Browsing by Subject "survival"
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Item Dynamics And Distribution Of Cyanophages And Their Effect On Marine Synechococcus Spp(1994-09) Suttle, Curtis A.; Chan, Amy M.; Suttle, Curtis A.; Chan, Amy M.Cyanophages infecting marine Synechococcus cells were frequently very abundant and were found in every seawater sample along a transect in the western Gulf of Mexico and during a 28-month period in Aransas Pass, Tex. In Aransas Pass their abundance varied seasonally, with the lowest concentrations coincident with cooler water and lower salinity. Along the transect, viruses infecting Synechococcus strains DC2 and SYN48 ranged in concentration from a few hundred per milliliter at 97 m deep and 83 km offshore to ca. 4 x 10(5) ml(-1) near the surface at stations within 18 km of the coast. The highest concentrations occurred at the surface, where salinity decreased from ca. 35.5 to 34 ppt and Synechococcus concentrations were greatest. Viruses infecting strains SNC1, SNC2, and 838BG were distributed in a similar manner but were much less abundant (<10 to >5 x 10(3) ml(-1)). When Synechococcus concentrations exceeded ca. 10(3) ml(-1), cyanophage concentrations increased markedly (ca. 10(2) to > 10(5) ml(-1)), suggesting that a minimum host density was required for efficient viral propagation. Data on the decay rate of viral infectivity d (per day), as a function of solar irradiance I (millimoles of quanta per square meter per second), were used to develop a relationship (d = 0.2610I-0.00718; r(2) = 0.69) for conservatively estimating the destruction of infectious viruses in the mixed layer of two offshore stations. Assuming that virus production balances losses and that the burst size is 250, ca. 5 to 7% of Synechococcus cells would be infected daily by viruses. Calculations based on contact rates between Synechococcus cells and infectious viruses produce similar results (5 to 14%). Moreover, balancing estimates of viral production with contact rates for the farthest offshore station required that most Synechococcus cells be susceptible to infection, that most contacts result in infection, and that the burst size be about 324 viruses per lytic event. In contrast, in nearshore waters, where ca. 80% of Synechococcus cells would be contacted daily by infectious cyanophages, only ca. 1% of the contacts would have to result in infection to balance the estimated virus removal rates. These results indicate that cyanophages are an abundant and dynamic component of marine planktonic communities and are probably responsible for lysing a small but significant portion of the Synechococcus population on a daily basis.Item Letter to H.B. Stenzel from Thurlow C. Nelson on 1943-01-29(1943-01-29) Nelson, Thurlow C.Item Small RNA Discovery Using Conservation Analysis Enhancement(2016-04-19) Chou, Brendan; Contreras, Lydia M.Small noncoding RNAs (sRNAs) have been described as posttranscriptional regulators of many cellular systems in bacteria, notably environmental stress responses. However, sRNAs are small and difficult to detect due to the lack of uniformity in which they are encoded in the genome. Since they may be found inn the 5' and 3' untranslated regions of genes and in intergenic regions, identification and characterization of sRNAs has been challenging. These elusive gene expression regulators may aid in explaining the interesting survival mechanisms of Deinococcus radiodurans under ionizing radation of > 12,000 Gy, while most bacteria find 1,000 Gy of radiation to be lethal. This study takes advantage of high-throughput experimental methods and computational prediction methods to develop a pipeline for more efficient sRNA discovery. Intergenic regions in 13 well-annotated bacterial species were analyzed for conservation levels to increase the likelihood that candidate intergenic regions would code for sRNAs. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicated that sRNAs are found more abundantly in longer and highly conserved intergenic regions. This workflow was used to discover novel sRNA in D. radiodurans. 199 potential sRNA candidates were generated from whole-transcriptome deep sequencing analysis, and 41 were confirmed using northern blotting and reverse transcription PCR. Analysis of sRNA expression levels during recovery after actute radiation resulted in 8 confirmed sRNAs which demonstrated varying expression levels due to irradiation. Conservation comparison of novel D. radiodurans sRNAs led to the discovery and confirmation of 7 homologous sRNAs in the closely-related species Deinococcus geothermalis.