Impact of wild-type and genetically modified Pseudomonas fluorescens on soil enzyme activities and microbial population structure in the rhizosphere of pea

The definitive version is available at www.blackwell-synergy.com. Copyright Blackwell Publishing DOI : 10.1046/j.1365-294x.1998.00367.xThe aim of this work was to determine the impact of wild type along with functionally and non-functionally modified Pseudomonas fluorescens strains in the rhizosphere. The wild type F113 strain carried a gene encoding the production of the antibiotic 2,4 diacetylphloroglucinol (DAPG) useful in plant disease control, and was marked with a lacZY gene cassette. The first modified strain was a functional modification of strain F113 with repressed production of DAPG, creating the DAPG negative strain F113 G22. The second paired comparison was a non-functional modification of wild type (unmarked) strain SBW25, constructed to carry marker genes only, creating strain SBW25 EeZY-6KX. Significant perturbations were found in the indigenous bacterial population structure, with the F113, (DAPG+) strain causing a shift towards slower growing colonies (K strategists) compared with the non-antibiotic producing derivative (F113 G22) and the SBW25 strains. The DAPG+ strain also significantly reduced, in comparison with the other inocula, the total Pseudomonas populations but did not affect the total microbial populations. The survival of F113 and F113 G22 were an order of magnitude lower than the SBW 25 strains. The DAPG+ strain caused a significant decrease in the shoot to root ratio in comparison to the control and other inoculants, indicating plant stress. F113 increased soil alkaline phosphatase, phosphodiesterase and aryl sulphatase activities compared to the other inocula, which themselves reduced the same enzyme activities compared to the control. In contrast to this, the -glucosidase, -galactosidase and N-acetyl glucosaminidase activities decreased with the inoculation of the DAPG+ strain. These results indicate that soil enzymes are sensitive to the impact of GMM inoculation.Peer reviewe

Altered expression of glutamate signaling, growth factor, and glia genes in the locus coeruleus of patients with major depression.

Several studies have proposed that brain glutamate signaling abnormalities and glial pathology have a role in the etiology of major depressive disorder (MDD). These conclusions were primarily drawn from post-mortem studies in which forebrain brain regions were examined. The locus coeruleus (LC) is the primary source of extensive noradrenergic innervation of the forebrain and as such exerts a powerful regulatory role over cognitive and affective functions, which are dysregulated in MDD. Furthermore, altered noradrenergic neurotransmission is associated with depressive symptoms and is thought to have a role in the pathophysiology of MDD. In the present study we used laser-capture microdissection (LCM) to selectively harvest LC tissue from post-mortem brains of MDD patients, patients with bipolar disorder (BPD) and from psychiatrically normal subjects. Using microarray technology we examined global patterns of gene expression. Differential mRNA expression of select candidate genes was then interrogated using quantitative real-time PCR (qPCR) and in situ hybridization (ISH). Our findings reveal multiple signaling pathway alterations in the LC of MDD but not BPD subjects. These include glutamate signaling genes, SLC1A2, SLC1A3 and GLUL, growth factor genes FGFR3 and TrkB, and several genes exclusively expressed in astroglia. Our data extend previous findings of altered glutamate, astroglial and growth factor functions in MDD for the first time to the brainstem. These findings indicate that such alterations: (1) are unique to MDD and distinguishable from BPD, and (2) affect multiple brain regions, suggesting a whole-brain dysregulation of such functions

Quasi-diffusion magnetic resonance imaging (QDI): A fast, high b-value diffusion imaging technique.

