Rhizosphere engineering: Innovative improvement of root environment

© 2017 Elsevier B.V.The ability of roots to extract water and nutrients from soil depends on the biophysical properties of the rhizosphere, which are strongly influenced by mucilage secretion. The aim of this study was to introduce the concept of rhizoligands to engineer the biophysical properties of the rhizosphere. A rhizoligand is defined as an additive that increases the wettability of the rhizosphere and links the mucilage network to main intimate contact with the root surface. We hypothesize that rhizoligands: i) facilitate the rewetting of the rhizosphere during repeated drying and wetting cycles; ii) enhance rhizosheath formation; iii) increase enzyme activities in the rhizosphere; and iv) increase plant biomass. A commercial surfactant was selected as the prototype rhizoligand to test the effect on the rhizosphere biophysical properties of white lupin grown in quartz sand and subjected to six drying-rewetting cycles. Half of the plants were irrigated with water and the other half with the rhizoligand solution. When plants were 50 days old, we measured: i) soil water content; ii) rhizosheath mass; iii) activity of selected enzymes; iv) carbon content in the rhizosphere; and v) plant biomass. Rhizoligand increased rewetting rate of the rhizosphere after drying and subsequent rewetting, resulting in a greater soil water content. Rhizosheath formation was improved in plants irrigated with rhizoligand and sand particles attached to the roots increased by 1.64 times compared to plants irrigated with water. Activity of the enzymes chitinase, sulfatase, and β-glucosidase were 4, 7.9, and 1.5 times greater in the rhizosphere of plants irrigated with rhizoligand than in the rhizosphere of plants irrigated with water. Plant biomass was 1.2 fold greater in samples irrigated with rhizoligand solution than in samples irrigated with water. We conclude that application of rhizoligand improves plant performance by influencing the water dynamics in the rhizosphere and the plant, increasing the mechanical stability of the rhizosheaths and increasing the enzyme activities in the rhizosphere. Such effects are probably triggered by the interaction between mucilage and the applied rhizoligand, which reduces mucilage swelling (possibly by cross-linking mucilage polymers) and thus by increasing its viscosity keeps the mucilage close to the root surface. We propose the rhizoligand concept as a strategy to engineer the rhizosphere properties and to improve plant tolerance to water shortage

Integrative genomic analysis of trisomy 12 abnormality in B-cell chronic lymphocytic leukemia

Background: Flow cytometry allows specific assessment of the expression of ZAP-70, a promising new prognostic factor in B-cell chronic lymphocytic leukemia (B-CLL), but suffers from a lack of multicenter standardization. Design and Methods: An optimized method for direct detection of ZAP-70 in flow cytometry was tested in a multicenter fashion. Adapted for frozen cells, this method includes a normalization step by addition of B cells from a pool of peripheral blood mononuclear cells collected from normal donors. ZAP-70 expression levels were assessed for 153 patients with typical B-cell chronic lymphocytic leukemia chronic lymphocytic leukemia. Results were expressed as the ratio of ZAP-70 mean fluorescence intensity between B-CLL cells and normal B cells. Results: The statistically optimized cut-off of ZAP-70 positivity was a ratio of 1.4. Concordance between ZAP-70 and CD38 expression was 67%. Concordance between the mutational status of IgVH genes and ZAP-70 or CD38 expression was 87% and 65%, respectively. ZAP-70 was significantly expressed in 28%, 54% and 61% of patients with Binet stages A, B and C B-cell chronic lymphocytic leukemia, respectively (p=0.008). The absence of ZAP-70 expression was associated with isolated del(13q14), a cytogenetic abnormality with a good prognosis, while most patients with the del(17p13) poor prognosis cytogenetic marker expressed ZAP-70 (p<10-5). ZAP-70 expression was not related to the other poor prognosis cytogenetic abnormality del(11q22.3) nor to trisomy 12. Conclusions: This new technique provides highly reliable results well correlated with the mutational status of IgVH genes, CD38 expression, Binet stage and cytogenetic abnormalities. This robust discriminative technique appears of particular interest for routine diagnosis and assessment of ZAP-70 expression in large, prospective, multicenter therapeutic trials

Kinetics of photoinduced ordering in azo-dye films: two-state and diffusion models

We study the kinetics of photoinduced ordering in the azo-dye SD1 photoaligning layers and present the results of modeling performed using two different phenomenological approaches. A phenomenological two state model is deduced from the master equation for an ensemble of two-level molecular systems. Using an alternative approach, we formulate the two-dimensional (2D) diffusion model as the free energy Fokker-Planck equation simplified for the limiting regime of purely in-plane reorientation. The models are employed to interpret the irradiation time dependence of the absorption order parameters extracted from the available experimental data by using the exact solution to the light transmission problem for a biaxially anisotropic absorbing layer. The transient photoinduced structures are found to be biaxially anisotropic whereas the photosteady and the initial states are uniaxial.Comment: revtex4, 34 pages, 9 figure

Mesoscopic organization reveals the constraints governing C. elegans nervous system

One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental stimuli. Investigating the intermediate or mesoscopic level of organization in the nervous system is a vital step towards understanding how the integration of micro-level dynamics results in macro-level functioning. In this paper, we have considered the somatic nervous system of the nematode Caenorhabditis elegans, for which the entire neuronal connectivity diagram is known. We focus on the organization of the system into modules, i.e., neuronal groups having relatively higher connection density compared to that of the overall network. We show that this mesoscopic feature cannot be explained exclusively in terms of considerations, such as optimizing for resource constraints (viz., total wiring cost) and communication efficiency (i.e., network path length). Comparison with other complex networks designed for efficient transport (of signals or resources) implies that neuronal networks form a distinct class. This suggests that the principal function of the network, viz., processing of sensory information resulting in appropriate motor response, may be playing a vital role in determining the connection topology. Using modular spectral analysis, we make explicit the intimate relation between function and structure in the nervous system. This is further brought out by identifying functionally critical neurons purely on the basis of patterns of intra- and inter-modular connections. Our study reveals how the design of the nervous system reflects several constraints, including its key functional role as a processor of information.Comment: Published version, Minor modifications, 16 pages, 9 figure

