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Understanding gene regulatory networks is essential to elucidate developmental processes and environmental responses. Here, we studied regulation of a maize (Zea mays) transcription factor gene using designer Transcription Activator-Like effectors (dTALes), which are synthetic type III TALes of the bacterial genus Xanthomonas and serve as inducers of disease susceptibility gene transcription in host cells. The maize pathogen Xanthomonas vasicola pv. vasculorum was used to introduce two independent dTALes into maize cells to induced expression of the gene glossy3 (gl3), which encodes a MYB transcription factor involved in biosynthesis of cuticular wax. RNA-seq analysis of leaf samples identified, in addition to gl3, 146 genes altered in expression by the two dTALes. Nine of the ten genes known to be involved in cuticular wax biosynthesis were up-regulated by at least one of the two dTALes. A gene previously unknown to be associated with gl3, Zm00001d017418, which encodes aldehyde dehydrogenase, was also expressed in a dTALe-dependent manner. A chemically induced mutant and a CRISPR-Cas9 mutant of Zm00001d017418 both exhibited glossy leaf phenotypes, indicating that Zm00001d017418 is involved in biosynthesis of cuticular waxes. Bacterial protein delivery of dTALes proved to be a straightforward and practical approach for the analysis and discovery of pathway-specific genes in maize.

Fungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungus Magnaporthe oryzae secretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here, we show that cytoplasmic effectors within BICs are packaged into punctate membranous effector compartments that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently labeled proteins in rice (Oryza sativa) showed that these effector puncta colocalize with the plant plasma membrane and with CLATHRIN LIGHT CHAIN 1, a component of clathrin-mediated endocytosis (CME). Inhibiting CME using virus-induced gene silencing and chemical treatments resulted in cytoplasmic effectors in swollen BICs lacking effector puncta. By contrast, fluorescent marker colocalization, gene silencing, and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector translocation. Effector localization patterns indicated that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by CME in BICs and suggests a role for M. oryzae effectors in coopting plant endocytosis.

Sessile organisms such as plants have adopted diverse reactive oxygen species (ROS) scavenging mechanisms to mitigate damage under abiotic stress conditions. Though CGFS-type glutaredoxin (GRX) genes are important regulators of ROS homeostasis, each of their functions in crop plants have not yet been well understood. We performed a targeted mutagenesis analysis of four CGFS-type GRXs (SlGRXS14, SlGRXS15, SlGRXS16, and SlGRXS17) in tomato plants (Solanum lycopersicum) using a multiplex clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system and found that Slgrxs mutants were more sensitive to various abiotic stresses compared to the wild-type tomatoes. Slgrxs15 mutants were embryonic lethal. Single, double, and triple combinations of Slgrxs14, 16, and 17 mutants were examined under heat, chilling, drought, heavy metal toxicity, nutrient deficiency, and short photoperiod stresses. Slgrxs14 and 17 mutants showed hypersensitivity to almost all stresses while Slgrxs16 mutants were affected by chilling stress and showed milder sensitivity to other stresses. Additionally, Slgrxs14 and 17 mutants showed delayed flowering time. Our results indicate that the CGFS-type SlGRXs have specific roles against abiotic stresses, providing valuable resources to develop tomato and, possibly, other crop species that are tolerant to multiple abiotic stresses by genetic engineering. This article is protected by copyright. All rights reserved.

In superconductors, vortices induced by a magnetic field are nucleated where some random fluctuations determine the nucleation position, and then may be pinned by impurities or boundaries, impeding the development of vortex-based quantum devices. Here, we propose a superconducting structure, which allows to nucleate and control vortices on-demand by controlling magnetic fields and currents. Using time-dependent Ginzburg-Landau theory, we study a driven vortex motion in two-dimensional Corbino geometries of superconductor-normal metal-superconductor Josephson junctions. We remedy the randomness of nucleation by introducing normal conducting rails to the Corbino disk to guide the nucleation process and motion of vortices towards the junction. We elaborate on the consequences of rail-vortex and vortex-vortex interactions to the quantization of resistance across the junction. Finally, we simulate the nucleations and manipulations of two and four vortices in Corbino networks, and discuss its application to Majorana zero mode braiding operations. Our study provides a potential route towards quantum computation with non-Abelian anyons.

