soybean-hairy-root-transformation-for-the-analysis-of-gene-function

Soybean Hairy Root Transformation for the Analysis of Gene Function

Soybean (Glycine max) is a valuable crop in agriculture that has thousands of industrial uses. Soybean roots are the primary site of interaction with ...

York University

Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.

Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33.

Yield stress materials flow if a sufficiently large shear stress is applied. Although such materials are ubiquitous and relevant for industry, there is no accepted microscopic description of how they yield, even in the simplest situations in which temperature is negligible and in which flow inhomogeneities such as shear bands or fractures are absent. Here we propose a scaling description of the yielding transition in amorphous solids made of soft particles at zero temperature. Our description makes a connection between the Herschel-Bulkley exponent characterizing the singularity of the flow curve near the yield stress Σc, the extension and duration of the avalanches of plasticity observed at threshold, and the density P(x) of soft spots, or shear transformation zones, as a function of the stress increment x beyond which they yield. We argue that the critical exponents of the yielding transition may be expressed in terms of three independent exponents, θ, df, and z, characterizing, respectively, the density of soft spots, the fractal dimension of the avalanches, and their duration. Our description shares some similarity with the depinning transition that occurs when an elastic manifold is driven through a random potential, but also presents some striking differences. We test our arguments in an elasto-plastic model, an automaton model similar to those used in depinning, but with a different interaction kernel, and find satisfying agreement with our predictions in both two and three dimensions.

Scaling description of the yielding transition in soft amorphous solids at zero temperature.

Failure of amorphous solids is fundamental to various phenomena, including landslides and earthquakes. Recent experiments indicate that highly plastic regions form elongated structures that are especially apparent near the maximal shear stress Σmax where failure occurs. This observation suggested that Σmax acts as a critical point where the length scale of those structures diverges, possibly causing macroscopic transient shear bands. Here, we argue instead that the entire solid phase (Σ<Σmax) is critical, that plasticity always involves system-spanning events, and that their magnitude diverges at Σmax independently of the presence of shear bands. We relate the statistics and fractal properties of these rearrangements to an exponent θ that captures the stability of the material, which is observed to vary continuously with stress, and we confirm our predictions in elastoplastic models.

Criticality in the Approach to Failure in Amorphous Solids.

We report the first measurements of the effect of pressure on vibrational modes in emulsions, which serve as a model for soft frictionless spheres at zero temperature. As a function of the applied pressure, we find that the density of states D(ω) exhibits a low-frequency cutoff ω^{*}, which scales linearly with the number of extra contacts per particle δz. Moreover, for ω<ω^{*}, our results are consistent with D(ω)∼ω^{2}/ω^{*2}, a quadratic behavior whose prefactor is larger than what is expected from Debye theory. This surprising result agrees with recent theoretical findings [E. DeGiuli, A. Laversanne-Finot, G. A. Düring, E. Lerner, and M. Wyart, Soft Matter 10, 5628 (2014); S. Franz, G. Parisi, P. Urbani, and F. Zamponi, Proc. Natl. Acad. Sci. U.S.A. 112, 14539 (2015)]. Finally, the degree of localization of the softest low frequency modes increases with compression, as shown by the participation ratio as well as their spatial configurations. Overall, our observations show that emulsions are marginally stable and display non-plane-wave modes up to vanishing frequencies.

Evidence for Marginal Stability in Emulsions.

The yielding transition of amorphous solids is a phase transition with a special type of universality. Critical exponents and scaling relations have been defined and proposed near the yield stress. We show here that, even in the initial stage of shear far below the yield stress, the stress-strain curve of amorphous solids also shows critical scaling with universal exponents. The key point is to remove the elastic part of the strain, and the shear stress exhibits a sublinear scaling with the plastic strain. We show how this critical scaling is related to the finite size effect of the minimum strain to trigger the first plastic avalanche after a quench. We point out that this sublinear scaling between the stress and the plastic strain implies the divergence of a high-order shear modulus. A scaling relation is derived between two exponents characterizing the stress-strain curve and the density distribution of the local stabilities, respectively. We test the critical scaling of the stress-strain curve using both mesoscopic and atomistic simulations and get satisfying agreement in two and three dimensions.

Universal scaling of the stress-strain curve in amorphous solids.

Academic institutions need to maintain publication lists for thousands of faculty and other scholars. Automated tools are essential to minimize the need for direct feedback from the scholars themselves who are practically unable to commit necessary effort to keep the data accurate. In relying exclusively on clustering techniques, author disambiguation applications fail to satisfy key use cases of academic institutions. Algorithms can perfectly group together a set of publications authored by a common individual, but, for them to be useful to an academic institution, they need to programmatically and recurrently map articles to thousands of scholars of interest en masse. Consistent with a savvy librarian's approach for generating a scholar's list of publications, identity-driven authorship prediction is the process of using information about a scholar to quantify the likelihood that person wrote certain articles. ReCiter is an application that attempts to do exactly that. ReCiter uses institutionally-maintained identity data such as name of department and year of terminal degree to predict which articles a given scholar has authored. To compute the overall score for a given candidate article from PubMed (and, optionally, Scopus), ReCiter uses: up to 12 types of commonly available, identity data; whether other members of a cluster have been accepted or rejected by a user; and the average score of a cluster. In addition, ReCiter provides scoring and qualitative evidence supporting why particular articles are suggested. This context and confidence scoring allows curators to more accurately provide feedback on behalf of scholars. To help users to more efficiently curate publication lists, we used a support vector machine analysis to optimize the scoring of the ReCiter algorithm. In our analysis of a diverse test group of 500 scholars at an academic private medical center, ReCiter correctly predicted 98% of their publications in PubMed.

