Author summarySignaling pathways describe how cells respond to external signals through molecular interactions. As we gain a deeper understanding of these signaling reactions, it is important to understand how molecules may influence downstream responses and how pathways may affect each other. As the amount of information in signaling pathway databases continues to grow, we have the opportunity to analyze properties about pathway structure. We pose an intuitive question about signaling pathways: when are two molecules "connected" in a pathway? This answer varies dramatically based on the assumptions we make about how reactions link molecules. Here, examine four approaches for modeling the structural topology of signaling pathways, and present methods to quantify whether two molecules are "connected" in a pathway database. We find that existing approaches are either too permissive (molecules are connected to many others) or restrictive (molecules are connected to a handful of others), and we present a new measure that offers a continuum between these two extremes. We then expand our question to ask when an entire signaling pathway is "downstream" of another pathway, and show two case studies from the Reactome pathway database that uncovers pathway influence. Finally, we show that the strict notion of connectivity can capture functional relationships among proteins using an independent benchmark dataset. Our approach to quantify connectivity in pathways considers a biologically-motivated definition of connectivity, laying the foundation for more sophisticated analyses that leverage the detailed information in pathway databases.Hypergraph-based connectivity measures for signaling pathway topologies PLOS Computational Biology | https://doi.org/10.

Our understanding of biological mechanisms and treatment options for traumatic brain injury (TBI) is limited. Here, we employed quantitative real-time PCR (QRT-PCR) and immunohistochemical analyses to determine the dynamic expression of cell proliferation and apoptosis in an effort to provide insights into the therapeutic window for developing regenerative strategies for TBI. For this purpose, young adult Sprague-Dawley rats were subjected to experimental TBI using a controlled cortical impactor, then euthanized 1-48 hours after TBI for QRT-PCR and immunohistochemistry. QRT-PCR revealed that brains from TBI exposed rats initially displayed nestin mRNA expression that modestly increased as early as 1-hour post-TBI, then significantly peaked at 8 hours, but thereafter reverted to pre-TBI levels. On the other hand, caspase-3 mRNA expression was slightly elevated at 8 hours post-TBI, which did not become significantly upregulated until 48 hours. Immunofluorescent microscopy revealed a significant surge in nestin immunoreactive cells in the cortex, corpus callosum, and subventricular zone at 24 hours post-TBI, whereas a significant increase in the number of active caspase-3 immunoreactive cells was only found in the cortex and not until 48 hours. These results suggest that the injured brain attempts to repair itself via cell proliferation immediately after TBI, but that this endogenous regenerative mechanism is not sufficient to abrogate the secondary apoptotic cell death. Treatment strategies designed to amplify cell proliferation and to prevent apoptosis are likely to exert maximal benefits when initiated at the acute phase of TBI.

Supplementary data are available at Bioinformatics online.

The pathophysiological changes that occur during ischemic stroke can have a profound effect on the surrounding nerve tissue. To this end, we advance the hypothesis that retinal damage can occur as a consequence of ischemic stroke in animal models. We discuss the preclinical evidence over the last 3 decades supporting this hypothesis of retinal damage following ischemic stroke. In our evaluation of the hypothesis, we highlight the animal models providing evidence of pathological and mechanistic link between ischemic stroke and retinal damage. That retinal damage is closely associated with ischemic stroke, yet remains neglected in stroke treatment regimen, provides the impetus for recognizing the treatment of retinal damage as a critical component of stroke therapy.