Physiological and Molecular Mechanisms of Differential Sensitivity of Palmer Amaranth (Amaranthus palmeri) to Mesotrione at Varying Growth Temperatures

Citation: Godar, A. S., Varanasi, V. K., Nakka, S., Prasad, P. V. V., Thompson, C. R., & Mithila, J. (2015). Physiological and Molecular Mechanisms of Differential Sensitivity of Palmer Amaranth (Amaranthus palmeri) to Mesotrione at Varying Growth Temperatures. Plos One, 10(5), 17. doi:10.1371/journal.pone.0126731Herbicide efficacy is known to be influenced by temperature, however, underlying mechanism(s) are poorly understood. A marked alteration in mesotrione [a 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor] efficacy on Palmer amaranth (Amaranthus palmeri S. Watson) was observed when grown under low- (LT, 25/15 degrees C, day/night temperatures) and high (HT, 40/30 degrees C) temperature compared to optimum (OT, 32.5/22.5 degrees C) temperature. Based on plant height, injury, and mortality, Palmer amaranth was more sensitive to mesotrione at LT and less sensitive at HT compared to OT (ED50 for mortality; 18.5, 52.3, and 63.7 g ai ha(-1), respectively). Similar responses were observed for leaf chlorophyll index and photochemical efficiency of PSII (F-v/F-m). Furthermore, mesotrione translocation and metabolism, and HPPD expression data strongly supported such variation. Relatively more mesotrione was translocated to meristematic regions at LT or OT than at HT. Based on T-50 values (time required to metabolize 50% of the C-14 mesotrione), plants at HT metabolized mesotrione faster than those at LT or OT (T-50; 13, 21, and 16.5 h, respectively). The relative HPPD: CPS (carbamoyl phosphate synthetase) or HPPD:beta-tubulin expression in mesotrione-treated plants increased over time in all temperature regimes; however, at 48 HAT, the HPPD:beta-tubulin expression was exceedingly higher at HT compared to LT or OT (18.4-, 3.1-, and 3.5-fold relative to untreated plants, respectively). These findings together with an integrated understanding of other interacting key environmental factors will have important implications for a predictable approach for effective weed management

Systems level analysis of two-component signal transduction systems in Erwinia amylovora: Role in virulence, regulation of amylovoran biosynthesis and swarming motility

<p>Abstract</p> <p>Background</p> <p>Two-component signal transduction systems (TCSTs), consisting of a histidine kinase (HK) and a response regulator (RR), represent a major paradigm for signal transduction in prokaryotes. TCSTs play critical roles in sensing and responding to environmental conditions, and in bacterial pathogenesis. Most TCSTs in <it>Erwinia amylovora </it>have either not been identified or have not yet been studied.</p> <p>Results</p> <p>We used a systems approach to identify TCST and related signal transduction genes in the genome of <it>E. amylovora</it>. Comparative genomic analysis of TCSTs indicated that <it>E. amylovora </it>TCSTs were closely related to those of <it>Erwinia tasmaniensis</it>, a saprophytic enterobacterium isolated from apple flowers, and to other enterobacteria. Forty-six TCST genes in <it>E. amylovora </it>including 17 sensor kinases, three hybrid kinases, 20 DNA- or ligand-binding RRs, four RRs with enzymatic output domain (EAL-GGDEF proteins), and two kinases were characterized in this study. A systematic TCST gene-knockout experiment was conducted, generating a total of 59 single-, double-, and triple-mutants. Virulence assays revealed that five of these mutants were non-pathogenic on immature pear fruits. Results from phenotypic characterization and gene expression experiments indicated that several groups of TCST systems in <it>E. amylovora </it>control amylovoran biosynthesis, one of two major virulence factors in <it>E. amylovora</it>. Both negative and positive regulators of amylovoran biosynthesis were identified, indicating a complex network may control this important feature of pathogenesis. Positive (non-motile, EnvZ/OmpR), negative (hypermotile, GrrS/GrrA), and intermediate regulators for swarming motility in <it>E. amylovora </it>were also identified.</p> <p>Conclusion</p> <p>Our results demonstrated that TCSTs in <it>E. amylovora </it>played major roles in virulence on immature pear fruit and in regulating amylovoran biosynthesis and swarming motility. This suggested presence of regulatory networks governing expression of critical virulence genes in <it>E. amylovora</it>.</p

Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

<p>Abstract</p> <p>Background</p> <p>Pearl millet [<it>Pennisetum glaucum </it>(L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community.</p> <p>Results</p> <p>A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags (ESTs). After clustering, unigene sequences (2175 singlets and 317 contigs) were searched for the presence of SSRs. We detected 164 sequences containing SSRs (at least 14 bases in length), with a density of one per 1.75 kb of EST sequence. Di-nucleotide repeats were the most abundant followed by tri-nucleotide repeats. Ninety primer pairs were designed and tested for their ability to detect polymorphism across a panel of 11 pairs of pearl millet mapping population parental lines. Clear amplification products were obtained for 58 primer pairs. Of these, 15 were monomorphic across the panel. A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations. Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny. Most new EST-SSR markers mapped to distal regions of linkage groups, often to previous gaps in these linkage maps. These new EST-SSRs are now are used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs.</p> <p>Conclusion</p> <p>This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet. As reported for other crops, EST-derived SSRs provide a cost-saving marker development option in pearl millet. Resources developed in this study have added a sizeable number of useful SSRs to the existing repertoire of circa 100 genomic SSRs that were previously available to pearl millet researchers.</p

Physiological and Molecular Characterization of Hydroxyphenylpyruvate Dioxygenase (HPPD)-inhibitor Resistance in Palmer Amaranth (Amaranthus palmeri S. Wats.)

Citation: Nakka, S., Godar, A. S., Wani, P. S., Thompson, C. R., Peterson, D. E., Roelofs, J., & Jugulam, M. (2017). Physiological and Molecular Characterization of Hydroxyphenylpyruvate Dioxygenase (HPPD)-inhibitor Resistance in Palmer Amaranth (Amaranthus palmeri S. Wats.). Frontiers in Plant Science, 8, 12. doi:10.3389/fpls.2017.00555Herbicides that inhibit hydroxyphenylpyruvate dioxygenase (HPPD) such as mesotrione are widely used to control a broad spectrum of weeds in agriculture. Amaranthus palmeri is an economically troublesome weed throughout the United States. The first case of evolution of resistance to HPPD-inhibiting herbicides in A. palmeri was documented in Kansas (KS) and later in Nebraska (NE). The objective of this study was to investigate the mechansim of HPPD-inhibitor (mesotrione) resistance in A. palmeri. Dose response analysis revealed that this population (KSR) was 10-18 times more resistant than their sensitive counterparts (MSS or KSS). Absorbtion and translocation analysis of [C-14] mesotrione suggested that these mechanisms were not involved in the resistance in A. palmeri. Importantly, mesotrione (>90%) was detoxified markedly faster in the resistant populations (KSR and NER), within 24 hours after treatment (HAT) compared to sensitive plants (MSS, KSS, or NER). However, at 48 HAT all populations metabolized the mesotrione, suggesting additional factors may contribute to this resistance. Further evaluation of mesotrione-resistant A. palmeri did not reveal any specific resistance-conferring mutations nor amplification of HPPD gene, the molecular target of mesotrione. However, the resistant populations showed 4- to 12-fold increase in HPPD gene expression. This increase in HPPD transcript levels was accompanied by increased HPPD protein expression. The significant aspects of this research include: the mesotrione resistance in A. palmeri is conferred primarily by rapid detoxification (non-target-site based) of mesotrione; additionally, increased HPPD gene expression (target-site based) also contributes to the resistance mechanism in the evolution of herbicide resistance in this naturally occurring weed species

Influence of fibre cross-section profile on the multi-physical properties of uni-directional composites