ReCiter: An open source, identity-driven, authorship prediction algorithm optimized for academic institutions.

The NAC (NAM, ATAFs, CUC) family of transcription factors (TFs) play a pivotal role in regulating all processes of the growth and development of plants, as well as responses to biotic and abiotic stresses. Yet, the functions of NACs from non-model plant species remains largely uncharacterized. Here, we characterized the stress-responsive effects of a NAC gene isolated from wintersweet, an ornamental woody plant that blooms in winter when temperatures are low. CpNAC68 is clustered in the NAM subfamily. Subcellular localization and transcriptional activity assays demonstrated a nuclear protein that has transcription activator activities. qRT-PCR analyses revealed that  was ubiquitously expressed in old flowers and leaves. Additionally, the expression of  is induced by disparate abiotic stresses and hormone treatments, including drought, heat, cold, salinity, GA, JA, and SA. Ectopic overexpression of  in  enhanced the tolerance of transgenic plants to cold, heat, salinity, and osmotic stress, yet had no effect on growth and development. The survival rate and chlorophyll amounts following stress treatments were significantly higher than wild type Arabidopsis, and were accompanied by lower electrolyte leakage and malondialdehyde (MDA) amounts. In conclusion, our study demonstrates that  can be used as a tool to enhance plant tolerance to multiple stresses, suggesting a role in abiotic stress tolerance in wintersweet.

Transgene  from Wintersweet () Improves Arabidopsis Survival of Multiple Abiotic Stresses.

Quantitative trait loci (QTLs) E and M are major soybean alleles that confer resistance to leaf-chewing insects, and are particularly effective in combination. Flavonoids and/or isoflavonoids are classes of plant secondary metabolites that previous studies agree are the causative agents of resistance of these QTLs. However, all previous studies have compared soybean genotypes that are of dissimilar genetic backgrounds, leaving it questionable what metabolites are a result of the QTL rather than the genetic background. Here, we conducted a non-targeted mass spectrometry approach without liquid chromatography to identify differences in metabolite levels among QTLs E, M, and both (EM) that were introgressed into the background of the susceptible variety Benning. Our results found that E and M mainly confer low-level, global differences in distinct sets of metabolites. The isoflavonoid daidzein was the only metabolite that demonstrated major increases, specifically in insect-treated M and EM. Interestingly, M confers increased daidzein levels in response to insect, whereas E restores M's depleted daidzein levels in the absence of insect. Since daidzein levels do not parallel levels of resistance, our data suggest a novel mechanism that the QTLs confer resistance to insects by mediating changes in hundreds of metabolites, which would be difficult for the insect to evolve tolerance. Collective global metabolite differences conferred by E and M might explain the increased resistance of EM.

Metabolomics Differences of  QTLs Resistant to Soybean Looper.

Glyceollins, isoflavonoid-derived antimicrobial metabolites, are the major phytoalexins in soybean (). They play essential roles in providing resistance to the soil-borne pathogen  and have unconventional anticancer and neuroprotective activities that render them desirable for pharmaceutical development. Our previous studies revealed that the transcription factors GmMYB29A2 and GmNAC42-1 have essential roles in activating glyceollin biosynthesis, yet each cannot activate the transcription of all biosynthesis genes in the absence of a pathogen elicitor treatment. Here, we report that co-overexpressing both transcription factors is also insufficient to activate glyceollin biosynthesis. To understand this insufficiency, we compared the transcriptome profiles of hairy roots overexpressing each transcription factor with glyceollin-synthesizing roots treated with wall glucan elicitor (WGE) from . GmMYB29A2 upregulated most of the WGE-regulated genes that encode enzymatic steps spanning from primary metabolism to the last step of glyceollin biosynthesis. By contrast, GmNAC42-1 upregulated glyceollin biosynthesis genes only when overexpressed in the presence of WGE treatment. This is consistent with our recent discovery that, in the absence of WGE, GmNAC42-1 is bound by GmJAZ1 proteins that inhibit its transactivation activity. WGE, and not GmMYB29A2 or GmNAC42-1, upregulated the heat shock family gene , the homolog of Arabidopsis  that directly activated the transcription of several glyceollin biosynthesis genes. Our results provide important insights into what biosynthesis genes will need to be upregulated to activate the entire glyceollin biosynthetic pathway.

Jie Lin

Department of Biology

York University

Soybean Hairy Root Transformation for the Analysis of Gene Function

Jie Lin

.css-o250i3{font-size:18px;font-family:Open Sans,sans-serif;line-height:21.6px;}Department of Biology

York University

Soybean Hairy Root Transformation for the Analysis of Gene Function

Department of Biology