High-throughput comparison of gene fitness among related bacteria

ABSTRACT: 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 to 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 strain (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 Tn insertions or had very few. For three of these nine genes, part of the annotated gene lacked Tn 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.L, STM14_2872, STM14_3360.RJ, 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 fitness among syntenic homologous genes. Further differences in fitness profiles among shared genes can be expected in other selective environments, with potential relevance for comparative systems biology.     

Nitrite oxidation in the Namibian oxygen minimum zone

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in ¹⁵N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO₂⁻ d⁻¹) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO₃⁻ was re-oxidized back to NO₃⁻ via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.     

EFFECTS OF COLCEMID ON HYDRA VIRIDIS WITH MULTIPLE-PEDUNCLE GRAFTS

The effect of Colcemid on multiple-graft Hydra viridis containing three peduncles (3p) grafted in tandem is reported. At grafting, the apical member of a 3p animal is a foot-less host, the middle member, an isolated peduncle, and the proximal member, a foot-bearing peduncle. In different experimental situations all three members are treated with Colcemid, the host member alone is treated, or the host member is not treated but the others are. Control animals have only non-treated members. Head and foot regeneration on graft pieces and the formation of waists and separations at the borders between these pieces are monitored and the significance of differences between frequencies tested by Chi square. Head formation on the middle and proximal peduncles is promoted by Colcemid when all pieces are treated, but animals with treated host pieces have significantly higher frequencies of heads on their non-treated proximal pieces than other experimental and control animals. Animals with Colcemid-treated proximal peduncles do not have significantly more heads on the most proximal peduncle compared to controls. Colcemid does not alter the frequency of foot formation significantly on the host peduncles of animals in the different categories, but foot formation is increased on the middle pieces of animals with three treated pieces and on animals with middle and proximal treated pieces. The rate of waist formation and graft separation is retarded when all three or just the host piece is treated, but not when only the middle and proximal pieces are treated. The direct action of Colcemid on nerves and on dividing cells may be responsible for these effects.     

Neuromuscular Systems in Molluscs

Molluscs have become increasingly popular in the study of centralneural mechanisms. More recently, there have been attempts torelate activity in central neurons with behavior in animalsof this phylum. The latter studies necessitate an understandingof the effectors of such behaviors. This requires not only informationabout the neuromuscular junction, but also an awareness of thecapabilities of the muscles themselves. Therefore, we have discussedsome structural and related functional characteristics of molluscanmuscle. We suggest that invertebrate mucles might be comparedon three scales: the amount of myofilament organization, theamount of vesicular specialization and organization, and theamount of paramyosin. We have considered some characteristicsof the widely-studied sustained contraction, known as "catch."Finally, we have discussed the neuromuscular junction—thetypes of junctions, the multiplicity of innervation, and someaspects of pharmacology. The results of such a study indicatedmany areas in which further research is essential before wecan understand behavior in terms of activity in the centralnervous system.