To enable application of non-Gaussian diffusion magnetic resonance imaging (dMRI) techniques in large-scale clinical trials and facilitate translation to clinical practice there is a requirement for fast, high contrast, techniques that are sensitive to changes in tissue structure which provide diagnostic signatures at the early stages of disease. Here we describe a new way to compress the acquisition of multi-shell b-value diffusion data, Quasi-Diffusion MRI (QDI), which provides a probe of subvoxel tissue complexity using short acquisition times (1-4 min). We also describe a coherent framework for multi-directional diffusion gradient acquisition and data processing that allows computation of rotationally invariant quasi-diffusion tensor imaging (QDTI) maps. QDI is a quantitative technique that is based on a special case of the Continuous Time Random Walk model of diffusion dynamics and assumes the presence of non-Gaussian diffusion properties within tissue microstructure. QDI parameterises the diffusion signal attenuation according to the rate of decay (i.e. diffusion coefficient, D in mm2 s-1) and the shape of the power law tail (i.e. the fractional exponent, α). QDI provides analogous tissue contrast to Diffusional Kurtosis Imaging (DKI) by calculation of normalised entropy of the parameterised diffusion signal decay curve, Hn, but does so without the limitations of a maximum b-value. We show that QDI generates images with superior tissue contrast to conventional diffusion imaging within clinically acceptable acquisition times of between 84 and 228 s. We show that QDI provides clinically meaningful images in cerebral small vessel disease and brain tumour case studies. Our initial findings suggest that QDI may be added to routine conventional dMRI acquisitions allowing simple application in clinical trials and translation to the clinical arena

Oligoclonal expansions of CD8(+) T cells in chronic HIV infection are antigen specific

Acute HIV infection is associated with a vigorous immune response characterized by the proliferation of selected T cell receptor V beta (BV)-expressing CD8(+) T cells. These 'expansions', which are commonly detected in the peripheral blood, can persist during chronic HIV infection and may result in the dominance of particular clones. Such clonal populations are most consistent with antigen-driven expansions of CD8(+) T cells. However, due to the difficulties in studying antigen-specific T cells in vivo, it has been hard to prove that oligoclonal BV expansions are actually HIV specific. The use of tetrameric major histocompatibility complex-peptide complexes has recently enabled direct visualization of antigen-specific T cells ex vivo but has not provided information on their clonal composition. We have now made use of these tetrameric complexes in conjunction with anti-BV chain-specific monoclonal antibodies and analysis of cytotoxic T lymphocyte lines/clones to show that chronically clonally expanded CD8(+) T cells are HIV specific in vivo

T2{}^2K2{}^2: The Twitter Top-K Keywords Benchmark

Information retrieval from textual data focuses on the construction of vocabularies that contain weighted term tuples. Such vocabularies can then be exploited by various text analysis algorithms to extract new knowledge, e.g., top-k keywords, top-k documents, etc. Top-k keywords are casually used for various purposes, are often computed on-the-fly, and thus must be efficiently computed. To compare competing weighting schemes and database implementations, benchmarking is customary. To the best of our knowledge, no benchmark currently addresses these problems. Hence, in this paper, we present a top-k keywords benchmark, T${}^2$K${}^2$, which features a real tweet dataset and queries with various complexities and selectivities. T${}^2$K${}^2$ helps evaluate weighting schemes and database implementations in terms of computing performance. To illustrate T${}^2$K${}^2$'s relevance and genericity, we successfully performed tests on the TF-IDF and Okapi BM25 weighting schemes, on one hand, and on different relational (Oracle, PostgreSQL) and document-oriented (MongoDB) database implementations, on the other hand

Improved reference tracts for unsupervised brain white matter tractography

Neighbourhood tractography aims to automatically segment equivalent brain white matter tracts from diffusion magnetic resonance imaging (dMRI) data in different subjects by using a “reference tract” as a prior for the shape and length of each tract of interest. In the current work we present a means of improving the technique by using references tracts derived from dMRI data acquired from 80 healthy volunteers aged 25–64 years. The reference tracts were tested on the segmentation of 16 major white matter tracts in 50 healthy older people, aged 71.8 (±0.4) years. We found that data-generated reference tracts improved the automatic white matter tract segmentations compared to results from atlas-generated reference tracts. We also obtained higher percentages of visually acceptable segmented tracts and lower variation in water diffusion parameters using this approach

Terrestrial laser scanning observations of geomorphic changes and varying lava lake levels at Erebus volcano, Antarctica

