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Impact of transgenic sugarcane overexpressing SoSPS1 gene on bacterial diversity, enzyme activity and minerals content in soil rhizosphere

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Journal of Crop Science and Biotechnology 2021年第1期24卷 61-69页

作者： Wulandari, Fitria Ekawati Suherman Handoyo, Tri Kim, Kyung-Min Sugiharto, Bambang Postgraduate Program in Biotechnology University of Jember Jl. Kalimantan No. 37 Kampus Tegalboto Jember 68121 Indonesia Laboratory of Molecular Biology and Biotechnology Center for Development of Advanced Science and Technology (CDAST) University of Jember Jl. Kalimantan No. 37 Kampus Tegalboto Jember 68121 Indonesia Division of Plant Biosciences School of Applied BioSciences College of Agriculture and Life Science Kyungpook National University Daegu South Korea Department of Biology Faculty of Mathematics and Natural Sciences University of Jember Jl. Kalimantan No. 37 Kampus Tegalboto Jember 68121 Indonesia

The transgenic sugarcane overexpressing SoSPS1 gene increased sugar content which may alter the root exudation that interact with soil rhizosphere microorganism. The microbial plays an important role in biochemical cycling and nutrient transformation in the soil. Therefore, it is important to investigate the potential risk of the transgenic sugarcane on soil ecosystem. This study is designed to evaluate the impact of overexpressing gene for sucrose-phosphate synthesis (SoSPS1) on the bacterial diversity, enzyme activity and nutrient contents. The transgenic sugarcane showed no significant difference in the population of culturable bacteria in the soil rhizosphere compared to non-transgenic counterpart. The populations of total, nitrogen-fixing and phosphate-solubilizing bacteria were similar in transgenic and non-transgenic sugarcane, although the bacterial population tends to increase at later sugarcane growth stage may due to the rise in nutrition from the root exudation. The PCR analysis showed no detection of horizontal gene flow in the bacteria. However, urease activity was significantly decreased in the transgenic sugarcane concomitant with lower nitrogen content in the soil rhizosphere at a later growth stage might due to the transgenic sugarcane lines increased nitrogen absorption for higher growth rate. Furthermore, the nutrient contents, such as organic carbon, phosphorus, potassium, magnesium and calcium, slightly varied in the soil rhizosphere but did not affected by the transgenic sugarcane. The results suggested that the transgenic sugarcane overexpressing SoSPS1 gene may not affect the bacterial diversity, nutrient contents and soil ecosystem. © 2020, Korean Society of Crop Science (KSCS).

关键词： Bacterial diversity Soil fertility Sucrose-phosphate synthase Sugarcane

OnsagerNet: Learning stable and interpretable dynamics using a generalized Onsager principle

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arXiv 2020年

作者： Yu, Haijun Tian, Xinyuan Weinan, E. Li, Qianxiao NCMIS LSEC Institute of Computational Mathematics and Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190 China School of Mathematical Sciences University of Chinese Academy of Sciences Beijing100049 China Department of Mathematics The Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mathematics National University of Singapore Singapore119077 Singapore Institute of High Performance Computing A*STAR Singapore138632 Singapore

We propose a systematic method for learning stable and physically interpretable dynamical models using sampled trajectory data from physical processes based on a generalized Onsager principle. The learned dynamics are autonomous ordinary differential equations parameterized by neural networks that retain clear physical structure information, such as free energy, diffusion, conservative motion and external forces. For high dimensional problems with a low dimensional slow manifold, an autoencoder with metric preserving regularization is introduced to find the low dimensional generalized coordinates on which we learn the generalized Onsager dynamics. Our method exhibits clear advantages over existing methods on benchmark problems for learning ordinary differential equations. We further apply this method to study Rayleigh-Bénard convection and learn Lorenz-like low dimensional autonomous reduced order models that capture both qualitative and quantitative properties of the underlying dynamics. This forms a general approach to building reduced order models for forced dissipative *** Codes 76E30, 34D20, 68T05/07, 82C35 Copyright © 2020, The Authors. All rights reserved.

关键词： Ordinary differential equations

Isotope effects in x-ray absorption spectra of liquid water

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arXiv 2020年

作者： Zhang, Chunyi Zhang, Linfeng Xu, Jianhang Tang, Fujie Santra, Biswajit Wu, Xifan Department of Physics Temple University PhiladelphiaPA19122 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

The isotope effects in x-ray absorption spectra of liquid water are studied by a many-body approach within electron-hole excitation theory. The molecular structures of both light and heavy water are modeled by path-integral molecular dynamics based on the advanced deep-learning technique. The neural network is trained on ab initio data obtained with SCAN density functional theory. The experimentally observed isotope effect in x-ray absorption spectra is reproduced semi-quantitatively in theory. Compared to the spectrum in normal water, the blueshifted and less pronounced pre- and main-edge in heavy water reflect that the heavy water is more structured at short- and intermediate-range of the hydrogen-bond network. In contrast, the isotope effect on the spectrum is negligible at post-edge, which is consistent with the identical long-range ordering in both liquids as observed in the diffraction experiment. Copyright © 2020, The Authors. All rights reserved.

关键词： Heavy water

Distributed branch points and the shape of elastic surfaces with constant negative curvature

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arXiv 2020年

作者： Shearman, Toby L. Venkataramani, Shankar C. Program in Applied Mathematics University of Arizona 617 N. Santa Rita Avenue TucsonAZ85721 United States Department of Mathematics University of Arizona 617 N. Santa Rita Avenue TucsonAZ85721 United States

We develop a theory for distributed branch points and investigate their role in determining the shape and influencing the mechanics of thin hyperbolic objects. We show that branch points are the natural topological defects in hyperbolic sheets, they carry a topological index which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating energy. We develop a discrete differential geometric (DDG) approach to study the deformations of hyperbolic objects with distributed branch points. We present evidence that the maximum curvature of surfaces with geodesic radius R containing branch points grow sub-exponentially, O(ec√R) in contrast to the exponential growth O(ec'R) for surfaces without branch points. We argue that, to optimize norms of the curvature, i.e. the bending energy, distributed branch points are energetically preferred in sufficiently large pseudospherical surfaces. Further, they are distributed so that they lead to fractal-like recursive buckling *** Codes 53C42(Primary) 53A70, 53C80, 35Q74, 74K99 (Secondary) Copyright © 2020, The Authors. All rights reserved.

关键词： Morphology

Reducing Stress Level Cases of Hypogalactia Using Electric and Massage Stimulation Models 4

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Reducing Stress Level Cases of Hypogalactia Using Electric a...

4th International Conference on Energy, Environment, Epidemiology and Information System, ICENIS 2019

作者： Maula, Sheyla Najwatul Widyawati, Melyana Nurul Suryono, Suryono Post Graduate Applied Science Midwifery Program Poltekkes Kemenkes Semarang Indonesia Physics Department Faculty of Mathematics and Natural Sciences Diponegoro University Semarang Indonesia

Postpartum stress is very likely to take place as there are fluctuations in terms of feelings, pressure, anxiety, and guilt that may result in hypogalactia without proper treatment. Hypogalactia itself is an issue breastfeeding mothers face that may stall toddlers' growth, and hence, the future of a nation. This research aims to lower stress levels in hypogalactia cases. It employs nor pharmacological methods of electric and massage stimulation models to activate the biomechanical, psychological, and neurological systems within the body. The electric stimulation model was performed for 10 minutes in acupoints SI, ST, and SP at 0.5 watts frequency. Meanwhile, the massage stimulation was performed for 30 minutes in acupoints GB, BL, ST, CV, and ST. Samples were divided into intervention and control groups, both characteristics and difference tests were performed. Paired t-test results show that there is a significant difference (p © The Authors, published by EDP Sciences, 2019.

关键词： Electrophysiology

Structured time-delay models for dynamical systems with connections to Frenet-Serret frame

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arXiv 2021年

作者： Hirsh, Seth M. Ichinaga, Sara M. Brunton, Steven L. Kutz, J. Nathan Brunton, Bingni W. Department of Physics University of Washington SeattleWA United States Applied and Computational Mathematical Sciences Program University of Washington SeattleWA United States Department of Mechanical Engineering University of Washington SeattleWA United States Department of Applied Mathematics University of Washington SeattleWA United States Department of Biology University of Washington SeattleWA United States

Time-delay embeddings and dimensionality reduction are powerful techniques for discovering effective coordinate systems to represent the dynamics of physical systems. Recently, it has been shown that models identified by dynamic mode decomposition (DMD) on time-delay coordinates provide linear representations of strongly nonlinear systems, in the so-called Hankel alternative view of Koopman (HAVOK) approach. Curiously, the resulting linear model has a matrix representation that is approximately antisymmetric and tridiagonal with a zero diagonal;for chaotic systems, there is an additional forcing term in the last component. In this paper, we establish a new theoretical connection between HAVOK and the Frenet-Serret frame from differential geometry, and also develop an improved algorithm to identify more stable and accurate models from less data. In particular, we show that the sub- and super-diagonal entries of the linear model correspond to the intrinsic curvatures in Frenet-Serret frame. Based on this connection, we modify the algorithm to promote this antisymmetric structure, even in the noisy, low-data limit. We demonstrate this improved modeling procedure on data from several nonlinear synthetic and real-world examples. © 2021, CC BY.

