Strain-specific differences in Neisseria gonorrhoeae associated with the phase variable gene repertoire

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited - © 2005 Jordan et al; licensee BioMed Central Ltd.Background: There are several differences associated with the behaviour of the four main experimental Neisseria gonorrhoeae strains, FA1090, FA19, MS11, and F62. Although there is data concerning the gene complements of these strains, the reasons for the behavioural differences are currently unknown. Phase variation is a mechanism that occurs commonly within the Neisseria spp. and leads to switching of genes ON and OFF. This mechanism may provide a means for strains to express different combinations of genes, and differences in the strain-specific repertoire of phase variable genes may underlie the strain differences. Results: By genome comparison of the four publicly available neisserial genomes a revised list of 64 genes was created that have the potential to be phase variable in N. gonorrhoeae, excluding the opa and pilC genes. Amplification and sequencing of the repeat-containing regions of these genes allowed determination of the presence of the potentially unstable repeats and the ON/OFF expression state of these genes. 35 of the 64 genes show differences in the composition or length of the repeats, of which 28 are likely to be associated with phase variation. Two genes were expressed differentially between strains causing disseminated infection and uncomplicated gonorrhoea. Further study of one of these in a range of clinical isolates showed this association to be due to sample size and is not maintained in a larger sample. Conclusion: The results provide us with more evidence as to which genes identified through comparative genomics are indeed phase variable. The study indicates that there are large differences between these four N. gonorrhoeae strains in terms of gene expression during in vitro growth. It does not, however, identify any clear patterns by which previously reported behavioural differences can be correlated with the phase variable gene repertoire.This study is funded by a Wellcome Trust Project Grant

Oyster Aquaculture Site Selection Using Landsat 8-derived Sea Surface Temperature, Turbidity, and Chlorophyll a.

Remote sensing data is useful for selection of aquaculture sites because it can provide water-quality products mapped with no cost to users. However, the spatial resolution of most ocean color satellites is too coarse to provide usable data within many estuaries. The more recently launched Landsat 8 satellite has both the spatial resolution and the necessary signal to noise ratio to provide temperature, as well as ocean color derived products along complex coastlines. The state of Maine (USA) has an abundance of estuarine indentations (~3,500 miles of tidal shoreline within 220 miles of coast), and an expanding aquaculture industry, which makes it a prime case-study for using Landsat 8 data to provide products suitable for aquaculture site selection. We collected the Landsat 8 scenes over coastal Maine, flagged clouds, atmospherically corrected the top-of-the-atmosphere radiances, and derived time varying fields (repeat time of Landsat 8 is 16 days) of temperature (100 m resolution), turbidity (30 m resolution), and chlorophyll-a (30 m resolution). We validated the remote-sensing-based products at several in situ locations along the Maine coast where monitoring buoys and programs are in place. Initial analysis of the validated fields revealed promising areas for oyster aquaculture. The approach used and the data collected to date show potential for other applications in marine coastal environments, including water quality monitoring and ecosystem management

Cyclic extensions of fusion categories via the Brauer-Picard groupoid

We construct a long exact sequence computing the obstruction space, pi_1(BrPic(C_0)), to G-graded extensions of a fusion category C_0. The other terms in the sequence can be computed directly from the fusion ring of C_0. We apply our result to several examples coming from small index subfactors, thereby constructing several new fusion categories as G-extensions. The most striking of these is a Z/2Z-extension of one of the Asaeda-Haagerup fusion categories, which is one of only two known 3-supertransitive fusion categories outside the ADE series. In another direction, we show that our long exact sequence appears in exactly the way one expects: it is part of a long exact sequence of homotopy groups associated to a naturally occuring fibration. This motivates our constructions, and gives another example of the increasing interplay between fusion categories and algebraic topology.Comment: 18 pages, 1 figur

Invertible braided tensor categories

We prove that a finite braided tensor category A is invertible in the Morita 4–category BrTens of braided tensor categories if and only if it is nondegenerate. This includes the case of semisimple modular tensor categories, but also nonsemisimple examples such as categories of representations of the small quantum group at good roots of unity. Via the cobordism hypothesis, we obtain new invertible 4–dimensional framed topological field theories, which we regard as a nonsemisimple framed version of the Crane–Yetter–Kauffman invariants, after the Freed–Teleman and Walker constructions in the semisimple case. More generally, we characterize invertibility for E1– and E2–algebras in an arbitrary symmetric monoidal ∞–category, and we conjecture a similar characterization of invertible En–algebras for any n. Finally, we propose the Picard group of BrTens as a generalization of the Witt group of nondegenerate braided fusion categories, and pose a number of open questions about it