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Solutes in native plants in the Arabian Gulf region and the role of microorganisms: future research

Journal of Plant Ecology 2018年第5期11卷 671-684页

作者： Roda Fahad Al-Thani Bassam Taha Yasseen Department of Biological and Environmental Sciences College of Arts&SciencesQatar UniversityDohaQatar present address:8 james court Dunstable RoadLuton LU40HNUK.

Aims One of the outstanding challenges facing humankind is increas-ing crop production under various types of severe environmental *** measures have been taken to adopt molecular and biotechnological approaches that lead to the development of transgenic plants able to deal with such harsh and polluted ***,such solutions could be very expensive and require considerable efforts and time to achieve these *** main objective of this review is to discuss the new biological solutions that have emerged in the last decade,as environmentally friendly approaches,perhaps to support and/or replace the present *** solutions based on plant-microbe interactions could be a lifeline and promising alternative strategy to create plants with a high resistance to the extreme *** During the last two decades research projects have been conducted to study the ecology,identify the features,and the ecophysiology of native plants and the associated microorganisms in the Arabian Gulf region and particularly in *** physiological and bio-chemical parameters have been determined,including organic sol-utes(amino acids like proline,glycinebetaine,soluble sugars,etc.),photosynthetic pigments,organic acids and inorganic ions espe-cially heavy metals,along with the physical and chemical proper-ties of the soil in various locations of the State of ***,the microorganisms adjacent to and associated with these native plants were identified to elucidate the possible roles in the soil biota in supporting these plants against extreme environmental *** Findings Investigations of native plants in the Arabian Gulf states during the last decade have shown that wild plants exhibit different abili-ties to accumulate organic solutes to cope with the harsh natural *** is a major factor stressing wildlife in this region due to the expansion of urban sectors and industrial activi-ties of oil and ***

关键词： Arabian Gulf region arid lands compatible solutes drought microorganisms modern approaches pollution salinity

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Construction of RNA nanotubes

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Nano Research 2019年第8期12卷 1952-1958页

作者： Hui Li Shaoying Wang Zhouxiang Ji Congcong Xu Lyudmila S. Shlyakhtenko Peixuan Guo Center for RNA Nanobiotechnology and Nanomedicine Division of Pharmaceutics and Pharmaceutical ChemistryCollege of Pharmacy/Department of Physiology & Cell BiologyCollege of Medicine/Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer CenterThe Ohio State UniversityColumbusOH43210USA UNMC Nanoimaging Core Facility Department of Pharmaceutical SciencesCollege of Pharmacy University of Nebraska Medical CenterOmahaNE68182USA present address: University of California San FranciscoCA94158USA present address: P&Z Biological Technology NewarkNJ07103USA

Nanotubes are miniature materials with significant potential applications in nanotechnological, medical, biological and material sciences. The quest for manufacturing methods of nano-mechanical modules is in progress. For example, the application of carbon nanotubes has been extensively investigated due to the precise width control, but the precise length control remains challenging. Here we report two approaches for the one-pot self-assembly of RNA nanotubes. For the first approach, six RNA strands were used to assemble the nanotube by forming a 11 nm long hollow channel with the inner diameter of 1.7 nm and the outside diameter of 6.3 nm. For the second approach, six RNA strands were designed to hybridize with their neighboring strands by complementary base pairing and formed a nanotube with a six-helix hollow channel similar to the nanotube assembled by the first approach. The fabricated RNA nanotubes were characterized by gel electrophoresis and atomic force microscopy (AFM), confirming the formation of nanotube-shaped RNA nanostructures. Cholesterol molecules were introduced into RNA nanotubes to facilitate their incorporation into lipid bilayer. Incubation of RNA nanotube complex with the free-standing lipid bilayer membrane under applied voltage led to discrete current signatures. Addition of peptides into the sensing chamber revealed discrete steps of current blockage. Polyarginine peptides with different lengths can be detected by current signatures, suggesting that the RNA-cholesterol complex holds the promise of achieving single molecule sensing of peptides.

关键词： RNA nanotechnology peptide sensing RNA nanotube nanobiotechnology

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CD8+T cell metabolic flexibility elicited by CD28-ARS2 axisdriven alternative splicing of PKM supports antitumor immunity

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Cellular & Molecular Immunology 2024年第3期21卷 260-274页

