Determining Protein Complex Connectivity Using a Probabilistic Deletion Network Derived from Quantitative Proteomics

Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex

Identifying Priority and “Bright-Spot” Counties for Diabetes Preventive Care in Appalachia: An Exploratory Analysis

Introduction: Type 2 diabetes mellitus (T2DM) prevalence and mortality in Appalachian counties is substantially higher when compared to non-Appalachian counties, although there is significant variation within Appalachia. Purpose: The objectives of this research were to identify low-performing (priority) and high-performing (bright spot) counties with respect to improving T2DM preventive care. Methods: Using data from the Centers for Medicare and Medicaid (CMS), the Dartmouth Atlas of Health Care, and the Appalachia Regional Commission, conditional maps were created using county-level estimates for T2DM prevalence, mortality, and annual hemoglobin A1c (HbA1c) testing rates. Priority counties were identified using the following criteria: top 33rd percentile for T2DM mortality; top 33rd percentile for T2DM prevalence; bottom 50th percentile for A1c testing rates. Bright spot counties were identified as counties in the bottom 33rd percentile for T2DM mortality, the top 33rd percentile for T2DM prevalence; and the top 50th percentile for HbA1c testing rates. Results: Forty-one priority counties were identified (those with high T2DM mortality, high T2DM prevalence, and low HbA1c testing rates), which were located primarily in Central and North Central Appalachia; and 17 bright spot counties were identified (high T2DM prevalence, low T2DM mortality, and high HbA1c testing rates), which were scattered throughout Appalachia. Eight of the 17 bright spot counties were adjacent to priority counties. Implications: By employing conditional mapping to T2DM, multiple variables can be summarized into a single, easily interpretable map. This could be valuable for T2DM-prevention programs seeking to prioritize diagnostic and intervention resources for the management of T2DM in Appalachia

Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription

SummaryYeast Rpd3 histone deacetylase plays an important role at actively transcribed genes. We characterized two distinct Rpd3 complexes, Rpd3L and Rpd3S, by MudPIT analysis. Both complexes shared a three subunit core and Rpd3L contains unique subunits consistent with being a promoter targeted corepressor. Rco1 and Eaf3 were subunits specific to Rpd3S. Mutants of RCO1 and EAF3 exhibited increased acetylation in the FLO8 and STE11 open reading frames (ORFs) and the appearance of aberrant transcripts initiating within the body of these ORFs. Mutants in the RNA polymerase II-associated SET2 histone methyltransferase also displayed these defects. Set2 functioned upstream of Rpd3S and the Eaf3 methyl-histone binding chromodomain was important for recruitment of Rpd3S and for deacetylation within the STE11 ORF. These data indicate that Pol II-associated Set2 methylates H3 providing a transcriptional memory which signals for deacetylation of ORFs by Rpd3S. This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation

Multiple Signals Converge on a Differentiation MAPK Pathway

An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors

Are Royalties Reasonable in Patent Infringment Suits? Using Hindsight at the Hypothetical Negotiating Table, 12 J. Marshall Rev. Intell. Prop. L. 241 (2012)

Reasonable royalties have become the primary form of relief in patent infringement lawsuits. Once a patent is found valid and infringed, royalties are calculated based on a hypothetical license negotiation between the patent owner and infringer said to take place at the moment infringement began. The calculations seek to arrive at a royalty amount the parties would have agreed upon had an actual license been negotiated. But there is disagreement among courts as to what information should inform the royalty amount. Some take the hypothetical negotiation literally and disallow post-infringement information from entering the calculations because such information would have been unknown to parties in an actual negotiation. Yet other courts view the hypothetical negotiation figuratively and allow both pre- and post-infringement information to play roles in arriving at a royalty amount. This comment examines the contradictive reasoning used by courts and proposes a set of judicial rules that, if applied, would aid in keeping reasonable royalty awards aligned with the statutory requirements of reasonableness and adequate compensation, while also helping to make damage awards more predictable

Are Royalties Reasonable in Patent Infringment Suits? Using Hindsight at the Hypothetical Negotiating Table, 12 J. Marshall Rev. Intell. Prop. L. 241 (2012)

Reasonable royalties have become the primary form of relief in patent infringement lawsuits. Once a patent is found valid and infringed, royalties are calculated based on a hypothetical license negotiation between the patent owner and infringer said to take place at the moment infringement began. The calculations seek to arrive at a royalty amount the parties would have agreed upon had an actual license been negotiated. But there is disagreement among courts as to what information should inform the royalty amount. Some take the hypothetical negotiation literally and disallow post-infringement information from entering the calculations because such information would have been unknown to parties in an actual negotiation. Yet other courts view the hypothetical negotiation figuratively and allow both pre- and post-infringement information to play roles in arriving at a royalty amount. This comment examines the contradictive reasoning used by courts and proposes a set of judicial rules that, if applied, would aid in keeping reasonable royalty awards aligned with the statutory requirements of reasonableness and adequate compensation, while also helping to make damage awards more predictable