Identification of biofilm proteins in non-typeable Haemophilus Influenzae

BACKGROUND: Non-typeable Haemophilus influenzae biofilm formation is implicated in a number of chronic infections including otitis media, sinusitis and bronchitis. Biofilm structure includes cells and secreted extracellular matrix that is "slimy" and believed to contribute to the antibiotic resistant properties of biofilm bacteria. Components of biofilm extracellular matrix are largely unknown. In order to identify such biofilm proteins an ex-vivo biofilm of a non-typeable Haemophilus influenzae isolate, originally from an otitis media patent, was produced by on-filter growth. Extracellular matrix fraction was subjected to proteomic analysis via LC-MS/MS to identify proteins. RESULTS: 265 proteins were identified in the extracellular matrix sample. The identified proteins were analyzed for COG grouping and predicted cellular location via the TMHMM and SignalP predictive algorithms. The most over-represented COG groups identified compared to their frequency in the Haemophilus influenzae genome were cell motility and secretion (group N) followed by ribosomal proteins of group J. A number of hypothetical or un-characterized proteins were observed, as well as proteins previously implicated in biofilm function. CONCLUSION: This study represents an initial approach to identifying and cataloguing numerous proteins associated with biofilm structure. The approach can be applied to biofilms of other bacteria to look for commonalities of expression and obtained information on biofilm protein expression can be used in multidisciplinary approaches to further understand biofilm structure and function

Genetic diversity and population structure of the threatened temperate woody bamboo Kuruna debilis (Poaceae: Bambusoideae: Arundinarieae) from Sri Lanka based on microsatellite analysis

Species of the temperate woody bamboo genus Kuruna Attigala, Kathriar. & L.G. Clark (Poaceae: Bambusoideae) distributed in Sri Lanka and southern India, are threatened due to deforestation and habitat fragmentation. The current study focused on the tetraploid woody bamboo Kuruna debilis (Thwaites) Attigala, Kathriar. & L.G. Clark, using twelve variable microsatellite loci to assess the genetic diversity and population structure in six known Sri Lankan populations. Due to the rarity of the species, an exhaustive sampling of accessible plants resulted in a total of only 28 individuals. Nonetheless, the allelic diversity was high at most loci and given the limited distances separating populations (\u3c 65 km apart), they exhibited a fairly high genetic differentiation (FST = 0.113) and strong isolation by distance. Structure, neighbour-joining, and neighbour-net analyses concur in grouping the six K. debilis populations into three genetic clusters consistent with the spatial proximity of the populations: one cluster comprised populations from the Piduruthalagala Mountain and Horton Plains, the second cluster consisted of the population from Adams Peak and the last comprised the populations from the Handapan Ella Plains. Due to multiple indicators of high allelic diversity, the population from the northern Horton Plains (LA124) should be targeted for conservation. Moreover, the population found in Adams Peak (LA159) is also genetically important and critical to the conservation of these species due to its unique genetic diversity. As the first population genetics study of Bambusoideae in Sri Lanka, we anticipate that our results will provide a foundation for future comparative population genetics and conservation studies in the country

Identification of IbeR as a Stationary-Phase Regulator in Meningitic Escherichia coli K1 that Carries a Loss-of-Function Mutation in rpoS

IbeR is a regulator present in meningitic Escherichia coli strain E44 that carries a loss-of-function mutation in the stationary-phase (SP) regulatory gene rpoS. In order to determine whether IbeR is an SP regulator in E44, two-dimensional gel electrophoresis and LC-MS were used to compare the proteomes of a noninvasive ibeR deletion mutant BR2 and its parent strain E44 in the SP. Four up-regulated (TufB, GapA, OmpA, AhpC) and three down-regulated (LpdA, TnaA, OpmC) proteins in BR2 were identified when compared to E44. All these proteins contribute to energy metabolism or stress resistance, which is related to SP regulation. One of the down-regulated proteins, tryptophanase (TnaA), which is regulated by RpoS in other E. coli strains, is associated with SP regulation via production of a signal molecule indole. Our studies demonstrated that TnaA was required for E44 invasion, and that indole was able to restore the noninvasive phenotype of the tnaA mutant. The production of indole was significantly reduced in BR2, indicating that ibeR is required for the indole production via tnaA. Survival studies under different stress conditions indicated that IbeR contributed to bacteria stress resistance in the SP. Taken together, IbeR is a novel regulator contributing to the SP regulation