作者： G.Aaron Holling Colin A.Chavel Anand P.Sharda Mackenzie M.Lieberman Caitlin M.james Shivana M.Lightman Jason H.Tong Guanxi Qiao Tiffany R.Emmons Thejaswini Giridharan Shengqi Hou Andrew M.Intlekofer Richard M.Higashi Teresa W.M.Fan Andrew N.Lane Kevin H.Eng Brahm H.Segal Elizabeth A.Repasky Kelvin P.Lee Scott H.Olejniczak Department of Immunology Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA Department of Medicine Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer CenterNew YorkNY 10065USA Center for Environmental Systems Biochemistry Department of Toxicology and Cancer Biology and Markey Cancer CenterLexingtonKY 40536USA Department of Cancer Genetics and Genomics Roswell Park Comprehensive Cancer CenterBuffaloNY 14263USA present address:University of Colorado Boulder BoulderCO 80309USA present address:Dana Farber Cancer Institute BostonMA 02215USA present address:Massachusetts Institute of Technology BostonMA 02139USA present address:Melvin and Bren Simon Comprehensive Cancer Center Indiana University School of MedicineIndianapolisIN 46202USA

Metabolic flexibility has emerged as a critical determinant of CD8+T-cell antitumor activity,yet the mechanisms driving the metabolic flexibility of T cells have not been *** this study,we investigated the influence of the nuclear cap-binding complex(CBC)adaptor protein ARS2 on mature T *** doing so,we discovered a novel signaling axis that endows activated CD8+T cells with flexibility of glucose ***2 upregulation driven by CD28 signaling reinforced splicing factor recruitment to pre-mRNAs and affected approximately one-third of T-cell activation-induced alternative splicing *** these effects,the CD28-ARS2 axis suppressed the expression of the M1 isoform of pyruvate kinase in favor of PKM2,a key determinant of CD8+T-cell glucose utilization,interferon gamma production,and antitumor effector ***,PKM alternative splicing occurred independently of CD28-driven PI3K pathway activation,revealing a novel means by which costimulation reprograms glucose metabolism in CD8+T cells.

关键词： Immunometabolism mRNA splicing CD8 T cells ARS2 PKM2

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Benchmarking the performance of Bayesian optimization across multiple experimental materials science domains

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npj Computational Materials 2021年第1期7卷 1742-1751页

作者： Qiaohao Liang Aldair E.Gongora Zekun Ren Armi Tiihonen Zhe Liu Shijing Sun james R.Deneault Daniil Bash Flore Mekki-Berrada Saif A.Khan Kedar Hippalgaonkar Benji Maruyama Keith A.Brown John Fisher III Tonio Buonassisi Massachusetts Institute of Technology CambridgeMAUnited States Boston University BostonMAUnited States Singapore-MIT Alliance for Research and Technology SingaporeSingapore Air Force Research Laboratory DaytonOhioUnited States Agency for Science Technology and Research(A*STAR)SingaporeSingapore National University of Singapore SingaporeSingapore present address:Aalto University EspooFinland present address:Northwestern Polytechincal University(NPU) Xi’anShaanxi P.R.China

Bayesian optimization(BO)has been leveraged for guiding autonomous and high-throughput experiments in materials ***,few have evaluated the efficiency of BO across a broad range of experimental materials *** this work,we quantify the performance of BO with a collection of surrogate model and acquisition function pairs across five diverse experimental materials *** defining acceleration and enhancement metrics for materials optimization objectives,we find that surrogate models such as Gaussian Process(GP)with anisotropic kernels and Random Forest(RF)have comparable performance in BO,and both outperform the commonly used GP with isotropic *** with anisotropic kernels has demonstrated the most robustness,yet RF is a close alternative and warrants more consideration because it is free from distribution assumptions,has smaller time complexity,and requires less effort in initial hyperparameter *** also raise awareness about the benefits of using GP with anisotropic kernels in future materials optimization campaigns.

关键词： optimization performance acceleration

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Spontaneous emission in non-local materials

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Light(Science & Applications) 2016年第1期5卷 1-10页

作者： Pavel Ginzburg Diane J Roth Mazhar E Nasir Paulina Segovia Alexey V Krasavin james Levitt Liisa M Hirvonen Brian Wells Klaus Suhling David Richards Viktor A Podolskiy Anatoly V Zayats Department of Physics King’s College LondonStrandLondon WC2R 2LSUK present address:School of Electrical Engineering Tel Aviv UniversityTel Aviv 69978Israel Department of Physics and Applied Physics University of Massachusetts LowellOne University AveLowellMA 01854USA present address:Department of Physics University of HartfordWest HartfordCT 06117USA

Light–matter interactions can be strongly modified by the surrounding ***,we report on the first experimental observation of molecular spontaneous emission inside a highly non-local metamaterial based on a plasmonic nanorod *** show that the emission process is dominated not only by the topology of its local effective medium dispersion,but also by the non-local response of the composite,so that metamaterials with different geometric parameters but the same local effective medium properties exhibit different Purcell factors.A record-high enhancement of a decay rate is observed,in agreement with the developed quantitative description of the Purcell effect in a non-local *** engineered material non-locality introduces an additional degree of freedom into quantum electrodynamics,enabling new applications in quantum information processing,photochemistry,imaging and sensing with macroscopic composites.

