of carbon fluxes for the production of a specific amino acid enantiomer. More knowledge has also become available concerning the function and structure of non-coding DNA positioned at or in the vicinity of promoters. In several cases the mRNA produced from this DNA contains a transcriptional terminator-antiterminator pair, in which the antiterminator can be stabilized either by uncharged tRNA or by interaction with a regulatory protein, thus preventing formation of the terminator so that mRNA elongation can proceed. Evidence has accumulated showing that also in LAB carbon catabolite repression in LAB is mediated by specific DNA elements in the vicinity of promoters governing the transcription of catabolic operons. Although some biological barriers have yet to be solved, the vast body of scientific information presently available allows the construction of tailor-made genetically modified LAB. Today, it appears that societal constraints rather than biological hurdles impede the use of genetically modified LAB.

Mal-Netminer: Malware Classification Approach based on Social Network Analysis of System Call Graph

As the security landscape evolves over time, where thousands of species of malicious codes are seen every day, antivirus vendors strive to detect and classify malware families for efficient and effective responses against malware campaigns. To enrich this effort, and by capitalizing on ideas from the social network analysis domain, we build a tool that can help classify malware families using features driven from the graph structure of their system calls. To achieve that, we first construct a system call graph that consists of system calls found in the execution of the individual malware families. To explore distinguishing features of various malware species, we study social network properties as applied to the call graph, including the degree distribution, degree centrality, average distance, clustering coefficient, network density, and component ratio. We utilize features driven from those properties to build a classifier for malware families. Our experimental results show that influence-based graph metrics such as the degree centrality are effective for classifying malware, whereas the general structural metrics of malware are less effective for classifying malware. Our experiments demonstrate that the proposed system performs well in detecting and classifying malware families within each malware class with accuracy greater than 96%.Comment: Mathematical Problems in Engineering, Vol 201