Evolution of a Canada Basin ice-ocean boundary layer and mixed layer across a developing thermodynamically forced marginal ice zone

A comprehensive set of autonomous, ice-ocean measurements were collected across the Canada Basin to study the summer evolution of the ice-ocean boundary layer (IOBL) and ocean mixed layer (OML). Evaluation of local heat and freshwater balances and associated turbulent forcing reveals that melt ponds (MPs) strongly influence the summer IOBL-OML evolution. Areal expansion of MPs in mid-June start the upper ocean evolution resulting in significant increases to ocean absorbed radiative flux (19 W m−2 in this study). Buoyancy provided by MP drainage shoals and freshens the IOBL resulting in a 39 MJ m−2 increase in heat storage in just 19 days (52% of the summer total). Following MP drainage, a near-surface fresh layer deepens through shear-forced mixing to form the summer mixed layer (sML). In late summer, basal melt increases due to stronger turbulent mixing in the thin sML and the expansion of open water areas due in part to wind-forced divergence of the sea ice. Thermal heterogeneities in the marginal ice zone (MIZ) upper ocean led to large ocean-to-ice heat fluxes (100–200 W m−2) and enhanced basal ice melt (3–6 cm d−1), well away from the ice edge. Calculation of the upper ocean heat budget shows that local radiative heat input accounted for at least 89% of the observed latent heat losses and heat storage (partitioned 0.77/0.23). These results suggest that the extensive area of deteriorating sea ice observed away from the ice edge during the 2014 season, termed the “thermodynamically forced MIZ,” was driven primarily by local shortwave radiative forcing

Community Impacts of Prosopis Juliflora Invasion: Biogeographic and Congeneric Comparisons

We coordinated biogeographical comparisons of the impacts of an exotic invasive tree in its native and non-native ranges with a congeneric comparison in the non-native range. Prosopis juliflora is taxonomically complicated and with P. pallida forms the P. juliflora complex. Thus we sampled P. juliflora in its native Venezuela, and also located two field sites in Peru, the native range of Prosopis pallida. Canopies of Prosopis juliflora, a native of the New World but an invader in many other regions, had facilitative effects on the diversity of other species in its native Venezuela, and P. pallida had both negative and positive effects depending on the year, (overall neutral effects) in its native Peru. However, in India and Hawaii, USA, where P. juliflora is an aggressive invader, canopy effects were consistently and strongly negative on species richness. Prosopis cineraria, a native to India, had much weaker effects on species richness in India than P. juliflora. We carried out multiple congeneric comparisons between P. juliflora and P. cineraria, and found that soil from the rhizosphere of P. juliflora had higher extractable phosphorus, soluble salts and total phenolics than P. cineraria rhizosphere soils. Experimentally applied P. juliflora litter caused far greater mortality of native Indian species than litter from P. cineraria. Prosopis juliflora leaf leachate had neutral to negative effects on root growth of three common crop species of north-west India whereas P. cineraria leaf leachate had positive effects. Prosopis juliflora leaf leachate also had higher concentrations of total phenolics and L-tryptophan than P. cineraria, suggesting a potential allelopathic mechanism for the congeneric differences. Our results also suggest the possibility of regional evolutionary trajectories among competitors and that recent mixing of species from different trajectories has the potential to disrupt evolved interactions among native species

A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns

We used a bi‐organellar phylogenomic approach to address higher‐order relationships in Pandanales, including the first molecular phylogenetic study of the panama‐hat family, Cyclanthaceae. Our genus‐level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellar genomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid‐based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well‐supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non‐photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/33/cla12417-sup-0025-TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/32/cla12417-sup-0017-FigS17.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/31/cla12417-sup-0004-FigS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/30/cla12417-sup-0019-FigS19.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/29/cla12417-sup-0020-FigS20.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/28/cla12417_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/27/cla12417-sup-0005-FigS5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/26/cla12417-sup-0012-FigS12.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/25/cla12417-sup-0007-FigS7.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/24/cla12417-sup-0022-FigS22.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/23/cla12417-sup-0029-TableS5.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/22/cla12417-sup-0010-FigS10.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/21/cla12417-sup-0011-FigS11.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/20/cla12417-sup-0014-FigS14.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/19/cla12417-sup-0002-FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/18/cla12417-sup-0001-FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/17/cla12417.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/16/cla12417-sup-0030-TableS6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/15/cla12417-sup-0021-FigS21.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/14/cla12417-sup-0023-FigS23.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/13/cla12417-sup-0009-FigS9.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/12/cla12417-sup-0031-TableS7.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/11/cla12417-sup-0006-FigS6.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/10/cla12417-sup-0003-FigS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/9/cla12417-sup-0024-FigS24.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/8/cla12417-sup-0008-FigS8.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/7/cla12417-sup-0028-TableS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/6/cla12417-sup-0016-FigS16.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/5/cla12417-sup-0013-FigS13.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/4/cla12417-sup-0018-FigS18.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/3/cla12417-sup-0026-TableS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/2/cla12417-sup-0015-FigS15.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162810/1/cla12417-sup-0027-TableS3.pd