The present work comprehensively examines the influence of fibre-matrix interface perimeter on the multi-physical properties of uni-directional composite materials. Three-dimensional microstructures (containing fibres of triangular, elliptical, rectangular, C-shape and two-lobe cross-section shape) are analysed to evaluate effective thermal conduction, thermo-elastic and piezo-electric properties. Each of these properties is normalised with the respective property of RVE with circular fibre cross-section; These normalised properties are, objectively, compared with the normalised fibre cross-section perimeter (shape factor). For all the considered properties and fibre cross-sectional shapes, a novel observation is that the property experiences a drop (or rise) in the initial range of the shape factor but rises (or drops) monotonically afterwards. This is in contrast with the existing literature observations, where properties are understood to have only a monotonic increase/decrease with the shape factor. Further, it is observed that the magnitude of the initial drop (or rise) is sensitive to the fibre volume fraction and the fibre-matrix property contrast. In accordance with the literature, a strong correlation is observed among the variation of in-plane shear moduli, transverse thermal conduction and transverse dielectric constants

A computationally efficient approach for generating RVEs of various inclusion/fiber shapes

A computationally efficient method for generating virtual periodic representative volume element (RVE), capable of handling arbitrary inclusion shapes, is developed. A universal collision/overlap detection and repair method is proposed, where each inclusion shape is represented as a union of n-Spheres (UnS). A constrained optimization problem is formulated and solved to remove inclusion overlaps; a closed-form solution is derived for calculating the degree of inclusions overlap and its gradient vector with respect to inclusion position. RVE generation is illustrated with circular, spherical, four non-circular and four non-spherical inclusion shapes. Computational efficiency is demonstrated using an elaborate RVE generation time study. The generated RVEs are evaluated using various statistical metrics; results confirm the random distribution of inclusions. Effective properties of RVEs, representing unidirectional composites, are determined using homogenization with various fibre cross-section shapes; obtained mechanical properties have shown transverse isotropy

A Six Degree-of-Freedom Spacecraft Dynamics Simulator for Formation Control Research

This paper presents a new six-degree-of-freedom robotic spacecraft simulator, the Multi-Spacecraft Testbed for Autonomy Research (M-STAR), for testing formation guidance, relative navigation, and control algorithms. The simulator dynamics are governed by five degrees of frictionless translational and rotational air-bearing motion and one degree of kinematic motion in the gravity direction with flight-like actuators, in a 1-g environment. M-STAR is designed to be modular and accommodates 3-DOF, 4-DOF, 5-DOF, and 6-DOF operation with minimal mechanical modifications. The simulator is modelled as a 3-D pendulum on a floating platform with sixteen thrusters and four reaction wheels as on-board actuators. Based on this plant model, a nonlinear hierarchical control law is proposed for position and attitude trajectory tracking. A weighted generalized pseudo-inverse strategy for control allocation to map control inputs to actuator inputs is discussed. The thruster actuation model for mapping smooth allocated input to non-smooth actuator input that achieves equivalent performance is derived. The control law, allocation scheme, and thruster model are tested on the simulator for real-time position tracking control using a Robot Operating System (ROS) based software framework

Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells

B cell responses are critical for antiviral immunity. However, a comprehensive picture of antigen-specific B cell differentiation, clonal proliferation, and dynamics in different organs after infection is lacking. Here, by combining single-cell RNA and B cell receptor (BCR) sequencing of antigen-specific cells in lymph nodes, spleen, and lungs after influenza infection in mice, we identify several germinal center (GC) B cell subpopulations and organ-specific differences that persist over the course of the response. We discover transcriptional differences between memory cells in lungs and lymphoid organs and organ-restricted clonal expansion. Remarkably, we find significant clonal overlap between GC-derived memory and plasma cells. By combining BCR-mutational analyses with monoclonal antibody (mAb) expression and affinity measurements, we find that memory B cells are highly diverse and can be selected from both low- and high-affinity precursors. By linking antigen recognition with transcriptional programming, clonal proliferation, and differentiation, these finding provide important advances in our understanding of antiviral immunity