Effective genome editing and identification of a regiospecific gallic acid 4-O-glycosyltransferase in pomegranate (Punica granatum L.).

Pomegranate (Punica granatum L.) trees are woody perennials that bear colorful and nutritious fruits rich in phenolic metabolites, e.g., hydrolyzable tannins (HTs) and flavonoids. We here report genome editing and gene discovery in pomegranate hairy roots using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9), coupled with transcriptome and biochemical analyses. Single guide RNAs (sgRNAs) were designed to target two UDP-dependent glycosyltransferases (UGTs), PgUGT84A23 and PgUGT84A24, which possess overlapping activities in β-glucogallin (a galloylglucose ester; biosynthetic precursor of HTs) biosynthesis. A unique accumulation of gallic acid 3-O- and 4-O-glucosides (galloylglucose ethers) was observed in the PgUGT84A23 and PgUGT84A24 dual CRISPR/Cas9-edited lines (i.e., ugt84a23 ugt84a24) but not the control (empty vector) or PgUGT84A23/PgUGT84A24 single edited lines (ugt84a23 or ugt84a24). Transcriptome and real-time qPCR analyses identified 11 UGTs with increased expression in the ugt84a23 ugt84a24 hairy roots compared to the controls. Of the 11 candidate UGTs, only PgUGT72BD1 used gallic acid as substrate and produced a regiospecific product gallic acid 4-O-glucoside. This work demonstrates that the CRISPR/Cas9 method can facilitate functional genomics studies in pomegranate and shows promise for capitalizing on the metabolic potential of pomegranate for germplasm improvement

Aharonov-Bohm effect in monolayer black phosphorus (phosphorene) nanorings

This work presents theoretical demonstration of Aharonov-Bohm (AB) effect in monolayer phosphorene nanorings (PNR). Atomistic quantum transport simulations of PNR are employed to investigate the impact of multiple modulation sources on the sample conductance. In presence of a perpendicular magnetic field, we find that the conductance of both armchair and zigzag PNR oscillate periodically in a low-energy window as a manifestation of the AB effect. Our numerical results have revealed a giant magnetoresistance (MR) in zigzag PNR (with a maximum magnitude approaching two thousand percent). It is attributed to the AB effect induced destructive interference phase in a wide energy range below the bottom of the second subband. We also demonstrate that PNR conductance is highly anisotropic, offering an additional way to modulate MR. The giant MR in PNR is maintained at room temperature in the presence of thermal broadening effect.Comment: 7 pages, 7 figure

Exploring the Phytochemical Landscape of the Early-Diverging Flowering Plant Amborella trichopoda Baill.

Although the evolutionary significance of the early-diverging flowering plant Amborella (Amborella trichopoda Baill.) is widely recognized, its metabolic landscape, particularly specialized metabolites, is currently underexplored. In this work, we analyzed the metabolomes of Amborella tissues using liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HR-ESI-MS). By matching the mass spectra of Amborella metabolites with those of authentic phytochemical standards in the publicly accessible libraries, 63, 39, and 21 compounds were tentatively identified in leaves, stems, and roots, respectively. Free amino acids, organic acids, simple sugars, cofactors, as well as abundant glycosylated and/or methylated phenolic specialized metabolites were observed in Amborella leaves. Diverse metabolites were also detected in stems and roots, including those that were not identified in leaves. To understand the biosynthesis of specialized metabolites with glycosyl and methyl modifications, families of small molecule UDP-dependent glycosyltransferases (UGTs) and O-methyltransferases (OMTs) were identified in the Amborella genome and the InterPro database based on conserved functional domains. Of the 17 phylogenetic groups of plant UGTs (A-Q) defined to date, Amborella UGTs are absent from groups B, N, and P, but they are highly abundant in group L. Among the 25 Amborella OMTs, 7 cluster with caffeoyl-coenzyme A (CCoA) OMTs involved in lignin and phenolic metabolism, whereas 18 form a clade with plant OMTs that methylate hydroxycinnamic acids, flavonoids, or alkaloids. Overall, this first report of metabolomes and candidate metabolic genes in Amborella provides a starting point to a better understanding of specialized metabolites and biosynthetic enzymes in this basal lineage of flowering plants

MAT: A Multi-strength Adversarial Training Method to Mitigate Adversarial Attacks

Some recent works revealed that deep neural networks (DNNs) are vulnerable to so-called adversarial attacks where input examples are intentionally perturbed to fool DNNs. In this work, we revisit the DNN training process that includes adversarial examples into the training dataset so as to improve DNN's resilience to adversarial attacks, namely, adversarial training. Our experiments show that different adversarial strengths, i.e., perturbation levels of adversarial examples, have different working zones to resist the attack. Based on the observation, we propose a multi-strength adversarial training method (MAT) that combines the adversarial training examples with different adversarial strengths to defend adversarial attacks. Two training structures - mixed MAT and parallel MAT - are developed to facilitate the tradeoffs between training time and memory occupation. Our results show that MAT can substantially minimize the accuracy degradation of deep learning systems to adversarial attacks on MNIST, CIFAR-10, CIFAR-100, and SVHN.Comment: 6 pages, 4 figures, 2 table

Evidence for the Formation of Quasi-Bound-State in an Asymmetrical Quantum Point Contact

Features below the first conductance plateau in ballistic quantum point contacts (QPCs) are often ascribed to electron interaction and spin effects within the single mode limit. In QPCs with a highly asymmetric geometry, we observe sharp resonance peaks when the point contacts are gated to the single mode regime, and surprisingly, under certain gating conditions, a complete destruction of the 2e^2/h, first quantum plateau. The temperature evolution of the resonances suggest non-Fermi liquid behavior, while the overall nonlinear characterizations reveal features reminiscent of the 0.7 effect. We attribute these unusual behaviors to the formation of a quasi bound state, which is stabilized by a momentum-mismatch accentuated by asymmetry.Comment: 5 pages, 5 figure

Attentive Tensor Product Learning

This paper proposes a new architecture - Attentive Tensor Product Learning (ATPL) - to represent grammatical structures in deep learning models. ATPL is a new architecture to bridge this gap by exploiting Tensor Product Representations (TPR), a structured neural-symbolic model developed in cognitive science, aiming to integrate deep learning with explicit language structures and rules. The key ideas of ATPL are: 1) unsupervised learning of role-unbinding vectors of words via TPR-based deep neural network; 2) employing attention modules to compute TPR; and 3) integration of TPR with typical deep learning architectures including Long Short-Term Memory (LSTM) and Feedforward Neural Network (FFNN). The novelty of our approach lies in its ability to extract the grammatical structure of a sentence by using role-unbinding vectors, which are obtained in an unsupervised manner. This ATPL approach is applied to 1) image captioning, 2) part of speech (POS) tagging, and 3) constituency parsing of a sentence. Experimental results demonstrate the effectiveness of the proposed approach