Increasing populations and temperatures are expected to escalate food demands beyond production capacities, and the development of maize lines with better performance under heat stress is desirable. Here, we report that constitutive ectopic expression of a heterologous glutaredoxin S17 from Arabidopsis thaliana (AtGRXS17) can provide thermotolerance in maize through enhanced chaperone activity and modulation of heat stress-associated gene expression. The thermotolerant maize lines had increased protection against protein damage and yielded a sixfold increase in grain production in comparison to the non-transgenic counterparts under heat stress field conditions. The maize lines also displayed thermotolerance in the reproductive stages, resulting in improved pollen germination and the higher fidelity of fertilized ovules under heat stress conditions. Our results present a robust and simple strategy for meeting rising yield demands in maize and, possibly, other crop species in a warming global environment.

We performed microwave spectroscopy of an InAs nanowire between superconducting contacts implementing a finite-length, multi-channel Josephson weak link. Certain features in the spectra, such as the splitting by spin-orbit interactions of the transition lines among Andreev states, have been already understood in terms of non-interacting models. However, we identify here additional transitions, which evidence the presence of Coulomb interactions. By combining experimental measurements and model calculations, we reach a qualitative understanding of these very rich Andreev spectra., Comment: (6+8) pages, (4+10) figures; added figure in SM

Purpose Photoacoustic (PA) microscopy has emerged as a useful tool in biomedical imaging applications such as visualization of microvasculature and hemoglobin oxygen saturation, single-cell, and label-free imaging of organs including cancer. Since the ultrasound transducers used for PA signal detection are not optically transparent, the integration of optical and acoustic modules for coaxial alignment of laser and acoustic beam fields in PA microscopy is complex and costly. Methods Here, we report a recently developed optically transparent focused transducer for combined PA and ultrasound (US) microscopy. All the acoustic layers including the acoustic lens are optically transparent, enabling simple integration of optical and acoustic modules for both imaging modalities. Results The mean light transmittance of the transducer’s backing layer and acoustic lens and of the transducer itself were measured at 92%, 83%, and 66%, respectively. Results from in vitro and in vivo experiments demonstrated the transducer to be suitable for both US and PA imaging. Conclusions The results of this study represent a step toward efficient construction of probes for combined PA and US microscopy.

Drought stress is an important crop yield limiting factor worldwide. Plant physiological responses to drought stress are driven by changes in gene expression. While drought-responsive genes (DRGs) have been identified in maize, regulation patterns of gene expression during progressive water deficits remain to be elucidated. In this study, we generated time-series transcriptomic data from the maize inbred line B73 under well-watered and drought conditions. Comparisons between the two conditions identified 8,626 DRGs and the stages (early, middle, and late drought) at which DRGs occurred. Different functional groups of genes were regulated at the three stages. Specifically, early and middle DRGs display higher copy number variation among diverse Zea mays lines, and they exhibited stronger associations with drought tolerance as compared to late DRGs. In addition, correlation of expression between small RNAs (sRNAs) and DRGs from the same samples identified 201 negatively sRNA/DRG correlated pairs, including genes showing high levels of association with drought tolerance, such as two glutamine synthetase genes, gln2 and gln6. The characterization of dynamic gene responses to progressive drought stresses indicates important adaptive roles of early and middle DRGs, as well as roles played by sRNAs in gene expression regulation upon drought stress.

Artificial miRNA technology enables the generation of siRNAs to regulate the expression of targeted genes. However, the application of siRNAs to alter gene expression is challenging due to their instability and requires a means to efficiently deliver siRNAs into the host. Here, we report that the siRNAs targeted to animal mRNAs can be heterologously expressed and stably produced in lettuce. We have modified rice miRNA precursors to produce siRNAs in lettuce with the potential to target mRNAs of mouse complement 3 ( C3) and coagulation factor 7 ( CF7). Expression of primary and mature siRNAs in the transgenic lettuce lines was confirmed via Sanger sequencing. Our study demonstrates an applicable tool to alter gene expression in the targeted host and has potential utility in siRNA-based oral therapeutics.

In this minireview, we outline the recent experimental and theoretical progress in the creation, characterization and manipulation of Majorana bound states (MBSs) in semiconductor-superconductor (SC) hybrid structures. After an introductory overview of the broader field we specifically focus on four of our recent projects in this direction. We show that the emergence of Fano resonances in the differential conductance in a normal lead-Majorana nanowire-quantum dot setup can be exploited to determine if a single MBS is contacted by the normal lead and the quantum dot providing an experimental test of the non-locality of MBSs. In the second project, the tunnel-coupling to two MBSs in ans-wave SC-Majorana nanowire Josephson junction (JJ) leads to a finite contribution of the MBSs to the equilibrium Josephson current probing directly the local spin-singlet contribution of the Majorana pair. We then shift our focus from MBSs forming in nanowire systems to MBSs forming in topological JJs. In a single sheet of buckled silicene with proximity induced superconductivity two local electric fields can be used to tune the junction between a topologically trivial and topologically non-trivial regime. In a Corbino geometry topological Josephson junction two MBSs harbored in Josephson vortices can rotate along the JJ and, in the course of this, will be exchanged periodically in the phase difference of the JJ. The tunneling current in a metal tip coupled to the JJ is shown to exhibit signs of the anyonic braiding phase of two MBSs.

Fungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungusMagnaporthe oryzaesecretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here we show that cytoplasmic effectors within BICs are packaged into vesicles that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently-labeled rice showed that effector vesicles colocalize with plant plasma membrane and with clathrin light chain-1, a marker for clathrin-mediated endocytosis (CME). Inhibition of CME using Virus-Induced Gene Silencing (VIGS) and chemical treatments results in cytoplasmic effectors in swollen BICs lacking vesicles. In contrast, fluorescent marker co-localization, VIGS and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector vesicle formation. Localization studies of two novel effectors, and of known effectors after CME inhibition, indicate that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by clathrin-mediated endocytosis in BICs and suggests a role forM. oryzaeeffectors in co-opting plant endocytosis.

There are many wafer level tests, such as Fail Bit Count (FBC), where conventional statistical analysis methods are inadequate because the associated data do not follow a normal distribution. This paper introduces a statistical failure analysis technique that does not rely on location and scale parameters and is thus able to handle such cases. It describes the math on which the method is based and explains how to determine effect size (ES) using the quantile comparison equivalence criteria (QCEC) and a statistical parameter, called the center of dispersion (CoD), that distinguishes between center difference and dispersion difference. It also includes a case study showing how the new method is used to assess the effect of a process change on dynamic random access memory test data and how it compares in terms of accuracy with conventional statistical techniques.

This paper proposes a scale recovery method for indoor mobile vehicles with monocular vision. We aim to solve the scale ambiguity problem which is the main weakness of monocular SLAM. The method is based on the detection and modeling of the ground plane under the constant camera height assumption which is suitable for ground mobile vehicles. The ground plane detection relies on vanishing points estimation, and the ground plane modeling is accomplished by point clouds on the ground complemented with vanishing directions estimation. The method is evaluated both on the self-collected indoor dataset and the KITTI benchmark dataset. The experimental results verify the effectiveness of our scale recovery method.

Significance Pathogenic bacteria acquire new virulence strategies for exploiting their hosts. This work reveals that the bacterial wheat pathogen Xanthomonas translucens uses a transcription activation-like (TAL) effector to promote virulence by directly activating the host gene 9-cis-epoxycarotenoid dioxygenase, the rate-limiting enzyme in biosynthesis of abscisic acid that is normally involved in water management within the host plant. Evolutionarily, TAL effectors are a relatively new class of virulence factors limited to a few species of pathogenic bacteria, and this work adds to the diversity of host susceptibility genes that can be exploited by pathogens through TAL effector gene function., Plants are vulnerable to disease through pathogen manipulation of phytohormone levels, which otherwise regulate development, abiotic, and biotic responses. Here, we show that the wheat pathogen Xanthomonas translucens pv. undulosa elevates expression of the host gene encoding 9-cis-epoxycarotenoid dioxygenase (TaNCED-5BS), which catalyzes the rate-limiting step in the biosynthesis of the phytohormone abscisic acid and a component of a major abiotic stress-response pathway, to promote disease susceptibility. Gene induction is mediated by a type III transcription activator-like effector. The induction of TaNCED-5BS results in elevated abscisic acid levels, reduced host transpiration and water loss, enhanced spread of bacteria in infected leaves, and decreased expression of the central defense gene TaNPR1. The results represent an appropriation of host physiology by a bacterial virulence effector.

Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

Drought stress is a major constraint in global maize production, causing almost 30–90% of the yield loss depending upon growth stage and the degree and duration of the stress. Here, we report that ectopic expression of Arabidopsis glutaredoxin S17 (AtGRXS17) in field grown maize conferred tolerance to drought stress during the reproductive stage, which is the most drought sensitive stage for seed set and, consequently, grain yield. AtGRXS17-expressing maize lines displayed higher seed set in the field, resulting in 2-fold and 1.5-fold increase in yield in comparison to the non-transgenic plants when challenged with drought stress at the tasseling and silking/pollination stages, respectively. AtGRXS17-expressing lines showed higher relative water content, higher chlorophyll content, and less hydrogen peroxide accumulation than wild-type (WT) control plants under drought conditions. AtGRXS17-expressing lines also exhibited at least 2-fold more pollen germination than WT plants under drought stress. Compared to the transgenic maize, WT controls accumulated higher amount of proline, indicating that WT plants were more stressed over the same period. The results present a robust and simple strategy for meeting rising yield demands in maize under water limiting conditions.

