Discovering maximal motif cliques in large heterogeneous information networks

We study the discovery of cliques (or "complete" subgraphs) in heterogeneous information networks (HINs). Existing clique-finding solutions often ignore the rich semantics of HINs. We propose motif clique, or m-clique, which redefines subgraphs completeness with respect to a given motif. A motif essentially a small subgraph pattern, is a fundamental building block of an HIN. The m-clique concept is general and allows us to analyse "complete" subgraphs in an HIN with respect to desired high-order connection patterns. We further investigate the maximal m-clique enumeration problem (MMCE), which finds all maximal m-cliques not contained in any other m-cliques. Because MMCE is NP-hard, developing an accurate and efficient solution for MMCE is not straightforward. we thus present the META algorithm, which employs advanced pruning strategies to effectively reduce the search space. We also design fast techniques to avoid generating duplicated maximal m-clique instances. Our extensive experiments on large real and synthetic HINs how that META is highly effective and efficient

Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness

Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development.This work was supported by grants from the Spanish Ministry of Economia y Competitividad BIO2014-57716-C2-2-R and receives partial support from the Generalitat de Catalunya SGR14/248. CIBER de Enfermedades Raras is an initiative of the ISCIII. CF group is partially financed by the Instituto de Salud Carlos III (IIS10/00014) and co-financed by Fondo Europeo de Desarrollo Regional (FEDER). We also acknowledge the support of COST Action BM1204 EUPancreas. E.V. was supported by a fellowship from the Gobierno Vasco, Spain

Toward standardized test methods to determine the effectiveness of filtration media against airborne nanoparticles

The filtration of airborne nanoparticles is an important control technique as the environmental, health, and safety impacts of nanomaterials grow. A review of the literature shows that significant progress has been made on airborne nanoparticle filtration in the academic field in the recent years. We summarize the filtration mechanisms of fibrous and membrane filters; the air flow resistance and filter media figure of merit are discussed. Our review focuses on the air filtration test methods and instrumentation necessary to implement them; recent experimental studies are summarized accordingly. Two methods using monodisperse and polydisperse challenging aerosols, respectively, are discussed in detail. Our survey shows that the commercial instruments are already available for generating a large amount of nanoparticles, sizing, and quantifying them accurately. The commercial self-contained filter test systems provide the possibility of measurement for particles down to 15 nm. Current international standards dealing with efficiency test for filters and filter media focus on measurement of the minimum efficiency at the most penetrating particle size. The available knowledge and instruments provide a solid base for development of test methods to determine the effectiveness of filtration media against airborne nanoparticles down to single-digit nanometer rang

Visualizing codon usage within and across genomes : concepts and tools

Cost and time of genome sequencing have plummeted over the last decade. This leads to explosive growth of genetic databases and development of novel sequencing-based approaches to study various biological phenomena. The database growth was particularly beneficial for investigation of protein-coding sequences at the codon level, requiring the access to large sets of related genomes. Such studies are expected to illuminate biological forces that shape primary structure of coding sequences and predict their evolutionary trajectories more precisely. In addition to fundamental interest, codon usage studies are of ample practical value, for example, in drug discovery and genomic medicine areas. Nevertheless, the depth of our understanding of codon-related issues is currently shallower as compared to what we know about nucleotide and amino acid sequences. Besides the lack of adequate datasets in the early days of molecular biology, codon usage studies, in our opinion, suffer from underdevelopment of easy-to-use tools to analyze and visualize how codon sequence changes along the gene and across the homologous genes in course of evolution. In this review, we aim to describe main areas of codon usage studies with an emphasis on the tools that allow visual interpretation of the data. We discuss underlying principles of different approaches, what kind of statistics lends confidence in their results and what has to be done to further boost the field of codon usage research