Capacity of a Simple Intercellular Signal Transduction Channel

We model the ligand-receptor molecular communication channel with a discrete-time Markov model, and show how to obtain the capacity of this channel. We show that the capacity-achieving input distribution is iid; further, unusually for a channel with memory, we show that feedback does not increase the capacity of this channel.Comment: 5 pages, 1 figure. To appear in the 2013 IEEE International Symposium on Information Theor

Finite-State Channel Models for Signal Transduction in Neural Systems

Information theory provides powerful tools for understanding communication systems. This analysis can be applied to intercellular signal transduction, which is a means of chemical communication among cells and microbes. We discuss how to apply information-theoretic analysis to ligand-receptor systems, which form the signal carrier and receiver in intercellular signal transduction channels. We also discuss the applications of these results to neuroscience.Comment: Accepted for publication in 2016 IEEE International Conference on Acoustics, Speech, and Signal Processing, Shanghai, Chin

Orientation-sensitivity to facial features explains the Thatcher illusion

The Thatcher illusion provides a compelling example of the perceptual cost of face inversion. The Thatcher illusion is often thought to result from a disruption to the processing of spatial relations between face features. Here, we show the limitations of this account and instead demonstrate that the effect of inversion in the Thatcher illusion is better explained by a disruption to the processing of purely local facial features. Using a matching task, we found that participants were able to discriminate normal and Thatcherized versions of the same face when they were presented in an upright orientation, but not when the images were inverted. Next, we showed that the effect of inversion was also apparent when only the eye region or only the mouth region was visible. These results demonstrate that a key component of the Thatcher illusion is to be found in orientation-specific encoding of the expressive features (eyes and mouth) of the face

Project Management Through Experiential Learning

Classroom-based projects are insufficient, in of themselves, when preparing students for positions in the digital media field today. David Kolb and Roger Fry argue that effective learning entails the possession of four different abilities: concrete experience, reflective observation, abstract conceptualization and active experimentation.2 Encouraging students to participate in community-based projects outside the classroom can help build the necessary skill sets in learning how to work in a real-world environment. Community-based learning teaches the student on three distinct levels: intellectually, socially, and emotionally including feelings, values, and meanings. Digital Media students should involve themselves in community projects to exercise their skills and broaden their experience. Working on community-based projects allows them to build their portfolio while affording the opportunity to start working under the constraints of actual projects with timelines and budgets. Students learn what an individual’s time is worth, what mistakes can cost, and how to deal with a client. Students also learn how to manage a real world project with deadlines. This paper describes our approach in having students come together to enhance their digital media skills by contributing in the development of a community-based animation festival. This paper also addresses how students learned to plan and manage a festival event while working with a community-based organization

Characterization of novel beta-galactosidase activity that contributes to glycoprotein degradation and virulence in Streptococcus pneumoniae.

The pneumococcus obtains its energy from the metabolism of host glycosides. Therefore, efficient degradation of host glycoproteins is integral to pneumococcal virulence. In search of novel pneumococcal glycosidases, we characterized the Streptococcus pneumoniae strain D39 protein encoded by SPD_0065 and found that this gene encodes a beta-galactosidase. The SPD_0065 recombinant protein released galactose from desialylated fetuin, which was used here as a model of glycoproteins found in vivo. A pneumococcal mutant with a mutation in SPD_0065 showed diminished beta-galactosidase activity, exhibited an extended lag period in mucin-containing defined medium, and cleaved significantly less galactose than the parental strain during growth on mucin. As pneumococcal beta-galactosidase activity had been previously attributed solely to SPD_0562 (bgaA), we evaluated the contribution of SPD_0065 and SPD_0562 to total beta-galactosidase activity. Mutation of either gene significantly reduced enzymatic activity, but beta-galactosidase activity in the double mutant, although significantly less than that in either of the single mutants, was not completely abolished. The expression of SPD_0065 in S. pneumoniae grown in mucin-containing medium or tissues harvested from infected animals was significantly upregulated compared to that in pneumococci from glucose-containing medium. The SPD_0065 mutant strain was found to be attenuated in virulence in a manner specific to the host tissue

The XRCC1 phosphate-binding pocket binds poly (ADP-ribose) and is required for XRCC1 function

Poly (ADP-ribose) is synthesized at DNA single-strand breaks and can promote the recruitment of the scaffold protein, XRCC1. However, the mechanism and importance of this process has been challenged. To address this issue, we have characterized the mechanism of poly (ADP-ribose) binding by XRCC1 and examined its importance for XRCC1 function. We show that the phosphate-binding pocket in the central BRCT1 domain of XRCC1 is required for selective binding to poly (ADP-ribose) at low levels of ADP-ribosylation, and promotes interaction with cellular PARP1. We also show that the phosphate-binding pocket is required for EGFP-XRCC1 accumulation at DNA damage induced by UVA laser, H2O2, and at sites of sub-nuclear PCNA foci, suggesting that poly (ADP-ribose) promotes XRCC1 recruitment both at single-strand breaks globally across the genome and at sites of DNA replication stress. Finally, we show that the phosphate-binding pocket is required following DNA damage for XRCC1-dependent acceleration of DNA single-strand break repair, DNA base excision repair, and cell survival. These data support the hypothesis that poly (ADP-ribose) synthesis promotes XRCC1 recruitment at DNA damage sites and is important for XRCC1 function