Ice and ocean velocity in the Arctic marginal ice zone: Ice roughness and momentum transfer

The interplay between sea ice concentration, sea ice roughness, ocean stratification, and momentum transfer to the ice and ocean is subject to seasonal and decadal variations that are crucial to understanding the present and future air-ice-ocean system in the Arctic. In this study, continuous observations in the Canada Basin from March through December 2014 were used to investigate spatial differences and temporal changes in under-ice roughness and momentum transfer as the ice cover evolved seasonally. Observations of wind, ice, and ocean properties from four clusters of drifting instrument systems were complemented by direct drill-hole measurements and instrumented overhead flights by NASA operation IceBridge in March, as well as satellite remote sensing imagery about the instrument clusters. Spatially, directly estimated ice-ocean drag coefficients varied by a factor of three with rougher ice associated with smaller multi-year ice floe sizes embedded within the first-year-ice/multi-year-ice conglomerate. Temporal differences in the ice-ocean drag coefficient of 20–30% were observed prior to the mixed layer shoaling in summer and were associated with ice concentrations falling below 100%. The ice-ocean drag coefficient parameterization was found to be invalid in September with low ice concentrations and small ice floe sizes. Maximum momentum transfer to the ice occurred for moderate ice concentrations, and transfer to the ocean for the lowest ice concentrations and shallowest stratification. Wind work and ocean work on the ice were the dominant terms in the kinetic energy budget of the ice throughout the melt season, consistent with free drift conditions. Overall, ice topography, ice concentration, and the shallow summer mixed layer all influenced mixed layer currents and the transfer of momentum within the air-ice-ocean system. The observed changes in momentum transfer show that care must be taken to determine appropriate parameterizations of momentum transfer, and imply that the future Arctic system could become increasingly seasonal

hHSS1: a novel secreted factor and suppressor of glioma growth located at chromosome 19q13.33

The completion of the Human Genome Project resulted in discovery of many unknown novel genes. This feat paved the way for the future development of novel therapeutics for the treatment of human disease based on novel biological functions and pathways. Towards this aim, we undertook a bioinformatics analysis of in-house microarray data derived from purified hematopoietic stem cell populations. This effort led to the discovery of HSS1 (Hematopoietic Signal peptide-containing Secreted 1) and its splice variant HSM1 (Hematopoietic Signal peptide-containing Membrane domain-containing 1). HSS1 gene is evolutionarily conserved across species, phyla and even kingdoms, including mammals, invertebrates and plants. Structural analysis showed no homology between HSS1 and known proteins or known protein domains, indicating that it was a truly novel protein. Interestingly, the human HSS1 (hHSS1) gene is located at chromosome 19q13.33, a genomic region implicated in various cancers, including malignant glioma. Stable expression of hHSS1 in glioma-derived A172 and U87 cell lines greatly reduced their proliferation rates compared to mock-transfected cells. hHSS1 expression significantly affected the malignant phenotype of U87 cells both in vitro and in vivo. Further, preliminary immunohistochemical analysis revealed an increase in hHSS1/HSM1 immunoreactivity in two out of four high-grade astrocytomas (glioblastoma multiforme, WHO IV) as compared to low expression in all four low-grade diffuse astrocytomas (WHO grade II). High-expression of hHSS1 in high-grade gliomas was further supported by microarray data, which indicated that mesenchymal subclass gliomas exclusively up-regulated hHSS1. Our data reveal that HSS1 is a truly novel protein defining a new class of secreted factors, and that it may have an important role in cancer, particularly glioma