The Beltline Emerald Necklace: Atlanta's New Public Realm

Proposes a corridor of transit, parks, and trails that will add more than 1,400 acres of green space to the city of Atlanta; connect 46 historic neighborhoods; provide a trail for running and bicycling; and include links to the existing transit network

SUMO monoclonal antibodies vary in sensitivity, specificity, and ability to detect types of SUMO conjugate

Monoclonal antibodies (MAb) to members of the Small Ubiquitin-like modifier (SUMO) family are essential tools in the study of cellular SUMOylation. However, many anti-SUMO MAbs are poorly validated, and antibody matching to detection format is without an evidence base. Here we test the specificity and sensitivity of twenty-four anti-SUMO MAbs towards monomeric and polymeric SUMO1-4 in dot-blots, immunoblots, immunofluorescence and immunoprecipitation. We find substantial variability between SUMO MAbs for different conjugation states, for detecting increased SUMOylation in response to thirteen different stress agents, and as enrichment reagents for SUMOylated RanGAP1 or KAP1. All four anti-SUMO4 monoclonal antibodies tested cross-reacted wit SUMO2/3, and several SUMO2/3 monoclonal antibodies cross-reacted with SUMO4. These data characterize the specificity of twenty-four anti-SUMO antibodies across commonly used assays, creating an enabling resource for the SUMO research community

Empowering the Planning Profession

Dwight Eisenhower once remarked, “Plans are worthless, but planning is everything” (1957). Indeed, plans that change nothing are worthless. There are a small number of plans however, that helped to change daily life for the better. The 1909 Plan of Chicago, for example, led to the widening of more than 100 miles of arterial streets and to the conversion of the shore of Lake Michigan into a nearly continuous twenty-four-mile strip of parkland. Plans can be useful, but as Eisenhower understood very well, anyone who wants to change anything must do more than publish a document—they must engage in a process that leads to actual changes to a neighborhood, city, suburb, or region. Sadly, today very few people who call themselves city planners engage in this sort of change-oriented activity and thus cannot be said to engage in planning

Post-translational regulation of the tumour suppressor IRF-1

IRF-1 (Interferon Regulatory Factor 1) is a transcription factor first identified as a regulator of Interferon expression. Two decades after its discovery, IRF-1 has been shown to be involved in numerous other pathways including apoptosis, cell cycle regulation, DNA damage/repair, immune cell development and inflammation. Transcriptional regulation of IRF-1 by a number of external agents has been extensively studied, however almost nothing is known about the posttranslational regulation of IRF-1 activity. In this study IRF-1 is shown to be phosphorylated at Thr180 by GSK3β (Glycogen Synthase Kinase 3β). Phosphorylated Thr180 promotes interaction with the ubiquitin E3 ligase SCFFbxw7u, (Skp1-Cu11-Fbxw7α) which increases turnover of IRF-1 protein. Phosphorylation dependent ubiquitination of IRF-1 was confirmed, as substitution of Thr180 to alanine reduced IRF-1 ubiquitination and increased stability. Enhanced phosphorylation of IRF-1 (by increasing GSK3β expression) promotes increased ubiquitination/degradation. Transactivation of the TRAIL (TNFα Related Apoptosis Inducing Ligand) promoter by IRF-1 was found to be dependent on GSK3β phosphorylation of Thr180 by use of reporter assays and inducible expression of IRF-1 in breast cancer cell lines. Importantly IRF-1 activity on the TRAIL promoter is dependent on proper turnover by the UPS (Ubiquitin Proteasome System), as chemical inhibition of the proteasome, or reduction in IRF-1 ubiquitination reduced activity in reporter assays. This suggests that phosphorylation of IRF-1 by GSK3β acts as a destruction signal through association with SCFFbxw7a. This signal dependent turnover of IRF-1 is required for proper transcriptional activation of the TRAIL promoter

A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response.

IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin immunoprecipitation coupled to a CpG island microarray (ChIP-chip). Using this approach we identified 202 new IRF1-binding sites with high confidence. Functional categorization of the target genes revealed a surprising cadre of new roles that can be linked to IRF1. One of the major functional categories was the DNA damage response pathway. In order to further validate our findings, we show that IRF1 can regulate the mRNA expression of a number of the DNA damage response genes in our list. In particular, we demonstrate that the mRNA and protein levels of the DNA repair protein BRIP1 [Fanconi anemia gene J (FANC J)] are upregulated after IRF1 over-expression. We also demonstrate that knockdown of IRF1 by siRNA results in loss of BRIP1 expression, abrogation of BRIP1 foci after DNA interstrand crosslink (ICL) damage and hypersensitivity to the DNA crosslinking agent, melphalan; a characteristic phenotype of FANC J cells. Taken together, our data provides a more complete understanding of the regulatory networks controlled by IRF1 and reveals a novel role for IRF1 in regulating the ICL DNA damage response

