The preparation and activity of a phenylanine ammonia-lyase inactivator from sunflower leaves

Isolated plastids from crude extracts of sunflower ( Helianthus annuus L. cv. Sungold) leaves released a factor on extraction with Triton X-100 that inactivated Rhodotorula glutinis L-phenylaine ammonia-lyase (PAL; EC 4.3.1.5) in vitro. This PAL-inactivating factor (PAL-IF) was found to be proteinaceous in nature when tested with pronase (EC 1.11.1.6), peroxidase (EC 1.11.1.7) and nitrate reductase and the protection of PAL from PAL-IF by ligands indicated its specificity towards PAL. The inactivated PAL inhibitors reported earlier. It is suggested that inactivation may play an important role in in vivo regulation of L-phenylalanine ammonia-lyase activity and phenolic biosynthesis.     

Hierarchical clustering of shotgun proteomics data

A new result report for Mascot search results is described. A greedy set cover algorithm is used to create a minimal set of proteins, which is then grouped into families on the basis of shared peptide matches. Protein families with multiple members are represented by dendrograms, generated by hierarchical clustering using the score of the nonshared peptide matches as a distance metric. The peptide matches to the proteins in a family can be compared side by side to assess the experimental evidence for each protein. If the evidence for a particular family member is considered inadequate, the dendrogram can be cut to reduce the number of distinct family members.     

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data

Tumors are characterized by properties of genetic instability, heterogeneity, and significant oligoclonality. Elucidating this intratumoral heterogeneity is challenging but important. In this study, we propose a framework, BubbleTree, to characterize the tumor clonality using next generation sequencing (NGS) data. BubbleTree simultaneously elucidates the complexity of a tumor biopsy, estimating cancerous cell purity, tumor ploidy, allele-specific copy number, and clonality and represents this in an intuitive graph. We further developed a three-step heuristic method to automate the interpretation of the BubbleTree graph, using a divide-and-conquer strategy. In this study, we demonstrated the performance of BubbleTree with comparisons to similar commonly used tools such as THetA2, ABSOLUTE, AbsCN-seq and ASCAT, using both simulated and patient-derived data. BubbleTree outperformed these tools, particularly in identifying tumor subclonal populations and polyploidy. We further demonstrated BubbleTree''s utility in tracking clonality changes from patients’ primary to metastatic tumor and dating somatic single nucleotide and copy number variants along the tumor clonal evolution. Overall, the BubbleTree graph and corresponding model is a powerful approach to provide a comprehensive spectrum of the heterogeneous tumor karyotype in human tumors. BubbleTree is R-based and freely available to the research community (https://www.bioconductor.org/packages/release/bioc/html/BubbleTree.html).