关键词： Time delay

Anomalous suppression of large-scale density fluctuations in classical and quantum spin liquids

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arXiv 2025年

作者： Chen, Duyu Samajdar, Rhine Jiao, Yang Torquato, Salvatore Materials Research Laboratory University of California Santa BarbaraCA93106 United States Department of Physics Princeton University PrincetonNJ08544 United States Princeton Center for Theoretical Science Princeton University PrincetonNJ08544 United States Materials Science and Engineering Arizona State University TempeAZ85287 United States Department of Physics Arizona State University TempeAZ85287 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Materials Institute Princeton University PrincetonNJ08540 United States Program in Applied and Computational Mathematics PrincetonNJ08544 United States

Classical spin liquids (CSLs) are intriguing states of matter that do not exhibit long-range magnetic order and are characterized by an extensive ground-state degeneracy. Adding quantum fluctuations, which induce dynamics between these different classical ground states, can give rise to quantum spin liquids (QSLs). QSLs are highly entangled quantum phases of matter characterized by fascinating emergent properties, such as fractionalized excitations and topological order. One such exotic quantum liquid is the Z2 QSL, which can be regarded as a resonating valence bond (RVB) state formed from superpositions of dimer coverings of an underlying lattice. In this work, we unveil a hidden large-scale structural property of archetypal CSLs and QSLs known as hyperuniformity, i.e., normalized infinite-wavelength density fluctuations are completely suppressed in these systems. In particular, we first demonstrate that classical ensembles of close-packed dimers and their corresponding quantum RVB states are perfectly hyperuniform in general. Subsequently, we focus on a ruby-lattice spin liquid that was recently realized in a Rydberg-atom quantum simulator, and show that the QSL remains effectively hyperuniform even in the presence of a finite density of spinon and vison excitations, as long as the dimer constraint is still largely preserved. Moreover, we demonstrate that metrics based on the framework of hyperuniformity can be used to distinguish the QSL from other proximate quantum phases. These metrics can help identify potential QSL candidates, which can then be further analyzed using more advanced, computationally-intensive quantum numerics to confirm their status as true QSLs. © 2025, CC BY-NC-ND.

关键词： Quantum entanglement

Harmonic analytic geometry on subsets in high dimensions - Empirical models

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Harmonic analytic geometry on subsets in high dimensions - E...

2018 International Congress of Mathematicians, ICM 2018

作者： Coifman, Ronald R. Department of Mathematics Program in Applied Mathematics Yale University United States

ISBN: (纸本)9789813272903

We describe a recent evolution of Harmonic Analysis to generate analytic tools for the joint organization of the geometry of subsets of Rn and the analysis of functions and operators on the subsets. In this analysis we establish a duality between the geometry of functions and the geometry of the space. The methods are used to automate various analytic organizations, as well as to enable informative data analysis. These tools extend to higher order tensors, to combine dynamic analysis of changing structures. In particular we view these tools as necessary to enable automated empirical modeling, in which the goal is to model dynamics in nature, ab initio, through observations alone. We will illustrate recent developments in which physical models can be discovered and modelled directly from observations, in which the conventional Newtonian differential equations, are replaced by observed geometric data constraints. This work represents an extended global collaboration including, recently, A. Averbuch, A. Singer, Y. Kevrekidis, R. Talmon, M. Gavish, W. Leeb, J. Ankenman, G. Mishne and many more. © ICM *** rights reserved.

关键词： Geometry

Liquid-liquid transition in water from first principles

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arXiv 2022年

作者： Gartner, Thomas E. Piaggi, Pablo M. Car, Roberto Panagiotopoulos, Athanassios Z. Debenedetti, Pablo G. Department of Chemistry Princeton University PrincetonNJ08544 United States Department of Physics Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Department of Chemical and Biological Engineering Princeton University PrincetonNJ08544 United States

A longstanding question in water research is the possibility that supercooled liquid water can undergo a liquid-liquid phase transition (LLT) into high- and low-density liquids. We used several complementary molecular simulation techniques to evaluate the possibility of an LLT in an ab initio neural network model of water trained on density functional theory calculations with the SCAN exchange correlation functional. We conclusively show the existence of a first-order LLT and an associated critical point in the SCAN description of water, representing the first definitive computational evidence for an LLT in water from first principles. Copyright © 2022, The Authors. All rights reserved.

关键词： Density functional theory