A Terrestrial Laser Scanning (TLS) instrument was used to image the topography of the Main Crater at Erebus volcano each December in 2008, 2009, and 2010. Our high-spatial resolution TLS scans provide unique insights into annual and decadal scale geomorphic evolution of the summit area when integrated with comparable data collected by an airborne instrument in 2001. We observe both a pattern of subsidence within the Inner Crater of the volcano and an ~ 3 m per-year drop in the lava lake level over the same time period that are suggestive of decreasing overpressure in an underlying magma reservoir. We also scanned the active phonolite lava lake hosted within the Inner Crater, and recorded rapid cyclic fluctuations in the level of the lake. These were sporadically interrupted by minor explosions by bursting gas bubbles at the lake surface. The TLS data permit calculation of lake level rise and fall speeds and associated rates of volumetric change within the lake. These new observations, when considered with prior determinations of rates of lake surface motion and gas output, are indicative of unsteady magma flow in the conduit and its associated variability in gas volume fraction.This material is based upon work supported by the National Science Foundation (Division of Polar Programs) under Grants ANT0838817 and ANT1142083. The Optech ILRIS 3D TLS instrument was provided by the UNAVCO Polar group with support from NSF grant award ANT0723223. CO receives additional support from the NEC Centre for the Observation and Modeling of Earthquakes, volcanoes and Tectonics (COMET). We gratefully acknowledge the following for assisting with fieldwork on Erebus: Nelia Dunbar, Bill McIntosh, Aaron Curtis, Nels Iverson, Matt Zimmerer, Melissa Kammerer, Nial Peters, Kayla Iacovino, Yves Moussallam, Tehnuka Ilanko, Anna Barford, and Harry Keys. We also acknowledge tremendous logistical support from the staff and the civilian contractors working out of McMurdo station on behalf of the Division of Polar Programs of NSF. We extend especial thanks to the helicopter support provided by PHI and Helicopters, New Zealand. We thank Mark Murray and Rick Aster for their comments on an early version of the manuscript, and Carolyn Parcheta and anonymous for formal reviews of the submitted manuscript.This is the final published version. It first appeared at http://dx.doi.org/10.1016/j.jvolgeores.2015.02.01

A facile method for the stain-free visualization of hierarchical structures with electron microscopy

Diblock copolymers form hierarchical morphologies with numerous applications in drug delivery and as nanoreactors. Yet, the visualization of these structures by electron microscopy can be extremely difficult, requiring complex staining techniques with associated health risks and the potential to alter structural morphology. Reported here is the synthesis of diblock copolymers by RAFT containing 3,5-bis(trifluoromethyl)phenyl functionality allowing for facile visualization of their resulting hierarchical structures by TEM with no further sample preparation.P.E.W. thanks the AWE and E.A. thanks Schlumberger for financial support, and J.d.B is grateful for a Marie Curie Intraeuropean Fellowship (project # 273807). This work was also supported by an ERC Starting Investigator Grant (ASPiRe) and a Next Generation Fellowship provided by the Walters-Kundert Foundation.This is the accepted manuscript. The final published version is available from Wiley at http://onlinelibrary.wiley.com/doi/10.1002/pola.27517/abstract

Interstellar Dust Close to the Sun

The low density interstellar medium (ISM) close to the Sun and inside of the heliosphere provides a unique laboratory for studying interstellar dust grains. Grain characteristics in the nearby ISM are obtained from observations of interstellar gas and dust inside of the heliosphere and the interstellar gas towards nearby stars. Comparison between the gas composition and solar abundances suggests that grains are dominated by olivines and possibly some form of iron oxide. Measurements of the interstellar Ne/O ratio by the Interstellar Boundary Explorer spacecraft indicate that a high fraction of interstellar oxygen in the ISM must be depleted onto dust grains. Local interstellar abundances are consistent with grain destruction in ~150 km/s interstellar shocks, provided that the carbonaceous component is hydrogenated amorphous carbon and carbon abundances are correct. Variations in relative abundances of refractories in gas suggest variations in the history of grain destruction in nearby ISM. The large observed grains, > 1 micron, may indicate a nearby reservoir of denser ISM. Theoretical three-dimensional models of the interaction between interstellar dust grains and the solar wind predict that plumes of about 0.18 micron dust grains form around the heliosphere.Comment: 2011 AGOS Taiwan meeting; accepted for publication in Earth, Planets and Spac