关键词： composite electromagnetic materials non-local optical properties plasmonic metamaterials quantum electrodynamics spontaneous emission

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Challenging Nanopores with Analyte Scope and Environment

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Journal of Analysis and Testing 2019年第1期3卷 61-79页

作者： Buddini I.Karawdeniya Y.M.Nuwan D.Y.Bandara Jonathan W.Nichols Robert B.Chevalier james T.Hagan Jason R.Dwyer Department of Chemistry University of Rhode IslandRichard E.Beaupre Center for Chemical and Forensic Sciences140 Flagg Rd.KingstonRI 02881USA present address:Department of Mechanical Engineering Lyle School of EngineeringSouthern Methodist UniversityDallasTX 75275USA present address:Nova Biomedical 200 Prospect StreetWalthamMA 02454-9141USA

Nanopores are nanofluidic channels formed through thin membranes that can deliver standout single-molecule and single-particle sensing *** targets include small molecules and nanoparticles,and the DNA,protein,and glycan biopolymers underpinning genomics,proteomics,and ***-notably even in the simplest implementation,resistive-pulse sensing-does not inherently require sample labeling and,thus,offers the potential for general sensing util-ity combined with the prospective benefits of reduced sample processing requirements.A key pursuit for biopolymer sens-ing is the characterization of monomer *** review article will provide an overview of the use of nanopores for general chemical sensing and-omics-related applications,*** broad analyte scope provides fertile ground for a discussion of principles governing nanopore sensing and considerations useful for guiding nanopore *** nanopores to be effective in the face of broad analyte scope,stringent requirements on analytical performance must be met within the particular analyte class without sacrificing the operational flexibility necessary to be responsive across classes presenting very different physical and chemical *** sample-driven challenges provide a unifying framework for discussing aspects of nanopore fabrication,properties,and integration;sensing paradigms,performance,and prospects;fundamental electrokinetic and interfacial phenomena;and practical challenges facing the use and further development of nanopore devices.

关键词： Nanopore Single-molecule sensing Nanofluidics Point-of-care Silicon nitride Resistive pulse Wearable sensors Quality assurance

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Myosin XI Is Required for Actin-Associated Movement of Plastid Stromules

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Molecular Plant 2009年第6期2卷 1262-1272页

作者： Senthil Kumar A. Natesan james A. Sullivan John C. Gray Department of Plant Sciences University of Cambridge Downing Street Cambridge CB2 3EA UK present address: Sir William Dunn School of Pathology University of Oxford South Parks Road Oxford OX1 3RE UK present address: School of Biological and Chemical Sciences Queen Mary University of London Mile End Road London E1 4NS UK

Stromules are highly dynamic stroma-filled tubules extending from the surface of plastids and occasionally interconnecting individual plastids, allowing the movement of complex biological molecules between the interconnected plastids. Experiments with inhibitors of cytoskeleton assembly have indicated the involvement of an actin-based system in stromule movement. However, the motor protein associated with the system had not been identified. Here, we present direct evidence that myosin XI is involved in the formation and movement of stromules in tobacco leaves. Application of 2,3-butanedione 2-monoxime, an inhibitor of myosin ATPase activity, resulted in the loss of stromules from tobacco leaf epidermal cells. Transient RNA interference of myosin XI in leaves of Nicotiana benthamiana also resulted in the loss of stromules from epidermal cells, without any effect on transcripts for actin or myosin VIII. Transient expression of a GFP- tagged myosin XI tail domain in tobacco leaf epidermal cells showed that the fusion protein localized to the chloroplast envelope, as well as to mitochondria and other organelles. Our findings identify myosin XI as a key protein involved in the formation and movement of stromules.

关键词： Chloroplast biology cytoskeleton organelle biogenesis/function tobacco.

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A Plant Immune Receptor Degraded by Selective Autophagy

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Molecular Plant 2019年第1期12卷 113-123页

作者： Fan Yang Athen N.Kimberlin Christian G.Elowsky Yunfeng Liu Ariadna Gonzalez-Solis Edgar B.Cahoon james R.Alfano Department of Plant Pathology University of NebraskaLincolnNE 68588-0722USA Center for Plant Science Innovation University of NebraskaLincolnNE 68588-0660USA Department of Bioohemistry University of NebraskaLincolnNE 68588-0664US Center for Biotechnology University of NebraskaLincolnNE 68588-0665USA present address:Department of Biochemistry University of MissouriColumbiaMQ 65211USA present address:College of Life Science and Technology University of GuangxiNanning 530004China

