High-throughput comparison of gene fitness among related bacteria

BACKGROUND: The contribution of a gene to the fitness of a bacterium can be assayed by whether and to what degree the bacterium tolerates transposon insertions in that gene. We use this fact to compare the fitness of syntenic homologous genes among related Salmonella strains and thereby reveal differences not apparent at the gene sequence level. RESULTS: A transposon Tn5 derivative was used to construct mutants in Salmonella Typhimurium ATCC14028 (STM1) and Salmonella Typhi Ty2 (STY1), which were then grown in rich media. The locations of 234,152 and 53,556 integration sites, respectively, were mapped by sequencing. These data were compared to similar data available for a different Ty2 isolate (STY2) and essential genes identified in E. coli K-12 (ECO). Of 277 genes considered essential in ECO, all had syntenic homologs in STM1, STY1, and STY2, and all but nine genes were either devoid of transposon insertions or had very few. For three of these nine genes, part of the annotated gene lacked transposon integrations (yejM, ftsN and murB). At least one of the other six genes, trpS, had a potentially functionally redundant gene encoded elsewhere in Salmonella but not in ECO. An additional 165 genes were almost entirely devoid of transposon integrations in all three Salmonella strains examined, including many genes associated with protein and DNA synthesis. Four of these genes (STM14_1498, STM14_2872, STM14_3360, and STM14_5442) are not found in E. coli. Notable differences in the extent of gene selection were also observed among the three different Salmonella isolates. Mutations in hns, for example, were selected against in STM1 but not in the two STY strains, which have a defect in rpoS rendering hns nonessential. CONCLUSIONS: Comparisons among transposon integration profiles from different members of a species and among related species, all grown in similar conditions, identify differences in gene contributions to fitness among syntenic homologs. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology

Reconsidering the Impact of Access to Transit on Local Land Markets

METRANS 11-08This research assesses the impact of new passenger rail stations on changes in land use intensity in Los Angeles County. In the county, employment outside downtown is concentrated in nodes with 3.2 million jobs (about half of all jobs in the metropolitan area). Making use of the employment centers as units of analysis reveals significant growth in both employment and population density around new stations. These results are useful for policy makers interested in assessing the indirect benefits of investment in new stations. The results are also informative for those using the Differences-in-differences approach in urban settings. While the effects of new stations are significant and positive, there is marked heterogeneity across stations, suggesting that more research is needed to understand the link between new stations and subsequent changes in land use

Ex vivo fucosylation improves human cord blood engraftment in NOD-SCID IL-2Rγ null mice

Delayed engraftment remains a major hurdle after cord blood (CB) transplantation. It may be due, at least in part, to low fucosylation of cell surface molecules important for homing to the bone marrow microenvironment. Because fucosylation of specific cell surface ligands is required before effective interaction with selectins expressed by the bone marrow microvasculature can occur, a simple 30-minute ex vivo incubation of CB hematopoietic progenitor cells with fucosyltransferase-VI and its substrate (GDP-fucose) was performed to increase levels of fucosylation. The physiologic impact of CB hematopoietic progenitor cell hypofucosylation was investigated in vivo in NOD-SCID interleukin (IL)-2Rγ null (NSG) mice. By isolating fucosylated and nonfucosylated CD34 + cells from CB, we showed that only fucosylated CD34 + cells are responsible for engraftment in NSG mice. In addition, because the proportion of CD34 + cells that are fucosylated in CB is significantly less than in bone marrow and peripheral blood, we hypothesize that these combined observations might explain, at least in part, the delayed engraftment observed after CB transplantation. Because engraftment appears to be correlated with the fucosylation of CD34 + cells, we hypothesized that increasing the proportion of CD34 + cells that are fucosylated would improve CB engraftment. Ex vivo treatment with fucosyltransferase-VI significantly increases the levels of CD34 + fucosylation and, as hypothesized, this was associated with improved engraftment. Ex vivo fucosylation did not alter the biodistribution of engrafting cells or pattern of long-term, multilineage, multi-tissue engraftment. We propose that ex vivo fucosylation will similarly improve the rate and magnitude of engraftment for CB transplant recipients in a clinical setting

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

The biological pump is a process whereby CO2 in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO2, which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.National Basic Research Program of China [2007CB815904]; National Natural Science Foundation of China [40632013/40841023]; SOA project [201105021/DY1150243]; Gordon and Betty Moore Foundation ; US National Science Foundation [648116, 0752972, 0851113, MCB-0453993]; French Science Ministry [ANR07 BLAN 016]; Netherlands Organisation for Scientific Research-Earth and Life Science

City charter of the city of Oakland, California : also general municipal ordinances of said city in effect December 12, 1903 /

Includes index.Mode of access: Internet

Jeannette Groeneveld (Mrs.Corsteiaan) Van Beek

Photograph shows studio portrait of Jeannette Groeneveld (Mrs. Corsteiaan) Van Beek, one of the Dutch settlers in the Gothland Colony near Alvin, Texas. Taken after she moved to California