Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes

Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous freestanding HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution

State Mandates, Housing Elements, and Low-income Housing Production

In order to create low-income housing opportunities and mitigate exclusionary zoning, in 1968 Congress mandated that municipalities receiving comprehensive planning funds must create a housing element. In tandem, many states mandated that municipal housing elements must accommodate low-income housing needs. After examining empirical research for California, Florida, Illinois, and Minnesota, this review found aspirational success because those states rewarded the municipal planning process. In order to increase low-income housing, this review argues for state housing policy reform. Under US Department of Housing and Urban Development’s revised fair housing rule, which requires an assessment of local data, states can no longer ignore the exclusionary behavior of municipalities

Foreclosures and crime: A city-level analysis in Southern California of a dynamic process

Although a growing body of research has examined and found a positive relationship between neighborhood crime and home foreclosures, some research suggests this relationship may not hold in all cities. This study uses city-level data to assess the relationship between foreclosures and crime by estimating longitudinal models with lags for monthly foreclosure and crime data in 128 cities from 1996 to 2011 in Southern California. We test whether these effects are stronger in cities with a combination of high economic inequality and high economic segregation; and whether they are stronger in cities with high racial/ethnic heterogeneity and high racial segregation. One month, and cumulative three month, six month, and 12-month lags of foreclosures are found to increase city level crime for all crimes except motor vehicle theft. The effect of foreclosures on these crime types is stronger in cities with simultaneously high levels of inequality but low levels of economic segregation. The effect of foreclosures on aggravated assault, robbery, and burglary is stronger in cities with simultaneously high levels of racial heterogeneity and low levels of racial segregation. On the other hand, foreclosures had a stronger effect on larceny and motor vehicle theft when they occurred in a city with simultaneously high levels of racial heterogeneity and high levels of racial segregation. There is evidence that the foreclosure crisis had large scale impacts on cities, leading to higher crime rates in cities hit harder by foreclosures. Nonetheless, the economic and racial characteristics of the city altered this effect

Assembly, organization, and function of the COPII coat

A full mechanistic understanding of how secretory cargo proteins are exported from the endoplasmic reticulum for passage through the early secretory pathway is essential for us to comprehend how cells are organized, maintain compartment identity, as well as how they selectively secrete proteins and other macromolecules to the extracellular space. This process depends on the function of a multi-subunit complex, the COPII coat. Here we describe progress towards a full mechanistic understanding of COPII coat function, including the latest findings in this area. Much of our understanding of how COPII functions and is regulated comes from studies of yeast genetics, biochemical reconstitution and single cell microscopy. New developments arising from clinical cases and model organism biology and genetics enable us to gain far greater insight in to the role of membrane traffic in the context of a whole organism as well as during embryogenesis and development. A significant outcome of such a full understanding is to reveal how the machinery and processes of membrane trafficking through the early secretory pathway fail in disease states

What Are the Determinants of Open-Space Ballot Measures? An Extension of the Research

This article comments on the findings of Romero and Liserio's "Saving Open Spaces." Their primary claim is that open-space ballots are not related in any way to actual land-use patterns. Copyright (c) 2004 by the Southwestern Social Science Association.

Cluster J mycobacteriophages: intron splicing in capsid and tail genes

Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution