Signaling pathways are a cornerstone of systems biology. Several databases store high-quality representations of these pathways that are amenable for automated analyses. Despite painstaking and manual curation, these databases remain incomplete. We present PATHLINKER, a new computational method to reconstruct the interactions in a signaling pathway of interest. PATHLINKER efficiently computes multiple short paths from the receptors to transcriptional regulators (TRs) in a pathway within a background protein interaction network. We use PATHLINKER to accurately reconstruct a comprehensive set of signaling pathways from the NetPath and KEGG databases. We show that PATHLINKER has higher precision and recall than several state-of-the-art algorithms, while also ensuring that the resulting network connects receptor proteins to TRs. PATHLINKER’s reconstruction of the Wnt pathway identified CFTR, an ABC class chloride ion channel transporter, as a novel intermediary that facilitates the signaling of Ryk to Dab2, which are known components of Wnt/β-catenin signaling. In HEK293 cells, we show that the Ryk–CFTR–Dab2 path is a novel amplifier of β-catenin signaling specifically in response to Wnt 1, 2, 3, and 3a of the 11 Wnts tested. PATHLINKER captures the structure of signaling pathways as represented in pathway databases better than existing methods. PATHLINKER’s success in reconstructing pathways from NetPath and KEGG databases point to its applicability for complementing manual curation of these databases. PATHLINKER may serve as a promising approach for prioritizing proteins and interactions for experimental study, as illustrated by its discovery of a novel pathway in Wnt/β-catenin signaling. Our supplementary website at http://bioinformatics.cs.vt.edu/~murali/supplements/2016-sys-bio-applications-pathlinker/ provides links to the PATHLINKER software, input datasets, PATHLINKER reconstructions of NetPath pathways, and links to interactive visualizations of these reconstructions on GraphSpace.

Conidia from the fungus Aspergillus fumigatus are notorious for their ability to stay airborne. This characteristic is believed to allow conidia to penetrate into the cleanest environments. Several hundred conidia are thought to be inhaled each day by a given individual and then expelled by mucociliary clearance. Given that airway epithelial cells make up a significant portion of the pulmonary-air interface, we set out to determine the percentage of conidia that are actually internalized after initial contact with airway epithelial cells. We determined this through an in vitro assay using an immortalized bronchial airway epithelial cell line known as BEAS-2B. Our results suggest a small fraction of conidia are internalized by BEAS-2B cells, while the majority stay adherent to the surface of cells or are washed away during sample processing. Internalization of conidia was observed at 6 h postchallenge and not prior. Our data also indicate conidia are rendered metabolically inactive within 3 h of challenge, suggesting BEAS-2B cells process a large number of conidia without internalization in this early time frame. We have also identified several host endocytosis markers that localize around internalized conidia as well as contribute to the processing of conidia. Understanding how these host endocytosis markers affect the processing of internal and/or external conidia may provide a novel avenue for therapeutic development.

The purpose of this study was to examine interference between concurrently performed speaking and driving tasks. Participants included 60 adults, 30 males and 30 females, with no history of communication disorders. They were divided into three different age groups of 20 participants each: younger (20s), middle-aged (40s), and older (60s). The participants were given a list of topics to consider and were instructed to select eight topics that they could talk about; they completed five practice trials of the driving simulator prior to the experimental recording to eliminate practice effects. Each participant completed the speaking task and driving task both separately and concurrently. The speaking task consisted of producing a monologue about the topics that they had selected. Dependent measures for speech included metrics relating to intensity, fundamental frequency, and the ratio of speaking to pausing time. The simulated driving task involved maintaining a constant speed and lane position on a freeway. Dependent measures for driving included metrics relating to speed, lane position, steering wheel position, and a count of steering wheel turns. Results indicated significant divided attention effects in speaking time ratio, intensity, speed, and steering wheel control. There was a significant age effect for intensity and fundamental frequency as the younger group had less variation with these variables compared to the other age groups. There was a significant age effect for lane position, steering wheel position, and speed as the younger group had less variation in lane and position compared to the other groups and the older group had more variation in speed and steering wheel position compared to the other groups. There was a significant gender effect for intensity and lane position as the females had less variation in intensity and more variation in lane position compared to the males. These findings suggest that divided attention conditions impact both speech and driving performance. The results also shed some light on the effects of age on concurrently performed speech and driving tasks. These findings imply that divided attention conditions should be incorporated in treatment to help patients generalize the skills learned in therapy to everyday communication.