Repetitive readout and real-time control of nuclear spin qubits in 171^{171}Yb atoms

We demonstrate high fidelity repetitive projective measurements of nuclear spin qubits in an array of neutral ytterbium-171 ($^{171}$Yb) atoms. We show that the qubit state can be measured with a fidelity of 0.995(4) under a condition that leaves it in the state corresponding to the measurement outcome with a probability of 0.993(6) for a single tweezer and 0.981(4) averaged over the array. This is accomplished by near-perfect cyclicity of one of the nuclear spin qubit states with an optically excited state under a magnetic field of $B=58$ G, resulting in a bright/dark contrast of $\approx10^5$ during fluorescence readout. The performance improves further as $\sim1/B^2$. The state-averaged readout survival of 0.98(1) is limited by off-resonant scattering to dark states and can be addressed via post-selection by measuring the atom number at the end of the circuit, or during the circuit by performing a measurement of both qubit states. We combine projective measurements with high-fidelity rotations of the nuclear spin qubit via an AC magnetic field to explore several paradigmatic scenarios, including the non-commutivity of measurements in orthogonal bases, and the quantum Zeno mechanism in which measurements "freeze" coherent evolution. Finally, we employ real-time feedforward to repetitively deterministically prepare the qubit in the $+z$ or $-z$ direction after initializing it in an orthogonal basis and performing a projective measurement in the $z$-basis. These capabilities constitute an important step towards adaptive quantum circuits with atom arrays, such as in measurement-based quantum computation, fast many-body state preparation, holographic dynamics simulations, and quantum error correction

Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis

Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species.Peer reviewe

Genome-editing based engineering of CESA3 dual cellulose-inhibitor resistant plants

The rapid appearance of herbicide-resistant weeds combined with a lack of novel herbicides being brought to market reduces crop production, thereby threatening food security worldwide. Here, we report on the use of the previously identified cellulose biosynthesis-inhibiting chemical compound C17 as a potential herbicide. Toxicity tests showed that C17 efficiently inhibits the growth of various weeds and widely cultivated dicotyledonous crops, whereas only slight or no growth inhibition was observed for monocotyledonous crops. Surprisingly, when exposed to a mixture of C17 and two well-known cellulose biosynthesis inhibitors (CBIs), isoxaben and indaziflam, an additive growth inhibition was observed, demonstrating that C17 has a different mode of action that can be used to sensitize plants towards known CBIs. Moreover, we demonstrate that a C17-resistant CESA3 allele can be used as a positive transformation selection marker and that C17 resistance can be obtained through genome engineering of the wild-type CESA3 allele using CRISPR-mediated base editing. This editing system allowed us to engineer C17 tolerance in an isoxaben-resistant line, resulting in double herbicide-resistant plants

Cell death regulation but not abscisic acid signaling is required for enhanced immunity to Botrytis in Arabidopsis cuticle-permeable mutants

Prevailing evidence indicates that abscisic acid (ABA) negatively influences immunity to the fungal pathogen Botrytis cinerea in most but not all cases. ABA is required for cuticle biosynthesis, and cuticle permeability enhances immunity to Botrytis via unknown mechanisms. This complex web of responses obscures the role of ABA in Botrytis immunity. Here, we addressed the relationships between ABA sensitivity, cuticle permeability, and Botrytis immunity in the Arabidopsis thaliana ABA-hypersensitive mutants protein phosphatase2c quadruple mutant (pp2c-q) and enhanced response to aba1 (era1-2). Neither pp2c-q nor era1-2 exhibited phenotypes predicted by the known roles of ABA; conversely, era1-2 had a permeable cuticle and was Botrytis resistant. We employed RNA-seq analysis in cuticle-permeable mutants of differing ABA sensitivities and identified a core set of constitutively activated genes involved in Botrytis immunity and susceptibility to biotrophs, independent of ABA signaling. Furthermore, botrytis susceptible1 (bos1), a mutant with deregulated cell death and enhanced ABA sensitivity, suppressed the Botrytis immunity of cuticle permeable mutants, and this effect was linearly correlated with the extent of spread of wound-induced cell death in bos1. Overall, our data demonstrate that Botrytis immunity conferred by cuticle permeability can be genetically uncoupled from PP2C-regulated ABA sensitivity, but requires negative regulation of a parallel ABA-dependent cell-death pathway.Peer reviewe

Rice plants respond to ammonium‐stress by adopting a helical root growth pattern

High levels of ammonium nutrition reduce plant growth and different plant species have developed distinct strategies to maximize ammonium acquisition while alleviate ammonium toxicity through modulating root growth. Up to now, the mechanism underlying plant tolerance or sensitivity towards ammonium remain unclear. Rice uses ammonium as its main N source. Here we show that ammonium supply restricts rice root elongation and induces a helical growth pattern, which is attributed to root acidification resulting from ammonium uptake. Ammonium-induced low pH triggers asymmetric auxin distribution in rice root tips through changes in auxin signaling, thereby inducing a helical growth response. Blocking auxin signaling completely inhibited this root response. In contrast, this root response is not activated in ammonium-treated Arabidopsis. Acidification of Arabidopsis roots leads to the protonation of IAA, and dampening the intracellular auxin signaling levels that are required for maintaining root growth. Our study suggests a different mode of action by ammonium on the root pattern and auxin response machinery in rice versus Arabidopsis, and the rice-specific helical root response towards ammonium is an expression of the ability of rice in moderating auxin signaling and root growth to utilize ammonium while confronting acidic stress

Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots.

Peer reviewe

Fine-Tuning Stomatal Movement Through Small Signaling Peptides

As sessile organisms, plants are continuously exposed to a wide range of environmental stress. In addition to their crucial roles in plant growth and development, small signaling peptides are also implicated in sensing environmental stimuli. Notably, recent studies in plants have revealed that small signaling peptides are actively involved in controlling stomatal aperture to defend against biotic and abiotic stress. This review illustrates our growing knowledge of small signaling peptides in the modulation of stomatal aperture and highlights future challenges to decipher peptide signaling pathways in guard cells

Mechanisms used by plants to cope with DNA damage

Because the genome stores all genetic information required for growth and development, it is of pivotal importance to maintain DNA integrity, especially during cell division, when the genome is prone to replication errors and damage. Although over the last two decades it has become evident that the basic cell cycle toolbox of plants shares several similarities with those of fungi and mammals, plants appear to have evolved a set of distinct checkpoint regulators in response to different types of DNA stress. This might be a consequence of plants' sessile lifestyle, which exposes them to a set of unique DNA damage-inducing conditions. In this review, we highlight the types of DNA stress that plants typically experience and describe the plant-specific molecular mechanisms that control cell division in response to these stresses