By coupling a superconducting weak link to a microwave resonator, recent experiments probed the spectrum and achieved the quantum manipulation of Andreev states in various systems. However, the quantitative understanding of the response of the resonator to changes in the occupancy of the Andreev levels, which are of fermionic nature, is missing. Here, using Bogoliubov-de Gennes formalism to describe the weak link and a general formulation of the coupling to the resonator, we calculate the shift of the resonator frequency as a function of the levels occupancy and describe how transitions are induced by phase or electric field microwave drives. We apply this formalism to analyze recent experimental results obtained using circuit-QED techniques on superconducting atomic contacts and semiconducting nanowire Josephson junctions., Comment: 22 pages, 14 figures

Bound states in superconductors are expected to exhibit a spatially resolved electron-hole asymmetry which is the hallmark of their quantum nature. This asymmetry manifests as oscillations at the Fermi wavelength, which is usually tiny and thus washed out by thermal broadening or by scattering at defects. Here we demonstrate theoretically and confirm experimentally that, when coupled to magnetic impurities, bound states in a vortex core exhibit an emergent axial electron-hole asymmetry on a much longer scale, set by the coherence length. We study vortices in 2H-NbSe2 and in 2H-NbSe1.8S0.2 with magnetic impurities, characterizing these with detailed Hubbard-corrected density functional calculations. We find that the induced electron-hole imbalance depends on the band character of the superconducting material. Our results show that coupling between quantum bound states in superconductors is remarkably robust and has a strong influence in tunneling measurements., This work was supported by the EU (ERC-StG-679080, ERC-2015-AdG-694097, ERC AdG Mol-2D 788222 and H2020-MSCAIF-2016-751047), by FET-OPEN program (grant 862893 FATMOLS), by EU program Cost (NANOCOHYBRI CA16218 and MOLSPIN CA15128), by Graphene Flagship (grant agreement number 881603, GrapheneCore3 project), by the Spanish State Research Agency (FIS2017-84330-R, RYC-2014-15093, MDM-2014-0377, MDM-2015-0538, CEX2018-000805-M, MAT2017-89993-R co-financed by FEDER and CEX2019-000919-M), by the Deutsche Forschungsgemeinschaft (DFG) under under Germany’s Excellence Strategy— Cluster of Excellence Advanced Imaging of Matter (AIM) EXC 2056—390715994, RTG 1995 and GRK 2247, by the Comunidad de Madrid through program NANOMAGCOST-CM (Program No.S2018/NMT-4321) and by the Generalitat Valenciana (Grupos Consolidados IT1249-19, Prometeo Programme, iDiFEDER/2018/061 and CDEIGENT/2019/022). J.J.B. acknowledges the Marie Curie Fellowship program (H2020-MSCA-IF-2016-751047). A.R. acknowledges support by the MPI-New York City Center for Non-Equilibrium Quantum Phenomena. H.S., E.H., and I.G. acknowledge SEGAINVEX at UAM for design and construction of STM cryogenic equipment. S.P. acknowledges Banco Santander - María de Maeztu program (ref. 102I0112).

It has been argued that fluctuations of fermion parity are harmful for the demonstration of non-Abelian anyonic statistics. Here, we demonstrate a striking exception in which such fluctuations are actively used. We present a theory of coherent electron transport from a tunneling tip into a Corbino geometry Josephson junction where four Majorana bound states (MBSs) rotate. While the MBSs rotate, electron tunneling happens from the tip to one of the MBSs thereby changing the fermion parity of the MBSs. The tunneling events in combination with the rotation allow us to identify a novel braiding operator that does not commute with the braiding cycles in the absence of tunneling, revealing the non-Abelian nature of MBSs. The time-averaged tunneling current exhibits resonances as a function of the tip voltage with a period that is a direct consequence of the interference between the non-commuting braiding operations. Our work opens up a possibility for utilizing parity non-conserving processes to control non-Abelian states., Published version: 7 pages, 3 figures + Supplemental material (10 pages, 3 figures)