Plants recycle non-activated immune receptors to maintain a functional immune *** Arabidopsis immune receptor kinase FLAGELLIN-SENSING 2 (FLS2)recognizes bacterial ***,the molecular mechanisms by which non-activated FLS2 and other non-activated plant PRRs are recycled remain not well ***,we provide evidence showing thatArabidopsis orosomucoid (ORM)proteins,which have been known to be negative regulators of sphingoUpid biosynthesis,act as selective autophagy receptors to mediate the degradation of *** plants overexpressing ORM 1 or ORM2 have undetectable or greatly diminished FLS2 accumulation,nearly lack FLS2 signaling,and are more susceptible to the bacterial pathogen Pseudomonas *** the other hand,ORM1/2 RNAi plants and orml or orrn2 mutants generated by the CRISPR/Cas9-mediated gene editing have increased FLS2 accumulation and enhanced FLS2 signaling,and are more resistant to *** proteins interact with FLS2 and the autophagy-related protein ***,overexpression of ORM1 or ORM2 in autophagydefective mutants showed FLS2 abundance that is comparable to that in wild-type ***, FLS2 levels were not decreased in Arabidopsis plants overexpressing ORM1/2 derivatives that do not interact with *** together,these results suggest that selective autophagy functions in maintaining the homeostasis of a plant immune receptor and that beyond sphingolipid metabolic regulation ORM proteins can also act as selective autophagy receptors.

关键词： Plant immunity selective autophagy pattern recognition receptor selective autophagy receptors

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Specific interaction of hepatitis C virus glycoproteins with mannan binding lectin inhibits virus entry

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Protein & Cell 2010年第7期1卷 664-674页

作者： Kristelle S.Brown Michael J.Keogh Ania M.Owsianka Richard Adair Arvind H.Patel james N.Arnold Jonathan K.Ball Robert B.Sim Alexander W.Tarr Timothy P.Hickling Institute of Infection Immunity and InflammationSchool of Molecular Medical SciencesThe University of NottinghamQueen’s Medical CentreNottinghamNG72UHUK The Medical Research Council-University of Glasgow Centre for Virus Research University of GlasgowChurch StreetGlasgowG115JRUK MRC Immunochemistry Unit Department of BiochemistryUniversity of OxfordOX13QUUK present address:Vitrology Biotech 5 South AvenueClydebank Business ParkGlasgowG812LGUK present address:Pfizer Technologies Ltd. Ramsgate RoadSandwichKentCT139NJUK

Mannan-binding lectin(MBL)is a soluble innate immune protein that binds to glycosylated *** acts as an opsonin and activates complement,contributing to the destruction and clearance of infecting *** C virus(HCV)encodes two envelope glycoproteins E1 and E2,expressed as non-covalent E1/E2 heterodimers in the viral envelope.E1 and E2 are potential ligands for *** we describe an analysis of the interaction between HCV and MBL using recombinant soluble E2 ectodomain fragment,the full-length E1/E2 heterodimer,expressed in vitro,and assess the effect of this interaction on virus entry.A binding assay using antibody capture of full length E1/E2 heterodimers was used to demonstrate calcium dependent,saturating binding of MBL to HCV *** with various saccharides further confirmed that the interaction was via the lectin domain of *** binds to E1/E2 representing a broad range of virus *** was shown to neutralize the entry into Huh-7 cells of HCV pseudoparticles(HCVpp)bearing E1/E2 from a wide range of *** were neutralized to varying *** was also shown to neutralize an authentic cell culture infectious virus,strain JFH-1(HCVcc).Furthermore,binding of MBL to E1/E2 was able to activate the complement system via MBL-associated serine protease *** conclusion,MBL interacts directly with HCV glycoproteins,which are present on the surface of the virion,resulting in neutralization of HCV particles.

关键词： hepatitis C virus neutralization mannose binding lectin chronic viral infection

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Natural orbital description of the halo nucleus 6He

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Nuclear Science and Techniques 2017年第12期28卷 237-243页

作者： Chrysovalantis Constantinou Mark A.Caprio james P.Vary Pieter Maris present address:Center for Theoretical Physics Sloane Physics LaboratoryYale UniversityNew HavenCT 06520-8120USA Department of Physics University of Notre DameNotre DameIN 46556-5670USA Department of Physics and Astronomy Iowa State UniversityAmesIA 50011-3160USA

Ab initio calculations of nuclei face the challenge of simultaneously describing the strong short-range internucleon correlations and the long-range properties of weakly bound halo nucleons. Natural orbitals, which diagonalize the one-body density matrix, provide a basis which is better matched to the physical structure of the many-body wave function. We demonstrate that the use of natural orbitals significantly improves convergence for ab initio no-core configuration interaction calculations of the neutron halo nucleus ~6He, relative to the traditional oscillator basis.

关键词： Neutron halo nucleus 6He Nuclear structure Nuclear theory

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