HIV-1 viral blips are associated with repeated and increasingly high levels of cell-associated HIV-1 RNA transcriptional activity

Objective:Some HIV+ patients, virally suppressed on ART, show occasional 'blips' of detectable HIV-1 plasma RNA. We used a new highly sensitive assay of cell-associated HIV-1 RNA to measure transcriptional activity in PBMCs and production of infectious virus from the viral reservoir, in patients with and without 'blips'.Design/methods:RNA and DNA extracted from cells in 6 ml of peripheral blood, from suppressed patients with one to two 'blip' episodes over the past 2 years of ART (n = 55), or no 'blips' (n = 52), were assayed for HIV-1 RNA transcripts and proviral DNA targeting the highly conserved 'R' region of the LTR. Follow-up samples were also collected. Purified CD4+T cells were cultured with anti-CD3/CD28/CD2 T-cell activator to amplify transcription and measure replication competent virus.Results:HIV-1 RNA transcripts ranged from 1.3 to 5415 copies/106white blood cells. 'Blip' patients had significantly higher levels vs. without blips (median 192 vs. 49; P = 0.0007), which correlated with: higher levels of inducible transcripts after activation in vitro, sustained higher HIV-1 transcription levels in follow-up samples along with increasing HIV-1 DNA in some, and production of replication-competent HIV-1.Conclusion:Viral 'blips' are significant reflecting higher transcriptional activity from the reservoir and contribute to the reservoir over time. This sensitive assay can be used in monitoring the size and activity of the HIV-1 reservoir and will be useful in HIV-1 cure strategies

Design and optimization of index-guiding photonic crystal fiber gas sensor

Globalization is becoming an important issue for most businesses in the world. Since globalization changes business trends and shortens product life cycles, it requires companies to be more innovative in developing new ideas, products and processes. Clustering is one of ways to promote innovation by facilitating sharing information and ideas between firms, attracting buyers and suppliers, and providing opportunities for joint training. Many researches in developed countries found that the proximity between companies facilitated collaboration and provided a more conducive environment for R&D and knowledge sharing which can develop culture of entrepreneurship and innovation. Then, the success of clusters in developed countries has led many government and companies to establish new clusters.Since products from China have been dominated Indonesia's market share with lower price, it is very difficult for Indonesian Small and Medium Enterprises to compete with lower price also. Therefore, to face the competition, innovation is perhaps as an alternative strategy for Indonesian SMEs. In facts, more than 50% of small and medium enterprises in Indonesia are located in clusters and most of them are located in Java, Bali and Nusa Tenggara. Even though they located in cluster but their innovations still very low and judging from technology perspective, most of them have low level of technologies and still remain in the underdeveloped stage. Therefore, in this research, the author tries to find (1). To what extend do cluster Indonesia promote innovation, (2). To find the reasons why clusters in Indonesia has not been working well in promoting innovation and (3). To investigate what aspects can be improved by Indonesian SMEs to boost their innovation

CSF and Brain Structural Imaging Markers of the Alzheimer's Pathological Cascade

10.1371/journal.pone.0047406PLoS ONE712

VPR-Bench: An Open-Source Visual Place Recognition Evaluation Framework with Quantifiable Viewpoint and Appearance Change

Visual place recognition (VPR) is the process of recognising a previously visited place using visual information, often under varying appearance conditions and viewpoint changes and with computational constraints. VPR is related to the concepts of localisation, loop closure, image retrieval and is a critical component of many autonomous navigation systems ranging from autonomous vehicles to drones and computer vision systems. While the concept of place recognition has been around for many years, VPR research has grown rapidly as a field over the past decade due to improving camera hardware and its potential for deep learning-based techniques, and has become a widely studied topic in both the computer vision and robotics communities. This growth however has led to fragmentation and a lack of standardisation in the field, especially concerning performance evaluation. Moreover, the notion of viewpoint and illumination invariance of VPR techniques has largely been assessed qualitatively and hence ambiguously in the past. In this paper, we address these gaps through a new comprehensive open-source framework for assessing the performance of VPR techniques, dubbed “VPR-Bench”. VPR-Bench (Open-sourced at: https://github.com/MubarizZaffar/VPR-Bench) introduces two much-needed capabilities for VPR researchers: firstly, it contains a benchmark of 12 fully-integrated datasets and 10 VPR techniques, and secondly, it integrates a comprehensive variation-quantified dataset for quantifying viewpoint and illumination invariance. We apply and analyse popular evaluation metrics for VPR from both the computer vision and robotics communities, and discuss how these different metrics complement and/or replace each other, depending upon the underlying applications and system requirements. Our analysis reveals that no universal SOTA VPR technique exists, since: (a) state-of-the-art (SOTA) performance is achieved by 8 out of the 10 techniques on at least one dataset, (b) SOTA technique in one community does not necessarily yield SOTA performance in the other given the differences in datasets and metrics. Furthermore, we identify key open challenges since: (c) all 10 techniques suffer greatly in perceptually-aliased and less-structured environments, (d) all techniques suffer from viewpoint variance where lateral change has less effect than 3D change, and (e) directional illumination change has more adverse effects on matching confidence than uniform illumination change. We also present detailed meta-analyses regarding the roles of varying ground-truths, platforms, application requirements and technique parameters. Finally, VPR-Bench provides a unified implementation to deploy these VPR techniques, metrics and datasets, and is extensible through templates