Post-translational regulation of the tumour suppressor IRF-1

IRF-1 (Interferon Regulatory Factor 1) is a transcription factor first identified as a regulator of Interferon expression. Two decades after its discovery, IRF-1 has been shown to be involved in numerous other pathways including apoptosis, cell cycle regulation, DNA damage/repair, immune cell development and inflammation. Transcriptional regulation of IRF-1 by a number of external agents has been extensively studied, however almost nothing is known about the posttranslational regulation of IRF-1 activity. In this study IRF-1 is shown to be phosphorylated at Thr180 by GSK3β (Glycogen Synthase Kinase 3β). Phosphorylated Thr180 promotes interaction with the ubiquitin E3 ligase SCFFbxw7u, (Skp1-Cu11-Fbxw7α) which increases turnover of IRF-1 protein. Phosphorylation dependent ubiquitination of IRF-1 was confirmed, as substitution of Thr180 to alanine reduced IRF-1 ubiquitination and increased stability. Enhanced phosphorylation of IRF-1 (by increasing GSK3β expression) promotes increased ubiquitination/degradation. Transactivation of the TRAIL (TNFα Related Apoptosis Inducing Ligand) promoter by IRF-1 was found to be dependent on GSK3β phosphorylation of Thr180 by use of reporter assays and inducible expression of IRF-1 in breast cancer cell lines. Importantly IRF-1 activity on the TRAIL promoter is dependent on proper turnover by the UPS (Ubiquitin Proteasome System), as chemical inhibition of the proteasome, or reduction in IRF-1 ubiquitination reduced activity in reporter assays. This suggests that phosphorylation of IRF-1 by GSK3β acts as a destruction signal through association with SCFFbxw7a. This signal dependent turnover of IRF-1 is required for proper transcriptional activation of the TRAIL promoter

SUMO, a small, but powerful, regulator of double-strand break repair

The response to a DNA double-stranded break in mammalian cells is a process of sensing and signalling the lesion. It results in halting the cell cycle and local transcription and in the mediation of the DNA repair process itself. The response is launched through a series of post-translational modification signalling events coordinated by phosphorylation and ubiquitination. More recently modifications of proteins by S mall U biquitin-like MO difier (SUMO) isoforms have also been found to be key to coordination of the response (Morris et al. 2009 Nature 462 , 886–890 ( doi:10.1038/nature08593 ); Galanty et al. 2009 Nature 462 , 935–939 ( doi:10.1038/nature08657 )). However our understanding of the role of SUMOylation is slight compared with our growing knowledge of how ubiquitin drives signal amplification and key chromatin interactions. In this review we consider our current knowledge of how SUMO isoforms, SUMO conjugation machinery, SUMO proteases and SUMO-interacting proteins contribute to directing altered chromatin states and to repair-protein kinetics at a double-stranded DNA lesion in mammalian cells. We also consider the gaps in our understanding. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.</jats:p

Viewpoints on Regaining Relevancy

In this piece, four planners from a diversity of backgrounds provide their views on the role and future of the planning profession. At times provocative and critical of the profession, these contributions are meant to encourage and provoke further conversation surrounding the purpose of our profession and the changes we need to make. Contains the following: Recovering What Makes Planning Relevant; Planners and Planning Trying to Find Their Way in the World; Empowering the Planning Profession; A View from a Private Sector/Public Sector Planne

GSK3β-SCFFBXW7α mediated phosphorylation and ubiquitination of IRF1 are required for its transcription-dependent turnover

IRF1 (Interferon Regulatory Factor-1) is the prototype of the IRF family of DNA binding transcription factors. IRF1 protein expression is regulated by transient up-regulation in response to external stimuli followed by rapid degradation via the ubiquitin-proteasome system. Here we report that DNA bound IRF1 turnover is promoted by GSK3β (Glycogen Synthase Kinase 3β) via phosphorylation of the T181 residue which generates a phosphodegron for the SCF (Skp-Cul-Fbox) ubiquitin E3-ligase receptor protein Fbxw7α (F-box/WD40 7). This regulated turnover is essential for IRF1 activity, as mutation of T181 results in an improperly stabilised protein that accumulates at target promoters but fails to induce RNA-Pol-II elongation and subsequent transcription of target genes. Consequently, the anti-proliferative activity of IRF1 is lost in cell lines expressing T181A mutant. Further, cell lines with dysfunctional Fbxw7 are less sensitive to IRF1 overexpression, suggesting an important co-activator function for this ligase complex. As T181 phosphorylation requires both DNA binding and RNA-Pol-II elongation, we propose that this event acts to clear " spent " molecules of IRF1 from transcriptionally engaged target promoters